Richard B. Hoppe posted Entry 2829 on January 10, 2007 01:05 AM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2819

The weblog of William Dembski is called “Uncommon Dissent Descent” (UD). It has a reputation for banning unwanted commenters (read: “evolution defenders”), but generally on the grounds that they’re obstreperous and disruptive. However, it’s becoming clear that it’s not just disruptive behavior that gets one banned: It’s also merely disagreeing, calmly and lucidly, with DaveScot.

Recently Dembski posted some remarks about ID in the United Kingdom and invited comment from UK residents. One UK resident, “Febble”, accepted the invitation. Febble remarked that she had no objection to intelligent design being taught in the UK, since under Dembski’s definition of “intelligent”, Darwinian natural selection is intelligent. She wrote

I am happy to accept “Intelligent Design” as a scientific hypothesis to account for the development of life, as proposed by yourself, Dr Dembski, as long as you stand by this definition of intelligence:

‘ by intelligence I mean the power and facility to choose between options–this coincides with the Latin etymology of “intelligence,” namely, “to choose between” ‘

From Intellligent Design Coming Clean

However, such a hypothesis need not (and should not) be presented as an “alternative to evolution” as it is described in the Truth In Science materials. Far from rejecting an agent “with the power and facility to choose between options”, this is exactly what the Theory of Evolution postulates as the agent of evolutionary change - a process of_selection_ (aka “choice”) between options.

That did not go over well. DaveScot, Dembski’s bouncer, first responded with sarcasm:

Survival of the survivors. Brilliant!

I guess we can all go home now. Case closed.

and then within minutes moved on to the core ID argument: ‘Computers are really complex and they’re designed, and cells are really really complex so they must be designed too’.

Well, that didn’t work. Febble (a Ph.D. neuroscientist, a Christian theist, and a knowledgeable evolution supporter) pointed out that she was only using Dembski’s own operational definition. She went on:

My own view is that life is a profoundly algorithmic phenonemon, and it is the richness of its algorithmic structure that gives rise to its “specified complexity”. It did not arise by chance, it arose from rules - algorithms. And a key algorithm is the if…then statement. In that sense, I consider Dr Dembski correct - biological systems are intelligent systems, arising from intelligent processes.

Where I part company from the ID movement, as opposed to the concept of ID itself, is the frequent implication that intelligent design is coterminous with intentional design. I am happy with Dr. Dembki’s operational definition of intelligence, which includes the concept of choice between options, but does not include consciousness or intention. Dr Dembski does not argue, as I understand him, that consciousness or intention are necessary to produce a pattern with “specified complexity”, merely the “power and capacity to choose between options”. (Italics original)

Note that Dembski (and DaveScot) can’t invoke intention as part of their ‘scientific’ ID – Dembski explicitly ruled the intentionality question out of bounds for science in the article Febble cited, “Intelligent Design Coming Clean”.

So DaveScot moved on to … wait for it … ‘Biological stuff is much more complicated than Darwin thought, and so it must have been designed’, throwing in “probabilities” (just the word, no numbers) for good measure.

Febble very calmly described the notion of cumulative selection, illustrating how evolution by natural selection is a sort of learning algorithm, and reminded DaveScot that chemistry is relevant to understanding how the genetic “code” in DNA is transcribed and translated into proteins that do stuff in cells..

DaveScot then launched a barrage of creationist fog:

* Natural selection works very strongly only in weeding out catastrophic mutations. It is exceedingly poor at fixing beneficial mutations.

* Thus in the fossil record we observe 999 out of 1000 species going extinct in an average of 10 million years without generating any new species during that time. (That’s a new one on me.)

* Natural selection is a conservative force. It works to keep species the same until enough less than disastrous mutations pile up so that extinction occurs at the first major environmental stress.

* The bit of evolution rm+ns can’t adequately explain is the abrupt origin of new species with markedly different and unique anatomical features which is also part of the indisputable testimony of the fossil record.

(Text DaveScot’s; formatting RBH’s)

And so on. I’m put in mind of Philip Kitcher’s term for ID: “dead science”. (Elaborating on the dead science theme, in his new book Living with Darwin Kitcher refers to ID proponents as “resurrection men”.)

Again, Febble responded calmly, dealing with the several misconceptions in DaveScot’s account. Salvador made a brief appearance with his normal derailing commentary, but Febble hauled the discussion back to the main point: Dembski’s operational definition of intelligence and its congruity with natural selection.

The exchange went on for several more posts, with Febble making her points calmly and with respect, and DaveScot responding that Febble doesn’t really understand this or that aspect, not of ID, but of his strawman caricature of evolution. Then, after two such posts by DaveScot within 10 minutes, abruptly and with no intervening posts by Febble, DaveScot posted this:

febble is no longer with us - anyone who doesn’t understand how natural selection works to conserve (or not) genomic information yet insists on writing long winded anti-ID comments filled with errors due to lack of understanding of the basics is just not a constructive member - good luck on your next blog febble

I encourage folks to read the exchanges for themselves, and judge the grounds for DaveScot’s precipitate banning of Febble. I’m not here suggesting that she should be reinstated on UD, but rather that the set of exchanges illustrates both the poverty of the arguments offered on UD, and more interesting, the paranoid defensiveness in the face of dissent from a Christian theist who dares disagree, on scientific grounds, with the UD bouncer. It’s really kind of a hoot: Uncommon Dissent Descent can’t bear to hear informed dissent.

Febble’s comments on UD constitute a sort of informal peer review – the testing of ideas by (in this case relatively friendly) critics. Febble is a self-identified (in that comment thread) Christian theist. She was calm and polite throughout. And what happened? Banned. So much for peer review.

Febble and I have corresponded about this affair, and we disagree. She suggests that what we’re seeing is the formation of a niche species within ID creationism on UD, while I argue it’s merely yet another a demonstration of the deployment of Freudian ego defense mechanisms by IDists.

I’ll note also that Febble’s argument that natural selection is “intelligent” on Dembski’s definition is not unique to her. In 1999 Wes Elsberry made a similar point at greater length, concluding that:

The “actualization-exclusion-specification” triad mentioned above also fits natural selection rather precisely. One might thus conclude that Dembski’s argument establishes that natural selection can be recognized as an intelligent agent.

RBH

Edited to add: A commenter pointed out that I called Dembski’s blog “Uncommon Dissent”, rather than “Uncommon Descent”. I’ve corrected that error. Perhaps it accounts for the intolerance of dissent there.

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Comment #154133

Posted by hhahaha on January 10, 2007 12:25 AM (e)

you’re trying to diss UD but you couldn’t even get their name right! what a doofus.

Comment #154135

Posted by RBH on January 10, 2007 12:45 AM (e)

hhahaha wrote

you’re trying to diss UD but you couldn’t even get their name right! what a doofus.

Yup, I called it “Uncommon Disssent”, rather than “Uncommon Descent”. I’ve corrected that, thanks. Perhaps that misreading on my part accounts for the false expectation that UD tolerates dissent. :)

RBH

Comment #154136

Posted by creeky belly on January 10, 2007 12:46 AM (e)

(Oops, make that “Descent”)

Freud would be proud.

Comment #154137

Posted by ArchetypeOfSagacity on January 10, 2007 1:01 AM (e)

They really are ban-happy over there at UD, aren’t they? I was banned there myself over a year ago.

I was one of several people who dared to suggest that the Dawkin’s quotes at http://tinyurl.com/ygbo9n were out of context and/or edited in such a way that they altered the point that Dawkins was trying to make. Like the others who commented on how out-of-context and edited those quotes were, I was not rude, I did not cuss or use any insults, or do anything else that any sane owner/operator of a blog would consider ban-worthy. I even made it clear as day that I was not accusing anyone (especially Dembski) of purposefully misquoting Dawkins, just that I thought that the quotes were not entirely accurate, and I explained why I thought as much as calmly as I could.

My post was deleted and I was banned without warning less than an hour after I posted my comment.

Yet, a few months later I believe it was, a post was made by Dembski that had a picture of Dawkins in it, and several of Dembski’s ID buddies made fun of Dawkin’s physical appearance. Those posters were not banned under the pretense that they were “not constructive members” and their posts were not deleted. How odd…

Comment #154139

Posted by Sir_Toejam on January 10, 2007 1:06 AM (e)

I think IDists have in fact, resurrected many of Freuds’s theories all by themselves.

Comment #154141

Posted by Steve Reuland on January 10, 2007 1:32 AM (e)

It has a reputation for banning unwanted commenters (read: “evolution defenders”), but generally on the grounds that they’re obstreperous and disruptive.

Eh, I got banned purely for being a PT contributor. That was my crime.

DaveScot’s rationale was that he was banned from here, so therefore I would be banned from there. Never mind that he was allowed to post here for many weeks, in spite of his extremely obnoxious behavior, until finally his threatening to hack the site got him the boot. Me, I just tried to respond to something that was criticizing one of my own posts and had my comment immediately deleted.

Comment #154142

Posted by Steve Reuland on January 10, 2007 1:38 AM (e)

Edited to add: A commenter pointed out that I called Dembski’s blog “Uncommon Dissent”, rather than “Uncommon Descent”. I’ve corrected that error. Perhaps it accounts for the intolerance of dissent there.

One of the IDist books is named “Uncommon Dissent“, so it’s an understandable error. In fact I believe that the book (or at least Dembski’s plugging it) preceded the blog. I also get the names mixed up sometimes.

Comment #154143

Posted by Troff on January 10, 2007 1:55 AM (e)

Febble and I have corresponded about this affair, and we disagree. She suggests that what we’re seeing is the formation of a niche species within ID creationism on UD, while I argue[…]

Can it be claimed that the public (primary?) leadership / face of Intelligent Design - Dembski (with his “publications”) and his Cerberus-like DaveScot are the “niche species”?

Well, so Intelligent Design is “niche” to begin with. Fine. But narrowing the scope of the view to the IDists alone…

Comment #154157

Posted by Christophe Thill on January 10, 2007 3:51 AM (e)

I don’t really understand why this apparently competent lady spent so much time trying to make her point. Perhaps she thought she was talking to scientists? Or just to people willing to listen to scientific arguments? Or just to intelligent people, perhaps…

Comment #154201

Posted by KL on January 10, 2007 6:44 AM (e)

I refered (and linked) to a NYTimes article that quoted a Templeton Foundation official saying that grant requests were solicited from DI and the ID “scientists” but none ever were submitted. After being told that I didn’t know what I was talking about, I offered to ask the Templeton Family (I taught Templeton’s grandniece and nephew as the family lives nearby) That was the end of me posting on UD. However, I’ve found that is much more fun looking from the outside at all the silliness at that site. It’s also very educational to see arguments disassembled on AtBC by people who REALLY know their stuff.

Comment #154208

Posted by Andrea Bottaro on January 10, 2007 7:06 AM (e)

Well, considering the abysmal level of argumentation UD stoops down to most of the time, including Professors of Theology proudly claiming authorship of flatulence-ridden animations, I find “Uncommon Descent” rather nicely evocative too.

Comment #154216

Posted by Torbjörn Larsson on January 10, 2007 7:08 AM (e)

Febble made a good argument, but more prominently she managed to parse out a real model from the ID fuzz. By sticking to one of Dembski’s definition and insist on testability - which Dembski has no intention to do. She even came up with a non-contradictory definition of ‘specified complexity’ (as the result of choice mechanisms), something Dembski never has managed.

I notice they have a tag team now, a Patrick mentioned he was a bouncer too. As if it wasn’t enough with Sal as repellent. :-)

Comment #154226

Posted by Duke York on January 10, 2007 7:25 AM (e)

I got banned from UD as well; I only wish I handled the frustration that DaveScot puts out with half the coolness Febble did. Kudos to her.

As I see it, we’re distilling the UD crowd. Every time DaveScot kicks someone who isn’t unruly and is making good points, everyone reading who isn’t completely brainwashed will have to actually look at the arguments that have to be defended by an prevaricators like DaveScot and his patron Dembski. Enough of that, and soon all that’s left on UD is syncophants, like the crud at the bottom of a soup-pot that’s been boiling all night.

The trouble is, new people come in and might be gulled by the ID’s facile tautologies, so we have to keep boiling the soup. Oh well. Dealing with someone like DaveScot is a price we pay for free speech.

Comment #154232

Posted by Michael Hopkins on January 10, 2007 7:55 AM (e)

I got banned for my one post. It was was when Dembski was claiming that Jeff Shallit was dropped by the ACLU as a Kitzmiller witness because he was an embarrassment. I pointed out that the real reason why Shallit did not testify and was promptly banned. Multiple other people tried to do so and where also banned.

Creationist sites are far more likely to censor forum or blog comments than noncreationist sites. I guess they are afraid of the truth. As many have pointed out, this is from those whose rhetoric (but not actions) is to present “both” sides.

Does anyone have a URL to the comment where DaveScot threatened to hack the Panda’s Thumb? Maybe it would be a good idea to call him “Dave ‘[insert quote here]’ Scot” to remind make sure people don’t forget his commitment to truth and the marketplace of ideas.

Comment #154233

Posted by bunjo on January 10, 2007 8:02 AM (e)

I too, as a UK resident, responded to the invitation concerning ID in the UK. I actually registered to do so.

My first post was added to the thread, my second post (sent 23:03 5 January, UK time, in response to comments made by Patrick) has not appeared. Here is the text of the unpublished post:

Patrick,

We were asked as UK residents to comment on the government response to ID being taught in schools. My caricature was a tad unkind (for the purposes of debate) but I don’t think it was unrepresentative of the likely reception in an ordinary state school. ID may get a warmer reception in our Academies (sponsored schools) as some of these have been funded by people with strong religious convictions.

200 years ago many of the clergy were also naturalists - the study of nature was seen as demonstrating God’s purpose and bounty. However the data and philosophical thought of the time ( e.g. Catastrophism vs Uniformitarianism) led to doubts about the literal accuracy of the Bible and the age of the Earth. This in turn has lead to a cultural recognition of the scientific world view, reinforced by social changes and the impact of two World Wars, and this is what ID is up against.

The bulk of the UK population is practically secular, despite the Queen being the head of the Established Church. ID must make its case based on science, there is little traction for a religious idea.

Saying that the Theory of Evolution cannot explain the appearance of design so Intelligent Design is the answer (even with the fragile concepts of IC and SC) is not enough to displace the evolutionary world view which has taken root in the UK over the last 150 years. You will have to prove who supplied the intelligence in ID, when it was done and how it was done.

I guess you could judge the comment to be mildly critical, but we were asked for our views…

Maybe my post went astray? Strangely enough I also posted a more critical comment on the Emerald Wasp thread (16:27 UK time, 5 January) and that has not appeared either.

Now I have to say that prior to this I was unimpressed by the general tone and content of Uncommon Descent, but I thought it worth the effort to try and contribute to the debates. For what it is worth I feel that I have proved to my own satisfaction that the site is nothing more than a cheerleaders club for ID, one that will not tolerate anything else but full on enthusiasm for team Dembski.

I wonder if I can de-register?

Comment #154236

Posted by Me on January 10, 2007 8:26 AM (e)

Well, to balance out the conversation a bit, as scientifically vacuous as ID may be I have challenged equally silly environmental notions on this site and seen my posts and the ensuing discussions removed. So, pick your metaphor, pots and kettles, glass houses, ivory towers…

I even feel the need to preface my comments with something such as “ID is nonsense” so that everyone can see I am in strong agreement with most things that are posted here so that my post can continue and has just has that greater chance of survivability. I do that because of past experience and it shouldn’t be necessary. If I did not also feel the hand of censure at my back when I have an opinion to express that is in disagreement with the majority here I would feel comfortable just saying it and not pandering to the masses before I express my opinion.

Comment #154237

Posted by Ric on January 10, 2007 8:35 AM (e)

DaveScot is pretty pathetic. But let me say that dissenting views aren’t just grounds for banning. Most of the time dissenting views never see the light of day.

Comment #154238

Posted by Raging Bee on January 10, 2007 9:17 AM (e)

Yo, “Me,” care to give us an example of the horrible hypocritical persecution you allege?

(Note: If you’re actually Larry Fafarman, please remember that you posted here with impunity for months, if not years, and were, if I’m not mistaken, banned for insistently posting nonsense, as well as unwarranted insults, that had nothing to do with the topic of the threads in which you were posting.)

Comment #154240

Posted by Me on January 10, 2007 9:31 AM (e)

Sorry, I don’t even know who Larry Farfarman is. This is just one of the sites I read, and mostly lurk and don’t post comments - and to ingratiate myself with the masses again: I enjoy immensely.

The one time I did post a few comments (I think it was about some weird Dolphin article I didn’t agree with) my posts and the discussion that followed got deleted so you may find it, or you may not. I ended up posting some kind of apology because dissent always seems to bring out the trolls that just have attack agendas. You may still find the post, I can’t even say I recall the article in much detail, all I recall was that I was deleted.

All I am saying is the one previous thread I posted in here was deleted and I didn’t do anything but (sarcastically) disagree with an article that was posted on the site. My point being that there is censorship here also.

Comment #154243

Posted by Raging Bee on January 10, 2007 9:59 AM (e)

In other words, “Me,” you have no case, otherwise you’d be citing the specific subject and at least a range of possible post-dates – As I would, and can, when I accuse UD of censoring me (last month, in a post regarding the fake-issue of Judge Jones’ “plagiarising” the ACLU’s PFOFs in his Dover ruling, I got banned for quoting Behe’s admission, under oath, that ID had no peer-reviewed work to its name – there’s posts here on that subject where I boldly boast of my trials and tribulations).

I suspect that if you were “censored” for anything, it was for posting off-topic; that’s happened to me more than once – my offending posts were simply moved to AtBC or the Bathroom Wall, and we all had the option of continuing the arguments there.

Comment #154244

Posted by Raging Bee on January 10, 2007 10:03 AM (e)

PS: Your last post didn’t have enough essense of Larryness to prove anything, therefore I take back, with apologies (for now at least), my allegation that you’re Larry. My bad.

Comment #154245

Posted by Paul Millington on January 10, 2007 10:06 AM (e)

RBH, you commented that “DaveScot then launched a barrage of creationist fog:”

Thus in the fossil record we observe 999 out of 1000 species going extinct in an average of 10 million years …

Hardly intelligent design then - as the poster above my desk says.

Comment #154246

Posted by Comstock on January 10, 2007 10:09 AM (e)

A couple points:

First, it’s great to see RBH mention Freudian ego defenses as a motivator for IDist behavior. Personally, I favor adding a psychological approach to understanding this conflict, as opposed to seeing it simply as a clash of competing ideas, and I’m glad to see it at least mentioned here.

Second, what’s the story on DaveScot? What’s his background? He was a character here, once upon a time, and is such a dominant force at UD, but I don’t know anything about the guy apart from his screen-name. I don’t mean personal info, just a sense of who he is and where he’s coming from intellectually.

Comment #154249

Posted by Darth Robo on January 10, 2007 10:17 AM (e)

“Me” may not be Larry, but I’m a wee bit surprised that a regular lurker of PT has never heard of him. I’ve also been put to the bathroom wall on occasion, but I’d hardly consider it to be the same treatment that people get on Dembski’s blog.

Comment #154250

Posted by DragonScholar on January 10, 2007 10:17 AM (e)

I certainly have to say Febbie handled herself professionally. I am deeply amused at her getting banned for “not understanding something” by DaveScott. So apparently if you don’t tow the line, you’re banned.

This has made me wonder if there’s ANYONE left at UD that can carry on an intelligent conversation. Yes, we joke about the bans we see, but there’s likely quite a few that we do NOT. At that rate, as noted here, you’re just going to end up with syncophants.

Which, in some ways, may explain things. Stay in the echo chamber long enough, and you’ll start believing the echos.

Comment #154260

Posted by W. Kevin Vicklund on January 10, 2007 11:17 AM (e)

Back in late July, there was a thread on a petition to save dolphins. The second comment is Wes explaining that he moved a bunch of metatalk to the Bathroom Wall. Look at the BW in the date range July 24-25, and see if your posts are there. My guess is that somebody else started spouting a bunch of “Darwinism is a cult and you can’t prove Darwin existed” BS and anything not dealing directly with the topic got axed.

Comment #154262

Posted by Peter on January 10, 2007 11:25 AM (e)

Enough of that, and soon all that’s left on UD is syncophants, like the crud at the bottom of a soup-pot that’s been boiling all night.

So they are essentially creating a memetic bottleneck.

Comment #154264

Posted by waldteufel on January 10, 2007 11:28 AM (e)

What’s the point in trying to intellectually engage with the clowns and DemskiBots at UD?

They have no original ideas, and none of them seem to have even a junior high school science student’s grasp of what science really is.

Comment #154267

Posted by Peter on January 10, 2007 11:40 AM (e)

I really have to say that after reading a fair amount of that UD entry with febble on it, it’s pretty appalling that they tossed her off declaring that she had some long-winded anti-ID comments. It seems to me that she was curious and wanted some real answers that she simply wasn’t getting. She responded in a detailed fashion that should promote constructive and educated discourse. Instead, she gets shut down by the Zhdanov to Dembski’s Stalin. Protect the dear leader.

Comment #154268

Posted by Darth Robo on January 10, 2007 11:43 AM (e)

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=45a51c071c28e3c9;act=ST;f=14;t=1272;st=630

For the record, most people who have their comments moved to here are not banned. It’s nice here at Pandas. :)

Comment #154270

Posted by Gary on January 10, 2007 11:43 AM (e)

Give me a break.
You jokers here and at KCFS and related sites ROUTINIELY ban people after smearing them.

POT. KETTLE. BLACK

Comment #154272

Posted by DragonScholar on January 10, 2007 11:50 AM (e)

Peter,

First of all “Memetic Bottleneck” would be a GREAT band name.

I’d say that’s a decent term, but I think of it as a case of where they’re massively lowering the diversity of information on the site. Any information that challenges certain preconceptions (apparently, anything DaveScot says), is eliminated and/or the sources of said information banned. Therefore information and discussion are extremely bounded, and the same cycles, ideas, and discussions repeat themselves without change - I’ve read UD since seeing the Vise, and frankly, its all the same. Its a place to go to have your conceptions reinforced, by and large.

The sad thing is that UD essentially is the embodiment of what many members claim to decry - the power-oriented, survival-of-the-fittest world that many of them inaccurately think Darwinian thought causes. A few Big Powers control membership, eliminate dissent, and promote themselves.

This leads to what one would expect - a lack of diversity and overall intellectual health and stability. If it was a gene pool instead of a blog it’d be highly inbred and reasonably docile population controlled by a few insecure Alphas eliminating any kind of diversity.

(And yes, the metaphors are a bit obnoxious, I admit. But illustrative).

Comment #154274

Posted by normdoering on January 10, 2007 11:54 AM (e)

I got banned after I pointed out Marvin Minsky’s book “The Society of Mind” which uses Dembski-like terminology before Dembski about “intelligent agents” but means by that “basically dumb computational circuits that work with other dumb agents to produce something smarter.”

I did however once sneak in a link to the Danny Hillis chapter of “Out of Control.”
http://www.kk.org/outofcontrol/ch15-d.html

Comment #154288

Posted by DragonScholar on January 10, 2007 12:44 PM (e)

It appears that the comment controversy is getting under DaveScot’s skin. Check this post here. Dembski’s rather amorphous comment policy is repeated, with some additional text from Dave.

The winning addition:

Uncommon Descent is not a soapbox for everyone with a chip on their shoulder against ID to repeat their trite, stale, and uninformed opinions. If you think that it should be a public dumping ground for anyone who has anything to say then go whine about it somewhere but whine about it somewhere else.

I would note with irony that UD is apparently the place for people who support ID to repeat their trite, stale, and uninformed opinions.

This brings up an irony of UD and the ID movement. Often I hear accusations thrown around about conspiracies to repress ID. However, I see very, very little commitment on the part of ID supporters to openc onversation and discussion. One may argue that Dembski wanting the blog to maintain a certain focus is appropriate (and to an extent, I feel it is understandable), but the creation of a prominent echo chamber seems to verge on hypocracy, considering.

I also feel, frankly, it weakens ID. After the Dover smackdown, it seems more and more apparent ID supporters are ready to engage in propaganda, PR, and smearing people - but not open and rational discussion. This just reinforces that image.

Comment #154291

Posted by Elizabeth Liddle on January 10, 2007 12:52 PM (e)

Hi, I’m Febble.

Thanks for all the comments. I’d just like to correct something that has appeared today on UD in response to this piece, and as, clearly, I no longer have right of reply at UD, you might have well have it right here, even though it has nothing to do with evolution (though a fair bit to do with decent data analysis).

DaveScot wrote: “…if you google her a bit you’ll find she’s a left-wing conspiracy theorist that thinks Bush stole the 2004 election by fraud. People like that are uneducable. Good riddance”

Actually I’m not and I don’t. In fact I spent a good part of the last year two years arguing that it is extremely unlikely that Bush stole the 2004 election by electronic fraud. I got involved because I realised that the exit pollsters had used a confounded measure of the magnitude of the the discrepancy between the poll and the count at precinct level, and suggested they reanalyse their data. Warren Mitofsky hired me to do so, and my conclusion (presented at the 2006 AAPOR conference in Montreal) was that the data strongly suggested a biased poll, and contra-indicated widespread electronic fraud.

Comment #154292

Posted by SDPaddlefish on January 10, 2007 1:06 PM (e)

If you really want to see some quick banning, try making an intelligent comment at Democratic Underground. If it doesn’t specifically refer to “Chimpy” and contain much hate language, you’re gone.

Comment #154293

Posted by Raging Bee on January 10, 2007 1:06 PM (e)

DaveScot wrote: “…if you google her a bit you’ll find she’s a left-wing conspiracy theorist that thinks Bush stole the 2004 election by fraud. People like that are uneducable. Good riddance”

But ID is about SCIENCE, not politics or religion, which is why people who don’t have the RIGHT religious or political opinions cannot be tolerated in an ID forum. _|:-O (Shocked Loser)

Comment #154295

Posted by secondclass on January 10, 2007 1:15 PM (e)

I got banned for calling Dembski’s bluff when he claimed that Freeman Dyson agreed with him on zero-energy information. If you ever play poker with Dembski, remember to always fold, or you’ll get kicked off the table.

Comment #154296

Posted by Peter on January 10, 2007 1:20 PM (e)

Febble/Elizabeth,
Thank you for the education. It would seem that no amount of reason or evidence is good enough for the UD folks…only assertions that reinforce the egoes of their demagoguery.
Feel free to stay and post. We can always invite you to our own religious wars where dissent is rampant and welcome.

Comment #154297

Posted by Elizabeth Liddle on January 10, 2007 1:40 PM (e)

SDPaddlefish: actually I’ve been posting what I regard as intelligent comments at Democratic Underground for quite awhile now, and I’ve never used the word “Chimpy” - not even once. There are a lot of intelligent posters there, and some real work gets done, although sometimes it feels like having a conversation on a battlefield.

If you are interested, here’s one of my posts on the exit polls:

http://journals.democraticunderground.com/Febble/3

I maintain the (probably unfounded belief) that you can have a proper conversation with anyone, anywhere, if you just ignore the crap, and stick to the argument. Although I have to say that belief has taken some knocks, largely, ironically from the “conspiracy theorists” of the left, but now, it seems from the right, as well.

Not from the Infidels, though, I must say.

Comment #154300

Posted by RBH on January 10, 2007 1:56 PM (e)

Gert Korthof reminds me that he also made the point that under Dembski’s definition of “intelligent”, natural selection is an intelligent agent. On the question of whether DNA is intelligently designed, Korthof concurs that it is:

Yes [Korthof agrees with Dembski], if ‘intelligent’ means ‘choosing between’ ! (p144), because natural selection chooses between genetically different individuals by differential reproduction. So according to Dembski’s definition natural selection is intelligent.

Italics original.

Wes Elsberry mentioned that Dembski had dismissed his version of that argument in the preface to one or another of his books. I know it wasn’t No Free Lunch – I have that book and it’s not there. Does anyone know where Dembski did his dismissing, and what the ground was?

Comment #154301

Posted by Mark Frank on January 10, 2007 2:00 PM (e)

I am another UK contributor who has gone through various stages of censorship on UD. I agree it really isn’t worth the effort of trying to post there - although I sometimes fall to temptation and sometimes the post gets through and sometimes it doesn’t.

I think the way it works there now is each of the contributors decides who gets banned for their own posts. I find the result is not so much that they eliminate anti-ID arguments - Jack Krebs seems to have no problem - but it is completely unpredictable when your post will get through if at all - which makes it pretty much unusable.

Maybe the error is to treat it as a forum for discussion about UD. After all Dembski says “This blog is for me mainly to get out news items about the ID movement and my work in particular.” It was never really intended as a two-way medium.

Comment #154302

Posted by DragonScholar on January 10, 2007 2:01 PM (e)

Elizabeth/Febbie,

Thanks for posting here. I hope you find the group here to be worth interacting with. I know I’ve learned a lot since I found this place.

I think actually conspiracy theorists are, in many cases, of a kind. Conspiracy theories are philosophical black holes that can suck anything into them. Example one is David Icke, a man capable of grafting ANYTHING to his convoluted theories.

The problem is that conspiracy theorists are very intolerant of dissenting worldviews. They often have various levels of personal/emotional investment in these theories. To challenge the theories is to challenge them.

It is my belief that the ID movement is partially a conspiracy theory movement - and rather openly in many cases. I feel that the recent losses in the American legal system are only reinforcing this feeling.

Comment #154303

Posted by Moses on January 10, 2007 2:13 PM (e)

Well, it seems like UD is still a wanker site. Until Demski grows up and deals with his flaws, including his inability to fire DaveScot, nothing will ever change at UD. Not that I mind. With a group like that presenting themselves as one of the players in the ID movement the ID movement can only diminish in crediblity.

OTOH, nice to see things are running smoothly at PT once again. The server issues drove me nuts and I decided to take a break from “the tubes.”

Comment #154305

Posted by Alison on January 10, 2007 2:22 PM (e)

Interesting that Dembski puts the blame on Wordpress for deleting comments. My version of Wordpress doesn’t do that.

I’ve tried posting on other pro-ID sites, and i’m wondering if Dembski gives out some kind of secret tutorial to ID bloggers that says “delete anyone who disagrees with you, especially if they’re making a rational point.” All the comments seem to be from one big happy family, with the occasional mention of the latest dissenter who was banned for being too stupid.

Comment #154307

Posted by Stevaroni on January 10, 2007 2:24 PM (e)

Febble is a self-identified (in that comment thread) Christian theist. She was calm and polite throughout. And what happened? Banned.

It speaks volumes that Feeble would be certainly welcomed, and probably engaged in great length, here on Pandas Thumb, in the very bosom of the enemy.

Yet among what should have been friends over at UD… well.

And that’s just the microcosm of the bigger picture. Science tolerates - actually, it encourages - skeptical analysis, in the belief that it keeps everybody honest and makes the product stronger. Creationism… not so much.

I ask you, deep down, which side knows that it’s on shaky ground?

Comment #154310

Posted by Nic George on January 10, 2007 2:33 PM (e)

Does anyone know who DaveScot actually is and what he does for a living?

Comment #154311

Posted by Raging Bee on January 10, 2007 2:34 PM (e)

It speaks volumes that Feeble would be certainly welcomed, and probably engaged in great length, here on Pandas Thumb, in the very bosom of the enemy.

I’m sorry, whose “enemy” are we again?

Comment #154315

Posted by GuyeFaux on January 10, 2007 2:44 PM (e)

The problem is that conspiracy theorists are very intolerant of dissenting worldviews. They often have various levels of personal/emotional investment in these theories. To challenge the theories is to challenge them.

Unfortunately, this is a side of effect both of a conspiracy theory being wrong and of a conspiracy theory being right; no matter what, the theorist ends up looking a bit pathological, as you have said.

For example, suppose that it really is the case that fluoridation of water is a secret communist conspiracy to sap your body of its precious bodily fluids, and that this fact really is known by only a few people, including yourself. Also suppose that you are willing to defend this “theory” tooth and nail; after all, you know that it is fact and that the future of your country depends on it. To everybody else, you’d come off pretty damned intolerant; in addition, since you’re one of the few people aware of the facts, you’re personally burdened by your “theory” and are more likely to take responsibility for it.

Comment #154317

Posted by GuyeFaux on January 10, 2007 2:49 PM (e)

…presenting themselves as one of the players in the ID movement the ID movement can only diminish in crediblity.

Reminds me of Voltaire’s prayer to God:
“I have never made but one prayer to God, a very short one: ‘O Lord, make my enemies ridiculous.’ And God granted it.”

Comment #154318

Posted by Dave Carlson on January 10, 2007 2:51 PM (e)

Elizabeth Liddle wrote:

Not from the Infidels, though, I must say.

That’s because everybody at IIDB thinks you rock. Well, I do anyway, and I bet I’m not the only infidel who does! :)
Dave aka someotherguy

Comment #154321

Posted by melatonin on January 10, 2007 3:01 PM (e)

***First, it’s great to see RBH mention Freudian ego defenses as a motivator for IDist behavior. Personally, I favor adding a psychological approach to understanding this conflict, as opposed to seeing it simply as a clash of competing ideas, and I’m glad to see it at least mentioned here.***

IF any contributors are of a psycholigical persuasion, Drew Westen’s recent imaging study in J. Cog Neuro. (18:11 1947+) on political partisanship and motivated processing (or the more freudian psychological defense) would be a good angle.

It basically shows that when information challenges strong pre-existing biases, little cold rational reasoning occurs (DLPFC), it’s an implicit emotional defense (amygdala, VMPFC, ACC etc).

Comment #154324

Posted by Me on January 10, 2007 3:10 PM (e)

Hello Raging Bee,

Sorry I don’t know who Larry is. I read the articles when they interest me and click the links when I want more detailed information. The names of the authors and participants really don’t interest me much so my apologies if I am not a careful enough reader.

Also, my apologies that I really don’t recall much about the article I read. I did manage to locate it here (http://www.pandasthumb.org/archives/2006/07/act_now_to_help.html) I understand that a poster (W. Kevin) further down in this discussion also found this article and commented that I may have had comments removed to the bathroom wall (whatever that is). It may be my comments still exist somewhere on this site, but they are not under the article that they were originally posted. So, even if I was incorrect about whether they were deleted or not (I guess, I don’t know anymore) I’d say that they were still censored. because they do not appear with the article where they originally appeared.

You’ll either have to take my word that I stop by this site on a regular basis to see what is going on in the anti science word of ID or believe that I don’t and I’m just here conspiring against you. It’s not really important to me, as your opinion of strangers and dissent has more impact on how relate to people. It just seems like the height of paranoia to conclude that I am someone I am not and I’m here lying to (presumably) discredit this board.

I guess the #1 rule for new posters is “always agree with the majority until they know you better, or expect the poison penned replies”.

At any rate, sorry to cause any cognitive dissonance - if it helps you feel better I shall recant everything and say that free speech reigns here and censorship has, and would never occur here, ever. I say it with all the sincerity it deserves.

Sorry for the interruption,

“Me”

Comment #154325

Posted by Flint on January 10, 2007 3:14 PM (e)

I guess I’m missing something here, but all of this extravagant breast-beating seems misdirected. UD exists as a religious and ideological mouthpiece, for the purpose of preaching a focused orientation. As such, it attempts to simulate “discussion” because this simulation can be organized in such a way as to make it appear that members of the public agree with the ideology. This is in contrast with creationist sites that present non-interactive materials as the format for their own sermons.

And this is why dissent is disappeared, rather than permitting it to be drowned out. Religions are based on consensus; even irrational, erroneous, or illiterate dissent would be disappeared because what’s persuasive to the target audience isn’t better evidence, better logic, or better deportment. What matters is *unanimity* - “there is only one side here, the right side, which we present.”

Perhaps if DaveScot were to change his name to Winston Smith, people on this forum would have a clearer idea of both what he does, and why he does it.

Comment #154326

Posted by IAMB on January 10, 2007 3:18 PM (e)

comstock wrote:

Does anyone have a URL to the comment where DaveScot threatened to hack the Panda’s Thumb?

Merry Christmas, late though it may be. I’ll let you put the vowels back in…

Comment #154334

Posted by Raging Bee on January 10, 2007 3:25 PM (e)

“Me;” if your comment is off-topic, it may be moved to the Bathroom Wall, especially if a lot of people are responding to it. Links to AtBC and the Bathroom Wall are on one of the lists on the right-hand side of the Main page here. If you can find where your post was moved (the site manager doing the moving normally announces it in a post of his/her own), you can find it and continue the debate with anyone else who wants to follow you there. It’s happened to my posts a few times. That may be a bit inconvenient, but “censorship” is clearly the wrong word to apply here – not just too strong a word, but totally off the mark.

Comment #154336

Posted by Robin Levett on January 10, 2007 3:29 PM (e)

Elizabeth, you said:

Hi, I’m Febble.

Thanks for all the comments. I’d just like to correct something that has appeared today on UD in response to this piece, and as, clearly, I no longer have right of reply at UD, you might have well have it right here, even though it has nothing to do with evolution (though a fair bit to do with decent data analysis).

DaveScot wrote: “…if you google her a bit you’ll find she’s a left-wing conspiracy theorist that thinks Bush stole the 2004 election by fraud. People like that are uneducable. Good riddance”

Hi, I’m Robin and I’m a blogaholic too…

I saw “tribune7”’s original post on that issue earlier today and tried to post an answer - but while my login still works, it appears I’m still banned…

Having said that, I think we can expect a recantation by DaveScot shortly…

Comment #154338

Posted by Stevaroni on January 10, 2007 3:40 PM (e)

I’m sorry, whose “enemy” are we again?

Well, Duh - The Judean Peoples Front!

(too obscure?)

Comment #154341

Posted by Laser on January 10, 2007 3:54 PM (e)

I thought it was the People’s Front of Judea?!

Comment #154342

Posted by Salvador T. Cordova on January 10, 2007 3:59 PM (e)

Salvador made a brief appearance with his normal derailing commentary, but Febble hauled the discussion back to the main point: Dembski’s operational definition of intelligence and its congruity with natural selection.

No! If Darwinian Natural Selection is itself self-contradictory or poorly stated (like the idea of “square circles”), then it is a moot point why any reconciliation should be attempted. There is no point in going further.

Note what I said:

I encourage your consideration of literature that is highly critical of of Darwinain evolution on simple theoretical and empirical grounds.

I think John Sanford argues extremely well that Darwinism has been falsified theoretically…
I think the literature out there both in peer-review and the popular press has made a devastating case against Darwinian evolution on theoretical and empirical grounds. Michael Denton’s book probably stands out as the classic scientific case agains Darwinian evoltution.

A good portion of Dembski’s argument is that Darwinian evolution is stated in a self contradictory way, like, “E = not-E”. Febble seemed unwilling to even look into important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution.

There is in direct theoretical and empircal contradiction to her hypothesis:

I consider the mechanism by which variance in our genetic inheritance interacts with natural selective pressures is an intelligent system.

For the record, I have no authority to ban anyone, and I had no part in her getting booted. I’m not aware than any PT contributor is banned from Uncommon Descent.

Anyway, thank you for letting me comment.

PS
And regarding the definition of intelligence, it can be left as an undefined primitive. The most fundamental parts of axiomatic systems and scientific theories usually are left as undefined primitives….

Comment #154347

Posted by Sir_Toejam on January 10, 2007 4:15 PM (e)

I guess the #1 rule for new posters is “always agree with the majority until they know you better, or expect the poison penned replies”.

sounds more like “poisioning the well” to me, but evidently not to “me”.

Comment #154348

Posted by Sir_Toejam on January 10, 2007 4:17 PM (e)

I thought it was the People’s Front of Judea?

bloody splitters!

Comment #154351

Posted by GuyeFaux on January 10, 2007 4:21 PM (e)

And regarding the definition of intelligence, it can be left as an undefined primitive.

I see. So Psychologists, economists, cognitive scientists and computer scientists have been wasting their time. Damn, wish I knew this before I got my AI degree.

Comment #154352

Posted by Sir_Toejam on January 10, 2007 4:25 PM (e)

Sal:

No! If Darwinian Natural Selection is itself self-contradictory or poorly stated

you mean deliberately misstated and poorly understood by yourself; don’t speak in generalities - say what you really mean.

Febble seemed unwilling to even look into important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution.

nooo…. she was unwilling to let you sidetrack her away from her actual point, which is something people suffering your particular form of dissonance constantly do as a defense mechanism.

Heck anybody who isn’t familiar with you, WD40, or Davetard can go check out endless examples in the AFDave thread on ATBC.

I’m not aware than any PT contributor is banned from Uncommon Descent.

you deliberatly blind yourself to a great many things; that’s also a result of your particular malady.

but then, you are mentally incapable of recognizing this, so I guess it’s rather pointless to mention it.

Comment #154372

Posted by GuyeFaux on January 10, 2007 4:51 PM (e)

Reflecting on this some more:

And regarding the definition of intelligence, it can be left as an undefined primitive.

This summarizes perfectly the vacuity of ID quite well. How can you say it’s not intelligence when intelligence is an undefined primitive?

So they quite wisely banned Febble for trying to give a definition to “their undefined primitive.”

Comment #154380

Posted by normdoering on January 10, 2007 5:03 PM (e)

GuyeFaux wrote:

Reflecting on this some more:

And regarding the definition of intelligence, it can be left as an undefined primitive.

This summarizes perfectly the vacuity of ID quite well. How can you say it’s not intelligence when intelligence is an undefined primitive?

So they quite wisely banned Febble for trying to give a definition to “their undefined primitive.”

And without a definition of “their undefined primitive” you run smack dab into the simple principle, as stated by David Brooks; “To explain the unknown by the known is a logical procedure; to explain the known by the unknown is a form of theological lunacy.”

Anyone want to try explaining that to Deepak Chopra:
http://www.huffingtonpost.com/deepak-chopra/survival-of-the-wisest-pa_b_38083.html

Feeble should try – at least she won’t get banned.

Comment #154382

Posted by Glen Davidson on January 10, 2007 5:08 PM (e)

No! If Darwinian Natural Selection is itself self-contradictory or poorly stated (like the idea of “square circles”), then it is a moot point why any reconciliation should be attempted. There is no point in going further.

But we don’t try to reconcile with your self-contradictory and poorly stated versions of evolutionary theory. There is no reason to try to deal with your imaginings of what natural selection is, nor your attempts to make it into some counterpart to your belief in revelation of “truth” to selected individuals.

A good portion of Dembski’s argument is that Darwinian evolution is stated in a self contradictory way, like, “E = not-E”. Febble seemed unwilling to even look into important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution.

This from the guy who calls simplicity “complexity” when it is improbable, and who claims that intelligence isn’t “natural”. I wonder how much more response anyone with such a confused understanding requires.

For the record, I have no authority to ban anyone, and I had no part in her getting booted. I’m not aware than any PT contributor is banned from Uncommon Descent.

Okay, so you’re too ignorant to comment on your allies’ dirty pool. Just as you’re too ignorant to comment on evolution.

Anyway, thank you for letting me comment.

You should appreciate it, since you guys don’t even allow the person or persons who are being maligned to respond in the forum in which it takes place. Double standard, yes.

PS
And regarding the definition of intelligence, it can be left as an undefined primitive.

Except to anyone with a scientific mind. Productive research continues into intelligence, while IDists shamelessly treat it as if it were Behe’s Black Box, or perhaps more to the point, as if it were a primordial spiritual phenomenon. This is another place where the religiosity of ID is more than a little apparent.

The most fundamental parts of axiomatic systems and scientific theories usually are left as undefined primitives….

This is why physics (like math) has such primitives, at least so far (it is not content with leaving them as such, however, since it is science), and biology does not. You have to delete knowledge for your “science” to begin to work even on paper.

Glen D
http://tinyurl.com/b8ykm

Comment #154383

Posted by SDPaddlefish on January 10, 2007 5:11 PM (e)

SDPaddlefish: actually I’ve been posting what I regard as intelligent comments at Democratic Underground for quite awhile now, and I’ve never used the word “Chimpy” - not even once. There are a lot of intelligent posters there, and some real work gets done, although sometimes it feels like having a conversation on a battlefield.

If you are interested, here’s one of my posts on the exit polls:

http://journals.democraticunderground.com/Febble…

I maintain the (probably unfounded belief) that you can have a proper conversation with anyone, anywhere, if you just ignore the crap, and stick to the argument. Although I have to say that belief has taken some knocks, largely, ironically from the “conspiracy theorists” of the left, but now, it seems from the right, as well.

Not from the Infidels, though, I must say.

If you haven’t used the word “chimpy” and hate language, nobody at DU knew what you were talking about and I assume, with good reason, that you received no responses. And unfortunately, your assumption about conversations with anybody, anywhere is wrong. Just go to DU and post something to the effect that the Bush’s are good people (and compared to Bill and Hillary they’re saints) but they are misguided on their policies, and you will be gone so fast that your kids will submit your will to probate.

Comment #154386

Posted by Doc Bill on January 10, 2007 5:25 PM (e)

I get it! Salvador works for Viewsonic and gets a kickback for every flat screen that’s wiped out by spewed coffee.

I must admit, after reading “undefined primitive” I got my screen, the plant and my sleeping cat! A new coffee spew record.

Oh, Sal, your entertainment value is First Class.

I’m thinking of using intelligence as an “undefined primitive” as a new pick-up line. What do you think?

“Hey, baby, I like a woman who shows a little undefined primitiveness.”

Could just work…

Comment #154387

Posted by DragonScholar on January 10, 2007 5:25 PM (e)

I see that this post is getting under the skin of people at UD, to judge by Sal’s recent post.

wrote:

And regarding the definition of intelligence, it can be left as an undefined primitive.

So technically, ID is about “Undefined Primitive Design.” Making it entirely meaningless at it’s core. If you’re going to talk Intelligence, you have to have something to talk about. Otherwise it’s meaningless.

Comment #154388

Posted by wright on January 10, 2007 5:26 PM (e)

I read the exchange (I guess it was an exchange of sorts) between Febble and DaveScot and found, unsurprisingly, that I couldn’t find how her banning made any sense. Having since read the stories of others who were banned from UD for, as far I can tell, raising interesting questions or quoting Dembski and Behe back at their supporters, I can only throw up my hands.

I’d say Flint’s comment pretty much hits it on the head.

Welcome, Febble. I’m no longer a Christian, but as a storyteller I very much enjoyed “Perhaps”.

Comment #154390

Posted by RBH on January 10, 2007 5:32 PM (e)

May I remind folks (this means you, Norm!) that it’s “Febble”, not “Feeble”. :)

RBH

Comment #154391

Posted by guthrie on January 10, 2007 5:32 PM (e)

Can no-one spell this poor womans name correctly?
Its not “feeble”, or any other variation you bozos can come up with!

Comment #154392

Posted by GuyeFaux on January 10, 2007 5:34 PM (e)

I guess it’s Christmas again. Sal “Undefined Primitive” Cordova has once again demonstrated that the best way to deal with the ID movement is to let it’s advocates talk.

Comment #154395

Posted by Elizabeth Liddle on January 10, 2007 5:49 PM (e)

Hi, Salvador

I appreciated your welcome and courtesy on UD, and I appreciate your courtesy here. So let me respond to your comment:

Salvador T. Cordova wrote:

No! If Darwinian Natural Selection is itself self-contradictory or poorly stated (like the idea of “square circles”), then it is a moot point why any reconciliation should be attempted. There is no point in going further.

I agree. So the first thing on the agenda should be an adequate statement of Darwinian Natural Selection. I invite you to state where you felt mine was inadequate, and/or what you consider an adequate statement. Then we can see where we might differ.

Salvador wrote:

A good portion of Dembski’s argument is that Darwinian evolution is stated in a self contradictory way, like, “E = not-E”. Febble seemed unwilling to even look into important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution.

There is in direct theoretical and empircal contradiction to her hypothesis:

Febble, on UD wrote:

I consider the mechanism by which variance in our genetic inheritance interacts with natural selective pressures is an intelligent system.

If you consider that there is a direct theoretical and empirical contradiction to this hypothesis, I would be delighted to hear it. Mine was concisely stated; I am sure the rebuttal can be stated with similar concision. I am certainly willing to look into any “important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution”, but I would like to know first why you find them convincing.

Salvador wrote:

And regarding the definition of intelligence, it can be left as an undefined primitive. The most fundamental parts of axiomatic systems and scientific theories usually are left as undefined primitives….

Well, my point is precisely that it can’t. As I see it, in conventional statistical terms Dembski’s null hypothesis apportions variance in the structure of life-forms thus: variance due to fundamentally stochastic factors, perhaps at the level of quantum particles - in other words truly “chance” or “random” factors; variance due to natural causes that we don’t yet know about - i.e. “natural” factors we believe may exist but we can’t model; and variance due to natural causes that we understand, and can model. The hypothesis he is testing (what would in conventional terms be the predictor of interest) is that additional variance is due to something called “intelligence”. Unusually, however, Dembski turns orthodox statistical testing methodology on its head, and, rather than modelling his hypothesis, he attempts to model his “error” terms, and on finding that these do not adequately account for the data, attributes “intelligence” to the remainder.

However, it is not this unorthodox approach to statistical hypothesis testing that I consider the major problem with his argument. Actually, I thought that was rather interesting. The problem as I see it is rather that “intelligence” itself may (and, in my view is) a product of both natural causes that we believe may exist but can’t model, and natural causes that we understand and can (and possibly even a contribution from true stochastic processes). So leaving “intelligence” as an “undefined primitive” entirely begs the question. A more productive approach, IMO, would be to consider the extent to which the “intelligence” manifest in the structure of life forms could have arisen through the kinds of “natural” algorithms that we know exist both inside and outside the realm of biology, indeed, which give the entire universe its structure.

I see no reason to believe it could not have done.

Cheers

Lizzie

Comment #154396

Posted by Robin Levett on January 10, 2007 5:55 PM (e)

Elizabeth:

The UDers are quoting your comment:

Regarding my “fraudster credentials”: I am a fraudster. I believe your election was inexcusably riggable and may well have been rigged. It was also inexcusably unauditable. I am convinced that there was real and massive voter suppression in Ohio, and that it was probably deliberate. I think the recount in Ohio was a sham, and the subversion of the recount is in itself suggestive of coverup of fraud. I think Kenneth Blackwell should be jailed.

as evidence that you believe the election was stolen…

Comment #154402

Posted by Jack Krebs on January 10, 2007 6:07 PM (e)

I’ve been browsing through this interesting set of comments and ran into this nice line from Lizzie:

I maintain the (probably unfounded belief) that you can have a proper conversation with anyone, anywhere, if you just ignore the crap, and stick to the argument.

This is a good rule to follow. It helps to have a good clear understanding of what your argument is, of course, but responding to crap, no matter how satisfying or necessary it may seem at the time, almost always leads the conversation into a downhill spiral.

It’s much better to do as Lizzie did, which was to stay relentlessly on-topic until the other side could take it no longer and had to punt by kicking her out of there.

Comment #154422

Posted by Elizabeth Liddle on January 10, 2007 6:45 PM (e)

Robin wrote:

Elizabeth:

The UDers are quoting your comment:

Regarding my “fraudster credentials”: I am a fraudster. I believe your election was inexcusably riggable and may well have been rigged. It was also inexcusably unauditable. I am convinced that there was real and massive voter suppression in Ohio, and that it was probably deliberate. I think the recount in Ohio was a sham, and the subversion of the recount is in itself suggestive of coverup of fraud. I think Kenneth Blackwell should be jailed.

as evidence that you believe the election was stolen…

I was incensed by Florida 2000. I was incensed again, by that footage on election day of long lines of (largely black) voters waiting for hours in the rain in Columbus, Ohio, to vote. I did not think it was a fair election. I do not think it was a fair election. I do not think your voting machines are reliable (electronic or otherways - maybe levers get a pass) and I think the election system in the US needs radical reform. I have been doing what I can to help people who are developing good random audit protocols. But I am not a conspiracy theorist, and I have taken a heck of a lot of flack, largely from the US left, for attempting to demonstrate that the exit poll discrepancy was not evidence of massive theft, and if anything, rather contra-indicates it. It drives me nuts that good evidence of unjust disenfranchisement has been sidelined because of irresponsibly flawed inferences made from the exit poll data.

I am confident Kerry would have done considerably better in Ohio had the playing field been level, and probably would have won New Mexico. But I have come to those conclusions after considering the evidence, not before. And having found myself in the extraordinary position of having been hired by Warren Mitofsky to re-analyse the actual exit poll data, I concluded from an extremely thorough examination of that data the evidence for a widespread conspiracy was simply not there. There was strong evidence in favor of the hypothesis that the poll had a pro-Democratic bias.

OK, back to the OP….

Comment #154425

Posted by Salvador T. Cordova on January 10, 2007 7:04 PM (e)

Febble suggested:

So the first thing on the agenda should be an adequate statement of Darwinian Natural Selection. I invite you to state where you felt mine was inadequate, and/or what you consider an adequate statement.

It seems your underlying premise is that Darwnian Natural Selection is the principle mechanism through which properties of biological reality have come to be. If this is your underlying assumption, and the assumption is false, further argumentation and attepmts at some sort of reconciliation is a moot point….

For starters, I will note, from first principles of population genetics alone, Motoo Kimura has demonstrated the impossiblity of that claim for the majority of molecular evolution. The full consequences of that are being elaborated by Geneticists like John Sanford at Cornell. I gave a link to Sanford’s book. Dawkins made passing reference to Kimura’s enigma in his book, Blindwatchmaker, but failed to give an adequate answer, and mostly evaded the issue with a few glib comments…

To be fair, a few have proposed non-Darwinian but naturalistic solutions to the evolution of life. In that sense it is not either Darwin or Design. However, imho, I think Sanford, ReMine, Dembski, Sternberg and others have made a good case that for sure Darwinian evolution could not possibly be the principle mechanism involved in the formation of life.

Therefore it is a moot point to even argue if Darwinian evolution can be likened to intelligence, since the hypothesized mechanism has been demonstrated theoretically to be mostly irrelevant to origins of the major features of biotic reality to the satisfaction of many in the ID community…

If you consider that there is a direct theoretical and empirical contradiction to this hypothesis, I would be delighted to hear it. Mine was concisely stated; I am sure the rebuttal can be stated with similar concision. I am certainly willing to look into any “important theoretical and empirical considerations that contradict the adequacy of Darwinian evolution”, but I would like to know first why you find them convincing.

I find the theoretical arguments convincing because they are logical and far more rigorously argued than what I see comming from the evolutionary community.

Trevors and Abel’s papers on Origin of Life and Self-Organization are a start, so is John Sanford’s book, and especially Michael Denton’s book.

PS
I wish to thank Richard Hoppe for allowing me to participate here, I am inquiring whether such reciprocity will be extended by Uncommon Descent to PT authors.

Comment #154426

Posted by Arden Chatfield on January 10, 2007 7:05 PM (e)

She suggests that what we’re seeing is the formation of a niche species within ID creationism on UD

What kind of niche species, exactly?

Comment #154428

Posted by Elizabeth Liddle on January 10, 2007 7:20 PM (e)

Salvador wrote:

It seems your underlying premise is that Darwnian Natural Selection is the principle mechanism through which properties of biological reality have come to be. If this is your underlying assumption, and the assumption is false, further argumentation and attepmts at some sort of reconciliation is a moot point….

No, it’s not my assumption. It’s a hypothesis. If you start by assuming your hypothesis is true, you are “begging the question”.

For starters, I will note, from first principles of population genetics alone, Motoo Kimura has demonstrated the impossiblity of that claim for the majority of molecular evolution.

Well, can you summarise his argument?

To be fair, a few have proposed non-Darwinian but naturalistic solutions to the evolution of life. In that sense it is not either Darwin or Design. However, imho, I think Sanford, ReMine, Dembski, Sternberg and others have made a good case that for sure Darwinian evolution could not possibly be the principle mechanism involved in the formation of life.

Well, again, I have to ask, can you make that case? I have attempted to explain what I consider to be the flaw in Dembski’s case, using his own operational definition of “intelligence”. With respect, I have not seen a rebuttal of my point. If the defining feature of an intelligent agent is “the power and capacity to choose [aka select] between options” (Dembski’s words) why is Natural Selection not a candidate for that intelligence?

I find the theoretical arguments convincing because they are logical and far more rigorously argued than what I see comming from the evolutionary community.

No, I meant, what is the content (not the quality) of the argument that convinces you?
Cheers

Lizzie

Comment #154431

Posted by Salvador T. Cordova on January 10, 2007 7:30 PM (e)

Febble wrote:

No, it’s not my assumption. It’s a hypothesis.

I apologize if I have misinterpreted your remarks, but to set the record straight, do you accept that Darwinain evolution by means of Natural Selection as the principle mechanism for the formation of life? Would that be fair of me to suggest that is your position, or at least the working hypothesis for the sake of discussion?

Comment #154433

Posted by Arden Chatfield on January 10, 2007 7:33 PM (e)

At any rate, sorry to cause any cognitive dissonance - if it helps you feel better I shall recant everything and say that free speech reigns here and censorship has, and would never occur here, ever. I say it with all the sincerity it deserves.

Well, given that you failed to produce a single real example of censorship here, I think we can be forgiven for not taking your claims of rampant censorship all that seriously.

“It happens ‘cuz I say so” isn’t too impressive, especially when it’s followed up by a sneery “oh okay, I’ll AGREE with you if that’s what you want”. You have a claim, be a grownup and back it up.

Comment #154438

Posted by Sir_Toejam on January 10, 2007 7:52 PM (e)

Syntax Error: mismatched tag 'quot'

Comment #154439

Posted by Salvador T. Cordova on January 10, 2007 7:56 PM (e)

Well, can you summarise his [Geneticist Kimura’s] argument?

In short: there are simply too many molecules for Natural Selection to effectively police and influence. For Natural Selection to police that many molecules, an appropriate number of organisms must be present. For Natural Selection to be effective, in general, there must be sufficient numbers of offspring that don’t see their lineage perpetuated. The number of offspring needed for Natural Selecition to work is dictated by the number of traits one wishes to preserve or evolve in the population. When the number of traits is prohibitively large, Natural Selection cannot possibly have the population resources it needs to evolve or even maintain properties of a population….

Kimura’s neutral theory is a well-developed scientific theory, but it’s full consequences have not been appreciated. In addition, it has it’s flaws because it too presumes naturalistic evoltution….

Via a “proof by contradiction” Kimura demonstrated the overwhelming majority of molecules in biotic reality cannot be subject to Natural Selection.

See: Motoo Kimura

With the advent of molecular biology, the study of evolution assimilated new techniques and ideas. One of the new ideas was introduced by Japanese biologist Motoo Kimura. Kimura is the father of the “neutral theory,” initially labeled “non-Darwinian theory” by its opponents. The neutral genetic theory Kimura introduced in 1960 is that a large majority of evolutionary changes at the molecular level are due to mutations that have no effect on fitness. When there is an effect, it is so small that the dynamics of these changes are determined mainly by genetic drift and not by natural selection. The vast majority of mutations, according to his theory, are selectively equivalent or neutral. For the neutral theory, the main factor directing evolution is not natural selection but random drift.

Kimura tried to assert the compatibility of his theory with Darwin, but in the modern day, that assertion seems increasingly implausible, especially if functionality is discovered in more and more sections of what has been previously deemed unnecessary evolutionary leftovers….

Geneticsit John Sanford builds on Kimura’s ideas. I pointed out Nachman’s U-Paradox at Uncommon Descent poses yet another problem, and so does Haldane’s dilemma.

You have requested a summary, I hope you can see, even a cursory survey of the reasons will not be done in one sitting. I do however invite you to read the literature.

Salvador

Comment #154440

Posted by normdoering on January 10, 2007 7:57 PM (e)

RBH wrote:

May I remind folks (this means you, Norm!) that it’s “Febble”, not “Feeble”. :)

Who are you to dare question the Microsoft Word spellchecker, RAH?

Comment #154441

Posted by Salvador T. Cordova on January 10, 2007 8:02 PM (e)

Febble asked:

No, I meant, what is the content (not the quality) of the argument that convinces you?
Cheers

The content is laid out in the follwoing books and aritcles:

Mystery of Life’s Origin by Thaxton, Bradley, Olsen

Evolution a Theory in Crisis by Denton

Genetic Entropy by Sanford

No Free Lunch by Dembski

“Biological function and the genetic code are interdependent” by Voie

“Chance and necessity do not explain the origin of life” by Trevors and Abel

By the way, have you watched, Unlocking the Mystery of Life (the video which caused the uproar in the UK)? That is a good introduction….

Comment #154442

Posted by Katarina on January 10, 2007 8:03 PM (e)

But evolutionary theory accepts random drift as a major factor. And you’re not telling us anything we don’t know: Natural selection selects organisms, not molecules. None of this contradicts evolution theory.

It’s true that dwindling populations are in trouble in an evolutionary sense. These are called “sink” populations.

You fail to make a relevant point, at any rate.

Comment #154443

Posted by Flint on January 10, 2007 8:07 PM (e)

do you accept that Darwinain evolution by means of Natural Selection as the principle mechanism for the formation of life?

I find the phrase “formation of life” ambiguous. Does this refer to biogenesis, or evolution? My understanding is that the proposed mechanisms for evolution purport to explain how life changes slightly from one generation to the next, rather than how it started.

I personally speculate that replication with variation, and thus selection, occurred long before the level of organization and sophistication had reached a point anyone today would consider “life”. But that’s perhaps beside the point. The point is, selection is an intelligent process if and only if there is a *pattern* of selection. Lottery winning numbers are surely selected, but the mechanism is carefully organized to make that selection as random as possible. If selection follows a pattern and exhibits rules, then it meets Dembski’s requirements.

My understanding of Salvadore’s axiomatic undefined primitive is, intelligent design is an inherent, basic, intrinsic property of life, no less so than mass. We observe it directly; it requires no complex theoretical explanation of how it may have developed. It didn’t develop. It just IS.

Comment #154444

Posted by Salvador T. Cordova on January 10, 2007 8:16 PM (e)

Febble asked:

the defining feature of an intelligent agent is “the power and capacity to choose [aka select] between options” (Dembski’s words) why is Natural Selection not a candidate for that intelligence?

Because the concept of selection in Natural Selection is being equivocated with the conception of Selection in the ID sense. This equivocation is a serious logical error.

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose. If one takes a population genetics book and tries to define “selection” from first principles, it will look nothing like the concept of selection that a conscious intelligent being does when that being selects. The question you pose is therefore fundamentally illogical.

Alternatively, it could be successfully argued, imho, that Natural Selection is an oxymoron and/or misnomer, therefore one could argue your question is like asking how a square circle can be round.

Furthermore, the issue still remains whether Natural Selection is the principle mechanism behind many of the features of life. One can begin with the question of the Origin of Life and the role of Natural Selection in the Origin of Life.

Comment #154445

Posted by Sir_Toejam on January 10, 2007 8:21 PM (e)

You fail to make a relevant point, at any rate.

welcome to the wonderful world of ID.

Comment #154446

Posted by KiwiInOz on January 10, 2007 8:23 PM (e)

Salvador asks “do you accept that Darwinain evolution by means of Natural Selection as the principle mechanism for the formation of life?” Yet again this is evidence that he is wilfully misconstruing what Darwinian evolution by NS is.

Once again for Salvador. Abiogenesis refers to the formation of life (from non life). Evolution (by NS and other mechanisms) is responsible for the DIVERSITY of life.

But then we expect nothing but cognitive dissonance and dissembling from our good friend Sal.

Comment #154447

Posted by H. Humbert on January 10, 2007 8:25 PM (e)

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose. If one takes a population genetics book and tries to define “selection” from first principles, it will look nothing like the concept of selection that a conscious intelligent being does when that being selects. The question you pose is therefore fundamentally illogical.

Ah, I think I see now. “Selection” in the ID sense means selection with planning and purpose.

So ok, Sal, what plan and what purpose has ID identified in biological structures?

Comment #154449

Posted by Steviepinhead on January 10, 2007 8:29 PM (e)

For Bog’s sake, Sal, you can’t even correctly “summarize” Dembski’s claims, much less correctly charactarize Kimura or the ToE.

Do you ever read what you right before you spin it off into the electronic void?

Comment #154450

Posted by Steviepinhead on January 10, 2007 8:30 PM (e)

And, one might fairly ask, do I ever read what I “right” before I punch “Post.”

Sigh.

Must be pizza time again…

Comment #154451

Posted by KiwiInOz on January 10, 2007 8:34 PM (e)

You’re right Steviepinhead. Anyone who spells summarise with a z should be ashamed of hitting the post button.

Comment #154452

Posted by Boo on January 10, 2007 8:35 PM (e)

Alternatively, it could be successfully argued, imho, that Natural Selection is an oxymoron and/or misnomer, therefore one could argue your question is like asking how a square circle can be round.

Please illustrate this argument.

Comment #154454

Posted by Sir_Toejam on January 10, 2007 8:36 PM (e)

hey Sal!

there’s a very interesting thread on abiogenesis which I’m sure your participation would be welcome in.

You can find it here:

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=45a5a274542d83b1;act=ST;f=14;t=3902

rather pointless to bring it up here, though.

Comment #154455

Posted by Tom Moore on January 10, 2007 8:40 PM (e)

That debate between Febbie and DaveScot was by far the best exchange I’ve seen on UD. I have mixed it up over there enough to come close to being banned, but nowhere near as masterfully as Febbie did it. She was so superbly lucid and persistent that DaveScot simply gave up in exasperation, unable to dismiss her arguments. So he dismissed her in the only way he could.

Still there are several folks over there who have been speaking out and defending the value of having evolutionists make their case on UD. But there is no way they will ever admit to having been bested, just as there is no one over here who would do so.

That suggests to me an open debate between the advocates, on a neutral site, with impartial judging by a lay group, such as the press. This may be the only way to get beyond dismissive rebuttals and name calling.

Comment #154457

Posted by H. Humbert on January 10, 2007 8:47 PM (e)

That suggests to me an open debate between the advocates, on a neutral site, with impartial judging by a lay group…

That already happened. Just look up “Kitzmiller v. Dover Area School District.”

Comment #154458

Posted by RBH on January 10, 2007 8:54 PM (e)

Salvador wrote

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose.

Sorry, Sal. Dembski emphatically ruled that out in “Intelligent Design Coming Clean”. The intentions of the designing agent are explicitly ruled to be not part of the ID “research program”. And Febble is arguing from Dembski’s definition, which does not include reference to a “conscious intelligent being”. This thread is about Febble’s attempt to explore the consequences of adopting Dembski’s definition, not yours. This is the kind of behavior I meant when I characterized your ‘contribution’ to the UD thread as a derailment. It’s a derailment here, too.

RBH

Comment #154459

Posted by Robin Levett on January 10, 2007 8:56 PM (e)

Elizabeth:

Thanks for the clarification - and, BTW, we don’t use electronic machines in Beckenham…

Sal:

Are you really trying to claim that Kimura’s work doesn’t count as evolutionary theory as the evolutionary biologists would define it simply because you insist on calling evolutionary biology “Darwinism”?

Can you produce a quote of Kimura claiming that:

In short: there are simply too many molecules for Natural Selection to effectively police and influence. For Natural Selection to police that many molecules, an appropriate number of organisms must be present. For Natural Selection to be effective, in general, there must be sufficient numbers of offspring that don’t see their lineage perpetuated. The number of offspring needed for Natural Selecition to work is dictated by the number of traits one wishes to preserve or evolve in the population. When the number of traits is prohibitively large, Natural Selection cannot possibly have the population resources it needs to evolve or even maintain properties of a population….

or even something equivalent to it? It sounds an ack-basswards way at best of putting neutral theory, which I understood (albeit I’m not a biologist) was directed at the fact that most mutations are neutral with respect to the organism’s environment - it’s to do with the effect of the mutations, not the number of molecules. That last phrasing is odd, of course; since the mutation happens to DNA, which is “a” molecule, and most mutations happen to regions of the DNA molecule that are not expressed - hence their neutrality.

Comment #154460

Posted by Dave Carlson on January 10, 2007 8:57 PM (e)

Derailment or not, I would be very interested in how Sal thinks the “purposeful reason” used by the intelligent designer can be scientifically discerned. Another time and place, perhaps.

Comment #154461

Posted by RBH on January 10, 2007 9:07 PM (e)

Salvador offered as his gloss of Kimura this bait and switch paragraph:

In short: there are simply too many molecules for Natural Selection to effectively police and influence. For Natural Selection to police that many molecules, an appropriate number of organisms must be present. For Natural Selection to be effective, in general, there must be sufficient numbers of offspring that don’t see their lineage perpetuated. The number of offspring needed for Natural Selecition to work is dictated by the number of traits one wishes to preserve or evolve in the population. When the number of traits is prohibitively large, Natural Selection cannot possibly have the population resources it needs to evolve or even maintain properties of a population….

Notice the switch? It’s from “that many molecules” to “number of traits”. Sorry, Sal. That ain’t Kimura; it’s word salad.

RBH

Comment #154462

Posted by Flint on January 10, 2007 9:15 PM (e)

This thread is about Febble’s attempt to explore the consequences of adopting Dembski’s definition, not yours.

But this is the key to why Febble got booted. She insisted on sticking strictly to Dembski’s definition, Dembski’s definition made natural selection an intelligent process, and this put DaveScot in the position of either admitting evolution has all the intelligence necessary for what we observe (intolerable), or admitting that Dembski was wrong (even more intolerable). He tried valiently to change the subject, but Febble didn’t bite. What alternatives did he have left? None he could possibly see, that’s for sure.

Comment #154464

Posted by Zachriel on January 10, 2007 9:31 PM (e)

Hi Everyone.

My name is Zachriel, and I’ve been banned three times.
http://zachriel.blogspot.com/2006/06/uncommon-dissent.html

Comment #154467

Posted by drerio on January 10, 2007 9:41 PM (e)

I don’t understand how Sal can say Kimura is against evolution. Kimura concludes his 1968 paper in Nature by saying:

To emphasize the founder principle but deny the importance of random genetic drift due to finite population number is, in my opinion, rather similar to assuming a great flood to explain the formation of deep valleys but rejecting a gradual but long lasting process of erosion by water as insufficient to produce such a result.

In other words, the genetic drift he proposes is precisely a slow gradual process that can change species. I can’t find anything in his writings to support Sal’s interpretation that Kimura thought evolution couldn’t happen or that mutation were not capable of creating diversity. Most of what I can find, rather, suggests that he thought the mutation rates must be much higher than expected, just mostly neutral.

Comment #154470

Posted by Henry J on January 10, 2007 9:56 PM (e)

And regarding the definition of intelligence, it can be left as an undefined primitive.

So DS on UD has an undefined primitiveness quotient of 150?

(Or am I misinterpreting that comment?)

Henry

Comment #154474

Posted by Salvador T. Cordova on January 10, 2007 10:20 PM (e)

Robin asked:

Are you really trying to claim that Kimura’s work doesn’t count as evolutionary theory

No. But the topic was natural seleciton, and furthermore, Kimura’s appeal to pure diffusion fails as an explanation as well. The selectonist camp is quite happy to point out fatal flaws in Kimura’s theories. Thus we have the delightful situation that the Neutralists (Kimura and friends) and the Selectionists have found fatal flaws in each other’s theories. Both are fundamentally wrong somewhere, although the edge definitely goes to Kimura regarding who is closer to the truth and the appropriate scientific methodologies to arrive at it…..

I said:

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose.

RBH objected:

The intentions of the designing agent are explicitly ruled to be not part of the ID “research program”.

There is a difference between saying “we don’t investigate what the plan or the identity of the Designer is” versus “the Designer has no identity nor plan or power of choice”. One can assert that an intelligent agency in general the power of choice or plan without actually investigating the details of the choice or the plan.

The fact remains, your respones is inadequate to refute my assertion that the word “selection” is being equivocated.

Finally, regarding undefined primitives, here is something RBH and John Lynch didn’t cite:

IS INTELLIGENT DESIGN A FORM OF NATURAL THEOLOGY? by Bill Dembski

At this point critics of intelligent design often protest that design theorists have yet to provide a careful definition of intelligence. While I agree that terms need to be defined as carefully as possible, the call for definition can itself become a subterfuge. Thus the call for definition can become a way of avoiding the challenge posed by an idea by endlessly requiring further clarification of key terms. The later Wittgenstein certainly thought the call for definition was overrated. Indeed, the finiteness of language itself implies that the call for definition must at some point either end or issue in circularity. Within intelligent design, intelligence is a primitive notion much as force or energy are primitive notions within physics. We can say intelligible things about these notions and show how they can be usefully employed in certain contexts. But in defining them, we gain no substantive insight.

The very word intelligence derives from the Latin words “inter” (a preposition meaning “between”) and “lego” (a verb meaning to “choose” or “select”). Thus strictly speaking intelligence refers to the capacity to choose or select. Yet unlike natural selection, which operates without goals or purposes, ordinarily when we think of an intelligence as choosing or selecting, it is with a goal or purpose in mind. We could therefore define intelligence as the capacity for rational or purposive or deliberate or premeditated choice. Have we therefore defined intelligence to the satisfaction of the critics of intelligent design? Hardly. When Howard Van Till, for instance, issues his call for definition, his worry is not what intelligence or design means as such, but what these terms mean in contexts where no embodied intelligence was acting and thus where his view of nature as a complete system of natural causes (cf. his fully gifted creation and robust formational economy) comes under pressure. Invariably I’ve found that the call to define intelligence by critics of intelligent design is not a call for clarification but a defensive move to relieve pressure from some aspect of the critic’s own worldview that intelligent design calls into question.

Comment #154479

Posted by Salvador T. Cordovaq on January 10, 2007 10:38 PM (e)

drerio wrote:

In other words, the genetic drift he proposes is precisely a slow gradual process that can change species. I can’t find anything in his writings to support Sal’s interpretation that Kimura thought evolution couldn’t happen or that mutation were not capable of creating diversity. Most of what I can find, rather, suggests that he thought the mutation rates must be much higher than expected, just mostly neutral.

The issue again was Natural Selection’s role in shaping biological reality. If the majority of biological reality (at least in terms of molecules) is not subject to selection, what does that say?

A subtlety that has not been sufficiently explored is what if Kimura is right that Natural Selection is not responsible for the majority of molecular evolution, but yet we find that these very same molecules serve a function? That is an empirical refutation the claim that Natural Selection was responsible for the design found in those molecules. What do we do then in light of the fact we may have found DESIGNS not made through Darwinian processes?

To quote Eric Davidson echoing Gould: “neo-Darwinism is Dead”.

Comment #154483

Posted by Sir_Toejam on January 10, 2007 11:09 PM (e)

No. But the topic was natural seleciton, and furthermore, Kimura’s appeal to pure diffusion fails as an explanation as well. The selectonist camp is quite happy to point out fatal flaws in Kimura’s theories. Thus we have the delightful situation that the Neutralists (Kimura and friends) and the Selectionists have found fatal flaws in each other’s theories. Both are fundamentally wrong somewhere, although the edge definitely goes to Kimura regarding who is closer to the truth and the appropriate scientific methodologies to arrive at it…..

Jeebus! could you have possibly fit more strawmen and nonsequitors into a single paragraph, Sal?

-natural selection is part and parcel to the ToE
-Kimura’s “appeal to pure diffusion” is a complete nonsequitor to the post you are responding to
-Kimura is not a “neutralist”, he merely proposed an alternative mechanism to generate variation. He does not say that he thinks it the only one, nor do “selectionists” (gees, it makes me ill just to type your idiotic constructions) think that natural selection acting on random mutations is the only mechanism that generates variability either.
-define “fatal”, given Kimura never used the term himself.

“appropriate” scientific metholodologies? what the hell does “appropriate” mean, considering that your ilk don’t appear to even understand what a theory is, let alone the scientific method? I challenge you to pick ten published articles that show how Kimura’s theories are more “appropriately” tested than any given ten articles demonstrating how natural (and/or sexual) selection shapes traits in any given population. Of course you won’t, because you simply can’t.
Unless, of course, you admit that your definition of “appropriate” is entirely an invention of your fevered imagination, much like how you guys like to reinvent the definitions of lots of commonly used words.

You idiots like to pretend there aren’t literally THOUSANDS of articles in the literature that are fantastic pieces of work demonstrating how selection actually works in the field, much like Behe likes to pretend there aren’t hundreds of articles demonstrating the evoltuion of the immune system and flagella.

really Sal, you haven’t got anything going for you but willfully imposed blindness and hyperbole.

put up or shut up doesn’t even register with you guys, does it. Hell, it can’t, or you would have had to recognize your delusions for what they were long, long ago.

Comment #154523

Posted by Henry J on January 10, 2007 11:30 PM (e)

What the heck does it mean to say that natural selection has to “police” molecules?

Henry

Comment #154524

Posted by PvM on January 10, 2007 11:31 PM (e)

When Wesley was one of the earlier ones to point out how Dembski’s own definitions could not eliminate natural selection as a designer, Dembski was forced to accept the existence of apparent versus actual specified complexity, where the former was without purpose and design (merely the result of an algorithm) while the latter one was caused by a ‘real designer’ with purpose and foresight in mind.
However, Dembski has yet to show how to distinguish between purposeful design and functional design.

Comment #154527

Posted by Sir_Toejam on January 10, 2007 11:37 PM (e)

What the heck does it mean to say that natural selection has to “police” molecules?

only Sal’s imagination can answer that question for you.

Comment #154528

Posted by Sir_Toejam on January 10, 2007 11:45 PM (e)

IS INTELLIGENT DESIGN A FORM OF NATURAL THEOLOGY?

could be.

It sure ain’t science.

Comment #154531

Posted by PvM on January 11, 2007 12:04 AM (e)

UcD apologetics are trying to claim that Febble took an informal definition of intelligence when quoting Dembski.
I am sure that many of them may be unaware with Dembski’s writings so here are some other examples:

In particular, evolution attributes intelligence, the power of choice, to a fundamentally irrational process, namely, natural selection. But nature has no power to choose. Real choices involve deliberation, that is, some consideration of future possibilities and consequences.

Nature surely has a power to chose, but the choice may not take into consideration future possibilities and consequences, but then again, perhaps neither do humans who may base their choices on lessons learned from the past.

Sadly enough, Dembski tends to be self contradicting in many of his comments. Defining choice suddenly to be something which requires a purpose, he undermines his own arguments about intelligent design.

or

By intelligence, here, I mean something quite definite, namely, the causal factors that change one probability distribution into another and thus, in the present discussion, transform a blind search into an assisted search. A logically equivalent, information-theoretic reformulation of this definition takes intelligence as those causal factors that induce a net increase in information as measured by the information measure I. Note that by a stochastic mechanism, here, I mean any causal process governed exclusively by the interplay between chance and necessity and characterized by unbroken deterministic and nondeterministic laws.
Intelligence acts by changing probabilities. Equivalently, intelligence acts
by generating information. For instance, a slab of marble temporarily has a
high probability of remaining unchanged. Then, without warning, Michelangelo
decides to sculpt David, and the probability of that marble slab taking on a new form (i.e., receiving new information) now changes dramatically.

But this is exactly what natural selection does…

Comment #154533

Posted by PvM on January 11, 2007 12:11 AM (e)

Why then did Kimura find its place in evolution textbooks, unlike other anti-Darwinists ?

* The Neutral Theory had testable consequences such as “changes in DNA that are less likely to be subject to natural selection occur more rapidly”.
* The growing evidence supporting the Neutral Theory
* The Neutral Theory made a lasting contribution to population genetics theory
* The Neutral Theory is more like a theory in physics or chemistry (predictions, laws)
* Kimura built his theory on accepted knowledge in genetics and population genetics and at the same time criticised it and extended it
* Kimura still allowed for negative selection to eliminate most new mutations
* Kimura did not deny the existence of natural selection on morphological levels

http://home.planet.nl/~gkorthof/kortho37.htm

From neutral to nearly neutral…
And of course, neutrality itself is a selectable trait…
And essential for evolvability

Neutrality and selection play quite nicely together, each their own role.

Comment #154577

Posted by Elizabeth Liddle on January 11, 2007 2:57 AM (e)

Robin: I only just noticed the source of your quote (an edit to DaveScot’s post on UD). I’d just like to point out that the next sentence of mine, following the part that DaveScot posted was:

However (and I’ll come clean now in case you want to read no further) I don’t believe the exit polls in themselves are evidence for fraud. I don’t think they are inconsistent with fraud, but I don’t think they support it either. Read on for my reasoning.

http://www.dailykos.com/story/2005/4/6/8028/83645

So his is a classic quote-mine. The word “fraudster” was current in DKos at the time because of an acrimonious debate between those who questioned the validity of the election, and those who wanted to “move on”. “Frauster” was coined for the first group (a pejorative). I allied myself with the “fraudsters” in the paragraph I wrote. But the point of my post was to debunk the argument that the exit polls indicated massive vote theft. The “snark-free” bit of the title was because my previous post (also arguing against bad statistical arguments made from the exit polls) had been a bit, well, snarky.

So it’s a quote mine. I also find it fairly hilarious, considering a quick google will indicate the degree of animosity I have engendered amoonst those who maintain the election was stolen. Sorry about another derail, but DaveScot must have tried quite hard to find a quote from me about exit polls that might imply that I that considered the 2004 election stolen, and this is my only opportunity to try and provide context.

There’s an informative interview with my colleague, Mark Lindeman, here, that might clear up the apparently willful misreading of my position by DaveScot. I remain a passionate advocate of election integrity.

http://www.neuralgourmet.com/2006/07/17/of_public_opinion_exit_polls_and_fraud_or_the_lack_thereof_an_interview_with_mark_lindeman_part_i

Comment #154602

Posted by Elizabeth Liddle on January 11, 2007 7:12 AM (e)

Salvador wrote:

Febble asked:

Febble wrote:

the defining feature of an intelligent agent is “the power and capacity to choose [aka select] between options” (Dembski’s words) why is Natural Selection not a candidate for that intelligence?

Because the concept of selection in Natural Selection is being equivocated with the conception of Selection in the ID sense. This equivocation is a serious logical error.

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose. If one takes a population genetics book and tries to define “selection” from first principles, it will look nothing like the concept of selection that a conscious intelligent being does when that being selects. The question you pose is therefore fundamentally illogical.

Thanks, Salvador, for the clarification of your point. My response:

If “selection in the ID sense pertains to an intelligence have [sic] at least some purposeful reason for making a choice” then the next question is: must Specified Complexity arise from such an “purposeful” intelligence or could it arise from mere “intelligence” as operationally defined by Dembski? I see nothing in Dembski’s argument that requires “purposeful” intelligence as the generator of CSI. My example of a filter showed that his Actualization-Exclusion-Specification conditions are fulfilled by any natural sorting mechanism. My favourite example is of Chesil Beach, an 18 mile beach on the south coast of England in which the pebbles are finely graded from course sand at the western end to small boulders at the east. There is Actualization (one out of a range of possible beaches was actualized); Exclusion (at any given point in the beach pebbles not conforming to tight size limits are excluded; and its pattern is Specified (it is both specified a priori – the actual pebbles are constantly being renewed and replaced, and yet the beach retains its sorted character – and can be inferred to be Specified a posteriori, by Dembski’s own reasoning – pebbles graded systematically from course sand to small boulders belong to a class of systematic arrangements of pebbles that forms an tiny subset of the total possible arrangements of pebbles. I doubt whether you, or Dembski, would categorize the combination of wind, tide and topography that generates this pattern of pebbles as “purposeful intelligence”. But those three factors together form an algorithm that has “the power and capacity to choose between options”. Small pebbles are chosen (selected), in preference to large pebbles at the eastern end, and large pebbles are chosen in preference to small at the Western end.

My question therefore is not illogical. It may have an answer, but I have yet to see Dembski (or anyone else) argue why intelligence must be “purposeful” to generate CSI. Indeed Dembski, as RBH has noted, specifically rules it out as a necessary condition.

Salvador wrote:

Alternatively, it could be successfully argued, imho, that Natural Selection is an oxymoron and/or misnomer, therefore one could argue your question is like asking how a square circle can be round.

Well, one could, but in that case Dembski’s definition of “intelligence” is also a misnomer. I’d be happy to rename Natural Selection “Natural Sorting”. But “sorting”, whether “natural” or “purposeful” would also generate CSI, as I have just demonstrated.

Salvador wrote:

Furthermore, the issue still remains whether Natural Selection is the principle mechanism behind many of the features of life. One can begin with the question of the Origin of Life and the role of Natural Selection in the Origin of Life.

Certainly the issue remains. The evidence seems to support the hypothesis; I have not seen it falsified. But all scientific models are provisional – falsifiability is a necessary property for a scientific hypothesis.

Thank you (and RBH) for the opportunity to continue this conversation, even if we still disagree.

Cheers

Lizzie

Comment #154603

Posted by Darth Robo on January 11, 2007 7:13 AM (e)

Sal said:

“By the way, have you watched, Unlocking the Mystery of Life (the video which caused the uproar in the UK)? That is a good introduction….”

This the one in those ID packs that were sent to UK schools? And were shown to ministers to see if they agreed if it was a suitable educational resource? And was instantly thrown out as rubbish? Yeah, ID is doing great over here!

Thanks, but you can keep your crap were it belongs - flushed down the toilet.

Comment #154606

Posted by Elizabeth Liddle on January 11, 2007 7:45 AM (e)

Salvador wrote:

I apologize if I have misinterpreted your remarks, but to set the record straight, do you accept that Darwinain evolution by means of Natural Selection as the principle mechanism for the formation of life? Would that be fair of me to suggest that is your position, or at least the working hypothesis for the sake of discussion?

I consider that the evidence supports the hypothesis that the variety of life on earth has been generated by the processes that are described in the Darwin’s Theory of Evolution, namely: replication with modification, and natural selection. I don’t see any reason to suppose that the same kind of algorithm (greater replication of whatever is best able to replicate) would not also apply to any self-replicating molecule, so my working hypothesis, were I in the field of abiogenesis, which I’m not, would be that the mechanism could also be responsible for the creation of life from non-life. Indeed I would consider the dividing line between the two somewhat blurred.

But, as I said, this is not a premise, it’s a hypothesis. But the hypothesis is of a mechanism that satisfies the conditions (sorting mechanism) necessary to generate CSI. Therefore, IMO, the detection of CSI does not falsify the hypothesis.

Comment #154608

Posted by Katarina on January 11, 2007 7:53 AM (e)

But the hypothesis is of a mechanism that satisfies the conditions (sorting mechanism) necessary to generate CSI. Therefore, IMO, the detection of CSI does not falsify the hypothesis.

Great point!

Comment #154617

Posted by caligula on January 11, 2007 8:19 AM (e)

Sal,

I want to express my regrets about the behavior of UD mods.

First, Febble’s original question about detecting intentionality from “design” was never answered nor treated with dignity. DaveScot retreated to rhetorics about the origin of life instead. (I’m glad that you are finally trying to respond Febble’s question though.) In general, both mods who replied clearly stepped on a sidetrack.

Second, no sensible reason has been given for silencing Febble. Only two illogical reasons were given.

Initially, DaveScot declared that Febble failed to make note of the fact that newly fixed alleles are destroyed by random mutations before subsequent mutations have time to accumulate in the same trait. According to DaveScot’s words, this demonstrates that Febble misunderstands the basics of ToE. In reality, DaveScot’s claim is alien both for evolutionary biology and for common sense. I asked DaveScot to provide evidence for his assertion, but my post was merely removed.

Later, in a new thread, DaveScot declared that Febble misunderstands the basics of ToE by claiming that “natural selection” can remember mistakes and good tricks. In reality, however, Febble said that “natural selection+replication with modification”, i.e. the adaptation process as a whole, has a memory. Which is quite sensible. Both DaveScot and Patrick kept asking: “how can natural selection remember not to repeat the same mutation again”. In reality, however, the “repeating” in Febble’s argument probably concerned reproduction, not mutation. A mistake is not repeated, but instead gets forgotten, when a harmful allele fails to increase its frequency, thus facing a genocide. A good trick is remembered by the adaptation process, more specifically by the gene pool of the population, when the frequency or a beneficial allele increases its frequency – and, indeed, becomes fixed in the population. Elizabeth will probably correct me if my interpretation of her writing is incorrect and if she indeed did mean that her “repeating” concerned subsequent mutations of identical type. She was never given an opportunity to clarify before banning.

It is ironic that, in this later thread, Patrick and DaveScot also asked rhetorical questions about how diseases persist in the human population (why not some wild population?). So, not only did DaveScot earlier fail to demonstrate that selection pressures change so quickly that they render newly acquired beneficial alleles useless or harmful (his original claim and reason for banning Febble), here he also contradicted the other part of his initial claim. I mean, do random mutations quickly destroy neutral/harmful sequences or do they not? Needless to say, there is little mystery about all this for evolutionary biology. First, harmful mutations don’t fare quite as well in the wild as they do among humans and their domesticated animals. Second, the average mutation rate of mammals is high enough to warrant that most of us carry a few novel harmful alleles (novel at least in the sense that they were not inherited) – natural selection can’t help this, but it certainly is capable of ensuring that these alleles do not become fixed in the wild. While sufficiently high mutation rates may keep up a marginal frequency for a harmful allele, purely due to subsequent mutations, each copy of this allele faces a quick genocide in the population.

Could you see to it that instead of continuing to silence their critics, the UD mods finally recognize that they mistreated Febble by both banning her and by avoiding her quite legitimate question, using rhetorics and “gymnastics”. Currently they are in a mental mode where they have to fabricate the “aftermath” by removing critical posts and self-declaring some sort of sorry victory.

Comment #154619

Posted by Mark Lindeman on January 11, 2007 8:58 AM (e)

Salvador, surely you must see the difficulty in complaining that some people have committed the “serious logical error” of “equivocation” with respect to the definition of intelligence, and complaining that other people are disregarding Dembski’s explanation of why it is unreasonable for critics to insist upon a definition.

But perhaps that objection is too abstract or vague, so let me offer this one. I would be willing to stipulate, for purposes of discussion, that “intelligence” entails having “a goal or purpose in mind.” I would be willing to stipulate, for purposes of discussion, a stipulation that it refers to “the causal factors that change one probability distribution into another,” or that lead to a “net increase in information.” However, I can’t think of any reason to stipulate that all these formulations actually mean the same thing.

So I must ask: has Febble committed the serious logical error of equivocation? or has Dembski? What is the point of an “undefined primitive” that nonetheless seems to take on different meanings in different places?

I hadn’t really registered the existence of Uncommon Descent until yesterday. Honestly, I don’t understand why Dembski allows his name to appear on it. He might as well rename it Stumbling Block.

Comment #154621

Posted by Elizabeth Liddle on January 11, 2007 9:02 AM (e)

caligula wrote:

Later, in a new thread, DaveScot declared that Febble misunderstands the basics of ToE by claiming that “natural selection” can remember mistakes and good tricks. In reality, however, Febble said that “natural selection+replication with modification”, i.e. the adaptation process as a whole, has a memory. Which is quite sensible. Both DaveScot and Patrick kept asking: “how can natural selection remember not to repeat the same mutation again”. In reality, however, the “repeating” in Febble’s argument probably concerned reproduction, not mutation. A mistake is not repeated, but instead gets forgotten, when a harmful allele fails to increase its frequency, thus facing a genocide. A good trick is remembered by the adaptation process, more specifically by the gene pool of the population, when the frequency or a beneficial allele increases its frequency – and, indeed, becomes fixed in the population. Elizabeth will probably correct me if my interpretation of her writing is incorrect and if she indeed did mean that her “repeating” concerned subsequent mutations of identical type. She was never given an opportunity to clarify before banning.

Yes, your interpretation is what I meant. It is possible that I took DaveScot’s shortand “rm+ns” to mean “replication with modification + natural selection”, but on reflection (not sure I can face returning to the thread) he may have defined it as “random mutation and natural selection”. Or I may just have been careless or unclear.

But yes, it is the system of replication with modification plus natural selection that, I argue, “remembers” both its mistakes and its successes.

Thank you very much for your support. Actually, thanks to everyone who has supported me over this, including Sal for coming over here and continuing the truncated conversation.

Cheers

Lizzie

Comment #154622

Posted by Dave Mescher on January 11, 2007 9:25 AM (e)

Salvador Cordova wrote:

Quoting WD:
The later Wittgenstein certainly thought the call for definition was overrated. Indeed, the finiteness of language itself implies that the call for definition must at some point either end or issue in circularity. Within intelligent design, intelligence is a primitive notion much as force or energy are primitive notions within physics. We can say intelligible things about these notions and show how they can be usefully employed in certain contexts. But in defining them, we gain no substantive insight.

The biggest mistake I can see with the analogy in the above statement (force & energy are primitives in physics, and intelligence is a primitive in ID) is that while force & energy are primitive, they are most certainly measurable and quantifiable, even though they are primitive, and further definition of either is not necessary for most applications.

Unfortunately, I’m unable to find any remotely useful means of quantifying intelligence except when the intelligence itself is known. (For example, I have found algorithms for comparing AI algorithms. However, for such algorithms to be useful, the set of possible decisions renderable by the AI must also be known.) To be able to apply those measurements to ID would require knowing or otherwise verifying some aspects of the designer’s identity/motives/purpose/limits/etc. something which WD (“I refuse to sink to your pathetic level of detail…”) and ID has refused to do, as far as I can tell.

Comment #154623

Posted by Raging Bee on January 11, 2007 9:40 AM (e)

I’m not aware than any PT contributor is banned from Uncommon Descent.

If Sal said that, then he has thereby flushed wnat little credibility he had down the toilet. This statement can only have come from a shameless liar who knowingly blinds himself to any fact, however obvious, that he finds inconvenient; and there really is no point in arguing with such a person. Whoever said this might just as well have said “I’m not aware of any proof that the Earth is round.”

(I guess we should be grateful that he’s actually trying to sound sciency, instead of vaguely pretending that a minority who reject evolution “says something significant.”)

PS to Sal: the word “coming” has one “M,” not two. Your misspelling of thst word can only be the result of reading too much bad Internet porn when you should have been studying either biology or morality.

Comment #154624

Posted by Torbjörn Larsson on January 11, 2007 9:41 AM (e)

I fail to see the point of trying to derail discussions, like Sal here trying to make out genetic drift as opposed to selection. It only shows the weakness of the original argument or claim.

SC wrote:

and so does Haldane’s dilemma.

Since you mentioned it. ;-)

It is true that ReMine’s latest answer to Talk Origin’s points has the most recent date. (Which I have notified T.O. about.) But he doesn’t really answer the old rebuttals, but instead continues to dodge the effects of just genetic drift and fixation among other things.

Since it doesn’t make a positive argument for creationism (nor a negative for evolution since it is faulty) you should not use it here.

SC wrote:

“Biological function and the genetic code are interdependent” by Voie

Voie’s paper, a paper relating to computer science, was published in a math journal on chaos. (“Chaos, Solitons, and Fractals”.) It has been critiqued by computer scientist Mark Chu-Carroll on his blog.

“Overall, it’s a rather dreadful paper. It’s one of those wretched attempts to take Gödel’s theorem and try to apply it to something other than formal axiomatic systems…. This stinker actually got peer-reviewed and accepted by a journal. It just goes to show that peer review can really screw up badly at times. Given that the journal is apparently supposed to be about fractals and such that the reviewers likely weren’t particularly familiar with Gödel and information theory. Because anyone with a clue about either would have sent this to the trashbin where it belongs.”
( http://scienceblogs.com/dispatches/2007/01/answering_cordova_on_ids_goals.php )

On another thread where Sal mentions this paper, Mark explains: “*Voie* formulates a meaningless distinction, and uses it to build an argument that conflates the distinct concepts of self-reference and self-referential paradox. My response was to point out that distinction: there are plenty of non-paradoxical self-references…. Voie *also* muddles the line between self-referential *statements* and self-referential *devices*. You *can* create self referential *statement* that contain Godel paradoxes. You *cannot* create self-referential *devices* that contain Godel paradoxes. The latter is a meaningless concept.”

You can find a link to this thread (“Answering Cordova on ID’s Goals”) where Sal tries to use turing equivalence as Behe tries to use interlocking complexity (with the same degree of success) at another of Sal’s assumedly active threads about turing: “Stupidity from our old friend Sal” ( http://scienceblogs.com/goodmath/2007/01/stupidity_from_our_old_friend.php#c312022 ). He hasn’t shown up today, though.

EL wrote:

the “intelligence” manifest in the structure of life forms

Well, that manifestation is pretty elusive. Phylogenetic and genetic trees are pretty much it.

That is why I liked your definition of “the result of selection”, though as genetic drift tells us it isn’t the whole story.

rather than modelling his hypothesis, he attempts to model his “error” terms,

Or as it is usually called, he is making noise.

Comment #154626

Posted by lurker on January 11, 2007 9:43 AM (e)

http://www.uncommondescent.com/archives/1945

Evidently dissent would not be allowed on Dr. Dembski’s biology department either, if he were president…

Comment #154625

Posted by Ric on January 11, 2007 9:43 AM (e)

For those of you crying that Panda’s Thumb censors too, here is a major difference:

All comments at Uncommon Descent start out censored until they eventually get the all clear from the mods, either by being hand-vetted or by having one’s name placed on a sycophant list.

At Panda’s Thumb, all comments start out as automatically appearing and one needs to work hard to earn a ban.

That’s a major difference.

Comment #154632

Posted by stevaroni on January 11, 2007 9:56 AM (e)

Hi Everyone.

My name is Zachriel, and I’ve been banned three times.

(everyone in a big ragged chorus)

Hi Zachriel!

(moderator)

Good! Remember, the first step is admitting that you have been banned.

Comment #154633

Posted by Torbjörn Larsson on January 11, 2007 10:05 AM (e)

WD wrote:

much as force or energy are primitive notions within physics

Axiomatic defined in particular physical theories, yes. A deeper understanding of energy and force is available from studying symmetries and action principles. These action principles in turn are understood as classical limits of quantum path integrals describing all possible paths of a system. Path integrals can be further generalized by non-commutative geometries. And so on.

So, given that primitive notions must be open to further analysis and theory instead of stopping inquiry, what is the difference between WD’s argument and ‘goddidit’? “Primitive notions”, indeed!

Comment #154636

Posted by Torbjörn Larsson on January 11, 2007 10:16 AM (e)

WD wrote:

much as force or energy are primitive notions within physics

Axiomatic defined in particular physical theories, yes. A deeper understanding of energy and force is available from studying symmetries and action principles. These action principles in turn are understood as classical limits of quantum path integrals describing all possible paths of a system. Path integrals can be further generalized by non-commutative geometries. And so on.

So, given that primitive notions must be open to further analysis and theory instead of stopping inquiry, what is the difference between WD’s argument and ‘goddidit’? “Primitive notions”, indeed!

Comment #154640

Posted by GuyeFaux on January 11, 2007 10:39 AM (e)

Axiomatic defined in particular physical theories, yes.

But even when you consider force and energy to be primitives, they’re still measurable. No one in the ID group has yet come up with a metric for intelligence, and Febble got the boot when she tried to suggest one.

Comment #154642

Posted by sparc on January 11, 2007 10:45 AM (e)

Has Allen MacNeill finally given up commenting at UD?
I can’t imagine they would dare to ban him.

Comment #154643

Posted by sparc on January 11, 2007 10:54 AM (e)

For those of you crying that Panda’s Thumb censors too, here is a major difference:

All comments at Uncommon Descent start out censored until they eventually get the all clear from the mods, either by being hand-vetted or by having one’s name placed on a sycophant list.

At Panda’s Thumb, all comments start out as automatically appearing and one needs to work hard to earn a ban.

That’s a major difference.

But the main difference is that at PD nuts are only occasionally commenting whereas at ID they are posting.

Comment #154644

Posted by sparc on January 11, 2007 10:56 AM (e)

Has Allen MacNeill finally given up commenting at UD?
I can’t imagine they would dare to ban him.

Comment #154645

Posted by caligula on January 11, 2007 11:02 AM (e)

TL wrote:

SC wrote:

and so does Haldane’s dilemma.

Since you mentioned it. ;-)

It is true that ReMine’s latest answer to Talk Origin’s points has the most recent date. (Which I have notified T.O. about.) But he doesn’t really answer the old rebuttals, but instead continues to dodge the effects of just genetic drift and fixation among other things.

Since it doesn’t make a positive argument for creationism (nor a negative for evolution since it is faulty) you should not use it here.

After reading pages and pages of ReMine’s rhetorics in an email exchange, I agree. Walter has never addressed e.g. “soft selection” and especially “intraspecific competition” properly, especially not with simultaneous substitutions at multiple loci. He should quit the rhetorics about “confusion factors”. The only person who needs confusion to survive is Walter himself.

Look at the CreationWiki page about Haldane’s dilemma. When discussing “soft selection”, Walter never actually explains what soft selection is. He only lists what it is not. Clarification indeed. Walter doesn’t even mention “intraspecific competition”. And while CreationWiki merrily links to Nunney’s highly relevant paper, where does it recognize the impact of that paper?

Comment #154648

Posted by KL on January 11, 2007 11:03 AM (e)

I have a question about the use of the word “intelligence”. A lot of this thread was over my head, but a theme I kept picking up on seemed to be the idea of “consciousness” or “self-awareness”. In other words, if there is purpose, would that imply intelligence? I the intelligence used by Dembski’s argument self-aware? Perhaps I am just getting hung up on terminology…

Comment #154650

Posted by Kevin nyc on January 11, 2007 11:10 AM (e)

and OT but this is the first time I’ve seen this:

SCIENCE NOW KNOWS THAT MANY OF THE PILLARS OF DARWINIAN THEORY ARE EITHER FALSE OR MISLEADING. YET BIOLOGY TEXTS CONTINUE TO PRESENT THEM AS FACTUAL EVIDENCE OF EVOLUTION. WHAT DOES THIS IMPLY ABOUT THEIR SCIENTIFIC STANDARDS?
– JONATHAN WELLS

from a wierd creationist site:

http://evolution-facts.org/New-material/survivalOfTheFakest.pdf

Article originally appeared in The American Spectator - December 2000 / January 2001

and at this point who really cares what Dumbski thinks?

.

Comment #154652

Posted by DragonScholar on January 11, 2007 11:20 AM (e)

Well I’ve caught up with this conversation today. Quite interesting still.

One thing in reading Sal’s posts caught my eye this morning. Namely, that in reading them I had to take time to parse through them, but frankly, I find very little actual content. I find some external references, questionably quoted, some verbal acrobatics, and talks of “subtleties” and of course various big words.

One of the trends I’ve noticed in ID discussions is a great deal of “contentless” discussions. There are references to a few other works by select individuals. I find various dodges (“if this is true” with no or little evidence said statement IS true), and attempts to find what is “logical” without looking at what has been found so far by science (the tornado-in-a-junkyard argument is logical, but its a terrible metaphor for the complex findings and studies of evolutionary biology).

A major aspect of science is the ability to effectively communicate information. It’s why records are kept, why math is used, why experiments are explained in painful detail (I still recall my days of people asking me what breed of hamster I used in my neural work*).

What I am finding in Sal’s case, and in much of ID’s case, is discussions that obscure the situation. I don’t care if Natural Selection “sounds unlikely,” or “if X is true” when there’s no evidence for X, or verbal acrobatics about undefined primitives. I want some numbers, data, research, hypotheses, tested theories, and documentation.

*It was disturbingly relevant when it came to trying to breed them. The two different gene pools had vastly different behaviors and maternal instincts.

Comment #154653

Posted by GuyeFaux on January 11, 2007 11:30 AM (e)

Perhaps I am just getting hung up on terminology…

This whole thread is about terminology, and in particular what is meant by intelligence.

For S. Cordova, intelligence is an “undefined primitive” so your questions about self-awareness and consciousness run into a brick wall. Febble’s notion of intelligence merely implies an algorithmic selection process, s.t. natural selection qualifies. Apparently Dembski has come up with definitions which are accept this.

Comment #154654

Posted by Raging Bee on January 11, 2007 11:32 AM (e)

(I still recall my days of people asking me what breed of hamster I used in my neural work*)

You may have given Sal his next talking-point: “Evolution is suspect because all of the experimenters used the wrong breed of hamster.” Then he’ll say DragonScholar just now accidentally blew the lid off the nefarious Darwinist conspiracy. Then Larry Fafarman will make a huge, convoluted and irrelevant legalistic argument out of it on his own blog…

Comment #154655

Posted by PvM on January 11, 2007 11:32 AM (e)

One thing in reading Sal’s posts caught my eye this morning. Namely, that in reading them I had to take time to parse through them, but frankly, I find very little actual content. I find some external references, questionably quoted, some verbal acrobatics, and talks of “subtleties” and of course various big words.

Yes, such is the typical response by ID activists when confronted with tough questions, especially questions which they feel have relevance and cannot be answered without putting as risk ID. Remember that Sal would ‘take a grenade for Dembski’… In other words, Sal suggested that he would protect Dembski at all cost. As such, the attention has to be distracted from Dembski’s flaws and towards issues or irrelevance such as neutral mutations, Haldane or some poorly written ID paper (Voie).

Which is why ID is scientifically (and theologically) vacuous and why ID activists have to cherry pick apparent disagreements in science as to the relative importance of neutrality versus selection while ignoring the larger picture, that ID does not even enter the picture as it fails to present ANY scientifically relevant hypothesis beyond X cannot be explained by Y thus Designed.

Pointing this out means a certain ban on blogs like UcD which insist on keeping its readers in the shades of our ignorance and who consider ‘teach the controversy’ to be a one way street.

Comment #154657

Posted by PvM on January 11, 2007 11:48 AM (e)

On UcD Davescot has a posting titled “Barbara Forrest: Will The Real Coward Please Stand Up”

Ironically, it was Davescot’s cowardly behavior which led him to ban Febble. As to Barbara Forrest debating Dembski. Dembski had his opportunity in court to apply his vise theory, sadly he decided to stand by at the sidelines.

Comment #154660

Posted by Blazer on January 11, 2007 11:59 AM (e)

Talk.Origins page about Haldane’s dilemma and ReMine does have some errors, check this post on T.O newsgroup:

http://tinyurl.com/yf6scm

Comment #154661

Posted by trrll on January 11, 2007 12:16 PM (e)

This is par for the course at UD. Whenever DaveScott cannot rebut somebody’s argument (which is pretty frequently), he bans them. He set up an entire topic based upon a comment I made, allowed me to make only one reply, then banned me. Once again, it was an entirely civil discussion. DaveScott simply didn’t like the points being made. You can see it here:

http://www.uncommondescent.com/archives/1627

In another highlight of this same thread, he banned Alan Fox for alerting the author of a paper to DaveScott’s mischaracterization of the author’s work.

Comment #154663

Posted by Peter on January 11, 2007 12:20 PM (e)

The IDC’s hermeneutic, ontological and pseudoscientific discourses, most notably Dembski’s and here Sal Cordova’s, shrouds its beinghood in the postmodern-dillemma-ridden communiques bound within discursive dialectical spaces wherein the heuristics fail to explicate their own obfuscatory methodological frameworks of parametric inflection.

Comment #154664

Posted by secondclass on January 11, 2007 12:21 PM (e)

Salvador wrote:

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice.

Obviously there are purposes and reasons for certain organisms being able to reproduce while others cannot. Whether this can be considered “intelligence” or not begs the question.

Salvador wrote:

Selection the modern Darwinian sense has nothing to do with planning or purpose. If one takes a population genetics book and tries to define “selection” from first principles, it will look nothing like the concept of selection that a conscious intelligent being does when that being selects. The question you pose is therefore fundamentally illogical.

I think the burden is on you to show the principled difference between human choices and natural evolutionary choices. We humans can certainly run through various scenarios more efficiently than nature, and we certainly employ more sophisticated algorithms, but I don’t see efficiency and sophistication as differences in kind. As far as I can tell, both processes are algorithmic, and they both easily fall within Dembski’s definition.

RBH wrote:

And Febble is arguing from Dembski’s definition, which does not include reference to a “conscious intelligent being”.

If it did, it would be quite circular.

Comment #154666

Posted by mark on January 11, 2007 12:59 PM (e)

Sal wrote:

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose.

This, of course, is the crux of anti-evolutionism. The argument is not whether undirected selection can produce the biodiversity seen today, but is all about purpose and meaning in existence. Without purpose, students will bring guns to school, the terrorists will have won, and the Surge to Save Christmas will have been lost.

Comment #154671

Posted by Alan Fox on January 11, 2007 1:44 PM (e)

Tom Moore wrote:

That debate between Febbie and DaveScot was by far the best exchange I’ve seen on UD. I have mixed it up over there enough to come close to being banned, but nowhere near as masterfully as Febbie did it. She was so superbly lucid and persistent that DaveScot simply gave up in exasperation, unable to dismiss her arguments. So he dismissed her in the only way he could.

Still there are several folks over there who have been speaking out and defending the value of having evolutionists make their case on UD. But there is no way they will ever admit to having been bested, just as there is no one over here who would do so.

That suggests to me an open debate between the advocates, on a neutral site, with impartial judging by a lay group, such as the press. This may be the only way to get beyond dismissive rebuttals and name calling.

I second the proposal and can offer spare server space if someone could help with setting it up (are you reading this, Lou)

If you build it, they will come.

Or will they?

I forgot to mention, kudos to Lizzie!

Comment #154676

Posted by alienward on January 11, 2007 2:29 PM (e)

Salvador T. Cordova wrote:

There is a difference between saying “we don’t investigate what the plan or the identity of the Designer is” versus “the Designer has no identity nor plan or power of choice”. One can assert that an intelligent agency in general the power of choice or plan without actually investigating the details of the choice or the plan.

If I found a “Plan for Building a Propulsion System for Bacteria from Scratch” I’d be thinking it would support Sal’s notion of intelligent agencies as well as support the falsification of those Darwinists’ claims the bacteria flagella came about through random chance purposeless processes. Why would anybody say they don’t investigate the plan when they know it would support their claims and falsify others?

Comment #154680

Posted by Torbjörn Larsson on January 11, 2007 3:15 PM (e)

Blazer wrote:

Talk.Origins page about Haldane’s dilemma and ReMine does have some errors, check this post on T.O newsgroup:

It seems the T.O. rebuttal could stand some revision. I don’t really know what Haldane modeled (I don’t need to - I’m not a biologist :-), I only noted that ReMine doesn’t care about later selection and fixation of drifted genes if the environment changes. But perhaps Haldane’s model is putting a limit on the rate of fixation by putting a limit on the rate of substitution?

It is interesting that Wilson mentions bottlenecks as causes for rapid evolution which exceeds Haldane’s limits. I’m reminded of the reports that introgression across mixing zones seems to have been important for human populations.

Comment #154682

Posted by Arden Chatfield on January 11, 2007 3:18 PM (e)

The IDC’s hermeneutic, ontological and pseudoscientific discourses, most notably Dembski’s and here Sal Cordova’s, shrouds its beinghood in the postmodern-dillemma-ridden communiques bound within discursive dialectical spaces wherein the heuristics fail to explicate their own obfuscatory methodological frameworks of parametric inflection.

That is exactly what I’ve always said!

Comment #154683

Posted by Raging Bee on January 11, 2007 3:23 PM (e)

In those very words?

Comment #154685

Posted by GuyeFaux on January 11, 2007 3:41 PM (e)

If I found a “Plan for Building a Propulsion System for Bacteria from Scratch” I’d be thinking it would support Sal’s notion of intelligent agencies as well as support the falsification of those Darwinists’ claims the bacteria flagella came about through random chance purposeless processes.

It wouldn’t falsify the Darwinian claim. It would simply be proof that a design could be arrived at both artificially and naturally. Think of the effort to create artificial spider silk, or adhesives based on gecko-feet. If these projects prove successful, it will not affect the hypothesis that spider silk and geckos arose via natural means.

In fact, finding such plans for propulsion systems, gecko’s feet and spider silk wouldn’t support Sal’s notion of intelligent agency either, if we know nothing about the designer (which is consistent with Sal’s position). We’d need to assume that the designer operated in ways similar to humans in order to conclude anything about the origin of the Propulsion system (reads English, understands drawings, sees in the visible spectrum, etc.).

Furthermore, such explicit plans already exist in the genotypes of certain bacteria, spiders, and geckos.

Comment #154697

Posted by caligula on January 11, 2007 4:53 PM (e)

A summary about “Haldane’s dilemma”.

Haldane’s model

In Haldane’s model, adaptations proceed through sudden changes in the environment, utilizing random variation that is present in all populations due to mutations, even if with tiny allele frequencies. Thus, quick adaptation, or high substitution rate, means more changes in the environment, i.e. more hostile environment or more intense selection. Haldane assumed that constant intense selection is likely to drive populations into extinction. Hence, he suggested that the average intensity of selection has a total selection coefficient of 0.1. Haldane handled simultaneous substitutions at multiple loci using so called multiplicative fitness interaction, which approximates additive fitness when individual coefficients are small. In practice, this means that 10 multiple beneficial alleles with coefficient 0.01 behave about the same way as a single allele with coefficient 0.1; they take ten times as long to fix.

Using the limit of 0.1 for selection coefficient, Haldane found that it will take about 300 generations per substitution. Walter ReMine’s “magic number” 1667 comes from 10,000,000 / 20 / 300, where 10 million (years) is the maximum time in years since humans and chimps diverged, 20 (years/generation) is the average generation time and 300 (generations) is the substitution time.

Soft selection

The idea behind soft selection is as follows. Darwin calculated that elephants, which are among the slowest breeders in the world, can produce a population of almost 19 million in mere 750 years, starting with a single mating couple. Obviously, exponential changes are so dramatic that unless populations spend most of their time at reproduction rate 1.0, they either go extinct or fill up the known space surprisingly quickly. Which is good to remember when considering the human condition. :) Now, what keeps the reproduction rate of wild populations at 1.0 most of the time? At least three options.

1) Predation. This is unlikely. Surely, the population size of prey does dramatically affect the population size of predators, but it is unlikely that the opposite is true, at least to the same extent.

2) Family planning. This sounds absurd to a layman, but I am not sure whether it can be (fully) dismissed without further investigation.

3) Ecological necessity. This is without doubt at least a major contributor to keeping population sizes stable. Each ecological niche has a limited carrying capacity. There is only so much food, shelter, territory, etc. available. If a population is overcrowded, excess mortality will follow. Well, most wild populations are likely overcrowded: each mating couple tries to maximize the replication of their genes by reproducing more than other couples. It is this mortality caused by excess reproduction being countered by excess mortality, called “background mortality”, that soft selection addresses.

Let us go back to Haldane’s model, but this time include “background mortality”. Assume a population has filled its ecological niche, and is reproducing at rate 2.0, i.e. an average of four offspring per parent. Since the environment can’t support any larger population, logically 50% of the population dies in any case, due to sheer lack of resources, no matter how well they are able to e.g. cheat predators. Now, assume a new predator arrives, imposing a new selective pressure with selection coefficient 0.1 on the population. Also, assume that a tiny subpopulation happens to possess an allele which helps them overcome this new challenge. What happens? In terms of total mortality or effective reproduction rate, not much. If we were to loyally follow Haldane’s model, we would increase the total mortality of the population beyond 50%, to account for the new selection pressure – and consequently, we should assume that the reproduction rate of the population needs to increase beyond 2.0, in order to keep the population size constant. But note that the original 50% mortality was largely due to overcrowding. Now, obviously the mortality remains constant in the new situation, and instead only the reasons behind juvenile deaths become more varied. The same amount of individuals would have died anyway, regardless of the appearance of the new selective pressure. It is said that “background mortality” serves as a “buffer” for natural selection. The population “pays” the “cost of selection”, but by doing so, it to the same extent is relieved from paying the cost due to overcrowding. So, in this case, the population could likely tolerate a selection much more intense than 0.1.

Intraspecific competition

Normally, evolutionary scenarios are concerned with the interaction between a population and its surrounding environment. But as there is a competition between individuals within a species for survival in a limited ecological niche, there is no reason to expect that beneficial alleles only concern overcoming challenges imposed by the environment. Many alleles may simply help their possessors to hog limited resources more efficiently than others in the population, and thus effectively surviving better than they do. Such alleles become fixed in the population just as any other beneficial allele – although their benefits are lost during the process, because the trick is no longer useful when everyone can do it. I have simulated this scenario a lot, and in fact posted my source code to ARN and urged Walter ReMine to study both the code and the results. (Alas, the response has been endless rhetorics and avoidance.) This “intraspecific competition” produces extremely impressive results, as there is no upper limit to the intensity of selection when simultaneous substitutions are studied at many, many loci – their total coefficient can go above 1.0 without problems. This is because the presence of beneficial alleles no longer requires any kind of excess mortality. To see why this is so, remember that in this scenario, survival is measured by possession of vital resources. The amount of resources remains the same – some individuals just get more of them than others – and so does the population size. To the extent the “have-not’s” die more often due to lack of vital resources, to the same extent the “have’s” die less often due to abundance of vital resources. The average fitness of the population remains constant even if individual fitness varies. And in practice, beneficial alleles spread in the population in such a smooth and even fashion that there are no extreme fitness differences.

Comment #154698

Posted by Salvador T. Cordova on January 11, 2007 5:05 PM (e)

Caligula asked:

Could you see to it that instead of continuing to silence their critics, the UD mods finally recognize that they mistreated Febble by both banning her and by avoiding her quite legitimate question, using rhetorics and “gymnastics”. Currently they are in a mental mode where they have to fabricate the “aftermath” by removing critical posts and self-declaring some sort of sorry victory.

It is not my weblog, and I am the low man in the administrative hierarchy (I have very limited administrative access to the site).

I can understand your objections, but I must also respect the wishes of the administrators there who give me the privilege of posting my writings on their weblog.

I could of course start my own weblog, but I have little inclination to do so.

I would again like to thank Richard Hoppe for his hospitality as I see that Febble wanted an opportunity to continue the conversation. However, I have directed readers at UD to this thread so they can see what Febble has to say. Regarding politics, character, and religion, unless a person volunteer’s it I think, for the sake of discussion of scientiftic issues, I personally prefer to be a bit circumspect on these peripheral issues. Thus, I will refrain from commenting issues outside of what Febble is discussing about ID.

Since some PT folks have asked, regarding Allen MacNeil, it is obvious the authors at UD have differing views. He said some things about Bill Dembski (a DI fellow) which I don’t think endeared him to Bill. MacNeill however has been very protective of the IDEA club at Cornell (and I’m affiliated with IDEA), so we have here a situation where there are conflicting perceptions at UD regarding MacNeill. I will continue to applaud MacNeil for all he has done and my sincere gratitude for him sticking his neck out for the Cornell IDEA club. I regret that there is apparently some friction between him and Bill Dembski….

Comment #154700

Posted by alienward on January 11, 2007 5:11 PM (e)

GuyeFaux wrote:

It wouldn’t falsify the Darwinian claim. It would simply be proof that a design could be arrived at both artificially and naturally. Think of the effort to create artificial spider silk, or adhesives based on gecko-feet. If these projects prove successful, it will not affect the hypothesis that spider silk and geckos arose via natural means.

I didn’t think I needed to say 4 billion year old plan and put the word support in uppercase bold and flashing.

In fact, finding such plans for propulsion systems, gecko’s feet and spider silk wouldn’t support Sal’s notion of intelligent agency either, if we know nothing about the designer (which is consistent with Sal’s position). We’d need to assume that the designer operated in ways similar to humans in order to conclude anything about the origin of the Propulsion system (reads English, understands drawings, sees in the visible spectrum, etc.).

Please at least go read some of Sal’s posts before you make a bogus claim like that. Here, let me help you.

Sal said:

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice. Selection the modern Darwinian sense has nothing to do with planning or purpose. If one takes a population genetics book and tries to define “selection” from first principles, it will look nothing like the concept of selection that a conscious intelligent being does when that being selects.

GuyeFaux wrote:

Furthermore, such explicit plans already exist in the genotypes of certain bacteria, spiders, and geckos.

I guess I also needed to say “very first” bacteria flagellum…

Do you really think that if we found that 4 billion year old plan for the very first bacteria flagellum the only thing Sal would say is “We don’t investigate plans – and that plan can’t be more than 6,000 years old anyway.”?

Comment #154701

Posted by caligula on January 11, 2007 5:18 PM (e)

caligula wrote:

an average of four offspring per parent

Apologies. I meant to say “four offspring per couple“.

Also, I should clarify this bit:

“unless populations spend most of their time at reproduction rate 1.0, they either go extinct or fill up the known space surprisingly quickly”

It would be better to say:

“unless populations sizes remain constant most of the time, populations either go extinct or fill up the known space surprisingly quickly”

Comment #154705

Posted by Dean Morrison on January 11, 2007 5:43 PM (e)

As another Brit I can also think of at least one good example of “Intelligent Design”.

It is true that if we can find a apparently ‘designed’ object that cannot possibly have arisen through the process of biological evolution, and which displays all the required characteristics of ‘specified complexity’ or whatever - then we should probably start looking around for a ‘designer’.

I was thinking that the Christian God fits the bill - he can’t possibly have arisen by biological evolution - there’s doesn’t appear to be any mechanism for DNA to code for ‘omnipresence’, ‘omnipotence’ or or any of the other supernatural powers. As we are ‘made in his image’ then he’s at least as complex as any human being. According to the Bible this is especially true of his emotional condition, where he displays all the usual human neuroses and more besides.

Therefore I claim the Christian God as the first proven example of ‘Intelligent Design’ - and I’ll go one further - I’ll identify not only the designers - but also their methods, motivations and actions in their production of their design. Crikey! I can even document the production of the ‘beta version’ that was worked on for a few thousand years before “God 2.0” was released.

Like all designs - the designers made a few flaws - but no matter - these are being ‘tweaked’ by a new generation of designers who are taking another link at earlier blueprints and are making new models fit for the 21st century.

I’m sure Mr Dembski will welcome my support for his insightful idea, and will welcome my support from across the pond - so I’m off to post this on ‘Uncommon Descent’ - where I’m sure I’ll get a warm and respectful welcome…..

Comment #154707

Posted by GuyeFaux on January 11, 2007 5:59 PM (e)

I didn’t think I needed to say 4 billion year old plan and put the word support in uppercase bold and flashing.

Well, since “four billion” in terms of your speculation is kind of an arbitrary number, it would’ve helped. There’s nothing in your post that would indicate that you were talking about something old.

Sal wrote:

Selection in the ID sense pertains to an intelligence have at least some purposeful reason for making a choice.

I wrote:

We’d need to assume that the designer operated in ways similar to humans…

What I was trying to say is that we’d need to know something about the designer in order to infer its purpose. This violates an ID taboo, but I guess it does vary day to day.

I guess I also needed to say “very first” bacteria flagellum

Yes, that would’ve helped. (Nit-pick: it’s either “very first bacterial flagellum,” or “very first bacterium’s flagellum”)

Do you really think that if we found that 4 billion year old plan for the very first bacteria flagellum the only thing Sal would say is “We don’t investigate plans – and that plan can’t be more than 6,000 years old anyway.”?

No, that would be extremely dogmatic of me, and I have no idea why you think I would think that. BTW, a four billion year old blueprint for bacterial flagella is an order of magnitude worse for the ToE than the proverbial misplaced rabbit.

Comment #154708

Posted by Sir_Toejam on January 11, 2007 6:06 PM (e)

That is exactly what I’ve always said!

Comment #154683
Posted by Raging Bee on January 11, 2007 3:23 PM (e)

In those very words?

Yes, he has said “That” many times before, and I’ve never seen him use any variant of the word.

;)

Comment #154709

Posted by Salvador T. Cordova on January 11, 2007 6:10 PM (e)

Febble asked:

must Specified Complexity arise from such an “purposeful” intelligence or could it arise from mere “intelligence” as
operationally defined by Dembski?

The falsifiably hypothesis is that specified complexity must ultimately regress to an intelligent agency. The intelligence can act through a surrogate (like a machine or factory), but it’s ultimate cause is intelligence. At least that is the hypothesis…

Formally speaking specified complexity is a property which is not derived from the presumption of intelligence. Consder what Dembski wrote:

The principal advantage of characterizing design as a complement of regularity and chance is that it avoids committing itself to a doctrine of intelligent agency.

Defining design as the negation of regularity and chance avoids prejudicing the causal stories we associate with the design inference.

William Dembskim Design Inference

Specified complexity can be an empircally measurable property given the approriate information. Even biologists colloquially say “such and such has a design.” That is consistent with the definition of Deisgn within ID theory.

Whether such designs can arise without the aid of intelligent agency somewhere in the pipeline is the question. ID theorists hypothesize that it can’t be done. The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default.

I think Dembski’s math had refuted anything by Dawkins and friends. I read the supposed refutations by Dembski’s critics, and I find them to be impressively written strawman takedowns and disingenuous distortions of what Dembski actually wrote. You’ll hear appeals by PT regulars to Shallit, Elsberry, Perakh, Avida, etc. They are mostly strawman misrepresentations. They do not qualify as theoretically sound rebuttals….

Comment #154710

Posted by Salvador T. Cordova on January 11, 2007 6:17 PM (e)

I pointed out the fact Kimura has shown the majority of molecular evolution cannot possibly be under the influence of selection. He had hoped that a reconciliation with Darwinian theory would be possible if adaptation (and thus functional evolution) were compartmentalized away from molecular evolution. One can see this is a brittle “truce” at best, especially if more and more functionality is discovered in regions of molecules which Kimura’s equations indicate must not be subject to selection. What if these regions are found functional then? The answer is we can infer these functional systems (dare we say designs) are not the product of Natural Selection. Tada!

Adding to this, Allen Orr astutely observed in his criticism of Dennett’s book, Darwin’s Dangerous Idea, that Natural selection does not correlate with designs in biology, Orr said, “selection does not trade in the currency of design”. I think Orr was sympathetic to the “Spandrels” explanation, which is really not much of an explanation at all….

So do we have evidence there is functionality in these regions presumed impossible to have function? See: DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins.

Comment #154711

Posted by Sir_Toejam on January 11, 2007 6:17 PM (e)

I think Dembski’s math had refuted anything by Dawkins and friends

of course you do!

duh, we already know what you think, Sal (hint: nobody cares), the real question you have obviously avoided for many years now is what EVIDENCE have you to support your thinking that Dembski has mathematically refuted anything, given that his book’s been blown out of the water not by one, but by myriads of mathemeticians and statisticians (note I didn’t even mention biologists)?

Most of us have seen your “answer” to THAT question before too, but maybe Febble would like to get a better idea of who exactly she thinks she is “debating” with, so she can stop wasting her time.

really, Dembski did her a favor.

Comment #154713

Posted by Sir_Toejam on January 11, 2007 6:31 PM (e)

I pointed out the fact Kimura has shown the majority of molecular evolution cannot possibly be under the influence of selection.

strawmen, Sal, remember?

several people pointed out your misinterpretation of Kimura’s work directly, which of course you chose to ignore and continue on in your obliviousness, rather much like how you claim to not be knowledgeable of what goes on at UD.

you simply are intellectually dishonest, Sal, either unconsciously or by “design”.

I do hope that Febble at this point doesn’t need me, or anyone else, to see that clearly.

Comment #154714

Posted by Coin on January 11, 2007 6:58 PM (e)

DragonScholar wrote:

Well I’ve caught up with this conversation today. Quite interesting still.

One thing in reading Sal’s posts caught my eye this morning. Namely, that in reading them I had to take time to parse through them, but frankly, I find very little actual content. I find some external references, questionably quoted, some verbal acrobatics, and talks of “subtleties” and of course various big words.

One of the trends I’ve noticed in ID discussions is a great deal of “contentless” discussions. There are references to a few other works by select individuals. I find various dodges (“if this is true” with no or little evidence said statement IS true), and attempts to find what is “logical” without looking at what has been found so far by science (the tornado-in-a-junkyard argument is logical, but its a terrible metaphor for the complex findings and studies of evolutionary biology).

A major aspect of science is the ability to effectively communicate information. It’s why records are kept, why math is used, why experiments are explained in painful detail (I still recall my days of people asking me what breed of hamster I used in my neural work*).

What I am finding in Sal’s case, and in much of ID’s case, is discussions that obscure the situation. I don’t care if Natural Selection “sounds unlikely,” or “if X is true” when there’s no evidence for X, or verbal acrobatics about undefined primitives. I want some numbers, data, research, hypotheses, tested theories, and documentation.

*It was disturbingly relevant when it came to trying to breed them. The two different gene pools had vastly different behaviors and maternal instincts.

PVM wrote:

Yes, such is the typical response by ID activists when confronted with tough questions, especially questions which they feel have relevance and cannot be answered without putting as risk ID. Remember that Sal would ‘take a grenade for Dembski’… In other words, Sal suggested that he would protect Dembski at all cost. As such, the attention has to be distracted from Dembski’s flaws and towards issues or irrelevance such as neutral mutations, Haldane or some poorly written ID paper (Voie).

I think these are some really critically important comments here.

I think a lot of pro-science blog people sort of “like” Sal because he actually breaks the DADT principle most of Intelligent Design is based around (and instead attempts to actually put forward arguments on the table which can then be refuted), and also because every time he is allowed to make his voice heard he winds up embarrassing the UD crowd tremendously.

But this makes it easy to overlook the role that Sal plays in a lot of these discussions, which is basically as a portable smokescreen. Sal drops into a conversation, and suddenly he’s claimed the center of attention; the original discussion topic is long-forgotten, and instead we have a discussion of Salvador T. Cordova. We see a great example of that here in this thread, where a conversation about the UD comment policy and Dembski’s slippery use of term definitions has now given way entirely to Cordova pushing creationist reinterpretations/quotemines of long-dead evolutionary biologists.

Comment #154716

Posted by alienward on January 11, 2007 7:26 PM (e)

GuyeFaux wrote:

Well, since “four billion” in terms of your speculation is kind of an arbitrary number, it would’ve helped. There’s nothing in your post that would indicate that you were talking about something old.

Sorry, I figured talking about finding a plan for a bacterial flagellum would have been enough to point out that I was talking about finding the original plan of the IDists intelligent designers and not some paper a nerd just wrote.

What I was trying to say is that we’d need to know something about the designer in order to infer its purpose. This violates an ID taboo, but I guess it does vary day to day.

The IDists are pretty consistent with their claims that intelligent designers make stuff with a purpose – like that motor and whip with a purpose to move bacteria around. But I do agree they are pretty inconsistent about stuff like whether the designer is really just one being or some kind of three-in-one being and if it made flagella 4 billion or 6,000 years ago.

No, that would be extremely dogmatic of me, and I have no idea why you think I would think that. BTW, a four billion year old blueprint for bacterial flagella is an order of magnitude worse for the ToE than the proverbial misplaced rabbit.

The IDists know this too. That’s why I’m asking why they would say (quoting Sal):

There is a difference between saying “we don’t investigate what the plan or the identity of the Designer is” versus “the Designer has no identity nor plan or power of choice”. One can assert that an intelligent agency in general the power of choice or plan without actually investigating the details of the choice or the plan.

Comment #154717

Posted by RBH on January 11, 2007 7:45 PM (e)

Dean Morrison wrote

Therefore I claim the Christian God as the first proven example of ‘Intelligent Design’ - and I’ll go one further - I’ll identify not only the designers - but also their methods, motivations and actions in their production of their design. Crikey! I can even document the production of the ‘beta version’ that was worked on for a few thousand years before “God 2.0” was released.

I’ve argued for years that if one put God through Dembski’s Explanatory Filter, it’d conclude “Designed!”

Salvador wrote

Specified complexity can be an empircally measurable property given the approriate information. Even biologists colloquially say “such and such has a design.” That is consistent with the definition of Deisgn within ID theory.

Then why does no one actually measure the specified complexity of anything? Some time back on ARN I noted that there is a perfect set of test data for ID “design detection” methods, the set of expression arrays of the programs evolved in Avida. Regardless of whether one thinks that research with Avida tells us anything about evolutionary processes, the outputs, in the form of evolved opcode programs, are perfect for validating and calibrating “design detection” methodologies. Yet no IDist has ever done so, on those programs or anything else. When will IDists stop talking about can be and show is? It’s vaporware so far.

Salvador wrote

Whether such designs can arise without the aid of intelligent agency somewhere in the pipeline is the question. ID theorists hypothesize that it can’t be done. The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default.

Magic (for that’s all intelligent design has offered by way of explanation) is “better by default”? Given the success of purely materialistic explanations in every domain of science for the last 300 years the “default” sure ain’t magic. That shifted a couple of centuries ago: Magic now bears the burden of proof and naturalistic explanations are the default.

RBH

Comment #154720

Posted by Henry J on January 11, 2007 9:25 PM (e)

Re “unless populations sizes remain constant most of the time, populations either go extinct or fill up the known space surprisingly quickly”

Or fluctuate within a constant range.

Henry

Comment #154721

Posted by Coin on January 11, 2007 9:26 PM (e)

What I was trying to say is that we’d need to know something about the designer in order to infer its purpose. This violates an ID taboo, but I guess it does vary day to day.

The IDists are pretty consistent with their claims that intelligent designers make stuff with a purpose – like that motor and whip with a purpose to move bacteria around.

Yes, but what purpose? I mean, you are correct that IDers are indeed ardent that the designer acted with a purpose, but they can never tell us what that purpose was. The Designer supposedly arranged the parts of the flagella purposefully to give that bacteria an outbound motor, but why? What was the motive in installing an outbound motor in a bacteria? Is installing outbound motors into objects an end in itself, and if so, why limit said outbound-motor-installing activities to the bacteria, rather than installing them in other places, such as viruses or rocks?

Rationalizing after the fact that X occurred with the purpose of allowing X to occur conveys to us no information. One might as well witness someone drowning in a lake, and conclude that the lake was formed expressly for that man to drown in.

Comment #154723

Posted by sparc on January 11, 2007 9:50 PM (e)

Dean Morrison:
I can even document the production of the ‘beta version’ that was worked on for a few thousand years before “God 2.0” was released.

Brilliant

… - so I’m off to post this on ‘Uncommon Descent’ - where I’m sure I’ll get a warm and respectful welcome…

Good luck or rather Happy Banning

Comment #154726

Posted by alienward on January 11, 2007 10:38 PM (e)

Coin wrote:

Yes, but what purpose? I mean, you are correct that IDers are indeed ardent that the designer acted with a purpose, but they can never tell us what that purpose was. The Designer supposedly arranged the parts of the flagella purposefully to give that bacteria an outbound motor, but why? What was the motive in installing an outbound motor in a bacteria? Is installing outbound motors into objects an end in itself, and if so, why limit said outbound-motor-installing activities to the bacteria, rather than installing them in other places, such as viruses or rocks?

Ummm, because rocks don’t need to move toward food? This isn’t too complicated – really. This purpose of the motor and whip is to move the bacteria. In that 4 billion year plan for the bacterial flagellum, that would support claims of intelligent designers, and support falsification of Darwinian random chance purposeless process, if we could find it, I would expect to see some kind of glyph with a meaning like “Purpose - move bacteria.”

Rationalizing after the fact that X occurred with the purpose of allowing X to occur conveys to us no information. One might as well witness someone drowning in a lake, and conclude that the lake was formed expressly for that man to drown in.

Now we don’t need to extend this from why do we need a motor with a whip on bacteria to why do we need to move the bacteria and all the way to why do we need a universe. We’re just talking the purpose of the designers that developed the plan for the flagellum - to move it. Finding that plan will be a holy grail for those IDists, and will have those Darwinists freaking out. It’s intellectually bankrupt enough IDEA clubs claim the age of the earth is irrelevant to ID, it looks like, according to Sal, IDEA clubbers also make the intellectually bankrupt claim the plans for any designs are irrelevant to ID too.

Comment #154733

Posted by PvM on January 12, 2007 12:13 AM (e)

I pointed out the fact Kimura has shown the majority of molecular evolution cannot possibly be under the influence of selection. He had hoped that a reconciliation with Darwinian theory would be possible if adaptation (and thus functional evolution) were compartmentalized away from molecular evolution.

And such a reconciliation is indeed possible, even though compartmentalization is not even needed.
Even if Kimura’s conclusions were to lead to a finding that ‘selection is dead’, we are still left with a scientific explanation for evolution, effectively banning ID’s ignorance. But the combination of selection and neutrality can indeed be a powerful mechanism as various authors have shown. I am sure that Sal must have seen the many references I have provided, relevant to this topic.

I forgot, ID can only survive by cherry picking scientific findings and quote mining.

Comment #154738

Posted by Mercury on January 12, 2007 2:59 AM (e)

I’ve been banned by UD twice.

I got involved in a few threads on UD discussing theistic evolution, since I happen to care more about the theological debate than the scientific one. The rulers of UD are no more friendly to theological discussion outside of their own viewpoints than they are to scientific discussion. I managed to sneak under the radar for a while and had quite a heavy discussion with a few participants, and even one of the lower-ranked moderators, Scott. But then DaveScot found the thread. He started retroactively adding notes to the ends of my posts, and I was promptly banned. Most of the exchange can still be read here. I’m especially happy with post 54.

Then, when DaveScot left to visit some girls and Denyse joined, statements were made that the forum was turning over a new leaf in how it dealt with dissent and previously-banned posters could once again participate. So, I tried again. (At first my posts under my old login were still being blocked, so I posted again under Max Kirk; then Denyse released my earlier post as Mercury from the spam filter.) But, my comments challenged the “big-tent” philosophy of ID, and this time I was banned by Dembski himself.

William Dembski wrote:

I’m afraid I’m not entirely happy what you bring to our discussion, so you’re out of here.

Comment #154741

Posted by Darth Robo on January 12, 2007 4:21 AM (e)

Sal said:

“The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default.”

Well RBH got there first, but better by “default”? That’s just incredible.

“I think Dembski’s math had refuted anything by Dawkins and friends. I read the supposed refutations by Dembski’s critics, and I find them to be impressively written strawman takedowns and disingenuous distortions of what Dembski actually wrote. You’ll hear appeals by PT regulars to Shallit, Elsberry, Perakh, Avida, etc. They are mostly strawman misrepresentations. They do not qualify as theoretically sound rebuttals….”

Okay, I believe you. Right after you show us EXACTLY WHY they do not qualify as theoretically sound rebuttals, other than just your say so. Hmm. That’s a lot of people you mentioned there - Dembski vs Shallit, Elsberry, Perakh, Avida, Dawkins (and friends). Please tell us where all these (qualified) people don’t um… qualify.

Comment #154742

Posted by caligula on January 12, 2007 4:22 AM (e)

SC wrote:

Whether such designs can arise without the aid of intelligent agency somewhere in the pipeline is the question. ID theorists hypothesize that it can’t be done. The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case

Salvador, may I ask that we briefly return to Dave Thomas’s genetic algorithm which generated MacGyvers for Steiner networks?

http://www.pandasthumb.org/archives/2006/08/take_the_design.html

I do not ask you to browse through the whole affair and the threads at PT and UD related to it. I merely remind you of your main objection as to why Thomas’s GA does not produce CSI. You said that the CSI is in reality generated by humans and hidden either (a) in the fitness criterium or at least (b) in hardware/OS/GA engine. Back then I asked you a very basic question. Since CSI is, supposedly, a measurable quantity, it should be possible to show discrete steps where the CSI gets copied into the “genome” of the GA from whatever its hiding place is. My question was never answered back then, although I think you admitted it was both an interesting and a relevant one. I agree. And it seems to be quite relevant concerning your sentence quoted above.

My response to your claim is: the ability of evolutionary processes to produce CSI in the genome has been proven many times over. The proof just hasn’t been accepted by yourself. Now, you are the boss of your own thoughts, of course. But if you insist that others should take your view seriously, you must take some burden of proof, too. So, could you please respond to my challenge above. If you are unable to do so, as I suspect, could you at least carefully explain why should anyone take your objections as anything more than assertions based on blind faith? I.e. what is your view based on if it is neither a concrete, testable claim nor blind faith/intuition?

Comment #154747

Posted by Torbjörn Larsson on January 12, 2007 6:17 AM (e)

Coin wrote:

a conversation about the UD comment policy and Dembski’s slippery use of term definitions has now given way entirely to Cordova pushing creationist reinterpretations/quotemines of long-dead evolutionary biologists.

I initiated an irrelevant (a negative argument against evolution doesn’t help Sal showing ID is useful) side discussion because I wasn’t aware that talk.origins group was discussing the quality of T.O. CC list.

If there is no room I can try to have it moved to AtBC, where it probably belongs.

Coin wrote:

a conversation about the UD comment policy and Dembski’s slippery use of term definitions has now given way entirely to Cordova pushing creationist reinterpretations/quotemines of long-dead evolutionary biologists.

caligula:

Thank you for very illustrative, lucid and thorough explanation on Haldane’s dilemma! (And I should thank Blazer as well for the link.) I am out of my depth on population models, but you made it very clear what is involved at a level I could assimilate it. Actually, you have whetted my appetite to look into this subject a bit, since I always liked dynamical models in math.

(There is another more farfetched reason too. Apparently some population models look like bayesian inference used in machine learning, with alleles as ‘hypotheses’ and the population as ‘theory’. Going back to Liddle’s observation of selection as a learning algorithm, of course. And apparently promising to give people a handle on what characterizes this information how evolutionary mechanisms picks it up (and forgets). I’m curious here too.)

caligula wrote:

Haldane assumed that constant intense selection is likely to drive populations into extinction. Hence, he suggested that the average intensity of selection has a total selection coefficient of 0.1.

Ah, so it includes putting a limit on fixation. It reveals my total ignorance, and makes my argument against ReMine faulty.

On the other hand, now I have a weak memory that it may be that neutral drift actually decreases variation in some cases. In any case, Haldane’s/ReMines model should not cover this.

caligula wrote:

Haldane handled simultaneous substitutions at multiple loci using so called multiplicative fitness interaction,

Explaining one of Wilson’s objections (Blazer’s link) on Isaak’s claim in CB121.

caligula wrote:

“background mortality” serves as a “buffer” for natural selection.

Ah.

caligula wrote:

Many alleles may simply help their possessors to hog limited resources more efficiently than others in the population, and thus effectively surviving better than they do.

So here possibly introgression and intraspecific competition interacts at times.

Adding up, soft selection and intraspecific competition from limits on populations, and bottlenecks (Wilson), non-independent fitness effects (Wilson), and possibly neutral drift and introgression are mechanisms of change in real populations that Haldane’s model doesn’t cover. Plenty of material for a revised T.O. article here. And rather revealing on the level of ‘research’ ID is about even on models that actually predicts things.

Comment #154748

Posted by ben on January 12, 2007 6:20 AM (e)

The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default

OK. Please let us know what this ID theory consists of. Maybe use the Wikipeda definition:

A theory is a logically self-consistent model or framework for describing the behavior of a related set of natural or social phenomena. It originates from and/or is supported by experimental evidence (see scientific method). In this sense, a theory is a systematic and formalized expression of all previous observations that is predictive, logical and testable.

What is the model? Please state it in a systematic and formal way, including some/any predictions it makes, and how it is testable. Oh, and please leave out any references to the supposed inadequacies of any other theories; that doesn’t bear on the matter (if for no other reason than that it violates the “logically self-consistent” parameter by introducing the fallacy of false dilemma.

My theory : You don’t have a scientific theory of ID.
Prediction: Requests for you to provide one will be met with some combination of silence, obfuscation, prevarication, or statement of something which does not constitute a scientific theory.
Falsifiablity: You state a scientific theory of ID that meets the above standards, someday, ever, eventually.

Comment #154752

Posted by Torbjörn Larsson on January 12, 2007 7:10 AM (e)

Sal wrote:

The falsifiably hypothesis is that specified complexity must ultimately regress to an intelligent agency.

It is only falsifiable if you can define your “SC”. Where is this unambiguous and predictive definition?

Sal wrote:

Specified complexity can be an empircally measurable property given the approriate information.

No calculation of SC has ever been done by ID to my knowledge, since the definition above is lacking.

For a comprehensive critique of SC, see http://scienceblogs.com/goodmath/2006/06/dembskis_profound_lack_of_comp.php .

Mark Chu-Carroll notes that Dembski avoids discussing complexity, and spends a lot of time to avoid defining specification. When he does discusses what specification could be, he happens to use Kolmogorov-Chaitin complexity. And it turns out that he needs to define specification and complexity to have the same, but opposite, property. “Something that possesses “specified complexity” is therefore something which is simultaneously compressible and non-compressible.” That is, one can never observe this property!

Liddle’s definition, as a result of choice, is better since you can observe phylogenetic trees when combined with other hypotheses of evolution.

Sal wrote:

I pointed out the fact Kimura has shown the majority of molecular evolution cannot possibly be under the influence of selection.

Not relevant, and you don’t listen. It was noted that Kimura’s theory is part of evolution theory.

Sal wrote:

See: DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins.

I wondered how long it would take for Pellionisz and ID to meet up, since science blogs have been negative against his PR comments. The negativity being that he misrepresents junk DNA and ‘postgenetic’ diseases, and have not presented any results from tests of his theory. (Reminds one of something, doesn’t it? ;-)

He makes such mistakes as including regulatory regions in junk DNA. He also presents any (ie all) diseases whose progress is affected by variation in DNA as a ‘postgene’ disease.

For example, he mentions that his co-author has multiple myeloma and calls it ‘postgene’. In fact, 50 % of cases are observed to have an immunoglobulin chromosomal abnormality. Where is the junk here? Not in the DNA, but in Pellionisz classification.

It is not surprising that two woo businesses have combined. Two woo or not to woo? Woo-woo!

Comment #154754

Posted by Torbjörn Larsson on January 12, 2007 7:18 AM (e)

“Something that possesses “specified complexity” is therefore something which is simultaneously compressible and non-compressible.”

That is a quote from Mark characterizing Dembski’s description of (yet another) possible definition, not Demsbki’s own description.

Comment #154755

Posted by Torbjörn Larsson on January 12, 2007 7:24 AM (e)

Oh, I also forgot to mention that Pellionisz refers to evolution (and ID) as ideology. Ie he has revealed himself to have a less than proper grasp of science in lieu of all his earlier papers.

Comment #154777

Posted by GuyeFaux on January 12, 2007 10:12 AM (e)

The IDists are pretty consistent with their claims that intelligent designers make stuff with a purpose – like that motor and whip with a purpose to move bacteria around.

Nit-pick:
IDists only talk about the purpose of the things made by the designer. They kind of forbid talking about why the designer designs things, though.

Comment #154778

Posted by Henry J on January 12, 2007 10:13 AM (e)

My theory : You don’t have a scientific theory of ID.
Prediction: Requests for you to provide one will be met with some combination of silence, obfuscation, prevarication, or statement of something which does not constitute a scientific theory.
Falsifiablity: You state a scientific theory of ID that meets the above standards, someday, ever, eventually.

LOL

Comment #154781

Posted by GuyeFaux on January 12, 2007 10:40 AM (e)

…he happens to use Kolmogorov-Chaitin complexity

This sounds interesting. Have people looked into this before? I.e. have people tried to estimate, say, the Kolmogorov complexity of the human genome? (I’m not abreast of these things.) In particular, does evolutionary theory predict that the Kolmogorov complexity of a genome tends to increase over time?

Comment #154782

Posted by Glen Davidson on January 12, 2007 10:48 AM (e)

But this makes it easy to overlook the role that Sal plays in a lot of these discussions, which is basically as a portable smokescreen. Sal drops into a conversation, and suddenly he’s claimed the center of attention; the original discussion topic is long-forgotten, and instead we have a discussion of Salvador T. Cordova. We see a great example of that here in this thread, where a conversation about the UD comment policy and Dembski’s slippery use of term definitions has now given way entirely to Cordova pushing creationist reinterpretations/quotemines of long-dead evolutionary biologists.

Yes, his mission is to derail every legitimate discussion of evolution and evidence that he can. His mode of operation is to make unsupported claims and accusations, and to refer to sources which he can’t summarize or really even discuss which supposedly “disprove” or make self-contradictory this or that well-established evolutionary phenomenon. It’s the standard IDist tactic, to bypass all evidence and to bring the focus on their incompetent criticisms of evolution, after which they claim to have won one for an “ID hypothesis” that remains forever without a speck of evidence in favor of it.

And we do allow this to happen too often. Because their claims are so lacking in substance, we want to demonstrate that this is the case, thus to refute them. Yet the fact that they really just are interested in bashing evolution means that any refutation of one bad claim or another only makes them look for another reason to fault evolution. One can never really win with people like Sal who only deny evidence, never once being open to what the evidence tells us. They don’t even care that they have no prospect of rivaling the explanatory ability of evolutionary theory, as explanations are their enemy—they want gaps in which to insinuate their God.

Let’s state it more forcefully: People like Sal who have no concern for explaining anything in biology via recognizable causal mechanisms cannot be reasoned with by discussing the explanatory ability of evolutionary theory or the lack thereof in “ID theory”. Sal is strictly an apologist, with no respect at all for the scientific enterprise when the issue is origins. He is fundamentally dishonest in the intellectual sense, wherever origins are discussed.

Glen D
http://tinyurl.com/b8ykm

Comment #154783

Posted by Raging Bee on January 12, 2007 10:51 AM (e)

Nit-pick:
IDists only talk about the purpose of the things made by the designer. They kind of forbid talking about why the designer designs things, though.

That’s not a nit-pick, that’s a fundamental flaw of creationist pseudoscience. When has any branch of any natural science ever explicitly ruled any avenue of inquiry “closed” or “out of bounds?” There have of course been many cases of “We don’t have the resources to go there yet;” and “Another branch is better equipped to go there;” but that’s very different from “We must all agree that it is forbidden to go there, don’t even ask about it.”

Comment #154785

Posted by caligula on January 12, 2007 11:19 AM (e)

TL wrote:

Thank you for very illustrative, lucid and thorough explanation on Haldane’s dilemma!

Thanks, glad you found it useful! Here’s some more, but apologies about the length.

TL wrote:

Explaining one of Wilson’s objections (Blazer’s link) on Isaak’s claim in CB121.

You must mean this one:

“He also assumed that two mutations would take twice as long to reach fixation as one, but because of sexual recombination, the two can be selected simultaneously and both reach fixation sooner.”

This claim is both right and wrong, in my opinion. Assume we have two loci, and a beneficial allele with coefficient 0.1 at both. These alleles will both fix, in parallel, in about the same time as a single allele with coefficient 0.1 would. (In principle, interference between loci, such as “hitchhiking”, is present in multi-locus population genetics, but I haven’t been able to reproduce effects which had much statistical impact in the long run – at least not when the loci are considered functionally independent of each other.) Thus, the two-locus scenario would indeed demonstrate double the substitution rate compared to the single-locus scenario. However, recall that Haldane’s model does not allow such intense selection. In fact, when Haldane is discussing multiple loci, he is implicitly assuming that their combined selective coefficient honors the limit 0.1. You can by all means have N simultaneous substitutions taking place, but in that case the average coefficient of each is 0.1/N at most, thus indeed taking N times as much time for each to fix. So, concurrency does not have the effect that two 0.05 substitutions would carry out faster than a single 0.10 substitution. Concurrency is relevant in another sense: it becomes important when the combined effects of selection at multiple loci exceed a value that no single allele could possibly have (i.e. their combined intensity goes to 1.0 and way beyond; read on!).

As I explained earlier, “soft selection” relaxes Haldane’s limit dramatically, and “intraspecific competition” lets the combined intensity of selection at multiple loci to jump through the ceiling. I will illustrate the latter case with an example.

The real power of concurrency

Assume a constant and large population size, and a “background mortality” of 50% (i.e. an average fitness of 0.5). Also, assume that this population suddenly has 100 tiny subpopulations, with just enough “critical mass” in their frequency to avoid the early genocide syndrome that haunts all new alleles, beneficial or otherwise. Each of these subpopulations possess a beneficial allele at separate locus which gives them a competitive edge worth coeffcient 0.05 over the rest of the population. I’m using multiplicative fitness interaction here, and equate selection coefficient “0.05” with a fitness multiplier 1.05.

(The sudden appearance of many alleles, each being possessed by more than one individuals is a simplification to ease the discussion here. When simulating these things, I create unique mutations on the fly, as indicated by a sensible mutation rate. Most of these mutations face a genocide before managing to build up enough “critical mass”.)

Initially, then, we have a large main population with fitness 0.5 (or, to be exact, slightly below 0.5) and 100 tiny subpopulations with fitness 0.5 *1.05 ~ 0.53. Note that the combined effects of selective pressures here, using multiplicative fitness interaction, is 1.05^100 ~ 132 ! What does this mean? In Haldane’s model, it would mean that the fitness of the main population would drop to 0.5/132 ~ 0.004 which means 99.6% mortality and clearly equals genocide. But this is not Haldane’s scenario we are studying. There is no new external selection pressure anywhere. There is merely a slight redistribution of vital resources going on, caused by intraspecific competition. A small fraction of the resources normally exploited by the main population gets hogged by the lucky ones possessing any one of the 100 beneficial alleles. Although the effects of these resources notably boosts the fitness of the lucky ones, it barely hurts the fitness of the much larger main population. The net effect is that the average fitness of the population remains exactly the same. Also note that although the combined effects of selective pressures is 132, there is no dramatic fitness difference between any two individuals in the population. Thus, we have a whole lot of selection taking place at a remarkable speed, but there is in fact nothing very dramatic going on in terms of (a) average fitness, (b) mortality, © reproduction rate required to keep the population size constant and (d) fitness differences between individuals.

If we step many generations forward, the beneficial alleles have obviously increased their frequencies in the population. Since they are at separate loci, they fairly soon start to meet in the same individuals due to Mendelian segregation. Even so, fitness difference between any two individuals remains fairly small, and the average fitness of the population remains constant. By the time some lucky bastard has managed to collect many of these beneficial alleles in their loci, the original main genotype, with no beneficial alleles at all, has likely already gone extinct; with random mating, alleles just tend to spread in a fairly even fashion. This is a sort of “internal arms race”. No one wins in the long run(*), because everyone eventually learns the same tricks, but a whole lot of substitutions take place at a fast pace regardless.

(*)Which ultimately applies to most evolutionary stories in one way or the other, of course. Despite all of our morphologic change and our “adaptation”, have we “won” the bacteria from which we have descended. (Rhetorical question.)

In terms of simulation, here is how I have implemented “intraspecific competition”. In the previous example, does population end up with (an absurd) fitness 0.5 * 1.05^100 ~ 61, after possessing all 100 beneficial alleles? No. As I said, the average fitness remains constant. To enforce this, I “renormalize” the fitness of the population every generation. This practice reflects the fact that whenever the fitness of any individual increases, due to increased effectiveness in hogging resources, it does so by decreasing the fitness of all others slightly. “Renormalization” means that I calculate the average fitness of the population after each reproduction phase, and then multiple all fitnesses with the constant ORIG_AVG_FITNESS/CURRENT_AVG_FITNESS. This effectively returns the average fitness to its original value. So, the value “61”, if anything, is merely some kind of rough and abstract measure of the amount of change the population has experienced, rather than an actual fitness value. If, instead, we were considering Haldane’s scenario over a long period of time, similarly either subsequent environmental changes or simply the finite carrying capacity of the ecological niche would keep the fitness of the evolving population at bay.

I hope this further clarifies the power of “intraspecific competition”, and why ReMine avoids it like a plague. Granted, I’m not qualified at all to judge how influential this scenario is for populations in real nature. However, it should be clear by now that Haldane’s own words (“I am quite aware that my conclusions will probably need drastic revision”) have come true. In fact, while ReMine calls Haldane/Kimura a “trade secret” of evolutionists, my text book (Ridley 2nd ed) merrily devotes a whole chapter for this topic, and considers the issue largely settled. We may not yet know the balance of power between various theoretical evolutionary scenarios, when it comes to real nature, but we do know that Haldane’s original model was very limited and that it has no special merit over more complex models that take more things into account. Kimura’s original argument has been weakened accordingly, as it largely depends on low rate of substitution for adaptations; neutral evolution trivially explains changes at non-coding DNA and fixation of silent mutations, but it is very likely not needed in explaining any morphologically meaningful evolution – there are enough adaptations to do the job. None of this applies to Walter ReMine’s quote mining project, of course. He just won’t listen. I hope Salvador does, at least. :)

Comment #154786

Posted by alienward on January 12, 2007 11:23 AM (e)

Coin wrote:

Nit-pick:
IDists only talk about the purpose of the things made by the designer. They kind of forbid talking about why the designer designs things, though.

No they don’t. Why, what, how, and when might be required questions to answer in a grade school science fair project, but they are only currently beyond the scope of ID, not forbidden. From the IDEA Center:

We may indeed one day be able to answer questions such as:
- what mechanism did the designer use to design?
- why did the designer design?
- how did the designer assemble the object?
- when was it designed? (this question may be informed through sciences which study chronology, such as the geological sciences, or through other biological dating methods. But intelligent design theory does not answer this question.)

But intelligent design theory will always be limited to what we can infer from the data. Currently these questions which lies outside the scope of intelligent design theory, but that fact does not discredit the claims that intelligent design theory actually does make.

Comment #154787

Posted by Jack on January 12, 2007 11:23 AM (e)

Zachriel may have been banned three times, but I got banned with my first post ever to Uncommon Descent. Here’s the off-topic, irrational, vulgarity ridden filth I attempted to spew there:

dodgingcars writes:
> > From admitting that science had to be redefined to include ID,
>
> Not quite. He’s actually saying that science was a broader term in
> the past and has been redefined to exclude ID now.

That is not at all what he claimed in his testimony. Behe recognizes
that ID is not a scientific theory and sought to change the definition
rather than address the aspects of ID that make it not qualify as
science. He then admitted under cross-examination that his definition
allows astrology to be called science as well.

> > The evidence about the peer review of his book (which I have
> > ordered, it isnt in my local shop) was pretty bad
>
> How was it bad?

If you read the testimony, you’ll see that he first claimed that his
book had been subject to the same level of peer review as are articles
in journals such as Nature and Science. In fact, one of the people
listed as a reviewer never even read the book, nor did he provide any
feedback. The feedback provided by other reviewers was without
exception unsupportive of ID, yet Behe changed nothing and published
the book anyway.

TheSun is absolutely correct, Behe got hammered.

I naively expected that someone with a PhD would have greater respect for the open exchange of ideas and a greater willingness to admit error.

Jack

Comment #154789

Posted by secondclass on January 12, 2007 11:40 AM (e)

Salvador wrote:

The falsifiably hypothesis is that specified complexity must ultimately regress to an intelligent agency.

How exactly is that falsifiable, considering that design detection is subject to false negatives? If you find an apparently unintelligent source at the root of the regress, how do you know that it’s actually unintelligent?

Salvador wrote:

Specified complexity can be an empircally measurable property given the approriate information.

Consider your bluff called.

Salavador wrote:

… it can be logically demonstrated that their theory is self-contradictory …

Consider this bluff called as well.

Salvador wrote:

I think Dembski’s math had refuted anything by Dawkins and friends.

And this one.

Salvador wrote:

I read the supposed refutations by Dembski’s critics, and I find them to be impressively written strawman takedowns and disingenuous distortions of what Dembski actually wrote. You’ll hear appeals by PT regulars to Shallit, Elsberry, Perakh, Avida, etc. They are mostly strawman misrepresentations. They do not qualify as theoretically sound rebuttals….

And this one.

You’re racking up quite a debt, Sal. Do you plan on ever making good on these claims?

Comment #154793

Posted by mark on January 12, 2007 12:09 PM (e)

Sal wrote:

…therefore ID theory is at least better by default.

No.
Numerous commenters have noted this.
The Flying Spaghetti Monster Theory is superior to the Theory of ID. If the Theory of ID is to be considered better than the FSM Theory, it had better provide some real esplanation (there’s no “theory” there.) No theory “wins by default.”
Would discussion of advantages of FSM over ID be acceptable to post at Uncommon D?

Comment #154803

Posted by GuyeFaux on January 12, 2007 1:19 PM (e)

Why, what, how, and when might be required questions to answer in a grade school science fair project, but they are only currently beyond the scope of ID, not forbidden.

Here’s the utter crap (Behe’s cross) that I get the idea that they don’t want to discuss the all important “why” question:

Q. Can you explain why would the intelligent designer design one irreducibly complex system and then another one to combat it or fight it?

A. The question of the intentions of the designer is a question that is separate from and beyond the question of whether there is design. We can know something that is designed without knowing what the designer intended for it. If I might just give an example from our everyday world, we can look at something like a gun or some such thing, realize immediately that it was designed, and not know what the purpose of it is for.

Q. But we do know a lot about the intentions, desires, motives, needs of the intelligent actors who designed those guns, correct?

A. I’m going to say I don’t think so. Certainly we know that if a gun were made by a human being and we know, we have other information from other sources about that, so from that other information we can certainly deduce, make good arguments about what those might be, but the case remains that that is separate information, separate from the structure of the gun, and we decide that the gun is designed by looking at the structure of it, or get away from guns, just any mechanical complex object.

And from the Minnich cross (which had a lot of content on this topic:

Is there any scientific intelligent design
research program going on to determine when the designer
acted or she acted or they acted; how he, she, or they
acted; why he, she, or they acted; or who he, she, or
they are?
A. No. No.

Comment #154804

Posted by Dave Mescher on January 12, 2007 1:35 PM (e)

Salvador Cordova wrote:

Specified complexity can be an empircally measurable property given the approriate information.

Then please, by all means, tell us what units “specified complexity” can be measured with, and what tools one would make a simple & easy measurement with. A sample measurement would be nice, too.

Force can be measured and has units for its measurement. (SI unit is Newton, 1 N = 1 kg*m/s^2)

Energy/Work can be measured and has units for its measurement. (SI unit is Joule, 1 J = 1N*m)

Power is measurable, too. (SI unit is Watt, 1 W = 1 J/s).

As far as I can tell, the primitives in physics are length (m/meter), mass (kg/kilogram), time (s/second), current (A/ampere), thermodynamic temperature (K/kelvin), substance (mol/mole), and luminous intensity (cd/candela). Every other measureable quantity in physics can be defined with these units. How does “specified complexity” fit in with these units, and if it requires a new unit, how would you measure it, even roughly?

Comment #154811

Posted by Salvador T. Cordova on January 12, 2007 1:51 PM (e)

caligula said:

None of this applies to Walter ReMine’s quote mining project, of course. He just won’t listen. I hope Salvador does, at least. :)

Can you tell me the average nucleotide fixation rate per generation under optimal conditions? Fixation defined as 100% uniformity of nucleotide at a loci position.

That was what ReMine’s argument boiled down to.

Thanks.

Comment #154813

Posted by Raging Bee on January 12, 2007 2:00 PM (e)

Sal: You haven’t answered any of our questions, so why should any of us answer yours?

Comment #154814

Posted by Coin on January 12, 2007 2:02 PM (e)

What was the motive in installing an outbound motor in a bacteria?…

Ummm, because rocks don’t need to move toward food? This isn’t too complicated – really. This purpose of the motor and whip is to move the bacteria.

Yes, but why is the intelligent designer interested in whether bacteria are able to move toward food?

I suppose what I should have said before is that while the IDers enthusiastically and immediately identify short-term purpose in all of the various things the Designer supposedly created, we’re essentially never given a hint of long-term motive. Until they produce some kind of long-term plan that the flagellum fits into like you suggest (you know, a theory), the tiny immediate purposes the designer is accused of now are meaningless; in a framework where the designer is expected to simply act in whatever arbitrary and capricious way strikes it at the moment, the unnamed designer might as well just be random chance.

I initiated an irrelevant (a negative argument against evolution doesn’t help Sal showing ID is useful) side discussion because I wasn’t aware that talk.origins group was discussing the quality of T.O. CC list.

Oh, I’m not complaining. I just find it fascinating this appears to happen in every conversation Sal enters.

Comment #154815

Posted by Elizabeth Liddle on January 12, 2007 2:04 PM (e)

Salvador T. Cordova wrote:

Febble asked:

must Specified Complexity arise from such an “purposeful” intelligence or could it arise from mere “intelligence” as operationally defined by Dembski?

The falsifiably hypothesis is that specified complexity must ultimately regress to an intelligent agency. The intelligence can act through a surrogate (like a machine or factory), but it’s ultimate cause is intelligence. At least that is the hypothesis.

Well, not really. You appear to be saying that if we find an example of specified complexity, and it does not regress to an intelligent agency, then the hypothesis is falsified.

Well, life (according to Dembski, and I agree) demonstrates specified complexity - so how do we test whether it regresses to an intelligent agency? Dembski’s position, as I understand it, is that we must infer an intelligent agency if we find an example of specified complexity. And of course you cannot assume what you set out to prove.

On the other hand, the proposition that Specified Complexity must be the result of an intelligent agency is falsifiable - I gave you the example of Chesil Beach, which exhibits Specified Complexity by Dembski’s definition, but which is the result of wind, tides and topography. It was not designed by an intelligence, in your sense, although it was designed, I have argued, by an intelligence as defined by Dembski.

Salvador wrote:

Formally speaking specified complexity is a property which is not derived from the presumption of intelligence. Consder what Dembski wrote:

The principal advantage of characterizing design as a complement of regularity and chance is that it avoids committing itself to a doctrine of intelligent agency.

Defining design as the negation of regularity and chance avoids prejudicing the causal stories we associate with the design inference.

William Dembskim Design Inference

Specified complexity can be an empircally measurable property given the approriate information.

Well, I accept that, up to a point, except that “the appropriate information” seems key. How is “appropriate” defined?

Even biologists colloquially say “such and such has a design.” That is consistent with the definition of Deisgn within ID theory.

Yes, and it is also consistent with the definition of intelligence as defined by Dembski. I think biologists would agree that in the sense that biological systems are “designed” they are designed by an agent “with the power and capacity to choose between options” namely, by natural selection.

Whether such designs can arise without the aid of intelligent agency somewhere in the pipeline is the question.

Well, my argument is that it isn’t. The question is how complex does a replicative if…then algorithm have to be before you call it intelligent? Sure, complex designs are the result of complex interactions. So is intelligence.

ID theorists hypothesize that it can’t be done.

And I agree. It can’t be done without the aid of an intelligent system.

The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default.

So the question arises as to whether Natural Selection is intelligent enough?

No, it isn’t. Even though it fulfills Dembski’s definition of being an agent with “power and capacity to choose between options” (Natural hazards determine who will live and who will die), it is not very intelligent. What IS arguably intelligent is the complete agent originally hypothesised by Darwin: natural selection plus replication with modification. It’s how our own intelligence works.

cheers

Lizzie

Comment #154816

Posted by Anton Mates on January 12, 2007 2:09 PM (e)

Coin wrote:

Yes, but why is the intelligent designer interested in whether bacteria are able to move toward food?

Whimsy.

Comment #154817

Posted by Elizabeth Liddle on January 12, 2007 2:15 PM (e)

Salvador T. Cordova wrote:

Febble asked:

must Specified Complexity arise from such an “purposeful” intelligence or could it arise from mere “intelligence” as operationally defined by Dembski?

The falsifiably hypothesis is that specified complexity must ultimately regress to an intelligent agency. The intelligence can act through a surrogate (like a machine or factory), but it’s ultimate cause is intelligence. At least that is the hypothesis.

Well, not really. You appear to be saying that if we find an example of specified complexity, and it does not regress to an intelligent agency, then the hypothesis is falsified.

Well, life (according to Dembski, and I agree) demonstrates specified complexity - so how do we test whether it regresses to an intelligent agency? Dembski’s position, as I understand it, is that we must infer an intelligent agency if we find an example of specified complexity. And of course you cannot assume what you set out to prove.

On the other hand, the proposition that Specified Complexity must be the result of an intelligent agency is falsifiable - I gave you the example of Chesil Beach, which exhibits Specified Complexity by Dembski’s definition, but which is the result of wind, tides and topography. It was not designed by an intelligence, in your sense, although it was designed, I have argued, by an intelligence as defined by Dembski.

Salvador wrote:

Formally speaking specified complexity is a property which is not derived from the presumption of intelligence. Consder what Dembski wrote:

The principal advantage of characterizing design as a complement of regularity and chance is that it avoids committing itself to a doctrine of intelligent agency.

Defining design as the negation of regularity and chance avoids prejudicing the causal stories we associate with the design inference.

William Dembskim Design Inference

Specified complexity can be an empircally measurable property given the approriate information.

Well, I accept that, up to a point, except that “the appropriate information” seems key. How is “appropriate” defined?

Even biologists colloquially say “such and such has a design.” That is consistent with the definition of Deisgn within ID theory.

Yes, and it is also consistent with the definition of intelligence as defined by Dembski. I think biologists would agree that in the sense that biological systems are “designed” they are designed by an agent “with the power and capacity to choose between options” namely, by natural selection.

Whether such designs can arise without the aid of intelligent agency somewhere in the pipeline is the question.

Well, my argument is that it isn’t. The question is how complex does a replicative if…then algorithm have to be before you call it intelligent? Sure, complex designs are the result of complex interactions. So is intelligence.

ID theorists hypothesize that it can’t be done.

And I agree. It can’t be done without the aid of an intelligent system.

The Darwinists argue Natural Selction can do this, and I respond, they have not proven their case and that it can be logically demonstrated that their theory is self-contradictory and therefore ID theory is at least better by default.

So the question arises as to whether Natural Selection is intelligent enough?

No, it isn’t. Even though it fulfills Dembski’s definition of being an agent with “power and capacity to choose between options” (Natural hazards determine who will live and who will die), it is not very intelligent. What IS arguably intelligent is the complete agent originally hypothesised by Darwin: natural selection plus replication with modification. It’s how our own intelligence works.

cheers

Lizzie

Comment #154819

Posted by JohnK on January 12, 2007 2:23 PM (e)

Just pointing out that as far back as 30 years ago, in
Solutions to the Cost-of-Selection Dilemma
Verne Grant and Robert H. Flake
Proc Natl Acad Sci U S A. 1974 October; 71(10): 3863–3865.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=434284

..the basic assumptions/limitations of Haldane’s original model were laid out and the various “solutions”, some excellently discussed in this thread, were summarized: soft selection/intraspecific competition, population structure, non-independent fitness effects (Mayr , Mettler and Gregg)/truncation selection (King, Maynard Smith, Crow, Felsenstein), gene linkage, and drift(Kimura) and introgression.

It gives the lie (surprised? thought not) to Remine’s claim that this was a “trade secret”.

caligula wrote
None of this applies to Walter ReMine’s quote mining project, of course. He just won’t listen. I hope Salvador does, at least. :)

You don’t know Cordova.
I had the privilege… what almost a decade ago… of seeing Remine “debate” David Sloan Wilson, Joel Felsenstein, et al in sci.bio.evolution, and I carried many of these insights over to ARN (along with professional popgen people who’d occasionally drop in.) I’m sure Cordova has seen them many times but the creationist memory hole/willful self-censorship something out of Oliver Sacks.
http://www.oliversacks.com/subj-a.htm

Comment #154820

Posted by Coin on January 12, 2007 2:25 PM (e)

Can you tell me the average nucleotide fixation rate per generation under optimal conditions?

I do not see why this question is particularly important to the current discussion. But my understanding from doing some basic checking is that average fixation rate as you describe it is known to vary depending on environment, species etc; and I seriously doubt “optimal conditions” can be meaningfully defined.

Comment #154838

Posted by Torbjörn Larsson on January 12, 2007 3:46 PM (e)

caligula wrote:

TL wrote:

Explaining one of Wilson’s objections (Blazer’s link) on Isaak’s claim in CB121.

You must mean this one:

“He also assumed that two mutations would take twice as long to reach fixation as one, but because of sexual recombination, the two can be selected simultaneously and both reach fixation sooner.”

That is Isaak’s claim, and Wilson objects: “This is nonsense. Haldane did _not_ _assume_ this. He _derived_ it from his other assumptions…. [The derivation] does _not_ assume that the mutations only become fixed one at a time, and it _does_ take full account of the role of sexual recombination…. [ReMine:] “If you average all these speeds, then the total rate can be one per 300 generations.” And this is an accurate description of what Haldane showed (given his assumptions).”

So yes, that was what I was referring to.

caligula wrote:

my text book (Ridley 2nd ed) merrily devotes a whole chapter for this topic

Googling I find on amazon.com Mark Ridley’s “Evolution” 2nd ed, “the premier undergraduate text in the study of evolution” with “strong, balanced coverage of population genetics”. Is that it? An undergraduate text would probably be just about right. :-)

caligula wrote:

Kimura’s original argument has been weakened accordingly, as it largely depends on low rate of substitution for adaptations; neutral evolution trivially explains changes at non-coding DNA and fixation of silent mutations, but it is very likely not needed in explaining any morphologically meaningful evolution – there are enough adaptations to do the job.

Well, that gives a new perspective. IIRC Moran on his blog proposes genetic drift as the strongest overall mechanism. This is more like “to each its own”.

Comment #154844

Posted by Torbjörn Larsson on January 12, 2007 3:54 PM (e)

Sal wrote:

Can you tell me the average nucleotide fixation rate per generation under optimal conditions?

Considering the different mechanisms undercutting the case of Haldane’s model used in the ‘dilemma’ as has been discussed here, what do you mean by “optimal conditions” and why is that relevant in this discussion?

You just confirm the picture of not listening. Instead, in light of the discussion, do you still think ‘Haldane’s dilemma’ is relevant, and why?

Comment #154846

Posted by Torbjörn Larsson on January 12, 2007 3:58 PM (e)

“An undergraduate text would probably be just about right. :-)”

Btw, besides reading a textbook, are there web resources available in population modeling?

Comment #154854

Posted by Doc Bill on January 12, 2007 4:30 PM (e)

From time to time I discuss the theory of evolution with my cat who has a short attention span. However, even after my best explanation my cat takes me back to square one with the question, “Meow?”

Sal, who is not nearly as endearing as my cat, uses the same mode in his “arguments.” Sal typifies how creationists address the theory of evolution at any level: unsupported assertions followed by diversion and topic-changing followed by semantic analysis of the word “is” followed by the vanishing act. Sal simple makes up stuff as he goes along which is why he gets trapped time and time again. Sal would not have survived as a mouse.

Sal is not a spokesman for the ID movement, nor does he represent the DI, nor is he considered a leading ID astrologer (like Dembski or Behe). Like me, Sal is a scientific gadfly but unlike me Sal isn’t interested in learning anything. Creationists, Sal included, are really bugged by the notion that the theory of evolution doesn’t require a designer, that we humans are not the end product and special, and that there is no plan or purpose to life other than complex chemical process that leads to survival.

For Sal that view makes his life meaningless.

For me that view gives me purpose. I am at the tip of a branch of organisms that can be traced back, unbroken, nearly 4 billion years. I am grateful and reverent to all my ancestors who survived calamity after calamity to enable me to exist today. I celebrate life and my place in the world and for the life of me I can’t understand Sal at all. What a poor, frightened creature he must be.

Comment #154855

Posted by secondclass on January 12, 2007 4:34 PM (e)

Dembski (as quoted by Salvador) wrote:

The principal advantage of characterizing design as a complement of regularity and chance is that it avoids committing itself to a doctrine of intelligent agency.

Actually, the principle advantage of that definition is that it avoids committing itself to anything. Not even mathematical or logical coherence.

Comment #154858

Posted by ben on January 12, 2007 5:00 PM (e)

Sal’s pathetic, infinitesimal, nitpicky criticisms of evolution are analagous to a librarian trying to tell us the Golden Gate Bridge is structurally unsound and near collapse by showing us a blurry close-up photo of a single rusty rivet. Except when pressed, he can’t or won’t tell you where the rivet supposedly is, he can’t offer any real evidence that that rivet is about to fail–hell, he can’t even demostrate that the rivet is part of the GGB to begin with. Plus you find virtually every piece of evidence he offers is easily googleable as having been quote-mined from engineering studies which unambiguously conclude that the bridge is sound.

Then once you really study the picture, you realize it’s just a really really low-quality jpg of that virgin mary grilled cheese sandwich on ebay. Meanwhile Sal has fled the discussion and is posting on all the librarian blogs how he blew all the bad guys out of the water with his rusty rivet argument, the blog czars helpfully delete all comments that point to the original discussion where his assertions were shredded by working structural engineers, and he gleefully declares victory while all the know-nothing sycophants (most of whom passionately believe it was impossible for the bridge to have ever been built to begin with) cheer his genius.

Sal, what’s your theory of ID? Put up or shut up.

Comment #154871

Posted by Torbjörn Larsson on January 12, 2007 5:15 PM (e)

GuyeFaux wrote:

In particular, does evolutionary theory predict that the Kolmogorov complexity of a genome tends to increase over time?

Well, this is a rather large question, and I’m no biologist. But this is what I can puzzle out from some discussions.

Describing “complexity” and ‘information’ isn’t relevant to describe evolution or life at large. Evolution models work without these descriptions, and phenotypes are described without it. This is where I think Liddle’s definition “result of choice” comes in, as a weak and tautological definition, though it will not cover all of the mechanisms behind phenotypes.

Cladistics have methods that touch on information theory, though. (Bayesian methods.)

Also, in some specific situations one can define and use complexity measures.

Intelligence are detected in forensics and SETI by having a model for intelligent behavior. (Refuting alienward’s naive assumption that it isn’t needed.) In SETI it is indeed complexity and information in signals that is used; small bandwidth (low Shannon information rate in the channel) and simplicity (low K-C complexity information content) is considered to characterize intelligent communication.

Another use of complexity is in characterizing (neural) networks, or neurons in brains. These systems are situated in between simplicity and complexity with order on all scales, just as glasses are situated in between crystals and amorphous materials. ( http://www.striz.org/docs/tononi-complexity.pdf )

This is apparently a common situation in natural systems, and it is akin to what Dembski tries (but fails) to do. Interestingly, here the “result of choice” returns, since network branching and glass interactions are results of components choosing different possibilities. Molecules in crystals and amorphous materials have less choices in bindings.

Turning to the genome, information in the genome doesn’t tell us how it is used, which is more like a complex language. But there have been some studies of information content, I assume KC, and PT has reported on them.

But this information doesn’t need to increase, since evolution works both ways. In Liddle’s analogy, evolution learns and forgets. And as I noted earlier, the adaptation process in some population models looks like bayesian inference used in machine learning, with alleles as ‘hypotheses’ and the population as ‘theory’.

Comment #154873

Posted by How's that? on January 12, 2007 5:19 PM (e)

Can you tell me the average nucleotide fixation rate per generation under optimal conditions?

somewhere near the mutation rate…

Comment #154881

Posted by Torbjörn Larsson on January 12, 2007 5:42 PM (e)

“These systems are situated in between simplicity and complexity”

Here I mean between regularity and non-regularity, since the measures used for complexity differs from KC. (They maximize between regularity and non-regularity instead.)

Comment #154883

Posted by GuyeFaux on January 12, 2007 5:49 PM (e)

But this information doesn’t need to increase, since evolution works both ways. In Liddle’s analogy, evolution learns and forgets.

What about Schneider’s GAs? I thought he proved that the Shannon information content of the genome should increase with selection.

I was just wondering if something similar could be showed for Kolmogorov complexity as well. As they say, the genome is mostly a repository of survival methods used by the organism’s ancestors. I just wonder how cumulative the “history” is.

Comment #154887

Posted by Dean Morrison on January 12, 2007 6:01 PM (e)

I’m sure Mr Dembski will welcome my support for his insightful idea, and will welcome my support from across the pond - so I’m off to post this on ‘Uncommon Descent’ - where I’m sure I’ll get a warm and respectful welcome…..

Strange - 24 hours later and they still haven’t posted my contribution??

On the other hand it seems to be rather quiet over there compared to the rather jolly debate on this blog.

Is that because ID doesn’t have many supporters, or is it because they ban and censor 90% of the people who post?

Do people like Sal just come here for the company? At least the saddos get some attention here I suppose??

Comment #154888

Posted by Torbjörn Larsson on January 12, 2007 6:03 PM (e)

“Turning to the genome, information in the genome doesn’t tell us how it is used, which is more like a complex language. “

Btw, not all of this information, either basic KC complexity or the complex real use of the genome, is contained in the genome. In reproduction cellular machinery (and maternal hormones in embryos) always encloses the genome, and contains further contingent information.

Comment #154902

Posted by Torbjörn Larsson on January 12, 2007 6:33 PM (e)

GuyeFaux wrote:

What about Schneider’s GAs? I thought he proved that the Shannon information content of the genome should increase with selection.

Ah yes, that is probably the PT article I remember. Okay, if it was Shannon information, it isn’t a “content”. Shannon information, or channel capacity, is characterizing the capacity of a communication channel. (See wikipedia on “channel capacity”.) The related Shannon entropy is also used as a sort of relative capacity measure.

GuyeFaux wrote:

I was just wondering if something similar could be showed for Kolmogorov complexity as well.

KC complexity is not a computable function. “However, it turns out that the fact that a specific string is complex cannot be formally proved, if the string’s length is above a certain threshold.” ( http://en.wikipedia.org/wiki/Kolmogorov_complexity ) Likewise, there is no general way to prove simplicity; there is generally always a possibility that another (simpler) algorithmic construction produces the same result.

But I don’t think Sal will listen, “information” and “complexity” is as holy as “intelligence”…

GuyeFaux wrote:

As they say, the genome is mostly a repository of survival methods used by the organism’s ancestors. I just wonder how cumulative the “history” is.

We seem to all (well, not Sal :-) agree on this. Actually, the analogy with alleles as hypotheses and the genome as theory is apparently considered by some biologists as a way to puzzle out some of what this ‘information’ and accumulation means in practical terms. ( http://golem.ph.utexas.edu/category/2006/12/back_from_nips_2006.html#c006690 )

Comment #154904

Posted by Torbjörn Larsson on January 12, 2007 6:42 PM (e)

“KC complexity is not a computable function.” - Apparently, KC complexity is not a computable function. (If I had realized earlier, I wouldn’t have suggested it.)

“the genome as theory” - the population as theory.

Comment #154905

Posted by Torbjörn Larsson on January 12, 2007 6:50 PM (e)

“KC complexity is not a computable function.” - Apparently, KC complexity is not a computable function. (If I had remember, I wouldn’t suggested it earlier.)

“the genome as theory” - the population as theory.

Comment #154923

Posted by Henry J on January 12, 2007 11:24 PM (e)

Torbjörn Larsson,
Re “In SETI it is indeed complexity and information in signals that is used; small bandwidth (low Shannon information rate in the channel) and simplicity (low K-C complexity information content) is considered to characterize intelligent communication.”

Huh. IOW they look for simplicity where it isn’t normally expected. After all, intelligent designers that we know of tend to avoid complexity where they can do so - things are simpler that way. (So to speak.)

————-

Coin,
Re “Yes, but why is the intelligent designer interested in whether bacteria are able to move toward food?”

And, what about the cases in which the “food” is us, our food plants and animals, and our pets? One could conclude that the “designer” (of bacterial flagella) is no friend of humanity…

Henry

Comment #154934

Posted by caligula on January 13, 2007 3:24 AM (e)

SC wrote:

Can you tell me the average nucleotide fixation rate per generation under optimal conditions? Fixation defined as 100% uniformity of nucleotide at a loci position.

What I can say is that the main limiting factor in intraspecific competition is the mutation rate for beneficial alleles. If one such mutation originated every generation, after an initial delay, we would get one fixation per generation as well.

But you talk about “optimal conditions” – alas, I’m hardly qualified to define them, or even to make a suggestion concerning them. I have to point you to Leonard Nunney’s paper “The cost of natural selection revisited”. You can’t miss it – it is linked by e.g. CreationWiki (although it seems no creationist / ID-advocate has actually discussed the impact of that paper!). It seems to me that Nunney’s simulation incorporates both the idea of soft selection and intraspecific competition. Nunney’s paper also contains an excellent discussion about the effects of all relevant parameters involved in these types of simulation. When I have the time, I should contact Nunney and request the specs of his simulation, in order to create an independent version of it and publish the source code.

PS. My main point of criticism concerning evolutionary scenarios involving a lot of concurrency is that we don’t really know the proper fitness interaction model for resolving the fitness of individuals with many beneficial alleles at separate loci. Multiplicative model is often used, but it is at best a vague estimate.

PPS. Did you notice #154742 ?

Comment #154939

Posted by Peter on January 13, 2007 7:46 AM (e)

I love this quotation from the IDists:
We may indeed one day be able to answer questions such as:
- what mechanism did the designer use to design?
- why did the designer design?
- how did the designer assemble the object?
- when was it designed? (this question may be informed through sciences which study chronology, such as the geological sciences, or through other biological dating methods. But intelligent design theory does not answer this question.)

Why? Why do I love it? Because it subjects the “unnamed designer” (Just cut the sham would you and say it in front of everyone?!?! “G-O-D.” It’s embarassing to watch!) to methodological naturalism…well…assuming they ever formulate any jeopardizable hypotheses.
In other words:

The resultant paradox contained within the definitional matrices of both “What is intelligence?” and “What is purpose?” lead, ultimately, to the unbound bind of the Deux ex natura of their Deus ex machina that diminishes the patina of the former’s resplendance by transmogrifying the amorphous into that which is hypothesized and therefore forced prostrate beneath the lens of methodological naturalism, a space wherein all is treated to the sharp blade of Occam’s Razor.
It represents a sub-order of homo sapiens’ - between the YEC/OEC/IDC v. Evolutionary Scientists - eternal conflict’s attenuation through meta-processed non-discrursive function along an illusive hegemonistic timescale not unlike Heidegger’s inquisition of the definitional parameters of “is” and thusly “not is.” The questions, then, are not, “What are our origins?” or “What are our ends?” but IS “How do we understand non-linear post facto extinction in time schemes disembodied from their semiotic foci?”

Got that Sal? I thought so.
To be perfectly blunt. That opacity is the essence of your argument. It might be grammatically/syntactically correct but it is, in essence, totally devoid of content.
Vapid.
Dodges.
Nonsense.
Dressed-up vacuity.
There are at least five solid questions waiting to be answered in this thread, not the least of which is from FEBBLE.
If one of William Dembski’s definitions of intelligence is the one that Febble keeps asking about, then why can’t natural selection be intelligent when it is clearly an “appropriate” (to use one of your words) candidate as an intelligent agency?
Now, it something to do with purpose, then please address what that purpose is and provide us with the data that support this alleged purpose?

Comment #154980

Posted by alienward on January 13, 2007 11:26 AM (e)

Torbjörn Larsson wrote:

Intelligence are detected in forensics and SETI by having a model for intelligent behavior. (Refuting alienward’s naive assumption that it isn’t needed.) In SETI it is indeed complexity and information in signals that is used; small bandwidth (low Shannon information rate in the channel) and simplicity (low K-C complexity information content) is considered to characterize intelligent communication.

Hey, I might be an alien but I don’t remember anything saying anything about SETI.

IDists claim “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” This implies that some features of living things aren’t best explained by an intelligent cause. Has anyone seen a list of some of the life features that aren’t best explained by an intelligent cause and the explanation of how IDists determined they weren’t intelligently designed?

Comment #154984

Posted by stevaroni on January 13, 2007 11:31 AM (e)

Peter loves the quote…

We may indeed one day be able to answer questions such as:
- what mechanism did the designer use to design?
- why did the designer design?
- how did the designer assemble the object?
- when was it designed? (…. But intelligent design theory does not answer this question.)

I love it too.

So as the “Theory of ID” currently stands, we have an unnamed designer using one or more unfamiliar mechanisms, unidentified methods and unspecified materials, for an unknown reason to make some, or all of the designs he may have designed at an unknown point in the uncharted past.

But, like any good scientific theory, ID does have it’s limits, since it will probably never be able to answer the imponderable “when”.

Well, that does it for me! Now that I bask in the sea of knowledge that is ID, how can I possibly begrudge teaching it to our kids?

Comment #154992

Posted by Torbjörn Larsson on January 13, 2007 12:40 PM (e)

TL wrote:

These systems are situated in between simplicity and complexity with order on all scales, just as glasses are situated in between crystals and amorphous materials.

I have gone on at length already, but I just saw an interesting comment bearing on this.

“A measure that corresponds much better to what is usually meant by complexity in ordinary conversation, as well as in scientific discourse, refers not to the length of the most concise description of an entity (which is roughly what AIC is), but to the length of a concise description of a set of the entity’s regularities. Thus something almost entirely random, with practically no regularities, would have effective complexity near zero. So would something completely regular, such as a bit string consisting entirely of zeroes. Effective complexity can be high only a region intermediate between total order and complete disorder.

There can exist no procedure for finding the set of all regularities of an entity. But classes of regularities can be identified.” Murray Gell-Mann, on his book “The Quark and the Jaguar”. ( http://golem.ph.utexas.edu/category/2006/12/common_applications.html#c006990 )

He goes on to discuss defining effective complexity, after which he concludes that “The effective complexity of the regularities can then be defined as the AIC of the description of the set of entities and their probabilities.” Also IIRC, AIC and some other complexity measures are discussed by mark Perakh on Talk reason.

alienward:

TL wrote:

Hey, I might be an alien but I don’t remember anything saying anything about SETI.

I was referring to your comment that “Why, what, how, and when might be required questions to answer in a grade school science fair project, but they are only currently beyond the scope of ID, not forbidden.” We can’t identify intelligence or its design without having a model of how the intelligence works. As Liddle pointed out, evolution provides us with such a model. And it predicts phylogenetic trees, which is what we observe.

And I’m sorry, but I can’t figure out what the remaining part of your comment is claiming and asking. The second sentence contradicts the first, assuming “this” points to it. That leaves me stumped.

Comment #155005

Posted by alienward on January 13, 2007 2:23 PM (e)

Torbjörn Larsson wrote:

I was referring to your comment that “Why, what, how, and when might be required questions to answer in a grade school science fair project, but they are only currently beyond the scope of ID, not forbidden.” We can’t identify intelligence or its design without having a model of how the intelligence works. As Liddle pointed out, evolution provides us with such a model. And it predicts phylogenetic trees, which is what we observe.

I’m saying that ID doesn’t even meet the requirements of grade school science, but IDists aren’t saying they won’t ever get around to the basics of science some day. I agree with you about needing to know how the intelligence works. Here’s some predictions of design from Sal’s club:

From the IDEA Center):

(1) High information content machine-like irreducibly complex structures will be found.
(2) Forms will be found in the fossil record that appear suddenly and without any precursors.
(3) Genes and functional parts will be re-used in different unrelated organisms.
(4) The genetic code will NOT contain much discarded genetic baggage code or functionless “junk DNA”.

Torbjörn Larsson wrote:

And I’m sorry, but I can’t figure out what the remaining part of your comment is claiming and asking. The second sentence contradicts the first, assuming “this” points to it. That leaves me stumped.

It’s my fault – let me try again.

IDists claim “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” They’re saying “certain features” not “all features”. So, what I ‘d like to know from IDists is what are some of the features of living things that are best explained by causes other than intelligent design, what are those causes, and how do IDists determine what isn’t intelligently designed?

Comment #155019

Posted by Torbjörn Larsson on January 13, 2007 4:14 PM (e)

alienward wrote:

Here’s some predictions of design from Sal’s club:

If ID have a theory (whatever it is), and agree that it is falsified if its predictions fails tests, it would be splendid. These predictions would be a start. But specifically here:

1) Interlocking complexity is predicted by evolution. So it would not be a decisive test - evolution explains this.
2) This is hard to establish, considering the randomness and scarcity of the fossil record. Probably not decisive.
3) Evolution predicts that (re)use will occur in related and unrelated organisms. (Same mutations, similar phenotype - ie bird’s and bat’s wings.) Also not decisive.
4) Decisive, since evolution predicts that some organisms may have much junk. (And also failed already.)

I guess I will have to wait for a new IDEA.

alienward wrote:

So, what I ‘d like to know from IDists is what are some of the features of living things that are best explained by causes other than intelligent design, what are those causes, and how do IDists determine what isn’t intelligently designed?

Wouldn’t we all? ;-)

Comment #155023

Posted by Elizabeth Liddle on January 13, 2007 4:28 PM (e)

The Theory of Evolution predicts everything that ID predicts because Replication with Modification plus Natural Selection is a very intelligent system. Slow, but brilliant. There is no disambiguating test because the predictions of both are identical.

Comment #155025

Posted by rossum on January 13, 2007 5:02 PM (e)

RBH wrote:

I’ve argued for years that if one put God through Dembski’s Explanatory Filter, it’d conclude “Designed!”

It does: God and the Explanatory Filter.

rossum

Comment #155037

Posted by Keith Douglas on January 13, 2007 6:22 PM (e)

And so S. Cordova demonstrates he knows as much about logic as he does about science; i.e. almost nil. An undefined primitive is contextual, first of all - nothing is absolutely an undefined primitive. So failing to mention the system in question makes his statement syntactic nonsense. Moreover, the idea that the ID guys have an axiomatic theory of anything … well, I won’t hold my breath.

Finally, to the extent that their nonsense is in hypothetico-deductive form, I suppose Elizabeth’s / Febble’s conclusion is the correct one - she found a consequence of their implicit definition. This is the danger of implicit (or axiomatic) definitions, after all: they may fail to capture some of the pretheoretical scope of the original idea.

Comment #155050

Posted by RBH on January 13, 2007 7:19 PM (e)

alienward remarked

IDists claim “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” This implies that some features of living things aren’t best explained by an intelligent cause. Has anyone seen a list of some of the life features that aren’t best explained by an intelligent cause and the explanation of how IDists determined they weren’t intelligently designed?

There’s no list, but around 1:35 or so into the talk linked here Behe says it’s an interesting question and part of a potential ID research program.

As an antidote, see this Nobel Intent post.

RBH

Comment #155071

Posted by Henry J on January 13, 2007 10:30 PM (e)

Re “(2) Forms will be found in the fossil record that appear suddenly and without any precursors.”

Seems to me that the earliest known fossils will always satisfy that “prediction”, regardless of I.D. or ToE.

Henry

Comment #155631

Posted by Salvador T. Cordova on January 17, 2007 1:19 AM (e)

Caligula wrote:

What I can say is that the main limiting factor in intraspecific competition is the mutation rate for beneficial alleles. If one such mutation originated every generation, after an initial delay, we would get one fixation per generation as well.

I appreciate your attempt to answer the question. However, under that premise with 180,000,000 base pair difference between humans and chimps, that implies 3.6 billion years at 20 years per generation which is clearly incompatible with Darwinian predictions.

The alternative is to invoke multiple nucleotide substitutions where there is somesort of synergistic effect, but how promising is that? For that scenario, for 5 million years (human chimp divergence time), we need to have on average fixations of 720 nucleotides per generation. How often will we expect 720 nucleotides to be synergistically selectable???? Not 100% of the time for sure, the answer is somewhere betweeen 1/4^720 and 1/1. It’s likely to be closer to 1/4^720 than 1, which is actually a WORSE scenario than the one nucleotide fixation at a time since 4^720 is an astronomically large number, even if fractionally smaller, one will not expect selectability of that group within supposed geological time of the Earth (4.5 billion years)….

I appreciate your comments. Sorry I’ve been delayed in responding.

Comment #155676

Posted by caligula on January 17, 2007 7:05 AM (e)

Sal,

Can you tell me what reason do we have to believe that most DNA differences between human and chimp are functionally significant? Surely you are aware of the discovery that only about 1% of the human/chimp DNA codes for genes. Although (a) a much larger part of DNA has been observed to regulate the coding part of the genome and (b) even the length of our junk DNA may in some places serve some function, no serious biologist claims that all or even most DNA sequences make a functional difference. It remains a fact that most DNA is junk, at least sequence-wise, to the best of our knowledge. In fact, it is known that even coding genes tolerate a lot of molecular change without any change in function; there is redundance in the genetic code which allows for silent mutations. (No, the news that some silent mutatations may not be entirely silent does not do away with the general conclusion. Just as the news that some non-coding DNA serves a selectable function does not do away with the conclusion that most of it does not, for mammals.)

The morphologic differences between humans and modern apes are not huge. Which is why ID advocates like ReMine have to resort to “Oh, come on!” and “You just don’t turn an ape into an opera admirer” type of emotional and intuitive arguments. In reality, evolutionary developmental biology (“evo-devo”) is increasingly demonstrating that animals share a more or less common genetic toolkit and different species are merely regulating this toolkit in a different way. For example, fairly recently, a mouse embryo grew bat’s fingers in the lab when the expression region of a single pre-existing mouse gene was manually expanded. As it happens, the corresponding gene naturally expresses itself in the limb buds of a bat embryo, accelerating finger growth. How many adaptations would you account for such a dramatic morphologic change, basing your estimate on mere intuition?

So, I am arguing that there is no molecular nor morphological argument which suggests that there must have occurred millions of functionally significant point mutations during the evolution of hominids, as opposed to what you are claiming. There is no evidence whatsoever that you can not turn an ape into an “opera admirer” with a couple of thousand adaptations. When argumentation is limited to little more than intuition and guessing, I’m sure many would join me in saying that a couple of thousand adaptations sound like a lot of morphologic evolution. And, as I’ve tried to explain, modern population genetics does not see any reason to accept Haldane/Kimura at face value any more. They have identified relevant factors that neither Haldane nor Kimura thought of, even if the contribution of these factors in historic evolution is not accurately known. So, instead of any number cut in stone, we are allowed to assume many thousand adaptations. An amount which happens to account for functionally significant molecular differences between human and chimp (or between human and the last common ancestor for human and chimp).

As for what can account for functionally insignificant molecular differences. Even though Kimura’s arguments have lost a lot of their initial punch – the part which downplays the role of adaptations – neutral change is of course still used to explain most of molecular evolution. After all, molecular clocks rely on the assumption that molecular change proceeds largely independently of morphologic change. Whether neutral evolution of hominids during the past few million years has involved mostly point mutations or chromosomal mutations, I do not know. However, the molecular change involved can be explained in principle by known mechanisms.

In summary. In my opinion, this topic follows the typical pattern of ID/evo debates. ID advocates declare that they have an observation for which there can’t be any Darwinian explanation, not even in principle. As it turns out, there can, even if it currently both lacks sufficient detail and is in practice extermely hard to test.

Comment #155695

Posted by caligula on January 17, 2007 9:37 AM (e)

Salvador,

Initially, I decided not to get sidetracked by making any note of the number (180 million SNPs) you threw in. But admittedly it did make me wonder: what on earth is going on this time. As you seem to concentrate on molecular differences, I decided to find out more. I then found your post at UD (Dec. 2006) which explains the fuzz.

I can but wonder how anyone can so utterly misinterpret a SciAm article repeating the term gene duplication like a dozen times. And it specifically says:

“The group estimated that humans have acquired 689 new gene duplicates and lost 86 since diverging from our common ancestor with chimps six million years ago. Similarly, they reckoned that chimps have lost 729 gene copies that humans still have.”

Now, you do know what a gene duplication (and, less significantly, gene deletion) is? It is something entirely different from a series of e.g. 1000 point mutations. It is a chromosomal mutation which duplicates a large sequence of DNA, including a whole coding gene, which is then subject to subsequent change independently of the original copy. As you should know, such mutations play a key role in explaining the evolution of genetic variety and, indeed, in explaining increases in genetic information. ToE postulates family trees not only for individuals and species, but also for genes and gene families.

Comment #155697

Posted by GuyeFaux on January 17, 2007 9:50 AM (e)

Let me see if I follow your point, Caligula (I’m not a biologist):

The 180,000,000 base pair difference over 5m years between chimps and humans is not caused by 720 point mutations per generation but by gene duplication? What does gene duplication deletion look like in terms of base-pair difference? And actually, now that I think about it, what does “180,000,000 base pair difference” even mean?

Comment #155703

Posted by Henry J on January 17, 2007 10:11 AM (e)

Re “we need to have on average fixations of 720 nucleotides per generation.”

Isn’t that fairly close to the sum of the average total mutation rate for the two species? And the total rate is what would be needed when comparing to the total amount of differences.

Comment #155708

Posted by Salvador T. Cordova on January 17, 2007 10:24 AM (e)

Caligula wrote:

Can you tell me what reason do we have to believe that most DNA differences between human and chimp are functionally significant? Surely you are aware of the discovery that only about 1% of the human/chimp DNA codes for genes.

That is a very good question. One friend of UD is Dr. Andras Pellioniz, internationally recognized DNA researcher. You might be interested by this article and his work. As it partially answers your question.

One Believer’s Junk Is Another Believer’s Treasure; Quest for Predictive Scientific Theories on the Function of ‘junkDNA’

“Genes” amount only to 1.3% of the hereditary material in human. Thus, the “genetic” difference between human and chimp is a slim one in ten thousand, while the difference in “junkDNA” is forty times larger. Is it a matter of belief or of scientific theory weather the 98.7% of the human DNA is “junk” or “a goldmine”?

The national debate about Darwinism (D) contra Intelligent Design/Extraterrestrial Intelligence (ID/ET) see http://www.junkdna.com/new_citationsl.html centers on the nature of predictive and thus refutable scientific theories.

Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”), while the ID/ET theory correctly predicted some yet to be decoded function of junkDNA. Debate is obsolete on “existence” of theories, once there is at least one with refutable precitions(s). The scientific challenge is already at its next stage, having stepped over the “existence question” and proceeded with the decoding junkDNA in order to understand its function.

The other issue is one ReMine and I have briefly discussed is the issue of HIGH uniformity (the term monomorphism is used, but I feel uncomfortable using it because it is definitionally problematic). Think about how difficult it is to achieve uniformity of duplicated genes. If not via Pelionisz’s argument for the functional significance of almost every nucleotide, then one is still faced with the problem of high uniformity at the nucleotide level. For duplicated genes to achieve an overtake of the population, one is dealing with the combinatorial problem I discussed above (recall the astronomically high figure of 4^720). How many duplicated genes go to fixation? Gene duplication does not rescue the problem of fixing that many nucleotides (720) per generation.

One also must assume a well stirred population. How hard is that to achieve even under moderate geographic dispersal. [in the extreme, think how hard it would be to evolve the human race via phyletic transfromation since a well-stirred population would involve mixing humans thousands of miles apart].

You pose good questions however. And I appreciate what you’ve put on the table….

Febble,

The Theory of Evolution predicts everything that ID predicts because Replication with Modification plus Natural Selection is a very intelligent system. Slow, but brilliant. There is no disambiguating test because the predictions of both are identical.

In terms of Darwinian evolution, not everyone agrees. See what Pellionisz said above about the ID/ET prediction prevaling over the Darwinists.

Thank you however for taking time to keep reading my posts. I appreciate your civil manner.

Salvador

Comment #155710

Posted by Raging Bee on January 17, 2007 10:39 AM (e)

Sal quoted someone thusly:

…the ID/ET theory correctly predicted some yet to be decoded function of junkDNA…The scientific challenge is already at its next stage, having stepped over the “existence question” and proceeded with the decoding junkDNA in order to understand its function.

If we still don’t understand the function of junk DNA, and still have yet to decode it, then how can anyone have “correctly predicted some yet to be decoded function of junkDNA?”

If you want to be taken seriously as an honest participant in this debate, then please explain this apparent contradiction.

Comment #155716

Posted by Henry J on January 17, 2007 11:00 AM (e)

Re “Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”)”

I thought that was a conclusion (inference from the data) rather than a prediction.

Henry

Comment #155717

Posted by Salvador T. Cordova on January 17, 2007 11:05 AM (e)

If we still don’t understand the function of junk DNA, and still have yet to decode it, then how can anyone have “correctly predicted some yet to be decoded function of junkDNA?”

If you want to be taken seriously as an honest participant in this debate, then please explain this apparent contradiction.

Pellionisz FractoGene has demonstrated at least one layer of linguistic architecture for the junk DNA. A linguistic structure suggest function even if the structure is not fully understood (like seeing an undecoded communication, the communication has function, but it is not understood). Furthermore, Fracis Collins called it hubris to say any part of the genome is junk.

My advice to you RagingBee, is to take the log out of thine own eye before trying to pullone out of mine. If Darwinists want to argue it’s junk, then it’s incumbent upon them to demonstrate it to be so if they want to be taken seriusly by the majority of the population in the USA, who happen to be ID friendly.

And regarding the functionality being uncovered, did you bother reading the threads on Pellionisz work at UD or visiting the junkDNA site?

Your line of argumentation reminds me of the days when Darwinists were part of creating a policy of removing of various organs out of little children since these organs were deemed junk. Now we know better, don’t we?

That disregard for “junkDNA” is impeding the progress of medical science. You ought to be encouraging the urgency of research into these regions rather than demanding that its function be demonstrated in every detail. If large “conserved” regions have an integrated linguistic architecutre, it his hard to argue they have no function, because language suggests design. Think about the Darwinist attitude toward intronic “junk” DNA. In 2002 it became apparent the Darwinists were wrong. Mattick declared that attitude was the greatest mistake in the history of Molecular Biology. Based on the stellar record of repeated failure by Darwinist biology, I would think on that basis alone, one ought to be inclined to think junkDNA is not junk.

Even disregarding the junkDNA issue, one is still confronted with the problem of uniformity (or deep “conservation”) within a species of junkDNA. It is still a problem for Darwinian evolution.

Comment #155724

Posted by caligula on January 17, 2007 11:25 AM (e)

Sal,

I don’t understand your logic about gene duplications at all. Gene duplication is a single mutation, not a series of point mutations.

Another thing. From the “180 million” articale, I was led to your “U-Paradox” article. I’d really like to discuss this one through, and I hope that PT contributors make note of this article of yours:

http://www.uncommondescent.com/archives/1911

It demonstrates what I find to be a hilarious misunderstanding.

First, let me assure you that natural selection has no problem at all to “purify” a gene pool from harmful mutations. Granted, new ones appear every generation, and not all harmful mutations disapperar during the very next generation due to selection (selection is a statistical force, after all). But selection and segregation certainly keep all naturally occurring rates of harmful mutations at bay. I have simulated this scenario as per request by one Life Engineer at ARN. In the simulated case, my harmful mutations were not exclusively deletrious, but that should only help their fixation. I generated harmful mutations at a rate which made an average individual possess, as it happens, 3 harmful mutations. None, and I repeat, none of the harmful alleles came anywhere near to fixation. As should be obvious and trivial to anyone who understands the basics of selection and Mendelian segregation.

Second, what was Nachman calling a “paradox” then? Well, he said it loud and clear, although you misinterpreted it somehow. Nachman estimates that U deletrious mutations reduce the fitness of an individual by 1 - e^-U. Following Haldane/Kimura models, this results in an unbearably low average fitness with even fairly small values of U and, consequently, an unbearably high mortality. Now, let us grant you all your wishes, Salvador. Let us call U=100 “optimistic”, even though you gave no reason for this at all, and although it contradicts the results of both Nachman et al. and Eyre-Walker et al. Also, let us assume that NS is, indeed, fully incompetent in “purifying” the gene pool of these extremely harmful alleles (which is utterly ridiculous).

With U=100, we get an average fitness of 7.3 * 10^-44. This means that each individuaal of the population survives the juvenile phase with probability, roughly, one in a billion billion billion billion billion. Given that even the current human population is only measured in billions, we would be so unbelievable lucky to have a single surviving couple (male+female) after the first generation that it is not worth mentioning. Also, let us assume that NS is on a holiday and these deletions start to accumulate. I hope I don’t have to mention the power of cumulative processes. Hope you are starting to see what the paradox really is. But you said you want more. Should U be 200? Or perhaps 1000? You do the math.

What you do not understand is that Nachman’s result does not address “macroevolution” at all. It addresses microevolution. The timescale we are observing is quite fast, too. With U=3, we would likely have a genocide in less than 15 generations, starting with a population of billions. How do you fit in 300 generations (from today back to 4000 BC), and how do you start with a population of 2? With the values of U=100 and the like, we would have some sort of weird Last Thursdayism. No generation at all would nearly survive so we would have to be the first generation with false memories.

Besides, I would think again before suggesting, with a straight face, that we all are likely missing a hundred genes or more.

Nachman’s results are not a problem for “evolution”. Natural selection continues to function just as it did before, and it indeed is capable of “purifying” (i.e. prevending the fixation of) harmful alleles. However, Nachman’s results are a problem for common sense. Clearly, the human population is much more than a dozen generations old, as opposed to the naive prediction of Nachman’s model. Hence, there must indeed be some factors which relax the effects of selection. Ironically, they seem to be pretty much the same factors that have been suggested for Haldane’s “dilemma”! No surprise, because “Nachman’s paradox” is produced by the same assumptions as “Haldane’s dilemma”. If anything, Nachman’s paradox demonstrates that Haldane/Kimura indeed must be wrong, and that the results of their overly simplistic model is against common sense.

Comment #155727

Posted by Salvador T. Cordova on January 17, 2007 11:44 AM (e)

Caligula inquired:

I don’t understand your logic about gene duplications at all. Gene duplication is a single mutation, not a series of point mutations.

That may be true that it is a single mutation, but what is the likelihood of fixation of a duplicated gene made of multiple-nucleotides? One must factor the probabilities of selection based on:

1. probability of activation
2. probability of positive selection after activation

If it the chance of fixation of a duplicated gene (say 720 nucleotides in length) is more remote than the sequential fixation of 720 single-insertion/point-mutations, then the single point mutation model is a far more optimistic picture than the gene duplication scenario. Thus the one-nucleotide-at-a-time model serves as a more generous model than the multi-nucleotides-at-a-time model, since on average multi-nucleotides-at-a-time model is slower based on probabilities.

If one argues fixation via drift of a duplicated gene, then that is yet another argument that natural selection had little to do with the fixation of that duplicated gene. But fixation via drift is not so easy either. Remember, we have to be fixing 720 nucleotides per generation while simultaneously maintaining deep uniformity.

Comment #155737

Posted by Raging Bee on January 17, 2007 12:09 PM (e)

A linguistic structure suggest function even if the structure is not fully understood…

So now you’re back to “inferring” and “suggesting” something you can’t actually PROVE. The existence of a structure suggests that something COULD have a particular function, but whether it’s actually used is another matter.

…(like seeing an undecoded communication, the communication has function, but it is not understood).

It LOOKS like something that has function: a sequence of nucleic acids. Like the unencoded text to which you compare it, however, its actual function depends on whether it is read and used, not merely on its structure. A message that no one reads is “junk,” not because it has no structure, but because it is not used.

(I also see you’re back to the standard IDist trick of saying “It reminds me of something that’s designed, therefore it’s designed.” Subjective comparisons don’t prove anything.)

Furthermore, Fracis Collins called it hubris to say any part of the genome is junk.

An opinion, albeit a valid one, but not, in itself, proof of anything. (Note: Collins is not an IDist.)

Your line of argumentation reminds me of the days when Darwinists were part of creating a policy of removing of various organs out of little children since these organs were deemed junk.

So…first you mention unspecified “days” when unspecified “Darwinists” were “part of creating” an unspecified policy of mutilating unspecified children in “various” unspecified ways. Then you equate my mere arguments to this alleged, unspecified, atrocity. Your facade of civility is thin indeed, if the name-calling, hatemongering, lying bigot pops out from under it so quickly.

Remember the Commandment: “Thou shalt not bear false witness against thy neighbor.”

Comment #155751

Posted by Salvador T. Cordova on January 17, 2007 1:15 PM (e)

This means that each individuaal of the population survives the juvenile phase with probability, roughly, one in a billion billion billion billion billion. Given that even the current human population is only measured in billions, we would be so unbelievable lucky to have a single surviving couple (male+female) after the first generation that it is not worth mentioning.

The interpreation you omit is the possiblity that everyone (or nearly everyone) receives a set of slightly deleterious mutation that does not result in death or non-reproduction. Thus the genomes continue to accumulate bad mutations which don’t get purified. The paradox deals how many population resources would be needed to clean out ALL bad mutations. The theoretical prediction then is that the genomes have been getting progressively worse since humans came into existence.

Recall the cobalt-bomb experients? Some organisms were differentially more fit than their peers, but they were all sick compared to their ancestors several generations back. That’s the problem with Darwinist genetics models, they have a hard time making such important comparisons to judge real fitness in the functional sense verus the sense of fitness in terms differential reproductive success among functionally degraded peers….

Comment #155754

Posted by Raging Bee on January 17, 2007 1:30 PM (e)

Ignoring my response to your logical fallacies and ad-hominem attacks, Sal? that’s typical of your cowardice. Man up already, willya? You’re starting to embarrass us.

Comment #155756

Posted by PvM on January 17, 2007 1:46 PM (e)

Sal wrote:

That disregard for “junkDNA” is impeding the progress of medical science.

But science is NOT disregarding junkDNA, certainly ID has done nothing to further our understanding of it. Despite vacuous claims by some IDers

Comment #155757

Posted by PvM on January 17, 2007 1:55 PM (e)

Sal wrote:

Pellionisz FractoGene has demonstrated at least one layer of linguistic architecture for the junk DNA. A linguistic structure suggest function even if the structure is not fully understood (like seeing an undecoded communication, the communication has function, but it is not understood). Furthermore, Fracis Collins called it hubris to say any part of the genome is junk.

Sure, and science has mostly reflected this position. Of course, a linguistic feature basically refers to Zipf’s law but then again words in random text also show Zipf’s law behavior.

Abstract
It is shown that the distribution of word frequencies for randomly generated texts is very similar to Zipf’s law observed in natural languages such as English. The facts that the frequency of occurrence of a word is almost an inverse power law function of its rank and the exponent of this inverse power law is very close to 1 are largely due to the transformation from the word’s length to its rank, which stretches an exponential function to a power law function

But then again, it seems to be Sal’s strawman that Junk DNA is all junk, scientists have considered “non coding” DNA to be partially explained by true junk, and such junk in the form of pseudogenes can be observed, but scientists have since long realized that some junk DNA must have function

Comment #155759

Posted by caligula on January 17, 2007 2:05 PM (e)

SC wrote:

That may be true that it is a single mutation, but what is the likelihood of fixation of a duplicated gene made of multiple-nucleotides? One must factor the probabilities of selection based on:

1. probability of activation
2. probability of positive selection after activation

Now that is another question altogether. I can see that at least Fyodor Kondrashov has studied the issue, but I would have to read his paper to get some bearings concerning this question. But note that now you are speculating without much data, having retreated from your original argument.

SC wrote:

The interpreation you omit is the possiblity that everyone (or nearly everyone) receives a set of slightly deleterious mutation that does not result in death or non-reproduction. Thus the genomes continue to accumulate bad mutations which don’t get purified. The paradox deals how many population resources would be needed to clean out ALL bad mutations. The theoretical prediction then is that the genomes have been getting progressively worse since humans came into existence.

Sal, I think you should read Nachman’s paper again. Nachman is clearly not talking about anything like what you write above. The real Nachman’s paradox is that combining the model of Haldane/Kimura with the estimated number of deletrious mutations in each human results in a rate of mortality that is against our direct observations and against common sense. Conclusion: either the measurements or, more likely, Haldane/Kimura’s overly simplistic models require drastic improvement. This conclusion is in line with Haldane’s own guess and with what modern population genetics has already pointed out, with concrete suggestions for improvement.

What you are suggesting above (“Cordova’s paradox” or, rather, “non-paradox”) is exactly what I already simulated at ARN: behavior of harmful but non-deletrious mutations. As I said, they just won’t fix with even remotely reasonable mutation rates. I challenge you to demonstrate for us how “genomes continue to accumulate bad mutations”. Of course, it is well known that sufficient mutation rates do maintain a marginal frequency for neutral and even harmful alleles. Why, Haldane’s substitution scenario relies on exactly such variation. Getting this harmful variation to fix is an entirely different thing. Now, you may be thinking: yes, but if the harmful mutations increased their frequency due to subsequent mutations ever so slightly each generation… shouldn’t that accumulate into something remarkable over many generations? No. Ask anyone. The effects of selection will grow as a function of the frequency of harmful alleles, and these factors will find an equilibrium which will keep the combined frequency of random variation at bay. Please do test it yourself. There are population genetics simulations available, and it is not all that hard to write one yourself if you know some programming.

Comment #155763

Posted by caligula on January 17, 2007 2:21 PM (e)

GuyeFaux wrote:

Let me see if I follow your point, Caligula (I’m not a biologist):

The 180,000,000 base pair difference over 5m years between chimps and humans is not caused by 720 point mutations per generation but by gene duplication? What does gene duplication deletion look like in terms of base-pair difference? And actually, now that I think about it, what does “180,000,000 base pair difference” even mean?

Neither am I a biologist. And neither is Sal. But a very good question. Where does this number 180 million come from? It seems it comes from another rather free interpretation by Salvador. The article he refers to at UD is in fact saying that humans differ from chimps in their number of genes more than expected previously. Perhaps Salvador can tell you exactly how his “magic number” follows from the article in question. I don’t quite get it, either.

As for how gene duplications show in terms of BP differences. I think the sequences of two species are re-aligned whenever there clearly is something extra (such as an extra gene) in the sequence of one species that the other one is missing, so as to allow the comparison to continue in a sensible fashion. I think this “extra” is then counted among the differences.

Comment #155767

Posted by GuyeFaux on January 17, 2007 2:52 PM (e)

I think the sequences of two species are re-aligned whenever there clearly is something extra (such as an extra gene) in the sequence of one species that the other one is missing, so as to allow the comparison to continue in a sensible fashion. I think this “extra” is then counted among the differences.

So it’s like diff.

So, from where does the 180 M come from?

Comment #155799

Posted by alienward on January 17, 2007 5:33 PM (e)

I’m no biologist, but I think it’s the # of base pairs of base pairs in all of the genes that are different between humans and chimps. For comparison, human males and females have around 55 million base pairs different between them. There’s almost as much differences between Sal and a male monkey than between Sal and his sister…

Comment #155832

Posted by Salvador T. Cordova on January 17, 2007 6:28 PM (e)

Regarding the base pair numbers. From Gen Bank

Homo Sapein Genome size = 3,4000,00,000
Pan Troglodytes= 3,577,500,000

That is technically a difference of 177,500,000.

Also, from scientific american Human-Chimp Gene Gap Widens from Tally of Duplicate Genes

A lot more genes may separate humans from their chimp relatives than earlier studies let on. Researchers studying changes in the number of copies of genes in the two species found that their mix of genes is only 94 percent identical. The 6 percent difference is considerably larger than the commonly cited figure of 1.5 percent……
The older value of 1.5 percent is a measure of the difference between equivalent genes in humans and chimps, like a difference in the spelling of the same word in two similar languages…..
The new research takes into account the possibility for multiple copies of genes and that the number of copies can differ between species, even though the gene itself is the same or nearly so. “You have to pay attention to more than just the genes that are shared,” says geneticist Matthew Hahn of Indiana University, Bloomington, lead author of the new report

I pointed out, there are problems with the scenario of duplicated genes propagating and fixating into a population withing geological time.

If the duplicated genes are selectively neutral, then drift mechanisms must fix them, and this is not easy. Problems are:

1. The population must be well stirred
2. Most such duplications could be lost by drift (gamblers ruin)
3. Probability of fixation is inversely proportional to population size

If we invoke selection, then we have the problems I mentioned above:

1. probability of activation
2. probability of being selectively advantage

If we are dealing with gene coding for a protein we then have the issue of the likelihood of protein functionality and protein usefulness in the context of the organism. I pointed out on the insanely generous assumption we could even select and fix 1 nucleotide per generation, and then assume we have 720 generations to fix 720 nucleotides, this is far more optimistic than the probability we could find on average 720 nucleotides in a gene duplication that would satisfy the above conditions in 720 trials by any reasonable stretch of the imagination.

Comment #155836

Posted by Steviepinhead on January 17, 2007 6:50 PM (e)

C’mon, guys, Sal’s having a hard enough time staying above water on Mark Chu-Carroll’s math blog.

Give him a little bit of a break here. It’s tough being out of your deptth. Being out of your depth in two different puddles at the same time can get truly frothy!

Comment #155881

Posted by Henry J on January 17, 2007 9:34 PM (e)

Re “and then assume we have 720 generations to fix 720 nucleotides, this is far more optimistic than the probability we could find on average 720 nucleotides in a gene duplication that would satisfy the above conditions in 720 trials by any reasonable stretch of the imagination.”

Huh? Unless I’m missing something, a duplicate (or deletion) event would be one mutation, therefore one trial, just as a base pair substitution is one trial.

Henry

Comment #155924

Posted by caligula on January 18, 2007 2:03 AM (e)

Sal,

You are doubtless as annoyed by the length of this comment page upon each refresh as I am. I suggest we continue this discussion elsewhere if you have the time. Either in another thread at PT or at UD. But in the latter case I would have to request a DMZ from the local mods! It is impossible to discuss if posts are being censored without good reason – seemingly on a random basis.

Here is a short summary of our discussion so far (from my POV of course!). Feel free to speak up if you find my summary unfair at some point.

The common denominator for the subtopics we have covered is your original claim to Febble that cumulative rounds of RM+NS do not produce CSI. You said (#154439) that “it has not been proven” and that instead it has been shown that ToE involves internal contradictions: “Haldane’s dilemma” and “Nachman’s paradox”.

1. Concerning your claim about lack of proof, I reminded you of GAs such as the one written by Dave Thomas. In the past, you have agreed that they do produce CSI but also claimed that this CSI is “smuggled in”. I asked you (#154742) to rigorously demonstrate for us how does CSI get smuggled in by humans. I believe that, so far, you have not replied anything to this important “challenge”.

2. Concerning “Haldane’s dilemma”, I have discussed (#154439 and #154785) the simplicity of Haldane’s model and the modern additions to this model (mainly “soft selection” and “intraspecific competition” which are sort of joined under the term “density-dependent selection”). I also suggest (#155676) that there is no known reason to assume that mere hundreds or thousands of adaptations could not account for the morphologic differences between humans and modern apes. And according to modern population genetics, several thousand adaptations may have occurred during the hominid evolution, as opposed to e.g. Walter ReMine’s “magic number”.

3. You suggested (#155631) that, on the other hand, there are just too many molecular differences to be accounted for by any theory, be it neutralist, selectionist or whatever. You threw in the number 180,000,000 SNPs, which you seem to have derived from this article:

http://www.sciam.com/article.cfm?chanID=sa003&articleID=9D0DAC2B-E7F2-99DF-3AA795436FEF8039

I pointed out that gene duplications are single events, and do not consist of a series of point mutations. You replied that in that case we have to study how likely it is that a gene duplication, which is supposedly a neutral mutation, becomes fixed in the population. I will have to study this issue somewhat before I can respond.

It was also asked how the number 180 million can be deduced from the SciAm article above. Indeed, the article speaks of a 6% difference in terms of number of genes, as opposed to in terms of SNPs (single nucleotide polymorhphisms). As coding genes form only about 1% of our DNA, it is impossible for 6% differences in coding genes to result in 180 million SNPs.

4. Concerning “Nachman’s paradox”, I am strongly claiming (#155724 and #155759) that you have grossly misinterpreted Nachman’s paper:

http://www.genetics.org/cgi/content/full/156/1/297

Nachman is in fact saying that if both his measurements and Haldane’s model were correct, then tehcnically we should be an extinct species. As we clearly are not, Nachman suggests that Haldane’s model requires revision. His suggestions are along the lines of “soft selection” and epistatic fitness interaction (what about intraspecific competition?), i.e. very similar suggestions that modern population genetics has provided earlier. So, instead of being evidence for a contradiction within modern ToE, Nachman merely gives further reason to doubt Haldane’s simplified model presented in “The cost of natural selection”(Haldane 1957).

As for the proposed inability of NS to prevent harmful mutations from fixing. While I am ready to demonstrate this further, I suggest you carefully study some basics of population genetics. It just isn’t the case. If you have some spare time, I can send you a population genetics simulation, source code and all, and demonstrate the invalidity of your assertion thoroughly to you. Also please note that this has nothing to do with Nahcman. Nachman did not claim that harmful mutations accumulate into our gene pool – they don’t – Nachman claimed that they don’t even need to, because we should go extinct due to the very background mutation rate!

Comment #155961

Posted by Salvador T. Cordova on January 18, 2007 3:30 AM (e)

Caligula wrote:

http://www.uncommondescent.com/archives/1911

It demonstrates what I find to be a hilarious misunderstanding.

First, let me assure you that natural selection has no problem at all to “purify” a gene pool from harmful mutations.

Yes, and we have sickle cell anemia, tay-sachs disease, diabetes, an increasingly large database of Single-Nucleotide Polymorphisms that are tied to inherited diseases, large numbers of diseases that have been persistent and not purified out of the population. You were saying about natural selection’s ability to have absolutely no problem purifying a gene pool from harmful mutations and hilarious misunderstandings? :-)

Comment #155967

Posted by Salvador T. Cordova on January 18, 2007 3:54 AM (e)

Caligula said:

Sal,

You are doubtless as annoyed by the length of this comment page upon each refresh as I am. I suggest we continue this discussion elsewhere if you have the time. Either in another thread at PT or at UD. But in the latter case I would have to request a DMZ from the local mods! It is impossible to discuss if posts are being censored without good reason – seemingly on a random basis.

That sounds reasonable. If UD is not amenable to you, you may suggest another place, and PT is fine unless of course the thread is hijacked by my enemies, and then we’re stuck again with an impossibly slow weblog. I have some personal weblogs but they are as slow as molasses going up hill. UD is faster.

First of all, are you banned at UD?

If not I can try to put a thread there. It would be better such an important discussion not be hidden away at an obscure place. I want to discuss this issue somewhere.

For what it’s worth, I’ve been wanting some critical review and discussion of Sanford’s work. Your criticisms have been about 5 orders of magnitude higher in quality than most of what I’m used to.

One way to calm down the mods at UD is to focus on the technical issues. I can take the lead and we can work through it. If you are unsatisfied with what takes place at UD, feel free to suggest another place. However, it would serve the conversation best if the discussion gets the most visibility on a high traffic site. So, if anyone reading this is on a high visibility weblog, I’m amenable to invitations to host the discussion.

Unfortunately, PT and UD, as far as I know, are the most visible sites. But before I proceeed, can you state something of your background and research interest? I wish to respect your privacy, so if you have to be little reserved about what you disclose, I respect that.

Comment #155971

Posted by Popper's ghost on January 18, 2007 4:16 AM (e)

Sal wrote:

my enemies

That would be anyone with a shred of sense and integrity.

Comment #155972

Posted by Popper's ghost on January 18, 2007 4:57 AM (e)

I think Dembski’s math had refuted anything by Dawkins and friends.

It doesn’t matter what a liar and an idiot claims to think.

I read the supposed refutations by Dembski’s critics, and I find them to be impressively written strawman takedowns and disingenuous distortions of what Dembski actually wrote.

It doesn’t matter what a liar and an idiot claims to think.

You’ll hear appeals by PT regulars to Shallit, Elsberry, Perakh, Avida, etc. They are mostly strawman misrepresentations.

You’re a liar and an idiot; they are no such thing.

They do not qualify as theoretically sound rebuttals….

You’re a liar and an idiot; they do so qualify.

Comment #155987

Posted by Popper's ghost on January 18, 2007 5:32 AM (e)

The Theory of Evolution predicts everything that ID predicts because Replication with Modification plus Natural Selection is a very intelligent system. Slow, but brilliant. There is no disambiguating test because the predictions of both are identical.

The ToE predicts everything that ID predicts because ID predicts nothing. A theoretical prediction is a logical inference. The set of logical inferences from the ToE most certainly is not identical to the set of logical inferences from ID.

Comment #155993

Posted by caligula on January 18, 2007 5:41 AM (e)

SC wrote:

Yes, and we have sickle cell anemia, tay-sachs disease, diabetes, an increasingly large database of Single-Nucleotide Polymorphisms that are tied to inherited diseases, large numbers of diseases that have been persistent and not purified out of the population. You were saying about natural selection’s ability to have absolutely no problem purifying a gene pool from harmful mutations and hilarious misunderstandings? :-)

What I found “hilarious” (a frank if admittedly not necessarily nice choice of wording) was how you misinterpreted Nachman’s paper and how, based on this misinterpretation and still without any good reason, you required that U should be increased beyond 100 – even though Nachman demonstrated that even value U=3 combined with Haldane’s model contradicts, not evolution per se but rather, our direct observations and our common sense. Nachman’s result does not refute evolution – it “refutes” our very existence under any other model than “Last Thursdayism” and the like. Yet you said you want a much bigger U!

As for your arguments about purification, I did not find them so much hilarious but simply off-topic in relation to Nachman’s paper, as well as invalid in general. Population genetics, as a mathematical model, plain and simply contradicts your assertion that harmful alleles could accumulate (become fixed) in the gene pool. Of course, NS does not purify our genomes, it only purifies the lineages starting from us, by disfavoring some of our alleles. If random mutations produce harmful variation, as they are known to do in any large population, then such variation does occupy tiny frequencies in our gene pool. What NS does is prevent such variation from fixing. I use the word “purify” in the latter sense, while I do not deny that all populations possess harmful random variation in small frequencies. As I’ve said many times already, Haldane even relied on such variation.

Concerning your examples above, here are some points worth considering:

1. Wild populations vs. civilization. I happen to suffer from Wolf-Parkinson-White type of heart problem. While I’m fairly certain I would have become a juvenile casualty in a wild environment (as much as it hurts my macho side to admit it!), it seems that I will likely spread my harmful allele in the modern civilization. NS just does not apply to the modern human population or its domesticated animals the way it did to our ancestors.

2. Fixed alleles vs. anomalies. Of the inherited diseases above, how many can be considered fixed in the human population? Anomalies do not contradict the predictions of population genetics, and anomalies have nothing to do with accumulation of harmful alleles. Accumulation of changes means fixation of a change and then subsequent changes.

3. Harmful vs. partially harmful. At least sickle cell anemia is known to be caused by an allele that has additional beneficial effects. It is the total selection coefficient of an allele that counts, not the individual effects. An allele is “pure” if it has a non-negative selection coefficient. In contrast, we would have to call an allele for increased muscularity in males “dirty” if our females happened to collectively prefer skinny guys.

Comment #156007

Posted by caligula on January 18, 2007 6:37 AM (e)

Sal,

I can log in at UD so I suppose I am not banned. I have no objection to continuing the discussion at UD per se. In fact, seeing that you have endured a lot of rhetorics on this page, I find it only fair that we continue in an environment where such extra burden is on my shoulders for a change. However, my past experience at UD suggests that censorship would prevent me from responding.

You know my writing style by now. I very much want to discuss technical issues, and I also want to get somewhere when doing so. (That’s why I wrote a summary about our past discussion, so as not to forget how the details are related to each other!) But I do not spend a lot of energy in excessive friendliness – I would find it somewhat pretentious of even sleazy. I speak up without much ceremony when I disagree, and if I find an argument ridiculous I say it loud and clear. I am also quite persistent – I don’t forget, and I don’t allow for distractions or retreats until provided with at least a sensible (if not a completely satisfactory) response. In turn, I don’t retreat with a smoke-screen myself. For example, your question about how gene duplications become fixed is quite valid and relevant, and it requires to be addressed. I have thought about it myself in the past. My current feeling is that the response does involve drift, but I will have to consult some professional papers before it is meaningful for me to respond; it is not my “hunch” you’re interested in, after all.

I do not know what offends UD mods – probably my direct way of presenting criticism and my persistence. But I have what I think is a legitimate fear that they will make my ability to discuss at UD unreasonably hard or even impossible. I would like you to do whatever you can to let me speak my mind, and to avoid getting sidetracked by the mods. (Sometimes they “let people understand” that the discussion is only allowed to proceed in some direction that is chosen exclusively by the mods, and is not necessarily a constructive direction if we truly want to get somewhere.) Upon entering, I have no intention to insult anyone, and currently I can’t even see any reason to criticize Dembski’s views. Dembski currently isn’t in the scope of our discussion. He might enter the picture, of course, in case he is involved in your hopefully forthcoming detailed explanation on how CSI is “smuggled in”.

Comment #156010

Posted by caligula on January 18, 2007 7:12 AM (e)

Oh, about myself. My real name is Esko Heimonen, and I use it in Finnish evo/crea debates openly. Although I use various callsigns at international servers, I have at least succeeded in creating the same nick at PT and UD, so that e.g. the mods of UD can associate my comments at PT to the person at UD. At ARN, I have written some stuff using the callsign Emuu.

My professional background is modest concerning these topics: IT. As it happens, there are precious few professional scientists in evo/crea web debates! So “research” does not apply to e.g. my population genetics simulations. I have been in modest email exchange with e.g. Dr. Warren Ewens, and I intend to also contact Leonard Nunney concerning his simulation. But I certainly am not planning to publish anything, not even on a self-administered web site.

I have followed the evo/crea debate for over a decade, so I know the various arguments quite well, and I have read quite a bit concerning the topic. But I’m perfectly aware that I’m no authority nor qualified to present strong arguments about scientific data. I do dare to present arguments concerning math, however. (GAs, neural networks, mathematical population genetics, “explanatory filter”, etc.) And finally, I have not read Dembski’s book X. Which is one of the recurrent questions at UD. I believe I have read Dembski’s core arguments, and frankly I don’t find them sophisticated enough to require one to read (and, in Finland, buy) all of Demsbki’s books in order to fully understand them. (Glad I said that here!)

Comment #156033

Posted by Salvador T. Cordova on January 18, 2007 9:25 AM (e)

Caligula,

I’m going to try putting up a thread there. If you’re consistently unable to get your messages through, post something here and we can try looking for another weblog.

I am considered like a guest columnist at UD. I’m not an administrator. If you’re comments get trapped in the spam buffer, I may not be able to get them out. Even my comments get trapped occasionally.

One thing that will improve the probability of getting your comments through is that they be short. If you have a long thread of thought, you may want to post it through multiple comments and watch each piece come up.

Links to various websites can get trapped in the spam buffer. Please save your work. If we can’t get it posted at UD, we can go somewhere else, but let’s give it a try.

I’ll try to get something up today. I’m usually out of town on the weekends, so I advise when I’m not at UD to wait till I return. I’ll try to post when I’m in or out. I think your criticisms of my ideas should get a fair hearing. If I feel you are being treated with an undue amount of harshness there, we can look for another place to continue the discussion. All the authors of PandasThumb are welcome to join the discussion with the exception of PvM who has been banned from UD.

Comment #156041

Posted by Raging Bee on January 18, 2007 9:46 AM (e)

Sal whined:

…and PT is fine unless of course the thread is hijacked by my enemies…

Excuse me, boy, but it seems you made at least one of us into enemies by trying to associate his argument (one you couldn’t refute, BTW) with an alleged surgical mutilation of children by “Darwinists.” (Can’t you at least specify what country that mutilation allegedly took place in? How about a continent?) If the thread got “hijacked” as a result, you have only yourself, not your “enemies,” to blame.

I find it telling that Sal offers to continue a debate on the one forum where he can count on his “enemies” being silenced. Sal is clearly nothing but a transparently dishonest kiss-up-kick-down courtier.

Comment #156056

Posted by Salvador T. Cordova on January 18, 2007 10:32 AM (e)

RagingBee demanded:
Excuse me, boy, but it seems you made at least one of us into enemies by trying to associate his argument (one you couldn’t refute, BTW) with an alleged surgical mutilation of children by “Darwinists.” (Can’t you at least specify what country that mutilation allegedly took place in? How about a continent?) If the thread got “hijacked” as a result, you have only yourself, not your “enemies,” to blame.

North America (including Canada), and one of the little children once upon a time long ago was a young child named Denyse O’Leary. This is her account: In science’s pecking order, evolutionary biology lurks somewhere near the bottom

in the 1950s, doctors believed that the tonsils and adenoids were vestigial organs left over from earlier stages of human evolution. I had mine taken out, along with huge wardsful of other children.

Only later did these minor organs’ role in combatting infection come to be considered. As it happened, I subsequently suffered from respiratory illnesses most of my life, some quite serious, because I have often lived in cold, damp conditions. My parents were once advised to move to Arizona, but we were Canadians.

That’s right, WARDSfull of kids having their organs removed because of Darwinist “medicine”.

Comment #156061

Posted by PvM on January 18, 2007 10:50 AM (e)

That’s right, WARDSfull of kids having their organs removed because of Darwinist “medicine”.

Nope because there was no detectable function for these organs and removing them would alleviate many real problems.

And remember “people were burnt as witches because of Christian “religion””. Perhaps Sal now appreciates the relevance of his claims?

Of course, it’s much easier for Sal to argue strawmen than real science since this would require hard work and research and would venture away from the oh so comfortable shroud of ignorance so commonly found surrounding ID proponents.

Comment #156062

Posted by Raging Bee on January 18, 2007 10:52 AM (e)

That’s not “Darwinist medicine,” because neither Darwin himself nor the theory of evolution ever explicitly endorsed anything like the policy you describe. Blaming “Darwinists” for this is typical of creationist demagoguery. Remember that Commandment about “false witness?”

Speaking of unnecessary surgery, are “Darwinists” to blame for circumcision, castration, foot-binding, etc. as well? Unnecessary mutilation kinda predates Darwin by, like, a few millenia. Oh, and don’t forget torture by Christian Inquisitors and Witch-Finders.

And you still haven’t made any attempt to justify linking my arguments to such mutilation. Other than your inability to refute them any other way, of course…

Comment #156063

Posted by PvM on January 18, 2007 10:53 AM (e)

Some real data on tonsils and adenoids

A tonsillectomy is performed to treat recurrent infections, especially if it is associated with a “Strep Throat,” which keeps coming back several times a year after antibiotic treatment. If medicine cannot treat or prevent the infections and the infections come back often, a tonsillectomy may be indicated. Several studies have shown that a tonsillectomy is an effective treatment for children with frequently recurring tonsillitis (chronic tonsillitis). View Abstract. Click on colored text for word definitions !!

The most common reason for tonsillectomy and adenoidectomy is is to remove enlarged tonsils and adenoids which block a child’s breathing passages. The nose may be so blocked by the adenoid (which is located behind the nose and above the back of the throat–see the below pictures) that a child can’t smell, has a congested nose, and talks like he has a cold all the time. If the tonsils are to large, a child may not eat well, taking only small, soft foods. The child may also have some choking and mouth breathing. Often, a child snores very loudly, may not breathe well while asleep, and may actually stop breathing for several seconds. If severe and not treated, this can put strain on the heart and lungs. It has been shown that removal of the tonsils and adenoids is effective in treating obstructive sleep apnea in children

and

What function do they serve? Aren’t they important? The tonsils and the adenoids are mostly composed of lymphoid tissue, which is found thoughout the gastointestinal tract and on the base of the tongue. Lymphoid tissue is composed of lymphocytes…which are mostly involved in antibody production. Since we generally consider antibody production to be a good thing, many studies have been performed to try to clarify the importance of the tonsils. To date, there seems to be no adverse effect on the immune status or health of patients who have had them removed. Any noticable effect has generally been positive. It appears that the tonsils and adenoids were not “designed” to effectively handle the multitude of viral infections that occur in children in an urban population. Rather, the immune system, including the tonsils and adenoids, developed during a era where the child was rarely exposed to a large number of other people and the germs they carried. It may also be that these organs are relatively more important in dealing with certain types of infections, such as worms or other parasites, that are relatively uncommon in today’s society. It is clear that in many cases, the tonsils and/or the adenoids become “dysfunctional” and are more of a liability than an asset.

Hope this helps lifting some of the “shroud”

Comment #156067

Posted by Raging Bee on January 18, 2007 11:13 AM (e)

North America (including Canada), and one of the little children once upon a time long ago was a young child named Denyse O’Leary…

This is telling: O’Leary is now a contributor to UD (which Sal does not mention). What’s happening here is obvious: “modern medicine” did something bad to O’Leary, and now she’s trying to destroy “modern medicine” and punish it for all of her current suffering, by trying to replace science with hackery and pseudoscience. I strongly suspect that this sort of scapegoating is one of creationism’s major driving forces.

Oh well, I guess that’s better than blaming the Jooos. Or not. Maybe.

Comment #156299

Posted by Scarlet Seraph, FOFOCD on January 18, 2007 9:40 PM (e)

Oh, Sal? While you are trying to avoid the issue, I note that Mark Chu-Carroll is still kicking your butt from here to the next world on this thread: http://scienceblogs.com/goodmath/2007/01/stupidity_from_our_old_friend.php#c319444”

I encourage everyone to read it; it provides a classic example of an ID believer’s complete and total inability to actually provide any sort of substance behind his hand-waving. In summary:

Sal: “various meaningless bafflegab”

Everyone else: “Sal, you must show the math. If you wish to use Shannon, you must do the math.”

Sal: “meaningless bafflegab”

Everyone else: “Sal, you must show the math….”

Repeat ad nauseum.

As I said, it is an excellent example of why there is no theory of ID: because there is no actual mathematics, science, or logic behind the fundamental concept.

Though, as usual, we must be clear to distinguish the movement and the concept.

The concept, that certain objects in the biological and non-biological realms are the product of conscious design, is undeniable: humans breed animals; termites build mounds; crows use tools to catch whatever the heck crows catch.

But no one, and I repeat no one has demonstrated that the biological objects can be identified (unless RBH has finished his work on the MDT).

Indeed, the interesting point here is that in the cases we know about - humans and their stock-keeping; termites and their aphids, etc. - the manufacturing mechanism is entirely indistinguishable from normal evolutionary mechanisms.

And given that Dembski relies on CSI to show design, and that design is the product of wholly natural manufacture, I’m willing to bet that a Russian Wolfhound would NOT show CSI, despite the fact that we know it’s designed.

I must think about that.

Anyway, go over to Good Math/Bad Math and watch Sal be eviscerated. It’s quite amusing, and very instructive.

Comment #156323

Posted by Salvador T. Cordova on January 18, 2007 11:29 PM (e)

Caligula,

Here is the thread. I had to tie it in somewhat to the readers there, but feel free to use my post as a lead in to anything you feel important to discussing. Let me know if you have problems.

http://www.uncommondescent.com/archives/1974

Sal

Comment #156336

Posted by Raging Bee on January 19, 2007 12:36 AM (e)

Sal: When you say you “had to tie it in somewhat to the readers there,” what, exactly, do you mean? And why the vague fuzzwords? It kinda sounds like you had to make some sort of unspecified compromise in order to get your post up – which would be rather odd, given that you’re a regular contributor at UD.

Comment #156373

Posted by caligula on January 19, 2007 5:30 AM (e)

Sal,

So far I have had rather thin results. I posted my first response to you a couple of hours ago and it was not published. Granted, it contains some links. And now that I look at it, it is rather long (although I only address a couple of details and postpone many other major subtopics). Here are the contents:

Sal,

First, thank you for your invitation to continue the discussion, which started at PT, here at UD.

The above article of yours is not exactly compatible with the discussion that inspired it at PT:

http://www.pandasthumb.org/archives/2007/01/dissent_out_of.html

which I tried to summarize in (#155924). Some of the 4 subtopics that I identify in the summary have been omitted by you here, some new ones have been added. Most importantly, you are here repeating claims that I believe were given in-depth responses, which you clearly did not even attempt to refute. I hope you will try to refute them here.

For starters, some comments about your article.

1. As you said yourself, a geographically complex population of 6,5 billion is not relevant when considering the evolution of Homo sapiens. Population sizes of the order 10,000 to 1,000,000 seem more realistic. Also, according to fossil evidence, it seems that this population has been geographically rather limited and well connected. In general, I suggest we acknowledge from the get-go that the current human civilization is not a typical wild population. I have pointed this out several times during our past exchanges.

2. I assume the figure 180,000,000 SNPs is solely based on this SciAm article that you have quoted in an earlier writing:

http://www.sciam.com/article.cfm?chanID=sa003&articleID=9D0DAC2B-E7F2-99DF-3AA795436FEF8039

Alas, you have misinterpreted the article. It does not refer to differences between human and chimp in terms of nucleotide differences over the entire genome. Note this key sentence:

“In humans and chimps, which have about 22,000 genes each, the group
found 1,418 duplicates that one or the other does not possess.”
(1418 / 22000 = 6%, roughly.)

Differences between human and chimp can be and have been calculated using many different criteria. Differences calculated with two entirely different criteria can’t be compared, of course. Talking in terms of SNPs, especially over the entire genome, is plain and simply nonsensical here. Using the typical 1000-sites-per-gene estimate, the above article would mean that humans and chimps differ by about 1,5 million sites (as opposed to your erroneous 180 million!). Now, does this really mean that we differ from chimps by only 0,05 %? Of course not. The number of coding genes that we do not share with each other tells us neither how many SNP differences there are over the entire genome nor even how many SNP differences there are over the coding genes that we do share with each other.

You asked for a better figure? Alas, I’m not qualified to give any accurate figure. But I believe that typical figures would be 30-60 million SNPs (1-2% difference). Of these differences, the vast majority are considered morphologically insignificant.

3. Haldane’s dilemma:

I have said quite a bit about this to you at PT already, but I will repeat my thoughts here. I will do it in a separate post, in order to prevent individual posts from becoming unwieldy, as you have adviced me.

4. Neuralists vs. selectionists:

See 3. I will pay special attention to this sentence of yours: “How do we account for designs that cannot possibly be the result of natural selection?” Indeed, you will have to show us what such design might be.

5. Nachman’s paradox: See 3.

6. Teleomorphic Recursivity:

This one I have to read more about. Do you have a link to the full text?

Comment #156374

Posted by caligula on January 19, 2007 5:47 AM (e)

Sal, now it was published. I regret for the length of my writings, but I just have a lot to say. I’m always surprised to see the length after posting – but at least I can’t find much rhetorics there. I want to be thorough, but I should work at being more brief nevertheless.

Comment #156381

Posted by Popper's ghost on January 19, 2007 6:22 AM (e)

I am also quite persistent – I don’t forget, and I don’t allow for distractions or retreats until provided with at least a sensible (if not a completely satisfactory) response.

So how long is it going to take you to grasp that Sal does not act in good faith?

Comment #156388

Posted by caligula on January 19, 2007 7:21 AM (e)

Popper's ghost wrote:

So how long is it going to take you to grasp that Sal does not act in good faith?

Don’t worry, I’m not as naive as you fear.

I merely like to discuss these issues, and I want to see where it leads. Admittedly, it is a lot of the time quite frustrating.

For example, Sal’s recent post at UD pretty much seems to pretend, as far as his arguments go, that the discussion here at PT never took place. His number 180 million has been shot down, and it has been clearly pointed out that even the more realistic number of SNPs involves mostly morphologically insignificant (i.e. neutral) differences. (And yes, I do wonder how the 180 million claim ever managed to get published at UD, because Sal’s mistake is hard not to spot by anyone who bothers to read the article it is based on.) Sal’s persistence to use the modern human population as an example of a wild population has been shown invalid many times. Nachman’s paradox does not support Sal’s agenda at all – it merely demonstrates that we have ever better reason to criticize Haldane/Kimura’s outdated models, because they clearly contradict even common sense. And about Haldane’s dilemma, I have presented quite a bit of information that Sal never even attempted to refute. As for finally showing us how CSI is “smuggled in”, Sal remains utterly silent. Sal has simply chosen to ignore all these facts in his “re-boot” at UD. Besides, he has spiced his article with quite a bit of both ungrounded and unnecessary rhetorics.

Of course I feel very silly being forced to repeat it all, in (vain?) hopes that Sal can’t ignore my points this time. But one has to be humble, I guess. If I can get even a single point across, I guess I’m somehow satisfied. And no, I’m not so naive as to think that this point I managed to made would necessarily be remembered very long at UD. But even a temporary admission – instead of avoidance – would be kind of rewarding. In short, debating is more fun to me than throwing mud, even deserved mud.

As for “good faith”, in this sense I suppose I am naive. I do believe that a lot of the activity by ID advocates is sincere in the sense that they can’t necessarily spot a lot of their intellectual dishonesty themselves.

Comment #156389

Posted by Zachriel on January 19, 2007 7:22 AM (e)

What are the speed limits of naturalistic evolution?
http://www.uncommondescent.com/archives/1974

Popper’s ghost:

So how long is it going to take you to grasp that Sal does not act in good faith?

This comment by scordova, a.k.a. Sal over at Uncommon Descent is very enlightening.

The reason part of the discussion moved here was that PandasThumb is incredibly slow in displaying long discussions (as you saw yourself).

As Uncommon Dissent Descent regularly suppresses opposing views, it appears that Sal has retreated to the comfort of the cloister. While LudwigK has already been threatened with the ban. His sin? Directly engaging the discussion.

LudwigK:

A random mutation shows up with a given probability per organism, so the same fraction of the population will bear the mutation regardless of how large the population is.

DaveScot:

That’s so hopelessy wrong I hardly know where to begin. I think you need to find a different blog.

Comment #156391

Posted by caligula on January 19, 2007 7:36 AM (e)

Zachriel wrote:

LudwigK:

A random mutation shows up with a given probability per organism, so the same fraction of the population will bear the mutation regardless of how large the population is.

DaveScot:

That’s so hopelessy wrong I hardly know where to begin. I think you need to find a different blog.

Yes, I found this bit quite, well, hilarious. LudwigK’s argument as a whole is incorrect, because he claims that “population size doesn’t matter”. Of course it matters, because in a small population, theoretic allele frequencies produced by the mutation rate will not manifest themselves as actual living genotypes on a regular basis. But instead of pointing this out, DaveScot quotes a perfectly correct sentence and threatens with a ban. A mod should be more careful with quotes when using such patronizing tone of voice.

Comment #156393

Posted by Raging Bee on January 19, 2007 8:11 AM (e)

As for “good faith”, in this sense I suppose I am naive. I do believe that a lot of the activity by ID advocates is sincere in the sense that they can’t necessarily spot a lot of their intellectual dishonesty themselves.

That’s certainly true of the rank-and-file followers, whose strong, and probably sincere and well-meaning, religious beliefs have been twisted by charlatans and bigots till they’re often not even loosely based on the words of Jesus. It is most certainly NOT true of the movement’s leaders, or of wannabee leaders like Sal: either they know full well what they’re doing, or they’re too ignorant and deluded to be qualified to lead anyone anywhere.

For example, Sal’s recent post at UD pretty much seems to pretend, as far as his arguments go, that the discussion here at PT never took place.

That’s how the creationists have worked since the nineteenth century: state an “objection” or “question” to the ToE, ignore the answers, and repeat the same objections or questions as if the subject had never before been brought up anywhere; then, when their honesty is questioned, say something like “What’s so dishonest about asking questions?” Fundamentalists, especially recent converts, do the same thing, especially when they pretend they’re the first people ever to have read the Bible.

…While LudwigK has already been threatened with the ban.

‘Nuff said. Forget the blithering about an “impossibly slow weblog” – this is Sal’s real reason for rebooting the debate at UD.

Comment #156405

Posted by caligula on January 19, 2007 8:52 AM (e)

RagingBee wrote:

this is Sal’s real reason for rebooting the debate at UD

Here I must defend Sal. It was I who suggested the relocation, it was I who mentioned UD as an option, and it was I who was given the final word about it. Frankly, I am disappointed about Salvador’s article in light of our past discussion. And I’m disappointed about the delays involved at UD before your post shows up. (Indeed, the most hilarious act of stupidity lately belongs to me by a wide margin: how on earth could I think that UD would speed up discussion compared to this thread!) But it is unfair to claim that Sal either forced or persuaded me to do it.

Comment #156407

Posted by Zachriel on January 19, 2007 8:57 AM (e)

caligula:

Yes, I found this bit quite, well, hilarious. LudwigK’s argument as a whole is incorrect, because he claims that “population size doesn’t matter”. Of course it matters, because in a small population, theoretic allele frequencies produced by the mutation rate will not manifest themselves as actual living genotypes on a regular basis. But instead of pointing this out, DaveScot quotes a perfectly correct sentence and threatens with a ban. A mod should be more careful with quotes when using such patronizing tone of voice.

A lot of people get turned around with discrete mathematics. Something that might apply to a continuum or to large finites may not apply to small numbers. But instead of DaveScot using this as an opportunity to discuss how alleles might fixate in populations of various sizes, he pretends as if the answer is self-evident and threatens to ban the commenter.

Assuming neutrality, some *unspecified* alleles are being fixed somewhere in populations of all sizes, which is what I think LudwigK might have been leading towards.

Comment #156413

Posted by Raging Bee on January 19, 2007 9:32 AM (e)

caligula: I have reread some of the above posts, and it seems you are right, and I was mistaken about who first proposed moving the debate to UD. My statements were mainly based on Sal’s comment #155967 above, in which, in accepting your offer, he chooses UD as his preference, for the clearly-stated reason that a debate on UD won’t be “hijacked” by his “enemies.” Furthermore, IIRC, he stated this preference and reason after you had mentioned the possibility of a debate being rigged by the selective banning that is well-known to take place there. He knew censorship was a problem at UD, he knew you were aware of it, and he chose UD anyway.

On top of all that, he never even came close to promising that no such censorship would take place; all he could promise was some vague talk about getting permission and “tying” a post to the audience, whatever the heck that means.

You wrote:

(Indeed, the most hilarious act of stupidity lately belongs to me by a wide margin: how on earth could I think that UD would speed up discussion compared to this thread!)

You had a very good reason for thinking that: the censors would have prevented Sal from having to answer for any of the ignorant, obfuscatory, or dishonest statements for which he is well-known; thus speeding up the discussion to the inevitable point of “No one who questions the Party Line is allowed here. End of argument!” Debates go much quicker when they’re not sidetracked by facts or logic.

I was clearly mistaken in some particulars, but Sal is still a coward.

Comment #156414

Posted by Zachriel on January 19, 2007 9:34 AM (e)

caligula

Here I must defend Sal. It was I who suggested the relocation …

I freely withdraw my comments concerning Sal’s ‘retreat’. I look forward to reading your discussion on Uncommon Dissent Descent.

You may already be aware, but there are a number of cites on the Talk Origins archives concerning rates of genomic and morphological change. (The observed rate of change must be greater than or equal to the change observed in the historical record. This is precisely the claim at issue.)

http://www.talkorigins.org/faqs/comdesc/section5.html

Comment #156415

Posted by Raging Bee on January 19, 2007 9:54 AM (e)

PS: I just had a quick look at the UD thread so far. I’m not in a position to follow this highly technical debate, but I can say for certain that Sal’s unctuous evasions cause me to doubt him as a source.

I notice he spends more time saying he welcomes an open dialogue than he does responding to your points.

I also notice he doesn’t take a firm stand against the banning of differing views: instead of saying “Please don’t ban comments,” or “If I want a commenter banned, I’ll ask you to do it,” he merely pretends to try to reason with DaveScot, then qualified even that request by allowing the banning of “spamming.” Sal is a named regular contributor to UD, with his own bio, f’chrissakes – is he really so low on their food chain that he can’t even control a debate on his own post? Does DaveScot respect him that little?

I guess that’s the price of being a suck-up, innit?

Comment #156428

Posted by Salvador T. Cordova on January 19, 2007 11:43 AM (e)

Caligula,

Have most of your comments gotten through. I’m trying to get the dialogue to flow over there so that the mods will not step in. The discussion may roll off the front page but it will continue.

Regarding your points at PT, I simply have not gotten around to discussing all of them. You claim the 180,000,000 figure was shot down, but I pointed out earlier chimps have 180,000,000 more nucleotides than humans, we must then account for the “fixation” of deletions. You might argue they are morphologically insignicant, but in response I point out it still leads to the enigma of sequence conservation.

So, I do appreciate your willingness to dialogue and your willingness to give me the benefit of the doubt as to whether I really am ignoring your objections. The previous paragraph points to substantial issues in favor of my position and the 180,000,000 figure, and I could also claim you are ignoring substative counter-objections on my part. I do not believe it is willful on your part as you do strike me as sincere and fair-minded. What I see is that you may believe the counter-objection is irrelevant since those regions have no apparent morpholoigcal significance (which is debatable, recall the whole JunkDNA controversy). Your position is a serious dismissal of a relevant issue as conserved sequences with no apparent immediate function are an evolutionary enigma that controvert both the selectionist and neutralist positions. And if those supposed insignicant positions prove to be signifcant, your thesis will be empirically refuted.

I think things could flow better here at PT if you will post administrative issues (like how long your comment was trapped in spam) and whether you want the discussion elsewhere. It would serve your interest well to discredit my arguments where I have home-field advantage at UD. It does not serve my interest to have any suggestions that the mods unfairly tipped the debate in my favor at UD, therefore I will continue to lobby you get a fair shot at my arguments.

We may slip off the front page at UD, but the arguments will remain as a historical record for all to see. Any one with technical background is welcome to try to post. I will continue to ask the mods for leniency if I think the comments are substantive.

Salvador

Comment #156434

Posted by Raging Bee on January 19, 2007 12:56 PM (e)

Salvador T. “Wormtongue” Cordova wrote:

Regarding your points at PT, I simply have not gotten around to discussing all of them.

That’s probably because you spent too much time equating my arguments about “junk DNA” with the surgical mutilation of children. Time-management tends to be a problem for people who aren’t willing to deal honestly with the real world.

It does not serve my interest to have any suggestions that the mods unfairly tipped the debate in my favor at UD, therefore I will continue to lobby you get a fair shot at my arguments.

“Lobby?” Is that all you can do? You’re a regular UD contributor, with your own bio, and you still need permission to have an open adult debate on your own post? Why can’t you just tell DaveScot “This is my post, don’t interfere unless I ask you to?” Not enough balls to stand up to DaveScot? Or not enough balls to step outside your dissent-free comfort-zone?

Comment #156437

Posted by Raging Bee on January 19, 2007 1:23 PM (e)

Oh, another thing, Sal:

I will continue to ask the mods for leniency if I think the comments are substantive.

So you have to decide a comment is acceptable to you BEFORE you “ask for leniency” (i.e., beg DaveScot not to erase it)? And you’ll do this on a comment-by-comment basis, without “asking” for freedom of speech in general?

Does caligula get the same privilege?

Comment #156443

Posted by Torbjörn Larsson on January 19, 2007 2:08 PM (e)

Hmm. We will se about commenting on UD, the usual banning censorship doesn’t make debates possible. And DaveScot’s behavior doesn’t bode well.

For now, next time Sal drops in he can riddle this:

Pellionisz wrote:

Debate is obsolete on “existence” of theories, once there is at least one with refutable precitions(s).

Note that Pellionisz hasn’t made any predictions that are verifiable (the first paper) or verified. So he hasn’t demonstrated any new functions in junk DNA.

Pellionisz discusses among other woo “fractal” genetics. Fractals generates self-similarity on all scales, which in turn are describable by power-law relationships. So does natural languages due to required redundancy. But investigations with Zipf’s analysis on patterns in junk-DNA has shown no power-law relationships.

Pellionisz has instituted what he calls “post-genetics”. As post-genetic sicknesses he lists very many, assumed or shown that variations in individuals genomes affects the sickness or its treatment. He doesn’t mention any such shown to be related to junk-DNA.

Why do you refer to woo like Pellionisz? It doesn’t strengthen your case on ‘science’.

Sal wrote:

Fracis Collins called it hubris to say any part of the genome is junk.

He was referring to the difficulties to distinguish between functional and non-functional genes in DNA assays without making errors. Some false positives and negatives are bound to happen, which are corrected later.

Sal wrote:

then it’s incumbent upon them to demonstrate it to be so

Junk DNA is an observation, and its a default function of DNA. It is your duty to show that all these DNA sequences has function, if you want to argue that the observation is incorrect.

Comment #156445

Posted by Scarlet Seraph, FOFOCD on January 19, 2007 2:15 PM (e)

Sal (at Uncommon Descent) wrote:

Thank you. Many of my critics have claimed I run fom the issues. This open dialogue will give me a chance to defend myself and have my day in court. I look forward to the opportunity.

Sal, I find this comment of yours puzzling. You have had innumerable opportunities to defend your position on innumerable threads and blogs.

I note, for example, that mark Chu-Carroll is eviscerating you right now over on Good Math/Bad Math.

By continually abandoning your threads when the conversation becomes difficult, or when you are faced by questions you cannot answer, you make yourself (and by extension the ID movement for which you claim the state of figurehead) look - as has been rightfully pointed out by other posters - cowardly, evasive, and ignorant.

Why continue to embarrass yourself in this fashion? Why continue to make the ID movement look foolish? Why not actually respond to the points your critics make instead of abandoning and running from conflict?

In all seriousness, why do you continue to make yourself look bad? Clearly you are aware of the low opinion that virtually everyone in the scientific blogsphere holds of you - why play into that opinion? Clearly this bothers you (I note the defensive, self-righteous tone in your post). Clearly this makes you feel as though you are behaving stupidly.

There’s a simple cure: actually engage your critics; respond to their questions; stop running and cowering over at UD whenever things become unpleasant.

Behave like a man, not a rabbit.

Or resign yourself to being laughed at.

Comment #156489

Posted by caligula on January 19, 2007 5:13 PM (e)

Sal, sorry about the late response. Time differences (I live at GMT+2!) will cause some unavoidable delays in responses because we are sometimes offline when the other one is “active”.

I’m glad to confirm that all of my posts have made it through at UD. Especially my “judgement” about Walter ReMine is such direct criticism that I wager it normally wouldn’t have made it through – you must have some influence at UD, after all. It is about bedtime for me, but tomorrow morning I will start responding to you at UD. I will also check what other reasons you find for “180 million” besides the SciAm article.

Comment #156503

Posted by RBH on January 19, 2007 5:52 PM (e)

Caligula and Salvador: If UD doesn’t work out, be aware that we have a moderated Formal Debates & Discussions forum on Infidels that’s available for your use. The moderation consists in ensuring that the debaters adhere to their own previously agreed terms and conditions for the debate.

RBH

Comment #156507

Posted by Salvador T. Cordova on January 19, 2007 6:05 PM (e)

Caligula and Salvador: If UD doesn’t work out, be aware that we have a moderated Formal Debates & Discussions forum on Infidels that’s available for your use. The moderation consists in ensuring that the debaters adhere to their own previously agreed terms and conditions for the debate.

RBH

Thank you RBH. Hopefully the discussion will continue somewhere. Thank you for letting me post here at PandasThumb.

Salvador

Comment #156508

Posted by RBH on January 19, 2007 6:19 PM (e)

Having now read the UD thread, I will add that the Infidels FD&D forum is immune to kibitzers in-thread. Only the participants in the debate/discussion can post in the debate thread. There may be a peanut gallery thread elsewhere (in this case it would be in E/C), but just the posts of the debaters appear in the debate thread. It makes for much more comprehensible exchanges, since the kibitzer noise is eliminated.

RBH

Comment #156616

Posted by caligula on January 20, 2007 3:32 AM (e)

I have earlier said that Nachman(2000) seems to provide further strong evidence that Haldane/Kimura’s models are outdated. But there is one thing about Nachman(2000) that puzzles me.

According to Nachman(2000), the multiplicative fitness of an individual possessing U deletrious mutations is reduced to e^-U. This formula comes from Kimura and Moruyama(1966), which in turn relies heavily on Haldane(1937) and Kimura(1961). Before diving into the world of ancient scrolls, I’d like to ask if someone who is already familiar with these sources can shed some light on what puzzles me.

Haldane(1957) calculates the multiplicative fitness of an individual exposed to U new selection pressures with coefficients d_i with the formula MUL(1 - d_i), i=1..U. (For individuals with a beneficial allele to counter any of the selection pressures, that particular coefficient is not applied, of course.) Haldane approximates this multiplicative formula with e^-SUM(d_i). Let us assume that all d_i are equal in magnitude, as the selection coefficients from deletrious mutations clearly are in Nachman(2000), to get e^-SUM(d_i) = e^-U*d_i.

Note that if U=U*d_i, the formulas from Haldane(1957) and Nachman(2000) become equivalent. This would obviously mean that d_i = 1.0.A selection pressure with coefficient (-)1.0 is lethal of course.

Now, assuming that the formula from Nachman(2000) indeed leads back to the classic multiplicative fitness formula, like I have done in the simple calculations above, it seems that Nachman considers all deletrious mutations lethal. What is the point of calculating the “fitness” of an individual with U lethal mutations? Granted, Haldane’s approximative formula returns a fitness slightly above zero for even lethal alleles, but the real formula it approximates does not. Exactly what does deletrious mean? If it is merely a synonym for harmful, why is the selection coefficient automatically -1.0? Do not harmful mutations have a wide scale of coefficients, just as beneficial ones?

Comment #156626

Posted by Douglas Watts on January 20, 2007 3:58 AM (e)

It seems the more a “scientific” ID person hones their “theory” to align with empirical data, the closer and closer it is going to resemble what we generally know as evolutionary biology, just with different nomenclature, ie. asymptotically.

I mean that in the sense that one could summarize the story of life as “overwhelming complexity arising from irreducible simplicity.”

The “irreducible complexity” phrase, to me is a restatement of Zeno’s Paradox and Lewis Carroll’s parable of Achilles being unable to outrun the tortoise, in other words, it is a very old and well-established “trick” of employing the rules of logic to seemingly negate those same rules.

Comment #156627

Posted by Douglas Watts on January 20, 2007 4:14 AM (e)

As an endnote, I welcome Salvador’s participation here and wish that others would exercise the option of either addressing his specific points or declining to do so. Ad hominem comments are distracting and serve no useful purpose.

The story of life as explained by evolutionary biological theory is vastly incomplete. Infinite surprises will always be just around the corner. For all we know, evolutionary biology may soon face its own plate tectonics moment, as geology faced during the 1960s, or as physics faced with the quanta.

In sensu strictu, it is always healthy to have folks playing Devil’s Advocate.

Comment #156633

Posted by Popper's ghost on January 20, 2007 4:34 AM (e)

As for “good faith”, in this sense I suppose I am naive. I do believe that a lot of the activity by ID advocates is sincere in the sense that they can’t necessarily spot a lot of their intellectual dishonesty themselves.

That may well be true, but it is not true of Sal, as has been demonstrated time and time again.

Comment #156634

Posted by Popper's ghost on January 20, 2007 4:42 AM (e)

That’s so hopelessy wrong I hardly know where to begin. I think you need to find a different blog.

That Sal does not denounce DaveScot and the blog (and the movement) that allows him to block commenters simply for (allegedly) being wrong is enough (although there is far more) to demonstrate his bad faith.

Comment #156636

Posted by Popper's ghost on January 20, 2007 4:59 AM (e)

scordova at UD wrote:

I found a commenter named Caligula who gave very substantive criticisms to my ideas in a precise and technical manner, and which I found worthy of giving a fair and civil hearing here at UD.

It’s remarkable that Caligula is the first person whom anyone at UD has even considered giving a fair and civil hearing, but if that actually happens, he will almost certainly be the last one.

Comment #156637

Posted by Douglas Watts on January 20, 2007 5:00 AM (e)

The moment ID was born, ie. when Creationists were forced for tactical reasons to externally sever any invocation of a Biblical Christian God, ID became an exercise in circular logic and self-refutation for the following reasons:

a) Any invocation of a “conscious” designer brings you right back to invocation of a God, leaving out the serious problem of how one can define “conscious” within this framework.

b) Invocation of a “non-conscious” designer brings you right back to the evolutionary theory of life; indeed, the two are different only in nomenclature.

Comment #156639

Posted by Popper's ghost on January 20, 2007 5:12 AM (e)

DaveScot wrote:

That’s so hopelessy wrong I hardly know where to begin. I think you need to find a different blog

scordova wrote:

I don’t necessarily want to scare away participants, but I don’t want this good discussion spammed either. One way to more objectively guage the worthiness of a comment is whether it addresses the fundamental issue of evolutionary speedlimits. […] If LudwigK can offer an estimate of the number of nucleotides per generation being fixed, then I would welcome his response. He can post it briefly. Is the answer

1, 2, 3… or .01, .001, .0001?

According to Sal, an “objective” gauge of worthiness is whether a comment fits his narrow framing – if one fails his test, they are “spamming” – it’s quite convenient for the UDites that they misunderstand that word in just such a way as to justify making dissent uncommon there. Perhaps that’s an example of the sort of bad faith passing as unrecognized intellectual dishonesty that caligula wrote about.

Comment #156641

Posted by Popper's ghost on January 20, 2007 5:20 AM (e)

And of course Sal does not apply the same “objective gauge” to the OT drivel that other UDites insert into his thread, such as “I applaud you Sal, I just went over there and saw the merciless (and logically weak) attacks they made on you. Keep it up.”

Comment #156678

Posted by Tom Moore on January 20, 2007 11:00 AM (e)

If UD doesn’t work out, be aware that we have a moderated Formal Debates & Discussions forum on Infidels that’s available for your use.”

While I agree that the Dover trial provided the best recent example of a fair debate, I’m not optimistic about how this is going to go at UD, and DaveScot has already fired an opening salvo by suggesting a different blog. So the above suggestion seems like a winner to me…

Comment #156693

Posted by Torbjörn Larsson on January 20, 2007 12:54 PM (e)

The “irreducible complexity” phrase, to me is a restatement of Zeno’s Paradox and Lewis Carroll’s parable of Achilles being unable to outrun the tortoise, in other words, it is a very old and well-established “trick” of employing the rules of logic to seemingly negate those same rules.

In all fairness to Zeno, it was just a “trick” of ignorance, because he run up against the problem of defining derivatives to discuss velocities and limits.

(and logically weak) attacks

Yes, it is only about logic. :-)

caligula:

My impression, perhaps mistaken, from your earlier exposition is that Haldane wants to study lethal mutations, or a set of deleterious ones adding up to lethality. In that case, but as you seem to show only in this case when they add up close to |1|, it works to replace multiplicative effects with additive.

Comment #156694

Posted by Raging Bee on January 20, 2007 1:17 PM (e)

Ad hominem comments are distracting and serve no useful purpose.

Pointing out evidence of one debater’s dishonesty and bad faith serves a very useful purpose – to people who care about honesty, logical integrity and facts, that is.

The story of life as explained by evolutionary biological theory is vastly incomplete.

It’s a lot more complete than “Poof, Goddidit, further questions about mechanisms and motives are not allowed, and we don’t need to do any actual science to prove our assertions.”

PS: if what you say is true, then why are so many creationists grudgingly accepting evolution, even as they pretend not to?

PPS to Sal: You still haven’t told us whether caligula has the same right as you do to have “spam” posts deleted on the UD thread. Whassamater, boy? Can’t think of a “Darwinist” atrocity to compare to my posts?

Comment #156721

Posted by caligula on January 20, 2007 4:51 PM (e)

TL wrote:

My impression, perhaps mistaken, from your earlier exposition is that Haldane wants to study lethal mutations, or a set of deleterious ones adding up to lethality.

It was Nachman who, among other things, seems to study deletrious mutations. (J.B.S. Haldane is long dead and was one of the famous scientists who are responsible for the modern synthesis.) And what puzzles me is that each of them alone seems to be lethal – so what’s the point of estimating how many are there per human? Obviously, since we are here, the answer is 0. Nachman’s calculations look like they are based on Haldane’s formulas (indirectly via Kimura), however. As you remember, Haldane himself did not allow for very intense selection, the limit being 0.1.

TL wrote:

In that case, but as you seem to show only in this case when they add up close to 1, it works to replace multiplicative effects with additive.

I’m not sure what you mean by this. But let’s put it this way. Haldane, and population genetics in general, seems to approximate a lot of things. With small coefficients d_i, i=1..N, it holds that MUL(1 - d_i) ~ 1 - SUM(d_i) ~ e^-SUM(d_i)

For example, let N=4 and all d_i=0.025. Then:
MUL(1 - d_i) = (1 - 0.025)^4 ~ 0.9
1 - SUM(d_i) = 1 - 4*0.025 = 0.9
e^-SUM(d_i) = e^-0.9 ~ 0.9

With Haldane’s magic limit 0.1 for combined selection pressures, and below, these funny approximations are possible for calculating fitness. Additive and multiplicative fitness are about equal, and you can even use a neat formula involving the Napier’s costant. (I’m tempted to think that it was for that reason Haldane chose the limit 0.1!) These approximations do not work if they are used with coefficients that are much higher. And that’s what I’m asking: is someone misusing Haldane’s formulas, or is the formula e^-U in Nachman(2000) based on some ideas by Kimura himself that I’m currently unaware of? And why are Nachman’s (and Kimura’s?) fitness penalties for deletrious mutations so severe?

Comment #156778

Posted by caligula on January 21, 2007 1:47 AM (e)

I think I now better understand Nachman’s (Kimura’s) reasoning, although I haven’t had time to read e.g. Kimura(1966), Kimura(1961) and Haldane(1937). I’m an ass. An average number of deletrious (lethal) mutations obviousbly doesn’t apply to all individuals. A small fraction can still be born without any. In this context, it makes sense to study how large the average number is, because it inversely affects the fraction of the population not bearing deletrious mutations.

Comment #156785

Posted by David Wilson on January 21, 2007 2:53 AM (e)

In comment #156616

caligula wrote:

I have earlier said that Nachman(2000) seems to provide further strong evidence that Haldane/Kimura’s models are outdated. But there is one thing about Nachman(2000) that puzzles me.

According to Nachman(2000), the multiplicative fitness of an individual possessing U deletrious mutations is reduced to e^-U…..

No, that isn’t the claim. U is Nachman and Crowell’s estimated deleterious mutation rate—i.e. the mean number of extra deleterious mutations an individual will acquire over and above those it inherits from its parents, and e-U is the mean population fitness relative to the optimal genotype (i.e. relative to an individual with no deleterious mutations) when the population has achieved mutation-selection and linkage equilibria. If the selection coefficients against the deleterious mutations are not very large, then at mutation-selection equilibrium most individuals will have many more than U deleterious alleles. If the mutations are all domininant, for instance, and have selection coefficients on the order of -0.01, then at mutation-selection equilibrium the mean number of deleterious alleles carried by an individual will be around 100 U.

Nachman and Crowell’s expression for the mean population fitness is only approximately correct if most of the mutations have degrees of dominance not too close to zero. It’s a very good approximation if the mutations are all completely dominant, and it’s not very sensitive to variations in their degrees of dominance as long as most of these are not too close to zero. If all the mutations were completely recessive, however, then the mean population fitness at mutation-selection and linkage equilibria would be e-(U/2) rather than e-U.

This formula comes from Kimura and Moruyama(1966), …

Nachman and Crowell are being a little naughty in citing this paper of Kimura and Moruyama’s without comment, since it gives a derivation of the formula only for the case of asexual reproduction (p.1343, equations 3.1-3.4), whereas they are claiming that it holds also for humans, who reprodroduce sexually. It’s very possible, though it’s not immediately obvious to me, that the formula for the case of sexual reproduction might be derivable by a method quite similar to Kimura and Moruyama’s, but if that’s what Nachman and Crowell were claiming, they should have at least included a note to that effect.

In any case, here’s a different derivation of the formula for the case of sexual reproduction. Let μi be the rate at which alleles at locus i suffer deleterious mutations, i = 1,2, …, L, and let the relative fitness factor for individuals with either one or both alleles deleterious at that locus be 1 - di. We then have U = 2 SUMi=1 .. L μi.

A standard formula from population genetics tells us that the frequency of the deleterious allele at locus i at mutation-selection equilibrium will be μi/di, and the fitness of an individual relative to the optimal genotype, assumimg multiplicative fitnesses, will be PRODi=1 .. L( 1 - di )Ii, where Ii = 0 if the individual is homozygous for the non-deleterious allele at locus i and Ii = 1 otherwise.

Now for a zygote chosen randomly from the population, Ii will be a random variable for each i, with Prob(Ii = 1 ) = (μi/di)2 + 2 ( 1 - μi/di ) μi/di = 2 μi/di - (μi/di)2 =approx 2 μi/di, since (μi/di)2 is neglible relative to μi/di for any reasonable values of μi and di, and Prob(Ii = 0 ) = (1 - μi/di)2. The mean fitness of the population is E(PRODi=1 .. L( 1 - di )Ii), where E denotes statistical expectation.

If the frequency distribution of the alleles at the loci 1,2, … , L is in linkage equilibrium, then the random variables Ii, and hence ( 1 - di )Ii, will be independent for i = 1,2, … , L, and the mean of the product of these latter must therefore be the product of their means. In other words the mean fitness of the population is PRODi=1 .. LE( ( 1 - di )Ii).

But since each of the random variables Ii assumes just two values, 0 and 1, with known probabilities, each term of this last product is easy to calculate: E( ( 1 - di )Ii) = ( 1 - di ) Prob( Ii = 1 ) + Prob( Ii = 0 ) = 1 - di Prob( Ii = 1 ) =approx 1 - 2 μi, and so the population mean fitness reduces to PRODi=1 .. L (1 - 2 μi) =approx PRODi=1 .. L e-2 μi = e-U.

Comment #156797

Posted by caligula on January 21, 2007 5:02 AM (e)

RBH:
Thank you for your suggestion, but I think it is not a good idea to relocate once again. We would resemble a wandering circus. :)

Comment #156820

Posted by caligula on January 21, 2007 8:56 AM (e)

David:
Now that shut my mouth! Thank you for a very thorough explanation and for a good demonstration on how equations should be presented in this medium. (I only now learned that KwickXML understands LaTeX, but I didn’t get eqn to work.) I failed to follow the very last line of your post, but apparently you are using properties of e^x that I can’t remember. I assume 1 - x approximates the infinite series representation of e^x and MUL(e^x_i) = e^SUM(x_i). I trust you in this.

My analysis of your post is that since d_i inversely affects the frequency of harmful alleles, it makes itself redundant for calculating the mean fitness. Nachman(Kimura) does not assume that always d_i=(-)1.0 was unfounded. Very well.

I now understand the difference between Haldane(1957) and Nachman(2000) or, rather, Kimura(1966). While Haldane’s formula e^-SUM(d_i) can be used to approximate the mean fitness of the population at the beginning of his scenario, Haldane’s formula can’t be used for mean fitness in later generation – it can only be used for calculating individual fitness.

Comment #156828

Posted by caligula on January 21, 2007 10:27 AM (e)

SC wrote:

I pointed out earlier chimps have 180,000,000 more nucleotides than humans

I could also claim you are ignoring substative counter-objections on my part.

Sal, I honestly haven’t been able to locate where this claim of yours is based on. So I find it hard to comment this at UD. Can you hold my hand and give me a pointer to your source?

Comment #156883

Posted by caligula on January 21, 2007 4:43 PM (e)

Sal,

Now a couple of my posts seem to have become stuck in the spam filter. Could you see if you can get them released, or at least some advice for me on why they became stuck? Unfortunately, I had ceased to keep copies of my posts “in good faith”, because things have been decently smooth thus far.

The first one addresses DaveScot’s claim about “soft selection” causing harmful mutations to fix. I ask DS to demonstrate this with a mathematical example.

The second one addresses DS’s claim in #55 and #57. I fail to see how it relates to Nachman’s paradox and how it fits the scope of the discussion in general. But as I don’t want to leave the impression that (a) I ignored DS’s claim by malice and that (b) I was unable to respond, I did eventually respond. It would be better to avoid getting sidetracked too much, though – wouldn’t it?

DaveScot claims that the “indisputable testimony of the fossil record” shows that:
(1) 99.9% of species have gone extinct
(2) without spawning new species

I think 99% is a more common estimate for (1), but let us accept DS’s number here. Also, I’m not sure what (2) means, as even so-called “baraminology” deals with groups of species with common ancestry (even if it considers the groups themselves distinct). But I assume DS generally refers to gaps in the fossil record below the family level, which he apparently interprets as “indisputable” evidence of “uncommon descent”.

My response to DS was something like this. Assume that the current, say, 10 million species represent only 0.1% of all species in the history of Earth; then there has lived as many as 10 billion species. Yet we only know the morphology of some hundred thousand extinct species by fossil evidence, so far. How does DaveScot know that none of the other 10 billion unknown species will fit the gaps in the fossil record, to “indisputably” demonstrate that they did not spawn new species?

PS. What would you respond to #58? It leaves me utterly speechless. Should domesticated animals both behave in a civil way and flourish when left to themselves, in order to demonstrate that sexuality does not prevent evolution?

Comment #156890

Posted by Scarlet Seraph, FOFOCD on January 21, 2007 5:48 PM (e)

Watts wrote:

As an endnote, I welcome Salvador’s participation here and wish that others would exercise the option of either addressing his specific points or declining to do so. Ad hominem comments are distracting and serve no useful purpose.

Unfortunately, I am not making ad-homs. Sal has a demonstrated and quite easily verified track record of evasive, incomplete, dishonest, and scientifically ignorant posts; his abandonment of threads whenever he can no longer obfuscate or evade confession that he is wrong is well-known.

While I appreciate Caligula’s patience, I feel it reasonable to caution he/she that Sal will not be engaging in an honest debate - based purely on the evidence that he has never done so.

Comment #156911

Posted by David Wilson on January 21, 2007 7:59 PM (e)

In comment #156820

caligula wrote:

I failed to follow the very last line of your post, but apparently you are using properties of e^x that I can’t remember. I assume 1 - x approximates the infinite series representation of e^x and MUL(e^x_i) = e^SUM(x_i)….

Yes, in the last line there is a hidden assumption that all the μis are “sufficiently small”. From standard results on Taylor series we know that   1 - xe-x ≤ 1 - x + x2/2   for non-negative x. For the approximation in the last line of my previous post to be reasonable it is necessary for the sum of the quadratic terms in the μis to be negligible—i.e. for   ∑i = 1 .. L μi2   to be close to zero. For typical values of the μi and L, this is in fact true. If all the μis are equal, for instance, they must all be equal to   U/(2 L), and then   ∑i = 1 .. L μi2 = U2/(4 L) = approx 9/(4 L) , for Nachman and Crowell’s estimate of U = 3. Since L is somewhere in the order of 20,000-100,000, the required condition is satisfied.

Comment #156943

Posted by David Wilson on January 22, 2007 1:43 AM (e)

In comment #156911

I wrote:

caligula wrote:

I failed to follow the very last line of your post, but apparently you are using properties of e^x that I can’t remember. I assume 1 - x approximates the infinite series representation of e^x and MUL(e^x_i) = e^SUM(x_i)….

Yes, in the last line there is a hidden assumption that all the μis are “sufficiently small”. From standard results on Taylor series we know that   1 - x  ≤  e-x  ≤  1 - x + x2/2   for non-negative x….

I have just realised that giving this approximation for   e-x   might have been more confusing than illuminating, since it isn’t much use for rigorously establishinng the approximation in the last line of my original post. The approximation one needs for that is   -x  ≤   ln(1 - x)  ≤  -x + x2/2   for   x ∈ [0,1).

Substituting   x = 2 μi   in these last inequalities, and summing over  i  from 1 to L we get   -U  ≤  ln( ∏i=1 .. L (1 - 2μi) )  ≤  -U + 2 ∑i=1 .. Lμi2. Taking exponentials then establishes the approximation   e-U  ≤  ∏i=1 .. L (1 - 2μi)  ≤  e-Ue2 ∑i=1 .. Lμi2 , and the factor   e2 ∑i=1 .. Lμi2   in the expression on the far right will be very close to 1 whenever the sum   ∑i=1 .. Lμi2   is sufficiently small.

Comment #156953

Posted by caligula on January 22, 2007 2:45 AM (e)

David:

Yes, thank you. My problem was not the exact accuracy of approximations, it was rather that I initially didn’t understand the background of Nachman’s formula. Your clear presentation drove the point home. The effect on average fitness of any harmful mutation is more or less constant, because its eventual frequency at equilibrium (yes, Sal, it is equilibrium, not fixation) depends inversely on the coefficient. (BTW. Momentarily finding MUL(e^x_i) = e^SUM(x_i) as an “exotic” rule was quite embarrassing. I was simply asleep. Being a project manager isn’t good for one’s math!)

I have to say that your kind posts have returned me firmly to the ground (in case my feet ever rose above it). What am I doing there, at UD? Of course, I never asked to be brought under the spotlight as some sort of a “champion” of the “evolutionists”. But I still feel ashamed that it is me who seems to be presented as the main opponent at the UD thread, instead of people who have sat through classes in evolutionary biology and now are, as I assume by the maturity of your mathematical treatments, teaching it. (Not that I didn’t know the other side of the “fence” almost exclusively consists of laymen.) I don’t care who “wins” the debate, I just want the avoidance at UD to stop and the endless exchange of shots to start finally getting somewhere. So Mr. Wilson, even at the risk of embarrassing a layman in public, if you have the time and if you follow the thread at UD, feel free to demolish any frogs that I spit out of my mouth. I do want to know.

Comment #157015

Posted by Raging Bee on January 22, 2007 8:39 AM (e)

Thank you for your suggestion, but I think it is not a good idea to relocate once again. We would resemble a wandering circus.

And this would be different from how creationists normally debate the issues…how?

Unfortunately, I had ceased to keep copies of my posts “in good faith”, because things have been decently smooth thus far.

That’s exactly what Sal, DaveScot, et al were counting on.

Comment #157024

Posted by caligula on January 22, 2007 9:26 AM (e)

Raging Bee wrote:

Unfortunately, I had ceased to keep copies of my posts “in good faith”, because things have been decently smooth thus far.

That’s exactly what Sal, DaveScot, et al were counting on.

I believe this claim is demonstrably wrong, as my posts have been released from the spam filter. And seems like it happened without Sal’s help this time, because he apparently has not become active at UD after his weekend pause yet.

Comment #157080

Posted by aiguy on January 22, 2007 3:43 PM (e)

RBH,

Thanks for the pointer to Febble’s great discussion. You may recall I have been making this and related points over at ARN for years. Dembski has actually provided many different definitions of “intelligence” besides the operational definition Febble cites. While he may have explicitly denied in “Intelligent Design Coming Clean” that mental attributes (intentionality, conscious purpose, and so on) are part of ID’s claims for the Designer, in “IS INTELLIGENT DESIGN A FORM OF NATURAL THEOLOGY?” for example he says

Dembski wrote:

We could therefore define intelligence as the capacity for rational or purposive or deliberate or premeditated choice.
- http://www.designinference.com/documents/2001.03.ID_as_nat_theol.htm

It is obvious that Dembski does not believe that intelligent causation means nothing more than merely “choosing between options”. It is abundantly clear that what he and all other IDists are talking about is mind. It is equally clear that ID has no way to even pretend that ascribing mental attributes such as “deliberate intent” to the Designer could be empirically supported, and so they simply equivocate on the definition of “intelligence”, and leaving all of the mentalistic connotations that we informally apply as implicit.

In fact, when pressed, ID proponents often readily admit that the notions of conscious reflection and libertarian free will are components of what they believe ID demonstrates as the cause of biological complexity.

I see this is the core confusion of the ID debates. Febble’s experience at UD demonstrates that uncovering this equivocation is very troubling to IDers. It does in fact reveal that ID’s sole explanatory concept, “intelligence”, is one of two things:

1) Intelligence means “the ability to choose”, or “the ability to output specified complexity”. As Dembski has also said:

For me, the key defining feature of intelligence is the ability to output specified complexity.
- William Dembski ( http://www.iscid.org/william-dembski-chat.php )

But of course this definition fails miserably. If intelligence is the ability to choose, then algorithmic processes are intelligent, and if intelligence is that which outputs CSI, then the claim of ID reduces to “CSI is created by that which outputs CSI”.

2) Intelligence means what we all informally and subjectively associate with mind - consciousness, free will, deliberation, beliefs, desires, and so on. But this definition is obviously impossible to support in a manner that even superficially resembles science.

It is this, in my opinion, that most clearly undermines the entire ID enterprise.

Comment #157084

Posted by Henry J on January 22, 2007 3:58 PM (e)

Maybe intelligence is the ability to take shortcuts that physical processes can’t - i.e., use mental simulation to get results that bypass physical steps that would be needed for a purely physical process to do the same thing? (And of course the later would be likely to leave physical evidence of those steps.)

Henry

Comment #157093

Posted by aiguy on January 22, 2007 4:31 PM (e)

Henry J wrote:

Maybe intelligence is the ability to take shortcuts that physical processes can’t - i.e., use mental simulation to get results that bypass physical steps that would be needed for a purely physical process to do the same thing? (And of course the later would be likely to leave physical evidence of those steps.)

Of course physical processes can do “mental simulations”, as they do every day in computer programs. Try as you might, I can guarantee you will not be able to find something that human (or any other kind of) intelligence can do that can not, in principle, be done algorithmically. (The basic argument for nonalgorithmicity of mind derives from Godelian arguments, like those of John Lucas or most recently from Roger Penrose, but these have been widely and well refuted, and are irrelevant to ID for other reasons).

As far as evidence of “mental simulations” taking place by demonstrating a lack of intermediate steps by physical processes: Well, no. If we observed a fully-formed complex functional structure appear suddenly in some species (fat chance of that), we might well question our current understanding of evolutionay mechanisms, and look for other processes that might account for it. But this would still in no way indicate that “mind” was at work.

Lightning seems to think ahead and take shortcuts when it looks around from the clouds, finds the highest point of ground, and aims directly for it (often a church steeple, as it turns out). Does this really evidence that some mind is aiming the lightning bolt? No - as it turns out, there are other mechanisms (that operate by regularity and chance like everything else) that give the appearance of mental shortcuts.

Comment #157144

Posted by Torbjörn Larsson on January 22, 2007 11:03 PM (e)

caligula wrote:

It was Nachman who, among other things, seems to study deletrious mutations.

Yes, my mistake. I was thinking of Haldane’s consideration of multiplicative effects, but they wasn’t to add up more than 0.1.

caligula wrote:

TL wrote:

In that case, but as you seem to show only in this case when they add up close to 1, it works to replace multiplicative effects with additive.

I’m not sure what you mean by this.

Yes, I was expressing that clumsy. I was really referring to “if U=U*d_i, the formulas from Haldane(1957) and Nachman(2000) become equivalent” for your comparison, and didn’t check the conditions for the multiplicative to (exponentially) additive conversion. (As done in David’s comments.)

caligula wrote:

e^-SUM(d_i) = e^-0.9 ~ 0.9

e^-SUM(d_i) = e^-0.1 ~ 0.9. Check!

caligula wrote:

A small fraction can still be born without any.

Now I’m confused. I thought Nachman (!) was studying extinctions, but here you wanted some survivors. In any case, I expect David’s derivation cleared this up.

Comment #157198

Posted by caligula on January 23, 2007 9:03 AM (e)

To David Wilson:
What do you think of Nachman(2000) in general, by the way? I just noticed that, quite understandably in 2000, the number of our genes is estimated at 70,000 as opposed to 20,000-25,000. Also, when I look at the calculations, the process somewhat looks like estimates nested inside estimates. Not to such researcj wasn’t useful and important, but do you consider these results reliable at all? I just pointed out at UD, for example, that if we are to argue based on Nachman’s paper, then U=3 should be updated to U=1 because U depends directly on the number of genes. It makes a huge difference concerning Nachman’s conclusions, of course, as the mean fitness increases from 0.05 to 0.37. Although, considering how much “sub-estimates” are involved in this, the resulting estimate might well increase again.

PS. You did your best here at PT, but I still wrote some really goofy comments about the timescale involved in Nachman’s paradox. Sorry!

Comment #157453

Posted by Salvador T. Cordova on January 24, 2007 7:53 PM (e)

Caligula,

It seems UD did not work out for our discussion. One of the chief moderators there has appeared to have made an informal ruling.

On the other hand, I don’t want your criticisms of my ideas suppressed, but rather put out in the open. It serves my side well to be congizant of challenges to their pro-ID position…

If you would like to take RBH up on his offer at infidels, I am amenable. To make things simple, I’ll let you moderate the discussion where you are the inquisitor and I will respond to your questions. I that will make the negotiations for format a lot easier.

The only provision is if I think the discussion is leading nowhere, I’ll call it quits, or we agree to disagree on a particular specific. Furthermore, I expect the discussion will take weeks as the subject matter is not easy and is deep.

I am interested in rigorous examination of the topics considered here. If people on your side wish to enter their discussion, you can field their objections, data points, or whatever through you with proper attribution. That way, you control what is in the discussion.

regards,
Salvador

Comment #157464

Posted by Salvador T. Cordova on January 24, 2007 8:39 PM (e)

Caligula wrote:
What am I doing there, at UD? Of course, I never asked to be brought under the spotlight as some sort of a “champion” of the “evolutionists”. But I still feel ashamed that it is me who seems to be presented as the main opponent at the UD thread, instead of people who have sat through classes in evolutionary biology and now are, as I assume by the maturity of your mathematical treatments, teaching it.

I’ve appreciated your participation nonetheless. I thought you were a bit abandoned by your comrades. You were quite valiant….

(Not that I didn’t know the other side of the “fence” almost exclusively consists of laymen.)

The keyword is almost. Those who have the ability and are in non-religious universities are reluctant to stick their necks out. Trust me, I know several pro-ID molecular geneticists. I dare not have them come forward for blogsphere exchanges, lest their identities be compromised. Not to mention, they care little for these sort of exchanges….

Salvador

Comment #157472

Posted by Brian McEnnis on January 24, 2007 9:48 PM (e)

Salvador T. Cordova wrote:

Those who have the ability and are in non-religious universities are reluctant to stick their necks out. Trust me, I know several pro-ID molecular geneticists. I dare not have them come forward for blogsphere exchanges, lest their identities be compromised. Not to mention, they care little for these sort of exchanges….

No, Salvador, I do not trust you. Your claim reeks of BS.

But assuming that you do “know several pro-ID molecular geneticists”, then simply refer us to the papers in which they publish the evidence in favor of their “pro-ID” positions. These scientists are, after all, the leaders of the new scientific paradigm. They must surely have published their revolutionary ideas by now.

They haven’t?

You’re right. The blogosphere is not the place for these exchanges. Let them submit their ideas to the free-for-all debate that is the peer-reviewed scientific literature. Let them argue their ideas before their peers at scientific conferences.

But it seems that these “pro-ID molecular geneticists” are cowards, afraid to spread their revolutionary ideas because of the threat of (unspecified) repercussions. Perhaps you could explain to them the concepts of “tenure” and “academic freedom.” If the “non-religious universities” in which they are employed fail to recognize those concepts, then AAUP will definitely be interested in knowing about it. Forward them the details, Sal.

Any academics who are “reluctant to stick their necks out” in support of their ideas don’t deserve to have their ideas considered.

Any commenter to this blog who relies on the authority of those “reluctant to stick their necks out” warrants exactly the same level of respect.

Comment #157482

Posted by Scarlet Seraph, FOFOCD on January 24, 2007 11:05 PM (e)

I must point out (it’s my civic duty!) that Sal continues to have his a$$ kicked from here to Kingdom Come over on Good Math/Bad Math by Mark Chu-Carroll.

Apparently, Sal is unable to mathematically define the supposed channel whose capacity to channel information from the environment to the genome is so crucial.

He shows up whenever someone remarks that he has abandoned the thread, pontificates some meaningless and completely non-mathematical dribble, and then flees again.

Sal, you were supposed to have studied math. What’s the matter? Lack of use making you rusty?

It’s not like Mark is asking for that difficult a task.

But boy is he making you look like an idiot.

Folks, check it out.

Comment #157503

Posted by RBH on January 25, 2007 2:17 AM (e)

Salvador wrote

If you would like to take RBH up on his offer at infidels, I am amenable. To make things simple, I’ll let you moderate the discussion where you are the inquisitor and I will respond to your questions. I that will make the negotiations for format a lot easier.

That’s not the way it works on Infidels. There the parties to the debate negotiate the debate/discussion terms and conditions between them, with the guidance of experienced moderators. Thereafter the moderators, neutral parties to the debate, do the moderation. Their only role is to ensure that the parties adhere to the mutually agreed question, terms, and conditions they themselves negotiated. See here for an example of such a negotiation.

Note that debaters have to be registered users on IIDB. That typically takes a day or less to accomplish. Registration is available through a link at the top of the main page.

RBH

Comment #157507

Posted by caligula on January 25, 2007 3:01 AM (e)

SC wrote:

caligula wrote:

What am I doing there, at UD? Of course, I never asked to be brought under the spotlight as some sort of a “champion” of the “evolutionists”. But I still feel ashamed that it is me who seems to be presented as the main opponent at the UD thread, instead of people who have sat through classes in evolutionary biology and now are, as I assume by the maturity of your mathematical treatments, teaching it.

I thought you were a bit abandoned by your comrades.

1. I don’t think I have “comrades”. I don’t participate in evo/crea discussions to make friends on either side of the “fence”.
2. I’m not ashamed of being “abandoned” by someone. Rather, I feel somewhat ashamed because I think there are more qualified people available, and because I doubt they would be as eager (as we are) in debating details that they are not formally qualified to debate. While I personally enjoy such somewhat intellectually loose debate, because it catalyzes my motivation to learn more, I feel somewhat awkward when the debate takes place “under a spotlight”.
3. I’m not sure how many people are allowed to participate in discussion at UD, even if they were willing and mostly qualified.

Comment #157511

Posted by caligula on January 25, 2007 3:27 AM (e)

SC wrote:

One of the chief moderators there has appeared to have made an informal ruling.

All in all, it wasn’t too bad. I think only about four of my posts were censored during my re-visit at UD. (It seems DS had banned me earlier!) Of those, I only regret the loss of my second response concerning the percentage of fossils found.

The last post that was censored was perhaps not as polite as it could have been, but I hardly think it was “uncivil”. Rather, I found “uncivil” GilDodgen’s mimicry of a mathematical argument which never contained any math (“Another form of ADD”). Responding to my censored post, GD clarified that:
(1) He never attempted to present a mathematical argument. He only wanted to mimic one. This was to make the point that
(2) no math is required in assessing such self-evident matters.

I exercise my freedom of opinion by seriously doubting his claim (1) and by strongly opposing his claim (2). Such exercise of freedom is not tolerated at UD, however.

I may have been hasty concering your willingness to respond. But yes, I find UD a tad too hostile environment for constructive discussion. I was made to understand that I’m on the verge of being banned because I’m an uncivil troublemaker, which I find an unfair assessment if you e.g. compare DaveScot’s own comments to mine in the “speed of evo” thread. Also, quite a few of my posts spent like half a day in spam filter, to appear much later than posts by others that were submitted later. This made discussion inconvenient.

Comment #157542

Posted by Raging Bee on January 25, 2007 7:30 AM (e)

Salvador T. “Wormtongue” Cordova once again shows his hypocricy and cowardice:

I thought you were a bit abandoned by your comrades.

Sal, YOU were the one who wanted to move the debate onto a forum where caligula’s “comrades” – people who support evolution and disdain creationism – are clearly unwelcome. caligula wasn’t “abandoned,” he was cut off, which we all know is what you and your fellow creationists intended from the start.

You were quite valiant…

As if standing up for evolution on UD is an act of extraordinary bravery. He was certainly braver than you are here, to be sure.

If you would like to take RBH up on his offer at infidels, I am amenable. To make things simple, I’ll let you moderate the discussion where you are the inquisitor and I will respond to your questions. I that will make the negotiations for format a lot easier.

Why are you so hung up on prearranged and controlled debate formats? Don’t you feel confident enough to stand up for your views in an open forum such as PT, where plenty of knowledgeable people can contribute their insight to a debate? You know you’re perfectly free to come here anytime, post just about anything you want, and let it stand or fall on its own merits. That’s how things work in the real world: once an idea is out, you don’t get to choose who supports or debunks it. (Besides, you always end up coming here when things go wrong on UD anyway.)

The only provision is if I think the discussion is leading nowhere, I’ll call it quits, or we agree to disagree on a particular specific.

You do that all the time anyway: whenever an argument of yours gets debunked, or your dishonesty is plainly exposed, you disappear, with or without some pathetic parting insult; and no one can force you to respond in any blog. Why must you insist on permission to do what you can’t be stopped from doing?

caligula wrote:

Rather, I feel somewhat ashamed because I think there are more qualified people available, and because I doubt they would be as eager (as we are) in debating details that they are not formally qualified to debate.

(That’s modesty, Sal; are you familiar with the concept?) That’s an interesting point, Sal: why won’t you debate someone more knowlegeable than caligula? Can’t hold your own with the big guys?

Man up, Sal. Stop pretending you want a debate (maybe, if we promise to go easy on you and the Moon is in the right phase); and just start debating already. Put up or shut up.

Comment #157552

Posted by Raging Bee on January 25, 2007 9:06 AM (e)

Oh, one more thing, Sal. You alleged:

Those who have the ability and are in non-religious universities are reluctant to stick their necks out. Trust me, I know several pro-ID molecular geneticists. I dare not have them come forward for blogsphere exchanges, lest their identities be compromised. Not to mention, they care little for these sort of exchanges…

So now we’re back to crying about “persecution” as an excuse for ID’s total lack of substance. If any of these persecution stories were real, the victims – and their friends, and the entire right-wing media and blogsphere – would be shouting names, dates, places, and specific charges all over the world, as PROOF of persecution by the Evil Darwinist Establishment. That’s how dissidents in China and the USSR responded to persecution – and their LIVES were on the line, not just their jobs.

Your refusal to provide specific charges – let alone proof – indicates that you know it’s all made up.

And demanding that we trust you, after all the laughably transparent dishonesty we’ve seen from you, is both insulting and funny.

Comment #157573

Posted by Salvador T. Cordova on January 25, 2007 11:52 AM (e)

RgD boasted:

I must point out (it’s my civic duty!) that Sal continues to have his a$$ kicked from here to Kingdom Come over on Good Math/Bad Math by Mark Chu-Carroll.

Apparently, Sal is unable to mathematically define the supposed channel whose capacity to channel information from the environment to the genome is so crucial.

He shows up whenever someone remarks that he has abandoned the thread, pontificates some meaningless and completely non-mathematical dribble, and then flees again.

Sal, you were supposed to have studied math. What’s the matter? Lack of use making you rusty?

It’s not like Mark is asking for that difficult a task.

But boy is he making you look like an idiot.

Folks, check it out.

Indeed check it out. Chu-Carroll is pathologically incapable of accurately representing my ideas and claims. He is forced to resort to strawman arguments and disingenous reprsentations of what I actually said. I called the readers to google and find statements Chu-Carroll attributed to me. Any success?

By all means check out the exchange:

Chu-Carroll vs. Cordova

I don’t intend to allow him to keep attributing statements to me which I never made or implied. Such a line of debate is disingenuous at best.

Comment #157576

Posted by Raging Bee on January 25, 2007 12:11 PM (e)

Sal flailed thusly:

I don’t intend to allow him to keep attributing statements to me which I never made or implied.

The way you linked “Darwinism” to the surgical mutilation of children? If you can’t take it, don’t dish it out.

Such a line of debate is disingenuous at best.

Which is why your word is worthless at best. Stop being a crybaby and start acting like a man.

Comment #157579

Posted by Salvador T. Cordova on January 25, 2007 12:22 PM (e)

Caligula:

I may have been hasty concering your willingness to respond.

Thank you.

But yes, I find UD a tad too hostile environment for constructive discussion. I was made to understand that I’m on the verge of being banned because I’m an uncivil troublemaker, which I find an unfair assessment if you e.g. compare DaveScot’s own comments to mine in the “speed of evo” thread. Also, quite a few of my posts spent like half a day in spam filter, to appear much later than posts by others that were submitted later. This made discussion inconvenient.

I valued your participation and your courage in visiting such a hostile an inconveniet place.

I felt your criticisms were fair and substantive, so much so I hope that people on my side of the discussion will study what you have to say. Your courage will help enlighten the readers on important counter-arguments which I think they should seriously consider.

I will continue to look into the criticisms you raised. I think they are worth addressing, especially soft selection and Haldane’s assumptions.

On behalf of the readers of UD who were interested in those topics, thank you for your participation there.

Comment #157589

Posted by Raging Bee on January 25, 2007 1:37 PM (e)

I valued your participation and your courage in visiting such a hostile an inconveniet place.

So now, after insisting on moving the debate to UD, you admit it’s a “hostile an inconvenient place.” That’s the most honest thing I’ve ever known you to say! Of course, you haven’t actually apologized for the hostility (which you implicitly condone by your continued presence as a contributor), nor did you take a meaningful stand against it; but hey, the journey of a thousand miles and all that…

I felt your criticisms were fair and substantive, so much so I hope that people on my side of the discussion will study what you have to say. Your courage will help enlighten the readers on important counter-arguments which I think they should seriously consider.

Wow – you’re not even accusing caligula of misrepresenting you, like you just accused Mark Chu-Carrol? caligula must have kicked your ass beyond any hope of obfuscation. Either that, or someone finally kick-started your sense of shame.

I will continue to look into the criticisms you raised. I think they are worth addressing, especially soft selection and Haldane’s assumptions.

Yep, sounds like it’s really over.

Comment #157601

Posted by Mark C. Chu-Carroll on January 25, 2007 3:27 PM (e)

Sal wrote:

Indeed check it out. Chu-Carroll is pathologically incapable of accurately representing my ideas and claims. He is forced to resort to strawman arguments and disingenous reprsentations of what I actually said. I called the readers to google and find statements Chu-Carroll attributed to me. Any success?

By all means check out the exchange:

Chu-Carroll vs. Cordova

I don’t intend to allow him to keep attributing statements to me which I never made or implied. Such a line of debate is disingenuous at best.

Yes, by all means, do come look at the comment thread over at my blog.

Sal’s idea of me attributing statements to him consists of my repeated request for him to mathematically define the “communication channel” that he repeatedly insists cannot carry enough information for evolution to occur.

What are the alleged misattributions?

After Sal babbled about communication channels and Shannon theory, I asked him for a mathematical definition of the Shannon channel. His reaction was “I never used the words Shannon channel” - thus avoiding the fact that he can’t do the math.

Repeat the above for various different phrasings of information channel. Including:

Sal wrote:

“The concept that “aspects of evolution are modellable as a channel for information” is not equivalent to saying “evolution as communication on a channel”.”

Just continually weaseling to avoid the fact that he made the claim that when evolution is modeled as a communication channel, the capacity of that channel is insufficient for evolution. He made the claim - and all I’ve done is repeatedly ask him to show the math: define the communication channel, and show a computation of the capacity of that channel, to back up his claim.

Witness the resulting faux outrage as he desparately tries to avoid the fact that he can’t do the math.

Comment #157606

Posted by Raging Bee on January 25, 2007 3:49 PM (e)

Oh well, at least he’s getting your name right. Baby steps, baby steps…

Comment #157608

Posted by Scarlet Seraph, FOFOCD on January 25, 2007 4:03 PM (e)

Sal wrote:

Indeed check it out. Chu-Carroll is pathologically incapable of accurately representing my ideas and claims. He is forced to resort to strawman arguments and disingenous reprsentations of what I actually said. I called the readers to google and find statements Chu-Carroll attributed to me. Any success?

By all means check out the exchange:

Chu-Carroll vs. Cordova

I don’t intend to allow him to keep attributing statements to me which I never made or implied. Such a line of debate is disingenuous at best.

At the risk of being uncivil, I must point out that Sal is lying. There is no other word to cover the case.

Sal has been asked to provide a mathematical definition of the channel of which he speaks so glibly, and of the amount of information it transmits.

He has been unable to do either.

Mark is correct: the bottom line here is that Sal, like Warren before him, resorts entirely to unsubstantiated claims about evolution that he cannot back up, cannot provide.

The worst part is that it’s math - something that Sal is supposed to know something about.

Truly, I recommend that anyone interested in seeing how scientifically ignorant and mathematically inept Sal is should read the post.

Sal looks like a fool.

And I haven’t even mentioned the faults in his logic. We can get to that.

Sal, you made a claim, a mathematical claim. You can either back it up or you can look like a laughingstock. Of course, you’re likely to look like a laughingstock either way.

Comment #157610

Posted by David B. Benson on January 25, 2007 4:23 PM (e)

Scarlet — What does ‘FOFOCD’ stand for?

But it is not clear to me that Sal is ‘lying’. To do that means to tell an untruth knowing that it is untrue. Perhaps you credit Sal with too much?

Comment #157613

Posted by Scarlet Seraph, FOFOCD on January 25, 2007 4:43 PM (e)

David Benson wrote:

Scarlet — What does ‘FOFOCD’ stand for?

Friend Of a Friend of Charles Darwin. It’s a joke based on my usual posting name, “Rilke’s Granddaughter”. Why I’m going with the Scarlet right now, I don’t know. I’m in my Winter wardrobe, maybe? %:->

But it is not clear to me that Sal is ‘lying’. To do that means to tell an untruth knowing that it is untrue. Perhaps you credit Sal with too much?

This is the problem I always have with characterizing the behavior of various IDists: are they really as stupid as they appear to be? Or are they simply lacking in ethics?

In Sal’s case, it’s relatively straightforward to demonstrate that he routinely misrepresents what is being posted, that he routinely contradicts himself, that he routinely reacts to accusations that he’s a moron.

No really stupid person would be capable of such activity. So actually, I’m giving Sal the benefit of the doubt; I’m assuming that he’s reasonably intelligent (just incapable of exercising logic with regard to his fundamental assumptions), rather than assuming he’s just too stupid to understand that what Mark has asked for it very straightforward.

Besides, he’s done this before. There’s a marvelous old thread on www.kfcs.org where Sal is trying to discuss Walt Brown’s stuff. He ducks and weaves and evades for dozens of posts while various folks demolish his nonsense point by point. Once he’s finally brought to it, and has to ‘show the math’ he manages to get it wrong. I don’t have the link in my bookmarks, but you can find it by searching for ‘mantle plumes’ over at www.kfcs.org.

And then, of course, it turns out that his posting were based on a gross misunderstanding of Brown’s book anyway.

No, Sal can’t have it both ways: he’s either a liar, a lunatic, or a fool.

I’m trying to be charitable: I think Sal knows he’s lying and evading and being unChristian. I think that’s nicer than being called dumb. Just me, of course.

Comment #157631

Posted by David B. Benson on January 25, 2007 7:21 PM (e)

Scarlet — Thank you. Of your three alternatives, the second, if I have to choose…

Comment #157804

Posted by Raging Bee on January 26, 2007 10:22 AM (e)

But it is not clear to me that Sal is ‘lying’. To do that means to tell an untruth knowing that it is untrue. Perhaps you credit Sal with too much?

At the very least, Sal is lying when he pretends to know or understand something that he clearly does not. He’s been to school, he’s met knowledgeable people, and he ought to know the limits of his knowledge.

Incorrect statements made under this pretense of authority are not just ignorant, they’re part of his deliberate pretense. In Rumsfeldese (Rummese?), he’s taking what he knows to be a known-unknown (which may be a known-known to an actual scientist) and pretending it’s a known-known to him.

If I make a factual claim about the brain that turns out to be wrong, that’s either ignorance or a mistake. If I claim professional knowledge or in-depth study about the brain which I know I don’t really have, as in “trust me, I learned this in med school,” that’s lying.

Comment #157828

Posted by David B. Benson on January 26, 2007 2:24 PM (e)

Raging Bee — To each their own amateur diagnosis. Personally, I question the “ought to know the limits” bit. So I’ll stick with the loose screw hypothesis…

Comment #157842

Posted by Scarlet Seraph, FOFOCD on January 26, 2007 4:02 PM (e)

I admit, the ‘loose-screw’ concept is comforting - but it then raises the question of what constitutes sanity.

In a way, Sal and his even less salubrious (like that one?) cohorts are a manifestation of a very old war: one against reason itself. Science, considered as a discipline, is very young - less that five centuries separate us from fundamental irrationality. As long as the majority of the species finds reason and logic emotionally unsatisfying, a constant effort to throw the microscopes and compasses and computers back into the furnace will exist.

We live on borrowed time.

Comment #157843

Posted by David B. Benson on January 26, 2007 4:10 PM (e)

Scarlet — I beg to differ. Mathematics and astronomy date back at least 5500 years in Southwest Asia with similar times in Ancient Egypt.

Granted, the enlightenment brought forth quite a flowering of science. But the origins of rational inquiry extend back into pre-history, IMO.

Comment #158293

Posted by Scarlet Seraph, FOFOCD on January 28, 2007 5:15 PM (e)

Dave wrote:

Scarlet — I beg to differ. Mathematics and astronomy date back at least 5500 years in Southwest Asia with similar times in Ancient Egypt.

Granted, the enlightenment brought forth quite a flowering of science. But the origins of rational inquiry extend back into pre-history, IMO.

But as a rationale discipline, rather than as an extension to religion or philosophy? I don’t think so. Science as science is a relatively recent invention (note that Egyptian mathematics was not concerned with the ‘theory’ of numbers, for example - merely with engineering problems.)

Oh, and Sal is still refusing to do anything more than look like a total chump over at Good Math/Bad Math. I’m going to use that link anytime Sal says anything stupid anywhere about his ability to actually use information theory to show anything.

Sorry Sal - you made the idiotic mistake of actually taking on someone who could handle the math. Now you’re indelibly etched as an incompetent. Not that you weren’t already?

Comment #158296

Posted by David B. Benson on January 28, 2007 5:30 PM (e)

The ancient astronomers wanted correct solutions to predict winter solstace and eclipses. And don’t knock the uses of mathematics in engineering. Both the Mesopotameans and the Egyptians were quite good at this.

Eventually, the classical Greeks developed especially plane geometry and also some number theory, all by 2300 years ago. Eudlid wrote it all down, organizing it quite beautifully in his “Elements”.

And all of the above was, and still is, completely rational. Naature has a way of not forgiving irrational solutions to engineering problems. Consider, for example, the pyramid at Meidum…

Comment #158298

Posted by David B. Benson on January 28, 2007 5:39 PM (e)

Oops, I hit Post before Check Spelling!

“solstice”

“Nature”

Comment #158445

Posted by Raging Bee on January 29, 2007 8:07 AM (e)

Scarlet & David: Don’t forget the advances made in math, medicine, and other sciences in the Islamic world prior to our Renaissance. (In fact, a good bit of our Renaissance was propelled by the translation of documents from Arabic to Latin starting in (IIRC) the tenth or eleventh centuries.)

And of course, the ancient Greeks gave us a lot in the way of rational inquiry, much of which was ignored or suppressed by both Christians and Muslims Hell-bent on ignoring St. Augustine’s advice.

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