PvM posted Entry 2221 on April 16, 2006 05:48 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2216

On The Design Paradigm Salvador Cordova ‘responds’ (sic) to various claims about evolution and irreducible complexity. As I will show, the response further establishes the scientific vacuity of Intelligent Design.

Salvador Cordova wrote:

You said, “You should also read up on existing evolutionary explanations for complexity such as scaffolding and Co-option “. No rather you should try to refute the well reasoned issues posed by the displacement theorem and the improbabilities associated with large scale co-option.

Nice redirection from examples of IC systems arising by natural pathways to yet another poorly developed concept of ID namely the displacement theorem. While the displacement theorem once again shows that ID is all about the supernatural, it also shows that as long as the system is ‘open’ to external information, there are no real issues. In other words, whether the external information is the environment or some supernatural or natural designer, it does not help ID’s cause. See Bad Math for more comments on Dembski’s claims.

As to the probabilities of ‘large scale co-option’ I notice the absence of much of any argument, calculations etc to support this claim.

Sal wrote:

Evolutionary algorithms are limited in the kinds of structures they can resolve, and that is a mathematical fact.

An unsupported assertion. Since Sal asserts that this is a ‘mathematical fact’ I am sure that he can support his claim, and show its relevance when it relates to biological evolution.

The presumption that biology is architected in a way that is amenable to evolutionary alogrithms is just a presumption, no where near a proven fact, and possibly quite wrong the more we learn about various molecular systems in biology.

Again wrong, read up on evolvability, neutrality etc which all show how evolution itself has evolved. And surprisingly neutrality which increases robustness also increases evolvability. There is much work which shows how evolvability, can evolve from simple processes. What is even more surprising is that neutrality is a selectable trait.

The case for the efficacy of blindwatchmaker evolution is far from closed.

So what? Such is science.

Ricardo Azevedo has addressed various other problems with Salvador’s claims in a posting titled Junk Science. Well worth reading. As are his contributions on robustness in Junk DNA is Junk. He got quite an education.

Science can explain issues of evolvability, neutrality, robustness etc, how does Intelligent design explain it? Please refresh my memory.

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Comment #96834

Posted by Registered User on April 16, 2006 6:41 PM (e)

Sal must not be aware of the reverse ordination refutation.

It is a devastating refutation of the ID peddlers “latest arguments” that life on earth did not evolve. Frankly, I don’t see how Sal or Dembski or anyone else is going to rebut the reverse ordination refutation of the so-caled displacement theorem (or any other creationist argument). They will be very disappointed when they try! Oh, so very disappointed …

Comment #96835

Posted by PvM on April 16, 2006 6:46 PM (e)

I agree, registered user, it will be quite a task for Sal or anyone else to address let alone rebut the reverse ordination refutation.
Would be fun to see them try though

Comment #96841

Posted by normdoering on April 16, 2006 7:09 PM (e)

What is the reverse ordination refutation?

I did a google on “reverse ordination” and got nothing that looked like an anti-ID argument.

Comment #96842

Posted by 'Rev Dr' Lenny Flank on April 16, 2006 7:10 PM (e)

Why oh why why why won’t Sal answer my simple questions ……?

Comment #96846

Posted by Glen Davidson on April 16, 2006 7:24 PM (e)

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

I just thought I’d ask this simple and basic question, the sort of essential question that IDists should answer before we even begin to consider anything else that Sal or other IDists have to say (IOW, they should not be allowed to dictate what is to be discussed–BTW, human tweaking of some structures hardly counts as such an intelligent designer for which I request evidence).

Glen D
http://tinyurl.com/b8ykm

Comment #96847

Posted by Gordon on April 16, 2006 7:36 PM (e)

Lenny Flank wrote:

Why oh why why why won’t Sal answer my simple questions ……?

Come on Sal and answer Lenny’s questions!!! Are you chicken? Bet its all “God did it!” “Poof!” Sal, at least you could make up some facts and other make believe world scenarios to Lenny’s questions - you don’t seem too shy when you make up rubbish from the Disco Institute for the benefit of the gullible. Reality is too harsh for you - is that it Sal?

Comment #96857

Posted by David B. Benson on April 16, 2006 8:31 PM (e)

Glen D: Do you mean human intelligent designer? If so, then designs produced by engineers are understandable. Designs evolved via so-called evolutionary algorithms are not, these designs just work, and surprisingly well….but maybe that wasn’t your question?

Comment #96862

Posted by Jaime Headden on April 16, 2006 9:09 PM (e)

Salvador wrote:

The presumption that biology is architected in a way that is amenable to evolutionary alogrithms is just a presumption, no where near a proven fact[.]

Yet for some reason, they’d like to think that biology IS architected, by an Intelligent Architect. They have this big problem with undirected processes that remain beholden to natural laws, which their presumed designer doesn’t have to pay homage to.

Comment #96869

Posted by steve s on April 16, 2006 10:40 PM (e)

Salvador Cordova wrote:

You said, “You should also read up on existing evolutionary explanations for complexity such as scaffolding and Co-option “. No rather you should try to refute the well reasoned issues posed by the displacement theorem and the improbabilities associated with large scale co-option.

Impudent comments like this often lead to hilarious cases of unintentional Irony. In the field of unintentional irony, the IDers are Supreme Grandmaster Hall of Famers. IDiots saying evolutionists haven’t done enough research. Mind boggling. Sal’s comment reminds me of this one a few days ago from Uncommonly Dense:

Materialists can’t avoid ID by pointing to it’s supernatural implications. In fact, their attempts to do so are what suggest to me that their scientific position is in bad shape, and they know it. The only way they can beat ID is by showing that the teleology that undeniably exists in nature can be plausibly accounted for by way of unintelligent causes. They need to stop throwing out the red herrings of possible supernatural connections to ID and get into the lab or go out into the field and do some research!

Comment by crandaddy — April 16, 2006 @ 7:03 am

When you read that, did your mouth fall open? mine did. In terms of unintentional irony, Intelligent Design is The Show. Those guys play at a rarified level. It’s the greatest thing on the internet.

Comment #96875

Posted by Anton Mates on April 17, 2006 12:20 AM (e)

I’ve said this before, but what the heck, Sal mentioned that displacement theorem paper of Dembski’s again.

On pages 5 and 6, Dembski gives his example of an assisted search:

Let us, therefore, define an assisted search as any search procedure that provides more information about candidate solutions than a blind search. The prototypical example of an assisted search is an Easter egg hunt in which instead of saying “yes” or “no” for each possible place where an egg might be hidden, one says “warmer” or “colder” depending on whether the distance to an egg is narrowing or widening. This additional information clearly assists those who are looking for the Easter eggs, especially when the eggs are well hidden and blind search would be unlikely to find them.

Then Dembski argues that for an assisted search to be better than a blind one, the responses made by the assistant must each at least indicate whether or not the searcher is directly on top of the target:

As Alice proposes candidate solutions x1,x2,…,xm, at each step k (1≤k≤m) Bob respondssith an item of information j(x1,…,xk) from the response space Λ.

In the scheme just outlined, blind search is represented (up to isomorphism) as follows: Λ = {0,1} and j(x1,…,xk) = 1 if xk is in the target T, 0 otherwise. Here 0 tells Alice that xk is not in the target, 1 that it is….Let us call such a j an indicator function for the target T.

Since assisted search is supposed to augment the information inherent in blind search, the information function associated with an assisted search needs to contain strictly more information than is contained in the indicator function of the corresponding blind search. This strict increase in information can be characterized as follows: An information function j´strictly augments the information in an indicator function j associated with a target T provided there is a function ϕ from Λ to {0, 1} such that ϕ ◦ j´= j and for any such ϕ there is no function ψ from {0, 1} back to Λ such that ψ ◦ ϕ ◦ j´= j´. In other words, composing j´with some function allows Alice to recover the indicator function for T, but j´cannot in turn be recovered from this composition.

And thus Dembski neatly contradicts his own “prototypical example” of an assisted search, the Easter egg hunt, since Alice cannot determine from Bob’s simple response of “warmer” whether she’s reached the egg. (“Cooler” at least tells her she’s not there yet.)

An error this obvious in the first few pages doesn’t bode well for the rest. I must admit I’ve never worked up the spiritual fortitude to carefully read through the entire paper, though. And the bit about

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.

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.”

didn’t really encourage me.

Comment #96880

Posted by buddha on April 17, 2006 2:11 AM (e)

normdoering wrote:

I did a google on “reverse ordination” and got nothing that looked like an anti-ID argument.

The sponsored links?

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trinity-edu.com

Comment #96882

Posted by djlactin on April 17, 2006 3:58 AM (e)

The prototypical example of an assisted search is an Easter egg hunt in which instead of saying “yes” or “no” for each possible place where an egg might be hidden, one says “warmer” or “colder” depending on whether the distance to an egg is narrowing or widening

By embarking on an analysis of whether ‘assisted search’ is better than ‘blind search’ Dembski reveals a serious lack of understanding of evolution.

The tone of this argument: (feedback regarding proximity to target) clearly indicates that Dembski (…err… naively?) assumes that an evolving population is aiming for a prespecified goal! Evolution does not have a goal; it simply a consequence of selection on population variation. The only ‘feedback’ that evolution provides in nature comes via selection (natural or sexual), and it is only in the form of “this phenotype is better/worse than the current wildtype”. It is certainly NOT in the form of “you’re getting closer to (e.g.) human”

Before launching into detailed mathematical analysis of such an appallingly fallacious teliological model, he should learn at least something about evolution!

All Dembski has shown is that intentional selection (‘breeding’) works faster than natural selection. This observation is certainly no major contribution to science, and it is totally irrelevant to the analysis of evolution in nature.

However, upon closer examination it does seem to deal a devastating blow to ID! It implies that an intelligent designer could have done it MUCH faster than nature did it. So why did the “intelligent” designer take 3.5 billion years to produce “us”?

Comment #96889

Posted by Corkscrew on April 17, 2006 6:07 AM (e)

I really have no idea what Dembski was going on about in the Displacement Theorem paper. The whole bloody point of evolution is that the algorithm is a function of the search space.

You could indeed characterise that as gathering information from the environment (for some sufficiently non-mathematical definition of “information”). However, since we already know that the environment for evolution exists (it’s called planet Earth, you may have heard of it), that presents no problem whatsoever.

I believe Dembski’s argument is something like “well, the information must be coming from somewhere so the environment must have been designed”. This completely ignores the fact that evolution works more or less regardless of the environment.

Claiming that evolution doesn’t work because of the displacement theorem is roughly equivalent to claiming that rainwater can’t create puddles because who designed the ground the puddles are forming on? If you want to use that as an argument for God then feel free, but I can see absolutely no way that it could ever in a million years be considered a mathematical argument.

Comment #96890

Posted by Corkscrew on April 17, 2006 6:09 AM (e)

I wrote:

the algorithm is a function of the search space

I meant, of course, the target space. Which is actually a fuzzy set rather than a classical set, if you want to get technical. It’s interesting that Dembski has completely ignored this subtlety.

Comment #96896

Posted by William E Emba on April 17, 2006 6:58 AM (e)

PvM wrote:

On The Design Paradigm Salvador Cordova ‘responds’ (sic) to various claims about evolution and irreducible complexity.

Sal also wrote some remarkably ignorant gibberish about Einstein and quantum mechanics. He seems to think QM is unverified and unverifiable, and that Einstein was just as stupid as Sal himself is on this point. Ergo, ID is science, just like QM!

Comment #96897

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 7:06 AM (e)

Sal tried to feed me some gibberish about QM, too. Near as I could decipher, he seems to think that, since things require an observer to exist, then the universe itself must have an observer to make it exist, therefore God – uh, I mean an Intelligent Designer – exists.

I immediately asked him what observer observed the Designer to collapse ITS wave function and bring it into existence.

No response yet. (shrug)

Comment #96903

Posted by wamba on April 17, 2006 7:58 AM (e)

[Gilbert&Sullivan]No one expects the reverse ordination refutation![/Gilbert & Sullivan]

Comment #96915

Posted by William E Emba on April 17, 2006 9:07 AM (e)

'Rev Dr' Lenny Flank wrote:

Sal tried to feed me some gibberish about QM, too. Near as I could decipher, he seems to think that, since things require an observer to exist, then the universe itself must have an observer to make it exist, therefore God — uh, I mean an Intelligent Designer — exists.

For the record, QM does not require an observer for things to exist. There are interpretations of QM that rely on observers. By choosing a different class of objects to single out as observers, you get a different interpretation of QM. It is completely legitimate, if somewhat odd, to limit the class of observers to all cats, or all amoebas, or all physics PhDs, or to a single person.

In other words, getting God out of QM is possible, if, like Sal, you know absolutely nothing about QM, and, as it seems also true in Sal’s case, absolutely nothing about God. Why some people like to share their incompetence and stupidity with the whole world, I’ll never figure out. No doubt it’s one of those meme things.

Comment #96916

Posted by Unsympathetic reader on April 17, 2006 9:10 AM (e)

Corkscrew wrote: “I really have no idea what Dembski was going on about in the Displacement Theorem paper.

It’s a backdoor way of smuggling in design that could fundamentally undermind his claim that humans create information as intelligent agents.

From another perspective, Denton would be the ultimate “Displacementist”.

Comment #96921

Posted by ag on April 17, 2006 9:21 AM (e)

Surely Cordova must be delighted that a thread specifically addressing his blabber appeared on PT - he thrives on such occurences. He is one of the most arrogant and impudent ignoramuses in the cyberspace, pretending to be an expert in all sciences, confidently judging real experts, licking Dembski’s boots, and generally emitting an annoying and meaningless noise. Rather than seriously discussing his illiterate piffle, he should be ignored - that is what will hit him the hardest.

Comment #96922

Posted by AR on April 17, 2006 9:37 AM (e)

Dembski’s “displacement problem” (which he presented in at least two different forms - one in his No Free Lunch book and another in the more recent article pointed to in this thread) - was promptly shown to be a flop, thus belonging in the same category as his so-called law of conservation of information (which plainly contradicts the 2nd law of thermodynamics), or his egregious misuse of the NFL theorems, or his several mutually incompatible definitions of complexity, etc. However, he himself as well as his acolytes (like the notorious Salvador) stubbornly stick to all that crap as if it is something at least partially accepted in the mainstream science. For a while it could be funny, but after many reapperances it has become boring. It must be of interest for psychologists.

Comment #96924

Posted by Admin on April 17, 2006 9:59 AM (e)

Metatalk moved to the Bathroom Wall.

Comment #96925

Posted by Glen Davidson on April 17, 2006 10:01 AM (e)

Glen D: Do you mean human intelligent designer? If so, then designs produced by engineers are understandable. Designs evolved via so-called evolutionary algorithms are not, these designs just work, and surprisingly well….but maybe that wasn’t your question?

No, I don’t think that was the question. More or less I was asking of Sal or any other IDer this:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

It’s one of those basic questions, are there any candidate “designers” that would operate to produce organisms? We’re always getting this false analogy from IDists/creationists, that humans produce machines, therefore designers must have made humans. But we haven’t made anything like humans, or plants, ever, and neither has any other “designer”. It’s a disanalogy, or perhaps a dysanalogy.

This is one of those empirically essential questions, one that IDists would have to properly affirm prior to even coming up with a “design” hypothesis–is there a reasonable explanation for any posited design in organisms (and btw, I don’t believe the claims that there is an appearance of “design” in organisms–very rare indeed has there been a mix-up between recognizing the difference between “designed objects” and organisms, while it has been rather more common that we have mistaken “natural objects” and animal creations as having been designed by humans)? The IDCists don’t want to have to explain anything, they simply want a poor analogy to “point to” an amorphous “Cause”.

I’m never too much in favor of answering IDCists on their own terms, since their terms are the first thing that they get wrong. So sure, no problem with pointing out Sal’s many errors, however I wish there would be more attempts to force them to answer first-principles questions, or be shown to fail to do so, as in fact would happen every time.

Glen D
http://tinyurl.com/b8ykm

Comment #96929

Posted by Glen Davidson on April 17, 2006 10:31 AM (e)

I don’t think anyone on the IDC side thinks that Panda’s Thumb is at all helpful to IDC causes. Of course the persecution claims, and the “running scared” tripe are standard IDC practice (as opposed to, for instance, research), and seem to work among the gullible such as the Afdaves. This goes to show that we probably are not altogether addressing the lurkers well when we discuss science, as we so often do, since a few pretenses at taking Galileo’s place, a clatter of non-empirically based calculations, and some put-downs are all that someone like Afdave thinks he needs.

I don’t especially accept this in full measure:

The tone of pro-science posts here ranges from extremely politeness to clever, civil satire (with the occasional mild insult used rarely, in frustration).

Nah, especially the head IDiots get called what they deserve to be called, charlatans, liars, and ignoramuses. We’ve done the analyses, collectively, and we’re still willing to engage those who will follow scientific standards in research and in discourse. But the shameful pseudoscientists who persist in spreading BS no matter how often and how well they are answered, deserve the harsh language that they frequently receive here. I make not the slightest apology for slamming IDiots like Afdave, and DaveScot (could be the same person, who cares?).

What’s the alternative? To respect fools and scammers? No, that’s no alternative at all. I remember Tucker Carlson on TV complaining that IDists are being treated like snake-oil salesmen, when he was sure they were rather better (to his credit, he didn’t pretend that ID was science). Why does he think they’re better than that? Apparently because they are “on his side”, and he simply can’t believe that they’re just snake-oil salesmen, when they seem so nice.

This is why we treat snake-oil salesmen like snake-oil salesmen, because most people accept scientific positions only on reputation. We could use the best anti-ID and evolutionary arguments whatsoever, and many people would accept one or the other based solely upon what scientific consensus was. Others would accept ID based solely upon what the religionists had to say, of course, but these people are already lost to the scientific worldview. It is much better if Tucker Carlson is defending IDists from the charge that they are snake-oil salesmen than that he be able to appeal to any respect accorded to IDCists as “alternative scientists”. IDCists must be on the defensive, not accorded any kind of respect that they don’t deserve.

I am entirely in favor of doing to IDCists what they earned, once they have shown themselves to be incapable of tackling the evidence against them. They have been shown to be snake-oil salesmen, even the very nice ones who quite sincerely place religion over and above biology when explaining life. Then we should treat them like the snake-oil salesmen that they are, and let IDiots like Afdave try to make this well-deserved contempt into a positive. Except among fellow idiots, it is not going to work.

Glen D
http://tinyurl.com/b8ykm

Comment #96931

Posted by Salvador T. Cordova on April 17, 2006 10:59 AM (e)

Ungresigtered wrote:

Sal must not be aware of the reverse ordination refutation.

I am not aware of it. If you can present where the refutation can be found, that would be helpful to the people here at PT trying to combat my claims.

So, for their sake, not mine, please provide more information.

ag wrote:

He [sal] is one of the most arrogant and impudent ignoramuses in the cyberspace,

Awh shucks, I can always count on PT to be filled with good will toward me. (sarcasm intended)

corkscrew had the one thoughtful comment:

I believe Dembski’s argument is something like “well, the information must be coming from somewhere so the environment must have been designed”. This completely ignores the fact that evolution works more or less regardless of the environment.

That is the unproven assumption of evolution. Such a “proof” is called affirmation of the consequent, and is a logical fallacy. The displacement theorem helps highlight that fallacy by showing the probability of selective forces to channel biology to high levels of innovation is remote. Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it. The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

Comment #96932

Posted by Bob O'H on April 17, 2006 11:09 AM (e)

Salvador T. Cordova wrote:

corkscrew had the one thoughtful comment:

I believe Dembski’s argument is something like “well, the information must be coming from somewhere so the environment must have been designed”. This completely ignores the fact that evolution works more or less regardless of the environment.

That is the unproven assumption of evolution. Such a “proof” is called affirmation of the consequent, and is a logical fallacy. The displacement theorem helps highlight that fallacy by showing the probability of selective forces to channel biology to high levels of innovation is remote. Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it. The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

Huh? Are you claiming that we haven’t shown that selection can operate? Or just that it can’t operate to produce new feature (such as, say, virulence to new pesticides, or ability to degrade nylon)?

Bob

Comment #96933

Posted by Rilke's Granddaughter on April 17, 2006 11:16 AM (e)

Syntax Error: mismatched tag 'quote'

Comment #96934

Posted by Rilke's Granddaughter on April 17, 2006 11:17 AM (e)

As usual, Sal’s post is long on bafflegab, light on content.

Sal wrote:

The displacement theorem helps highlight that fallacy by showing the probability of selective forces to channel biology to high levels of innovation is remote.

Meaningless. What is ‘high levels of innovation’? In what fashion does the displacement theorem show this (since it doesn’t appear to do so at all)?

Sal wrote:

Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it.

We’ve observed selection, Sal. Perhaps you haven’t because you’re not familiar with research or reality.

Sal wrote:

The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

“Stealth circularity”? Simply more bafflegab.

Enough with the rhetoric, Sal - explain what you mean or remain an apparent fool. Remember that you can always remove that moniker by dealing with the facts.

Comment #96935

Posted by Glen Davidson on April 17, 2006 11:18 AM (e)

Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it. The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

Deal with the predictions of evolution via natural selection and the other associated mechanisms, instead of resorting to the meaningless criterion of “directly observed it”. For once, then, try to deal honestly with the evidence from the beginning, rather than using faulty criteria to attack evolution without having first dealt with the evidence in favor of current evolutionary theory.

Or expect to be treated as well here as you have so richly deserved up to this point.

Glen D
http://tinyurl.com/b8ykm

PS: “Direct observation” means nothing philosophically. All observations are mediated, and all observations are delayed in time. We have a great deal of “direct evidence” (still not a philosophical distinction, but a useful one in science) in favor of evolution (the only “evolution” that has any empirical standing, RM + NS), including on the phylum scale, and we have also “directly observed” natural selection, albeit for more minor changes. What is more, the two mesh. That is, directly observed natural selection occurs essentially as predicted by current evolutionary theory, and the patterns of life also exist essentially as predicted by current evolutionary theory.

Comment #96939

Posted by Glen Davidson on April 17, 2006 11:45 AM (e)

Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it.

Then tell me how researchers are able to differentiate between “neutral changes” and selection. After all, the literature is rife with such distinctions.

Oh, that’s right, Sal’s (apparently) stupidly thinking of scientists assigning a near 100% chance of natural selection actually taking place, and mischaracterizing it as 100%. Indeed, there is just about 100% chance of natural selection occurring, which I suppose is why IDists like Dembski concede that it happens. But Sal, as usual, can’t keep his various apologetics straight, and ignores the fact that IDists such as Dembski and Behe also claim that natural selection occurred where is hasn’t been “directly observed”. Well, no matter, he can’t deal with science, so why not the bafflegab? Anything to attack, and to obscure his vacuousness.

One trouble with Sal is that he thinks in opposites, essentially dialectically. Someone points out (for the 112,529th time) that ID simply assumes design, and he lashes out with “you too”. He can’t understand how it is that evolution makes predictions, is observed to work in accordance with said predictions, and thus evolution is confirmed while phantom designers are not. In fact he calls the empirical gain in information “affirming the consequent”, as any glib ’60s French philosopher might do (if in a manner uncharacteristic of, say, Derrida). The fact is that once one has cut oneself off from empiricism, as Derrida and Sal have done, one claim becomes as good as another one.

And you can’t make a cat look at itself in a mirror. This is what we have to contend with in dealing with IDists, you can’t make them look at the evidence with unbiased eyes, and you can lead them to the facts, but you can’t make them think. They operate entirely outside the bounds of empirical confirmation, and have made their position impregnable by doing so (if not in the opinion of more open minds). It’s rather natural for most of them, since most have never really confronted empiricism in the raw, and have steeled themselves against problematic data in the interim. Therefore they will likely never take up the empirical attitude that they never had in the first place–and which they have learned is the spiritual enemy.

Which is why it is futile for Sal to come on here. We have to insult his ignorance, because that is about all he exhibits. He has to use fakery and ungrounded philosophical gas to pretend to have anything behind his claims, but of course we’re well aware of the tactics of bad philosophy and pseudoscience, so are simply insulted at such stupidity. There is only one thing that could change these discussions with him–he would have to unlearn much, and learn much more. And he clearly is not inclined to do this.

Glen D
http://tinyurl.com/b8ykm

Comment #96942

Posted by Salvador T. Cordova on April 17, 2006 11:56 AM (e)

Then tell me how researchers are able to differentiate between “neutral changes” and selection. After all, the literature is rife with such distinctions.

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance.

Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm. It is analogously the multi-password-like structures which IDers call “irreducibly complex” that is being discussed here.

Darwinian logic affirms the consequent: “selective forces existed in the past to work such wonders because were obviously here, because we are here such selective forces must have obviously existed in the past”.

It has not been demonstrated that such selective forces had been at all pervasive in the past, it is just assumed. Heck, Darwinists hardly even realize they need to be investigating the question!

Comment #96943

Posted by PvM on April 17, 2006 12:10 PM (e)

Sal wrote:

I believe Dembski’s argument is something like “well, the information must be coming from somewhere so the environment must have been designed”. This completely ignores the fact that evolution works more or less regardless of the environment.

That is the unproven assumption of evolution. Such a “proof” is called affirmation of the consequent, and is a logical fallacy. The displacement theorem helps highlight that fallacy by showing the probability of selective forces to channel biology to high levels of innovation is remote. Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it. The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

Sal’s comments once again make some ad hoc claims which remain fully unsupported. Let’s look at the simple ID claim which is easily disproven by science that regularity and chance cannot explain the creation of CSI (Complex Specified Information). In biology specification is given by function and is thus trivial, the problem with complex information is that, as defined by ID activists, complexity disappears the moment it can be explain by a natural process (let’s ignore for the moment that if natural intelligent design explains the system, complexity should also disappear). However when applying scientific concepts of complexity and information such as Shannon entropy, it is trivial to show how processes of mutation and selection can in principle explain increase in complexity, and information.

As to innovation, again science comes to the rescue. In RNA (and more recently DNA) it has been shown that sequence space is ‘scale free’. This means that there are a few phenotypes which are very common and many phenotypes which are much less common. The scale free nature of sequence space means that these phenotypes are closely within any of the other phenotypes. How can this be? Well, much of sequence space is neutral, which means that the genetic sequence can ‘diffuse’ while the phenotype remains in stasis. Occasionally, such diffusing genotypes get close to a new phenotype and with a single mutation an innovative phenotype can be accessed. In other words, long periods of apparant stasis (although at the genetic level much variation is happening) followed by quick innovations. All explained by good old science. No need for miracles.

Sal makes much of the fact that science does not always get to observe directly these selective forces. Of course that’s the problem with looking back in history trying to unravel the evolutionary pathways. And yet, through intelligent dissemination of data and hypotheses, science can not only identify genes under selective pressure but can also reconstruct likely pathways followed in evolution. In the mean time, ID, fully incapable of any scientifically relevant contributions, sits at the sidelines whining that the evolutionists are still unable to provide sufficiently detailed descriptions. Of course forgetting that when it comes to comparing ‘competing hypotheses’ ID has NOTHING to offer.
It’s this kind of envy which seems to frustrate many ID activist, leading them to make inflated claims as to what ID or evolution can or cannot explain.

So in short, in spite of the ‘displacement theorem’ science has shown that evolutionary processes can in fact explain innovation, increase in information and complexity, disproving a major anti-evolutionary claim by ID and exposing the scientific vacuity of ID which is unable to present ANY competing explanation. After all, design merely means that we cannot explain it using natural mechanisms and since evolution proposes such mechanisms, ID is even at this fundamental level unable to compete. But things get worse, ID is even unable to compete with the null hypothesis of ‘we don’t know’. Showing how vacuous ID really is.

Left with little positive evidence, ID has no choice but to downplay the relevance of science and invent ‘scientifically sounding concepts’ such as CSI, IC, law of conservation of complex information, etc or make up strawmen pathways (Behe/Snoke for binding sites, Dembski for proteins) or downplay scientific knowledge (evolution of genetic code, origin of DNA, Cambrian explosion etc).

And finally, Avida is a powerful tool at laying to rest the vacuous claims of ID activists. Problem is that they often do not even understand the tool or the scientific arguments based on Avida work. Which is too bad because science, especially in the last decade or so has acquired much data and knowledge in many of the areas in which ID sees weaknesses, while ID has failed to contribute much of anything scientifically.

Think about this. Anyone interested in science should be worried. Anyone interested in theology would be even more worried by a concept which makes faith subject to disproof.

Comment #96944

Posted by k.e. on April 17, 2006 12:13 PM (e)

Gee Sal THAT was a tour de force ….laff laff

So what’s it to be? No free lunch from Luskin ,again. snicker

You just have to get some more serious people backing your scam er YEC youth camp er love in for idiots er what the heck are you doing anyway, every time you come by here you get enough egg on your face to feed a small nation in Africa.

But back to the serious people for a minute, you know someone more serious than GWB, it seems he is caught between Iraq and a hard place at the moment so how about all those nice new Justices on the Supreme Court?
Got something in the sewer line Sal?
No?
Pity really , you must really love egg.

Now pray tell what is the difference between your hero “Count” Demquixote and other pseudoscience pedlers ?

Phil Karn of Qualcomm fame has a similar observation on a couple of pseudoscientists

Tom Bearden is one of the best known crackpots in the field of “free energy”, the modern incarnation of the age-old futile quest for perpetual motion. Bearden has published an amazing amount of utter nonsense.

He is surrounded by a loyal band of cheering sycophants who go out of their way to threaten and silence their critics. This is rather ironic given their constant complaints that a vast conspiracy has successfully suppressed (and continues to suppress) all information about “free energy” because what it would do to established energy interests.

Another idiot who thought Claude Shannons Theories were going to make them millions.
The VMSK Delusion.

So Sal what are you going to do when ‘Count’ Dembski “the Uri Geller of information science” stops being ‘Count’ Dembski? Go back to the fame and glory of being a nobody ?

Say here’s an idea once you find the ‘Donatello Versace’ of the universe you could impose upon her to give you supernatural powers and the claim ‘The JREF Million’ and get some flash new moses robes at the same time.

Oh and look up Freudian projection before you deny evidence and acuse your oponents of doing what you do.

Comment #96945

Posted by Bob O'H on April 17, 2006 12:17 PM (e)

Salvador T. Cordova wrote:

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance….

Darwinian logic affirms the consequent: “selective forces existed in the past to work such wonders because were obviously here, because we are here such selective forces must have obviously existed in the past”.

Do you really mean selective forces? i.e. do you mean that we can’t demonstrate the advantage of having a defence response or a means of being motile, for example?

The problem with this is that it may not be clear a priori whether a large innovation or a small change is needed: either way the selective pressure is the same.

I suspect you’re confused between the selective landscape and the mutational landscape (which gives the probablity of producing different phenotypes).

Bob

Comment #96948

Posted by Glen Davidson on April 17, 2006 12:33 PM (e)

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance.

Since you missed it the first time, I wrote this:

But Sal, as usual, can’t keep his various apologetics straight, and ignores the fact that IDists such as Dembski and Behe also claim that natural selection occurred where is hasn’t been “directly observed”.

Not that Dembski and Behe are authorities in the least, but for those who prefer words over evidence…

Also, you ignored the predictions of RM + NS (as you always have) in discussing the issue. You missed the fact that one theory encapsulates both small selected changes and the larger tree of life. But then, you can hardly acknowledge that sort of evidence, even when it is called to your attention.

And finally, large changes are documented in the DNA, whether these be accumulations of small changes, or considerable rearrangements. It would do you some good to read the literature on DNA and genetics, such as may be found in Nature, but then I don’t suppose that it fits your agenda.

Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm. It is analogously the multi-password-like structures which IDers call “irreducibly complex” that is being discussed here.

No, it is not, because you don’t get to decide what is going to be discussed. Either deal with the totality of the evidence, or accept that you tacitly are admitting defeat of your lame belief. You are not dealing with the evidence and predictions of evolution, rather you are demanding that we take your unevidenced assertions as the starting point.

I’ll have to add that even if you were able to show that current evolutionary theory were inadequate that it would bring not one iota of evidence forward for ID. I asked:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

Btw, quite obviously my question is about the totality of design, not the overlap between design and evolution which is possible in some cases. Tacitly you admit that you have not achieved this starting point essential to ID every time that you fail to adequately answer the question.

Darwinian logic affirms the consequent: “selective forces existed in the past to work such wonders because were obviously here, because we are here such selective forces must have obviously existed in the past”.

This is not accurate or honest. I did mention predictions, but you, as usual, fail to engage in proper discourse. Scientists believe because of the evidence, which you tacitly allow when you repeat the same BS after having been challenged on it.

It has not been demonstrated that such selective forces had been at all pervasive in the past, it is just assumed.

You have no shame. We happen to know of evolution which happens according to quite different principles, notably language evolution, and sometimes textual evolution. These do not occur via RM + NS, and they do not portray the same paterns of inheritance, splitting, and descent which are seen in biological evolution. Besides which, we can differentiate between robust natural selection among free-living organisms, and the reduced selective pressures existing among most parasites.

We don’t simply assume that natural selection was operative in the past, we demonstrate it through the evidence of the kind of evolution that has occurred. We wouldn’t do ill to simply assume pervasive natural selection, of course, but we don’t have to assume, we have the evidence that similar forces were at work.

Your YEC beliefs are showing again. We are, you know, familiar with the old “can’t know the past” nonsense, which apparently only matters when it is evolution which is at issue, or anything related to it. Apparently we are supposed to be able to discern out-of-the-ordinary events in the past, like Jesus being resurrected, while ordinary events looking completely like what we see today are supposedly in question. Well, you’ve got that backward, as you tacitly acknowledge whenever you ignore the claims of different religions.

Heck, Darwinists hardly even realize they need to be investigating the question!

Of course they know that natural selection in the past must be investigated, but not on your terms. We utilize the predictions of RM + NS to differentiate between “neutral changes” and selected changes, as I noted before. What you want us to do is to invalidate the tests of natural selection that it has already passed, and to accept unevidenced claims instead. This we will not do.

Glen D
http://tinyurl.com/b8ykm

Comment #96949

Posted by PvM on April 17, 2006 12:35 PM (e)

Sal wrote:

Then tell me how researchers are able to differentiate between “neutral changes” and selection. After all, the literature is rife with such distinctions.

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance.

And yet Behe considered such limited changes as impossible for evolution. Boy was he wrong.

Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm. It is analogously the multi-password-like structures which IDers call “irreducibly complex” that is being discussed here.

So the argument is as follows? IC systems can be created by evolution so there is apparant IC and real IC? The problem is that if a 2 character IC system can evolve then there is at least nothing in principle which can build on this IC system to add another 2 character IC system. Or the co-option of a 20 part IC system for instance.

Darwinian logic affirms the consequent: “selective forces existed in the past to work such wonders because were obviously here, because we are here such selective forces must have obviously existed in the past”.

A very plausible assumption. Contrast this with ID’s position. While we know that selective forces exist we can never be sure that they played a role in evolution in the past which means that it must have been intelligently designed.

It has not been demonstrated that such selective forces had been at all pervasive in the past, it is just assumed. Heck, Darwinists hardly even realize they need to be investigating the question!

Seems Sal is somewhat unfamiliar with evolutionary theory and research but let’s even assume his ever shifting position. Sal now admits that evolution could explain IC systems but that we lack the evidence that such selective forces were present in the past. A valid objection but it also undermines ID’s position since we cannot reject nor accept the hypothesis and thus any ID inference has been blocked. If ID had something positive to offer which could be compared to the scientific hypotheses then we could resolve which one performs better. But ID is not about hypotheses, it’s all about ignorance.

For instance let’s look at the marvelous evidence of the transition from water to land. Science has a fascinating series of transitional fossils, genetic data inferred from existing organisms, understanding of the developmentary pathways involved, all that is lacking according to Sal, is the proof that it was selective forces (only) which were present. But even there, science comes to the rescue as it finds how transitional forms were found in areas where such pressures must have existed with significant likelihood. In other words it’s the complete picture which is so compelling.

Compare this with ID’s hypothesis. Poof…. Any questions?

Comment #96950

Posted by Corkscrew on April 17, 2006 12:44 PM (e)

Salvador T. Cordova wrote:

Corkscrew had the one thoughtful comment:

I believe Dembski’s argument is something like “well, the information must be coming from somewhere so the environment must have been designed”. This completely ignores the fact that evolution works more or less regardless of the environment.

That is the unproven assumption of evolution. Such a “proof” is called affirmation of the consequent, and is a logical fallacy.

Uh, it’s no more unproven than the corresponding assertion about raindrops - given a vaguely continuous fitness function (landscape), evolutionary algorithms will find a local optimum and form a stable population in the same way that raindrops find a local minimum and form a puddle. In the case of real-world organisms, the fitness function doesn’t need to be designed - it can be taken directly from the environment (incidentally, the purpose of Avida was to simulate this arrangement). I’ll happily write programs to confirm my assertions here, if you so wish - it’s not exactly rocket science.

The displacement theorem helps highlight that fallacy by showing the probability of selective forces to channel biology to high levels of innovation is remote.

Only if the selective forces in question don’t naturally aim for high levels of innovation. Is innovation good for an organism’s survival? Why, I do believe it is. Can natural selection therefore home in on innovative solutions? It would seem so.

Darwinists however affix a value of 100% probability to such selctive forces existing even when they’ve never directly observed it. The amount of stealth circularity in Darwinian proofs such as Avida is distressing.

No, we’ve observed natural selection. We’ve observed natural selective processes causing differentiation in organisms as a result of differing environments. We’ve observed speciation in sufficiently differentiated organisms. We’ve observed random mutation giving rise to entirely new and valuable traits ex nihilo, and we’ve observed the effect of cumulative selection of even minor mutations. None of this is even remotely in doubt.

We’ve observed fossil records of transitions between wildly differing species, and what we’ve noted is that even the most dramatic transition can be broken down into smaller steps that are well within the scope of selective forces. We’ve noted that hypotheses based on the premise that there exists an evolutionary path often produce confirmed predictions. We’ve noted that conjectures based on alternative premises (such as “Goddidit”) generally fail to produce any predictions whatsoever, let alone confirmed ones.

From this we conclude that “Darwinism” is a scientifically useful premise and ID isn’t. If you wish to challenge this conclusion, the easiest and most productive approach would be to create an ID hypothesis that actually makes predictions not made by the corresponding evolutionary hypothesis. Then go away and test that prediction, and if it’s confirmed we’ll agree that ID is scientifically useful.

If you can’t do this, why on earth would we bother with ID? What would be the point?

(Note: I’m a maths student myself, so I would generally be inclined to accept a mathematical disproof of evolution if one were presented. As documented above, Dembski’s paper does not qualify.)

Comment #96951

Posted by Don Baccus on April 17, 2006 12:52 PM (e)

Sal Cordova wrote:

Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm.

Of course it does, if the algorithm’s general. It just takes longer.

How much longer? Sal assumes exponentially longer.

However, history teaches us that with early versions of VAX/VMS it was possible to write a program that would determine the password to an account in time linearly proportionate to the length of the password. Had to run on the same system, but it was a nifty way for non-admins to get admin access to the box. Very nifty trick and blindingly obvious once it was pointed out. Easy to fix, too, fortunately for Digital.

And it didn’t even require violating the 2nd law of thermodynamics to do it, by golly! Nor the invocation of God (other than the use of His Name in vain when this “feature” was discovered).

One needs to be careful of one’s assumptions when making probablistic arguments, and those assumptions had better be well-supported by observed data. Otherwise it’s just handwaving.

Comment #96954

Posted by Jason on April 17, 2006 1:24 PM (e)

'Rev Dr' Lenny Flank wrote:

Sal tried to feed me some gibberish about QM, too. Near as I could decipher, he seems to think that, since things require an observer to exist, then the universe itself must have an observer to make it exist, therefore God — uh, I mean an Intelligent Designer — exists.

I immediately asked him what observer observed the Designer to collapse ITS wave function and bring it into existence.

No response yet. (shrug)

The thing about this is that what collapses a wavefunction isn’t observation but interaction.

Observation is a type of interaction, but not the only type, obviously. Interaction is what collapses a wavefunction.

And I’m not even sure if you can take the universe as a whole and define a wavefunction for it. I mean, the only one who might be able to do that would be God (or maybe Q).

Comment #96957

Posted by E. Bergen on April 17, 2006 1:33 PM (e)

The debate over irreducible complexity is itself becoming irreducibly complex. Look at all this new-fangled jargon: displacement theorem, co-option, exaptation, scaffolding, reverse ordination, and stealth circularity. Who can keep up with all this stuff ?

Comment #96959

Posted by Rilke's Granddaughter on April 17, 2006 1:43 PM (e)

E Bergen wrote:

The debate over irreducible complexity is itself becoming irreducibly complex. Look at all this new-fangled jargon: displacement theorem, co-option, exaptation, scaffolding, reverse ordination, and stealth circularity. Who can keep up with all this stuff?

Not Sal, apparently. Remember, this is the fellow who said

The critical thinking and precision of science began to really affect my ability to just believe something without any tangible evidence

and

Intelligent design doesn’t have any theology to it.

and “Intelligent design, Cordova notes, does not even attempt to prove the type of deity involved, it just points to some sort of supernatural intervention.”

His ability to reason is demonstrably impaired.

Comment #96961

Posted by Raging Bee on April 17, 2006 1:58 PM (e)

The debate over irreducible complexity is itself becoming irreducibly complex. Look at all this new-fangled jargon: displacement theorem, co-option, exaptation, scaffolding, reverse ordination, and stealth circularity. Who can keep up with all this stuff?

We’re not supposed to keep up with it; we’re supposed to be bowled over by a new wave of smart-sounding buzzwords, woven into “arguments” that can’t be refuted because there’s really nothing of substance to refute.

They’re still trying to baffle us with bullshit, with a new brand of perfume added to the same old mix.

Comment #96967

Posted by Salvador T. Cordova on April 17, 2006 2:25 PM (e)

corkscrew wrote:

given a vaguely continuous fitness function (landscape),

GIVEN? That is affirmation of the consequent. Your statements starts off by assuming the very thing that’s in question for large scale IC.

Salvador

Comment #96968

Posted by k.e. on April 17, 2006 2:31 PM (e)

egg Sal remember ?
Clutching at a straw there boy.
You know what you are doing is a logical fallacy, don’t you?
10 points for the correct one Sal (smirk)
Oh and please stay longer this time
As the premier representative (giggle) for the DI you’re doing a splendid job.
More egg for Sal please.

Comment #96969

Posted by Salvador T. Cordova on April 17, 2006 2:37 PM (e)

Don Baccus writes regarding passwords:

How much longer? Sal assumes exponentially longer.

However, history teaches us that with early versions of VAX/VMS it was possible to write a program that would determine the password to an account in time linearly proportionate to the length of the password.

Are you suggesting the operating system had a security flaw, thus the natural expectation of exponentially longer search times was thwarted? What did I say about anticipatory information?

Hey PvM do you buy that from Don? How about you Corkscrew or Glen Davidson? Are you going to let this sort of stuff pass without any skepticism?

If Don is referring to a hacker’s trick based on his knowledge of an operating system flaw, such password intrusion is anything but Darwinian, but rather intelligent design.

Comment #96970

Posted by Rilke's Granddaughter on April 17, 2006 2:38 PM (e)

Sal wrote:

GIVEN? That is affirmation of the consequent. Your statements starts off by assuming the very thing that’s in question for large scale IC.

Gee, Sal - are you claiming that natural selection doesn’t take place either? Amazing.

Comment #96971

Posted by BorkBorkBork on April 17, 2006 2:40 PM (e)

So is anyone going to clarify what the “reverse ordination refutation” is, or is this some sort of rhetorical snipe hunt? Google only brings up sites on finding vocations, of which I don’t find myself in any particular need.

Comment #96972

Posted by Rilke's Granddaughter on April 17, 2006 2:41 PM (e)

Sal wrote:

If Don is referring to a hacker’s trick based on his knowledge of an operating system flaw, such password intrusion is anything but Darwinian, but rather intelligent design.

No, he’s not. Perhaps you should read for comprehension, Sal; you’re doing a very poor job of it on this thread.

Maxson claims ID ‘theory’ makes predictions and has been tested. What predictions? What tests?

Comment #96973

Posted by harold on April 17, 2006 3:01 PM (e)

Glen Davidson -

I said -

“The tone of pro-science posts here ranges from extremely politeness to clever, civil satire (with the occasional mild insult used rarely, in frustration).”

You disagreed with me, saying that the most notorious purveyors of ID are referred to as “IDiots”, “ignoramouses”, “charlatans”, and “liars”.

Seriously, dude, with the possible exception of “liar”, those ARE mild insults, and they are used here as the result of frustration, and there are a lot of pro-science posters who don’t even go that far (not that I’m saying they shouldn’t).

This is the internet for designer’s sake. Land of over-the-top, misspelled racist and homophobic epithets, sexual vulgarities, impotent but disturbing threats of violence, etc. Which is how a lot of “Christian” creationists handle things. Check out the feedback sections at TalkOrigins.

Believe me, we make our point a lot better this way than if we used the “intuligint desine sux, yu (perform unusual sexual act) with (species of farmyard animal), don’t yu, yu fukken (misspelled epithet)” approach.

Comment #96975

Posted by Jaime Headden on April 17, 2006 3:17 PM (e)

Salvador Cordova wrote:

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance.

This is yet another area that many critics of evolution cannot grasp. It is fine for them to accept “microevolution” because there is so much evidence for it in the lab they cannot ignore it, and for the untrained, it is very easy to distill micro-e down to “small scale 1 or 2 amino acid substitutions” so as to assuage the implications of macro-e, which operates as the accumulation of micro-e events, not some other specified event. How do you think macro-e works? It doesn’t work without the individuals breeding, and without that genetic heritage, no scale of heritage occurs, no genome refinement or introduction of positively or negatively selective changes spread through the genome occurs. But it does. Macro-e acts within a breeding population, through mechanisms of selection and environment, by simple “large scale” perspective of thousands on thousands of micro-e changes occuring between each breeding pair and their descendants.

Evolution critics think that to get an amphibian, a fish has to simply pop legs, differentiate the skull from the shoulder, pop a neck, and WHAM! it’s a tetrapod! But these steps all occured as selective advantages that did not kill the populations that had them, and the animal specimens that we find that hve them are simply providence of recovery through a staggeringly unlucky fossilization process. We get descendants of ancestors in the fossil record, as it is impossible to point at them and get “ancestorA of descendantA” without running into evidenciary problems. But these changes that get us descent through modification, natual selection through interactive ecology, and selective breeding (e.g., “that bird has too much white on its tail to be a good breeding partner, lets find someone else!” resulting in a population that favors white tails over gray tails; and if there is selective advantage in one, the gray tails will disappear, leaving only the white – even though in time and space, they coexisted, none of that confused gabble of “Why are there still apes!?”).

To get around these issues and their unwillingness to study the processes of the scale, one turns to the refuge of the devout: Probabilities. It is only through probability math that a person can argue for the existence of something that no other testable observation can find evidence for. Thus Dembski seeks God in the machine, hoping, wishing for God to smile back with a little letter of recommendation into Heaven, leading to the axiom: Those who seek God do so because they are afraid they will not find Him; A man who KNOWS God exists does not try to look for Him.

Comment #96976

Posted by Bill Gascoyne on April 17, 2006 3:29 PM (e)

wamba in Comment 96903 wrote:

[Gilbert&Sullivan]No one expects the reverse ordination refutation![/Gilbert & Sullivan]

Don’t you mean Monty Python? Or did Python parody some G&S I’m not aware of?

Comment #96978

Posted by Salvador T. Cordova on April 17, 2006 3:50 PM (e)

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

I just thought I’d ask this simple and basic question, the sort of essential question that IDists should answer before we even begin to consider anything else that Sal or other IDists have to say

Glen D

Yes, and even before we knew they existed in the cell:

1. Turing Machines
2. Analog to Digital Converters
3. Compilers
4. Operating Systems
5. Digital Error Correction
6. Spectral Analyzers
7. Feed Back Control Circuits
8. Rotary Motors
9. Aritificial Languages constructed with Backus-Normal Forms

etc.

Comment #96979

Posted by harold on April 17, 2006 3:59 PM (e)

Salvador Cordova wrote -

“Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm.”

This has been refuted at the literal level, in terms of computer science, above.

Perhaps even more importantly, it reveals that Salvador Cordova really doesn’t known anything about the theory of evolution.

His implication is clear - a one or two nucleotide sequence difference between alleles or a forty nucleotide sequence difference between alleles both had to happen in a single step.

Well, technically, that could occur quite easily. And it does all the time.

But the other thing that can happen is that a single smaller change can occur, and be replicated and selected for. Then, in one of the many descendants with that change, another change can occur and be selected for. Repeat many times.

Why does Salvador Cordova spend years commenting uninsightfully on the theory of evolution, when a single semester’s worth of reading in molecular biology, genetics, and population biology would be far more than enough to allow him to avoid such errors*?

Comment #96980

Posted by Jaime Headden on April 17, 2006 4:22 PM (e)

Salvador Cordova wrote:

The context of my mention of selective forces was in regards to large scale biological innovations, not small scale 1 or 2 amino acid substitutions as seen in development of various kinds of antibiotic resistance.

This is yet another area that many critics of evolution cannot grasp. It is fine for them to accept “microevolution” because there is so much evidence for it in the lab they cannot ignore it, and for the untrained, it is very easy to distill micro-e down to “small scale 1 or 2 amino acid substitutions” so as to assuage the implications of macro-e, which operates as the accumulation of micro-e events, not some other specified event. How do you think macro-e works? It doesn’t work without the individuals breeding, and without that genetic heritage, no scale of heritage occurs, no genome refinement or introduction of positively or negatively selective changes spread through the genome occurs. But it does. Macro-e acts within a breeding population, through mechanisms of selection and environment, by simple “large scale” perspective of thousands on thousands of micro-e changes occuring between each breeding pair and their descendants.

Evolution critics think that to get an amphibian, a fish has to simply pop legs, differentiate the skull from the shoulder, pop a neck, and WHAM! it’s a tetrapod! But these steps all occured as selective advantages that did not kill the populations that had them, and the animal specimens that we find that hve them are simply providence of recovery through a staggeringly unlucky fossilization process. We get descendants of ancestors in the fossil record, as it is impossible to point at them and get “ancestorA of descendantA” without running into evidenciary problems. But these changes that get us descent through modification, natual selection through interactive ecology, and selective breeding (e.g., “that bird has too much white on its tail to be a good breeding partner, lets find someone else!” resulting in a population that favors white tails over gray tails; and if there is selective advantage in one, the gray tails will disappear, leaving only the white – even though in time and space, they coexisted, none of that confused gabble of “Why are there still apes!?”).

To get around these issues and their unwillingness to study the processes of the scale, one turns to the refuge of the devout: Probabilities. It is only through probability math that a person can argue for the existence of something that no other testable observation can find evidence for. Thus Dembski seeks God in the machine, hoping, wishing for God to smile back with a little letter of recommendation into Heaven, leading to the axiom: Those who seek God do so because they are afraid they will not find Him; A man who KNOWS God exists does not try to look for Him.

Comment #96983

Posted by steve s on April 17, 2006 5:29 PM (e)

Why does Salvador Cordova spend years commenting uninsightfully on the theory of evolution, when a single semester’s worth of reading in molecular biology, genetics, and population biology would be far more than enough to allow him to avoid such errors*?

Salvador is a committed Young Earth Creationist. If Jesus himself were to descend from heaven to tell Sal that evolution was true, Sal would argue with him.

Comment #96985

Posted by Glen Davidson on April 17, 2006 5:40 PM (e)

Seriously, dude, with the possible exception of “liar”, those ARE mild insults, and they are used here as the result of frustration, and there are a lot of pro-science posters who don’t even go that far (not that I’m saying they shouldn’t).

Ah, looks like we’re not very far apart at all on this issue. And I’ll add that it is true that this forum tends to be more polite and science-oriented than something like TalkOrigins. Which is good, since whatever epithets are called for here, getting back to the science is what we do best.

Glen D
http://tinyurl.com/b8ykm

Comment #96986

Posted by Glen Davidson on April 17, 2006 5:41 PM (e)

I should have written “TalkOrigins NG” above.

Glen D
http://tinyurl.com/b8ykm

Comment #96998

Posted by Bill Gascoyne on April 17, 2006 6:20 PM (e)

My guess would be that Sal is just as able and willing to scroll past and ignore that long repetitive post of yours as the rest of us are. IOW, it would appear that through ad nauseum repetition, he and we have “evolved” an immunity to it, which has rendered it ineffective. I suggest you try something else. Please.

Comment #97000

Posted by Glen Davidson on April 17, 2006 6:23 PM (e)

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

I just thought I’d ask this simple and basic question, the sort of essential question that IDists should answer before we even begin to consider anything else that Sal or other IDists have to say

Glen D

Yes, and even before we knew they existed in the cell:

1. Turing Machines
2. Analog to Digital Converters
3. Compilers
4. Operating Systems
5. Digital Error Correction
6. Spectral Analyzers
7. Feed Back Control Circuits
8. Rotary Motors
9. Aritificial Languages constructed with Backus-Normal Forms

etc.

So I guess the answer is “no”, you do not know of any intelligent designer that produces the forms and “machines” that we find in living organisms. However, you do not mind calling one thing by the name of another and basing a pseudoscience upon those words.

Not only did religious folk know the difference between machines and living organisms well even in ancient times, but there are virtually no scientists today who would confuse the two. IDists must confuse the two to make a pretense at science, but they can’t show a single organ that is anything like what known intelligent designers produce–the exhibit of this fact is above.

Even good ol’ Homer wrote of Hephaestus making automatons to serve the gods back in his day (iow, they knew the difference between life and non-life (which remains proper even though we know that at some levels of reductionism the distinction is no longer clear)). The Greeks, did not generally tell of the gods making life, rather life was produced via other life, and sometimes morphed (very crudely, they evolved–note Ovid’s Metamorphoses, whose sources were almost entirely Greek myth). Nor did God make robots in Genesis, rather he did make a sculpture (a sculpture, not a machine) and then breathed the spirit of life into Adam–then Eve was made out of (morphed) Adam’s rib in the second version of creation.

Aristotle definitely made the distinction between techne and the forms found in life–after all, the two are not similar, except in rather crude aspects. Fortunately, Christians, like most other religious folk, maintained the distinction between techne and life down to the age of modern science, and actually the demise of vitalism is probably the most intensive undermining of traditional religion that ever occurred, being far more erosive of religion than mere evolution, which has plenty of scope for God (but what is God to do if life doesn’t exist beyond the bounds of science?). Evolution is just the scapegoat for the loss of belief in spirit which so thoroughly pervades ID notions.

Nietzsche said it: God is dead. The best evidence of this is that many religious folk see God as some kind of Star Trek god/superior being, who engineered life like some soulless Dr. Frankenstein. Of course one might protect religion via this move, but the spiritual realm that is supposed to animate religion is undercut more surely than through any kind of “naturalistic evolution”. We at least maintain the distinction between animal and robot, even if we do not see it as an unbreachable barrier, while the IDists’ God is relegated to a role analogous with humans.

Oh well, it is up to the theists to destroy their religious bases. However, I do not think that the destruction of religion is solely the responsibility of IDists and their ilk, and that they do as much disservice to genuine Christians as they do to science. My main concern is that science not be thrown out along with the spiritual realm that IDists so callously mischaracterize, that we moderns should still be able to differentiate between the very different realms of engineering and biology, and that one should be able to continue to believe in some sort of religion–or not–based on the obvious fact that life is quite different than are machines.

Btw, Berlinski is one who undermines the ID/Frankenstein argument that life is just tubes, Turing machines, rotary motors, iow, machinery. His arguments in Commentary and elsewhere claim that life isn’t even based on the physical, let alone that it is engineered by some exalted DaveScot. Berlinski writes (in his abiogenesis article):

But whether it has been immeasurably improved in a way that vigorously confirms the daring idea that living systems are chemical in their origin and so physical in their nature–that is another question entirely.

Ignoring here the obvious non-sequitur above, I can heartily agree with his notion that life is different from machines–which must be the case if life is not certainly “physical” (my point is that this difference between life and machines is easily explained via evolution, not by destroying physics). Do you guys really intend to continue to support people who disagree completely with the ID position that life is just a bunch of machinery? In any case, you’d think that if you were serious about science and scientific arguments that you would be most intent on disagreeing with Berlinski’s Platonic vitalism, not with those of us who believe that in principle life could be made by humans.

And of course I realize that at some point humans or their descendants might in fact be capable of making some sort of life, though not the specific complexity that we see, by utilizing first principles (rather than merely copying what we know). But even this future possibility would not (partially) answer my question any more than Sal did, for even then one would have to establish that such intelligences existed when life arose.

Not that it matters to them, since Sal and other IDists only try to confuse the issue (whether as a self-affirmation of their own confusion, or otherwise), not to develop a coherent rational model. The above is for lurkers and any other readers, not for the dedicated foes of science.

Glen D
http://tinyurl.com/b8ykm

Comment #97002

Posted by Glen Davidson on April 17, 2006 6:29 PM (e)

Well gee, how many hundreds of times have I asked Sal (and Nelson, and Beckwith, and Heddle, and every other IDiot who comes here) my simple questions?

Oh yeah, I recognize what you’re doing, and largely agree with at least the principle. However, I thought I’d ask a different question, one that I think cuts closer to the bone and any putative “basis” for ID–though not necessarily a better question. That it was different was meant to avoid the sentiments written by Gascoyne, however appropriate or not.

Glen D
http://tinyurl.com/b8ykm

Comment #97003

Posted by Salvador T. Cordova on April 17, 2006 6:33 PM (e)

Salvador wrote: Establishing that someone can crack a 2 character password by a search algorithm does not imply a 40 character password can be resolved by the same algorithm.

Harold wrote: This has been refuted at the literal level, in terms of computer science, above.

26^40 = 3.97 * 10^56, do you care to back your assertion in light of that, Harold?

Comment #97006

Posted by Salvador T. Cordova on April 17, 2006 6:44 PM (e)

Glen’s original question:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

To which I answered yes.

Note: the question was not originially about “any intelligent designer that produces the forms and ‘machines’ that we find in living organisms”.

Glen couldn’t even get his own question straight. He had to re-write it after I gave a pointed response.

Glen misrepresents his own question and my supposed answer a few posts later.

Glen’s revision:

So I guess the answer is “no”, you do not know of any intelligent designer that produces the forms and “machines” that we find in living organisms.

Huh? I said “yes” to one question, and then you insert a “no” from me from another question which I didn’t respond to. What’s up with that?

Comment #97008

Posted by Salvador T. Cordova on April 17, 2006 6:50 PM (e)

Pim van Meurs (pvm) worte:

As to innovation, again science comes to the rescue. In RNA (and more recently DNA) it has been shown that sequence space is ‘scale free’. This means that there are a few phenotypes which are very common and many phenotypes which are much less common. The scale free nature of sequence space means that these phenotypes are closely within any of the other phenotypes. How can this be? Well, much of sequence space is neutral, which means that the genetic sequence can ‘diffuse’ while the phenotype remains in stasis. Occasionally, such diffusing genotypes get close to a new phenotype and with a single mutation an innovative phenotype can be accessed. In other words, long periods of apparant stasis (although at the genetic level much variation is happening) followed by quick innovations. All explained by good old science. No

Pim fails to mention the source of that “proof”. At the end of A Testable Genotype-Phenotype Map:
Modeling Evolution of RNA Molecules
the paper he got it from, by Shuster, it says:


From analyzing and modelling prokaryotic evolution to an understanding of multicellular organisms is still a very long way to go and we do not know
yet whether or not generic properties of simple genotype-phenotype mappings can be used as models. Progress, however, is fast and molecular genetics of
development is witnessing a true explosion of new insights into the enormous complexity of higher organisms. At the current state of our knowledge it seems certainly premature to generalize the concepts developed here to evolution of plants and animals

Pim did exactly what the authors warned against, tried to generalize this to complex evolution. Furthermore, the scale free argument ends up just being a red herring and obfuscation as it won’t really help much the issue of large scale biological innovations involving multiple proteins.

Comment #97012

Posted by Don Baccus on April 17, 2006 7:01 PM (e)

Sal Cordova wrote:

26^40 = 3.97 * 10^56, do you care to back your assertion in light of that, Harold?

Yet passwords are cracked in large numbers every day. Again, you’re arguing from a false premise.

Sal Cordova wrote:

1. Turing Machines
2. Analog to Digital Converters
3. Compilers
4. Operating Systems
5. Digital Error Correction
6. Spectral Analyzers
7. Feed Back Control Circuits
8. Rotary Motors
9. Aritificial Languages constructed with Backus-Normal Forms

As someone who wrote compilers professionally for nearly three decades, and who has a rich background in formal language theory, you make me laugh.

Please give us an example in each category so we can laugh at you some more.

Comment #97013

Posted by steve s on April 17, 2006 7:10 PM (e)

AFDave, your highly off-topic comment does not belong on this thread. Ergo, I have created a new topic for you at After the Bar Closes, the free-for-all forum this site maintains for just such occasions:

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=4443e7c5adba0e88;act=ST;f=14;t=1938

Comment #97014

Posted by the pro from dover on April 17, 2006 7:24 PM (e)

I really dont think sal wants to be educated. He wants to hone his arguments more sharply to present them to up-and-coming debaters to press the challenge to evolution. What matters here is the saving-of-souls for the rapture not America’s continued hegemony in science and technology for generations to come. Who cares about mutating bird flu in the face of the antichrist. So I get to ask a question as well. Sal the theory of evolution can be tested given technology already available and I want your best guess of the outcome and why to this experiment. Lets take 2 groups of 5 mammals. No tricks here. The mothers all secrete milk to feed their young and they all have hair on some part of their bodies at some time in their lives. The theory of evolution will predict that the DNA of one of these groups of 5 will be much closer among the species than the DNA of the other group will be to theirs based on the fossil record. No tricks here either, all the living species as well as the fossils in question meet the criteria for “mammal”. They all have synapsid skull structures, 3 ossicles and a mandible made of a single dentary bone. In group #1 we’ll put the spiny anteater, the banded anteater, the scaly anteater, the giant anteater, and the aardvark. In group #2 the arctic fox, the giant panda, the mink, the walrus, and the tiger. Evolution will clearly predict one of these groups will have more closely similar genomes than the other. What would ID have to say beyond “anything is compatible with ID”. In short it explains everything and predicts nothing. That is what is meant by “scientifically vacuous.”

Comment #97015

Posted by Glen Davidson on April 17, 2006 7:32 PM (e)

Note: the question was not originially about “any intelligent designer that produces the forms and ‘machines’ that we find in living organisms”.

Of course it was:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

The two say much the same thing (though I realize that the second is actually inferior–but as it happens the two mean essentially the same thing, since we have no other examples of forms and machines “like” those we find in organisms except those found in organisms–sort of my point (I do recognize how Sal takes offense, as he claims otherwise, despite the actual evidence)), and I merely re-wrote because that is what good writers do. I don’t simply repeat myself, with an interspersed falsehood every now and then, as the unimaginative Sal does.

Now it is true that I added context well before Sal’s “answer”, because I know how badly IDCists misuse words. This was what I added, though it should have been obvious to anyone not stupid or prejudiced:

Btw, quite obviously my question is about the totality of design, not the overlap between design and evolution which is possible in some cases. Tacitly you admit that you have not achieved this starting point essential to ID every time that you fail to adequately answer the question.

Naturally Sal ignored those qualifications, and simply spouted a moronic list exhibiting the marked confusion of IDCists.

Glen couldn’t even get his own question straight. He had to re-write it after I gave a pointed response.

How idiotic of Sal to characterize a somewhat different re-write (for stylistic reasons) as meaning that I couldn’t get my own question straight. To be sure, anyone stupid or dishonest enough to claim that his confusion of biological parts with human-made machines
“answered my question” is not going to be able to understand why one might slightly re-write instead of simply repeating.

Well it’s just attack, attack, attack from the IDiots. He hasn’t answered any pertinent questions at all well, but resorts to the one thing IDists are capable of doing, libel.

Glen misrepresents his own question and my supposed answer a few posts later.

Glen’s revision:

So I guess the answer is “no”, you do not know of any intelligent designer that produces the forms and “machines” that we find in living organisms.

Huh? I said “yes” to one question, and then you insert a “no” from me from another question which I didn’t respond to. What’s up with that?

ID is rotting your brain, Sal. No one with a speck of integrity will believe that I misrepresented my question. And it’s absurd that you think that your confusion about biology and its “analogies” with human-designed objects and systems backed up your “yes”. For people who understand the English language it is not difficult to understand my reply, which is that your insipid cut-and-pastes show that you cannot answer the question, thus your list implies that your answer is “no” (however much you may believe that “yes” is true).

Of course the big problem is not that you don’t understand normal English, stylistic reasons for re-writes, or that attacks on individuals do not back up ID as science. The biggest problem is that you again ignored a vast number of issues and questions raised in my various posts, tacitly admitting that you have no more answer for these than for the question that you “pointedly answered”.

Look, I’ve been harsh, but let me try to make a small appeal. No one here (at least on the evolution side, which is most of us, and by far the most intelligent posters) thinks that you answered my question. Do you really think that it is because you are so much more intelligent than us, that somehow we do not understand analogies and comparisons, and that we also don’t know how to debunk false analogies and comparisons? Do we in fact discuss science without knowing the philosophy and empiricism which have gone into the making of science, and that we may somehow be enlightened by a list made by people who get so many things wrong? Does it ever occur to you that we have studied the relevant sciences, along with the related courses, and simply disagree because you have not engaged us on our level?

Do you really think that you can only learn from IDists, and that we know nothing? If not, please, please learn some of the relevant science, and if you can, some of the philosophy of science as well. Then we might begin to have a reasonable discussion of the issues.

Glen D
http://tinyurl.com/b8ykm

Comment #97016

Posted by Corkscrew on April 17, 2006 7:36 PM (e)

Uh, there’s a post of mine floating around in the moderator system. It mentions Lipschitz continuity. It fails to mention that, for the definition I use to be even remotely useful, there’d need to be a prespecified value of K.

Basically, the definition could be more simply restated as “in the majority of cases, a small change in genotype will not result in a radical change in phenotype”. Or something like that. Apologies for the confusion - blame the booze :P

Comment #97017

Posted by Moses on April 17, 2006 7:38 PM (e)

Comment #97009

Posted by afdave on April 17, 2006 06:58 PM (e)

I can see that the Flank and Davidson have read the book ‘How to Win Friends and Influence People’ … I have an idea for a simple, fun exercise. I’m an Electrical Engineer and business man and I used to fly AF jets. I like simple, uncomplicated arguments and I like people to cut to the chase … fast. Let’s say I was undecided about where life on earth came from or how it began. I hear the YECs and the ID people saying it came from an Intelligent Agent/God or whatever. I hear the Darwinists saying it happened by chance evolution. And everybody quotes all these long-winded academic sources. I would love to hear from each of you, everybody in YOUR OWN WORDS, not referring to a single outside source what YOUR theory is and WHY you believe it in 5 simple statements, i.e. the top 5 reasons for your belief. Take me from when and how it all began to where you think its going and why … very short and simple so my pea brain can understand it … try explaining it nicely and politely.

Honestly, I wouldn’t waste my time as I smelling a hypocrite and a trouble maker. Nothing like coming in from a hostile premise including your Darwinist appellation typically indicative of a closed mind. I don’t see why anyone should jump through your little hoop and give “polite” answers (or much slack) to people who play polite yet use the word “nigger” (Darwinist) in their posts.

But most importantly, evolution can’t be proven to someone who suffers from a bumper-sticker mentality and thinks anyone can really sum up the arguments for evolution in five bullet-points suitable for a Power Point presentation. If you’re truly interested, do what any educated person has done - get educated - here’s a start:

29+ Evidences for Macroevolution
The Scientific Case for Common Descent
Version 2.87
Copyright © 1999-2006 by Douglas Theobald, Ph.D.
[Last Update: March 29, 2006]

http://www.talkorigins.org/faqs/comdesc/

Comment #97018

Posted by harold on April 17, 2006 7:40 PM (e)

Salvador Cordova wrote -

“26^40 = 3.97 * 10^56, do you care to back your assertion in light of that, Harold?”

I guess 26^40 is a reference to the maximum possible number of combinations an algorhythm would have to check to “crack” a password of forty character length, with letters of the alphabet being the only characters, not case-sensitive.

His point was that Don Bacchus contradicted his irrelevant assertion that an algorythm to “crack” a two digit password wouldn’t be able to “crack” a forty digit password. I merely referred to Don’s post. Of course, Sal is right that it takes longer (much longer) to crack a longer password, but Don is more right, because it’s obvious that an algorythm can be designed to crack any length of password based on finite and known character combinations - it’s just a matter of how long it takes. Sal seems to make the valid point that it would take far longer (with current computers, that is) to crack such a long password, than the scientifically predicted lifespan of the sun or indeed, the universe, in any meaningful sense, for an algorhythm to crack such a password.

However, Sal is being very, very evasive. None of this has anything to do with the theory of evolution; it’s just an irrelevant discussion of passwords and computer programs. In fact, the real point of my post was that this analogy, used by Sal, reveals a profound misunderstanding of the theory of evolution, as well as of genetics and molecular biology.

I don’t want to tie Sal up, because he’s got 31 or so questions from Lenny Flank to answer, plus he never did tell me whether he agrees that HIV is the cause of AIDS, and he’s got those IDEA club kids to keep an eye on.

However, if Sal gets through with all of that, I’d love to hear whether he has anything to say about the actual substance of my post. One of them may have busted out and tried to post as “afdave” today, although more likely that was DaveScot.

Going on and on about password-cracking algorhythms will be interpreted as more evasion.

Naturally, I’m not arguing with Sal’s religion, which is his own business, but with his endorsement of the logically and scientifically vacuous “ID”, which he himself vehemently insists is not a religious idea.

Comment #97019

Posted by PvM on April 17, 2006 7:41 PM (e)

Pim fails to mention the source of that “proof”. At the end of A Testable Genotype-Phenotype Map: Modeling Evolution of RNA Molecules the paper he got it from, by Shuster, it says:

At the current state of our knowledge it seems certainly premature to generalize the concepts developed here to evolution of plants and animals

Yes, that’s why it is so interesting that much of what Schuster et al have found for RNA also seems to apply to DNA evolution. And thus I stated

. In RNA (and more recently DNA) it has been shown that sequence space is ‘scale free’. .

So rather than extrapolating from RNA to DNA I actually stated that recent research supports the scale free nature of DNA as well.

That Sal is unfamiliar with these details should not have been a reason for him to suggest that I am not aware of the limitations outlined in 2002. Perhaps Sal does not appreciate how fast research moves in 4 years. He could have chosen to ask for clarifications, instead he makes yet again unsupported assertions.

Furthermore, the scale free argument ends up just being a red herring and obfuscation as it won’t really help much the issue of large scale biological innovations involving multiple proteins.

Now that’s ironic hearing Sal complain about obfuscation and red herrings. But rather than accept his unsupported assertion, I will do better and show that Sal is wrong. Scale free networks, evolvability, neutrality will all combine quite nicely.
But rather than hastily present these arguments, I will address them in more detail soon. After all, showing how natural processes can deal with ID ‘objections’ to evolutionary theory can be a good learning experience for those toying with the idea of taking ID seriously.

Comment #97020

Posted by harold on April 17, 2006 7:47 PM (e)

Oops.

I fall victim to the nectar of the malt - a common affliction among posters here.

This was the intended meaning of a possibly mysterious sentence in my post above…

“I don’t want to tie Sal up, because he’s got 31 or so questions from Lenny Flank to answer, plus he never did tell me whether he agrees that HIV is the cause of AIDS, and he’s got those IDEA club kids to keep an eye on. One of them may have busted out and tried to post as “afdave” today, although more likely that was DaveScot.”

Actually, I just noticed more evidence that it was DaveScot. Sorry kids.

Comment #97022

Posted by Glen Davidson on April 17, 2006 7:56 PM (e)

Note: the question was not originially about “any intelligent designer that produces the forms and ‘machines’ that we find in living organisms”.

My first rendition:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

At the risk of beating this to death, I want to make clear that the change in wording reflects the fact that the only forms and “machines” that are like those we find in organisms are to be found in organisms. That Sal cannot understand this is the major problem between our recent conflict.

The only backtracking I’m willing to make is that when Sal pointed out the change I did understand why he didn’t like it, and probably wouldn’t have written it that way if I had gone through the pain of “thinking like Sal”–which I wrote before, but include again to keep it clear. That said, the “change” was legitimate in the scientific sense because any intelligent and knowledgeable person knows that nothing is “like” what we find in organisms except what we find in organisms–notably because of their two very different origins. As I wrote, Berlinski recognizes this fact (though one has to work through his statements to show this), while the other antievolutionists applaud him while relying on their faulty analogies to claim quite the opposite.

And it is because the “parts” and systems of organisms are not “like” anything we have ever made that Sal’s “answering list” is so laughable. Yet it appears that only “our side” the sense to laugh at it.

Glen D
http://tinyurl.com/b8ykm

Comment #97023

Posted by afdave on April 17, 2006 8:10 PM (e)

Yeah, I’m truly interested, but only in your own words. Everybody and their brother refers me to TalkOrigins.

So what’s the polite term to call you folks at PT if not Darwinists?

Comment #97024

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 8:12 PM (e)

He wants to hone his arguments more sharply to present them to up-and-coming debaters to press the challenge to evolution.

He’s a day late and a dollar short. ID has already been killed, dead, in Dover. (shrug)

Comment #97025

Posted by steve s on April 17, 2006 8:19 PM (e)

Comment #97023

Posted by afdave on April 17, 2006 08:10 PM (e)

Yeah, I’m truly interested, but only in your own words. Everybody and their brother refers me to TalkOrigins.

Do you go to physics sites and ask people to explain relativity to you only in their own words?

Comment #97026

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 8:20 PM (e)

I can see that the Flank and Davidson have read the book ‘How to Win Friends and Influence People’ …

Um, in case you didn’t notice, my side has already won. In a courtroom in Dover, Pennsylvania. Your side had its chance ot puit its money where its mouth is. Your side had the opportunity to present any evdiecne it wanted, to put forth any witnesses you felt would help, and to question and cross-examine everything put out by the “evilutionists”. And when all was said and done, your side lost —– so crushingly and embarrassingly that even your pals in Ohio subsequently fled from you in terror.

That may, of course, have had something to do with the simple fact that nobody, nobody at all, has ever been able to give us any scientific theory of ID or explain how such could be tested using the scientific method.

WHY you believe it in 5 simple statements, i.e. the top 5 reasons for your belief.

Evolution is no more “a belief” than is gravity or the mass of an electron. (shrug)

Comment #97028

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 8:23 PM (e)

So what’s the polite term to call you folks at PT if not Darwinists?

How about “the people who kicked ID ass in Dover”?

Comment #97029

Posted by Salvador T. Cordova on April 17, 2006 8:26 PM (e)

Syntax Error: mismatched tag 'url'

Comment #97031

Posted by Don Baccus on April 17, 2006 8:32 PM (e)

harold wrote:

Sal seems to make the valid point that it would take far longer (with current computers, that is) to crack such a long password, than the scientifically predicted lifespan of the sun or indeed, the universe, in any meaningful sense, for an algorhythm to crack such a password.

The false premise here is that people chose random passwords. They don’t. Even when forced to include digits or non-alphanumerics in their passwords, they frequently choose to base their choice on words. Perhaps substituting “1” for “l”, etc.

If people chose random passwords, then even 6 to 8 character passwords would be very time-consuming to crack. As it is, dictionary attacks are still fruitful, as there are far fewer than (say) 26^8 words in the average person’s vocabulary, even including obvious non-letter substitutions.

The VAX/VMS password attack I mentioned earlier made a linear algorithm possible. In this case, a program could figure out each letter of the password one at a time. In other words, rather than query “is this password correct” the security flaw made it possible to ask “is the first letter ‘a’? ‘b’?” and after getting a “yes” answer, ask “is ‘a’ the password?”. If you got a “no”, move to the second, determine it in linear time, then ask if that’s the correct password. If not, continue the process until you get a “yes” answer to the entire password.

So the false premise of the naive probabilistic argument in this case is that you can only get yes/no answers to the whole password. Unless you know this to be true for a fact, you shouldn’t assume it.

harold wrote:

However, Sal is being very, very evasive. None of this has anything to do with the theory of evolution; it’s just an irrelevant discussion of passwords and computer programs. In fact, the real point of my post was that this analogy, used by Sal, reveals a profound misunderstanding of the theory of evolution, as well as of genetics and molecular biology.

The only usefulness of his password analogy is to show that when trying to calculate the probability of an event you can’t just make assumptions, you have to have data to back up those assumptions. Probabilities used to “prove” specified complexity or whatever suffer from false premises in the same way, as has been detailed by many people on many occasions.

Comment #97032

Posted by Salvador T. Cordova on April 17, 2006 8:32 PM (e)

Don boasted:

As someone who wrote compilers professionally for nearly three decades, and who has a rich background in formal language theory, you make me laugh.

Please give us an example in each category so we can laugh at you some more.

You may now eat crow.

IEEE: Two operative concepts for the post-genomic era : the “mémoire vive” of the cell and a molecular algebra

Basic Gene Grammars

David Searles and the Linguistics of DNA

Stochastic Grammars and Graph Grammars

Oh, and last but not least, a somewhat speculative, but interestring treatment of the issue was given in Godel, Escher, Bach

Comment #97034

Posted by Don Baccus on April 17, 2006 8:37 PM (e)

Uh, Sal, I didn’t say that grammars can’t be used to describe genetic material. Of course they can. Any string can be trivially generated by a grammar that says “generate this string”.

Read your claims again … no wonder you don’t comprehend what others say, you’re not even aware of what YOU say.

Comment #97035

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 8:37 PM (e)

Hey Sal, why don’t we see the designer in operation today?

Is God dead?

Comment #97036

Posted by Salvador T. Cordova on April 17, 2006 8:58 PM (e)

Don said:

Uh, Sal, I didn’t say that grammars can’t be used to describe genetic material. Of course they can. Any string can be trivially generated by a grammar that says “generate this string”.

Read your claims again … no wonder you don’t comprehend what others say, you’re not even aware of what YOU say.

You apparently didn’t even read the first paper, if you did, you didn’t pick up on some important points. So perhaps spoon feeding it to your CRT will ensure you won’t miss it.

The architecture of informatics systems is based on two main concepts: memory and programming languages. The analogy that will be developed between living systems and informatics systems is based on these concepts. The cell working-space memory is the physicochemical space in which the processes take place. The elements of the active memory or main memory are: circulating ligands, membrane receptors, cytosol molecules and transcription factors in the nucleus, which are capable of catalytic and regulatory action. They can be seen as a set of variables and positioned pointers in the volatile memory of the cell. These elements of cell memory do not pre-exist to their value, i.e. to the variable that they represent. However, these variables may then represent several values during the process, for instance activated or inactivated. These variables may be endogenous or exogenous, local or global.

In fact, the processes are observable when they are taking place in the intra- and inter-cellular spaces which play the role of active memory due to their capacity to maintain and transmit information. We are attempting to learn the underlying language for this program, including syntax, semantics and alphabet.

This molecular algebra was first developed to describe the series of operations: “Biological Binding Operators” (Bentolila 1996) that leads to the expression /repression of a gene in a cell. In fact the two main mechanisms are Repressible Systems and Activable Systems, they are symmetric : the repressor or the activator is currently expressed, and a co-factor acts as an external signal who turn off or on the mecanism. This grammar was applied to 4 examples : i) Lactose operon, an instance of a repressible inducible system, moreover a repressible system may be activated. ii) The regulation of metallothionein, an instance of an alternative activable system. iii) Yeast galactose metabolism, a combination of repressible and activable mechanisms. iiii) Tryptophan operon, an instance of a repressible system. This grammar has now been expanded in two directions of signal pathway : i) to the chain reaction which leads to the transmission of a signal destined to activate (or inactivate) a metabolic pathway for the delivery of necessary substances; ii) to the integration of the various types of inter-cellular activities in a multicellular organism which is mainly performed by the nervous system, the endocrine system and the immune system. This first grammar was context-sensitive because it requires a Turing Machine which is capable of reading and writing symbols. If we suppose that the semantics of biological binding operators is already implemented (using a database language or any other functional implementation of the compiler), it is sufficient to write a context-free grammar. Therefore an other extension of the present paper is the description of the whole machine including a memory device. Indeed, the implementation of the notion of variable as utilized by the logic of predicates and context-free grammar implies elements of memory…..

1/ Cell main memory or working-space memory, 2/
DNA database as storage memory, 3/ Regulation mechanisms as a molecular algebra (language : syntax, semantics and alphabet), 4/ A minimal set of genes as the operating system, 5/ Biochimicals as hardware, 6/ Attempt at reprogramming life 7/ Input-output cell management.

And from Denton, Evolution a Theory in Crisis

We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly process involving the principle of prefabrication and modular construction.

In fact so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.

There, there, Don, get the picture now. Still want to pretend I have not basis for my claims? What part of the above don’t you understand?

Comment #97038

Posted by Kenneth Baggaley on April 17, 2006 9:04 PM (e)

What 3 books should an interested person read?

There have been comments here about what afDave and Sal should ‘look up’. TalkOrigins (a great site, IMHO) is often referenced. And I know some individuals simply choose not to learn, and for them any references made will be ignored.

But say someone with a fundamentalist/evangelical background decided, in earnest, to read about Evolution for real. Given the rapid advance of science, what 3 books would PT regulars recommend?

Assume the adult individual is 1.) sincere, 2.) reasonably intelligent, and 3.)has very little science background. Rather than a website, what 3 books would PT regulars suggest he/she read?

Assume also you don’t want to attack Christianity or religion, other than the overt fallacy of abject Biblical literalism (a lost cause in any reality-based scientific endeavor).

I’ve had this discussion with several folks of various backgrounds. I know what I’d recommend for folks trapped in ‘literal’ Bible mode. But for biology/genetics/evolution, apart from referring to TO and college classes, I wouldn’t know the best books to recommend.

In the opinion of PT regulars, what 3 books are best today?

Comment #97039

Posted by Freelurker on April 17, 2006 9:07 PM (e)

…why don’t we see the designer in operation today?

Speaking for myself, I see the evidence for a telic universe most every day, because I have a thermos bottle. When I put hot drinks in it, it keeps them hot. But when I put cold drinks in it, it keeps them cold. Somehow, it just knows.

It’s probably all related to the 2nd Law of Thermodynamics.

Comment #97041

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 9:35 PM (e)

Assume the adult individual is 1.) sincere, 2.) reasonably intelligent, and 3.)has very little science background. Rather than a website, what 3 books would PT regulars suggest he/she read?

Assume also you don’t want to attack Christianity or religion, other than the overt fallacy of abject Biblical literalism (a lost cause in any reality-based scientific endeavor).

The three I’d recommend?

“Finding Darwin’s God”, by Kenneth Miller.

“What Evolution Is”, by Ernst Mayr.

“The Demon-Haunted World” by Carl Sagan.

Comment #97043

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 9:44 PM (e)

And from Denton, Evolution a Theory in Crisis

Speaking of Denton, Sal, would you mind explaining to everyone (1) why Denton’s very next book explained why his previous one was full of crap, and (2) why Denton asked to be removed from Discovery Institute’s masthead?

And while you’re at it, Sal, how about explaining to everyone why, when the Templeton folks offered to fund any scientific investigations that DI was willing to undertake, DI was unable to present any?

Why *does* DI get funded only by Howie Ahmanson and a handful of other fundamentalist extremist nutters, Sal? Isn’t DI supposed to be all about SCIENCE and not about religion?

Or is DI (like you) just lying to us about that, Sal?

Comment #97044

Posted by Anton Mates on April 17, 2006 9:48 PM (e)

Kenneth Baggaley wrote:

But say someone with a fundamentalist/evangelical background decided, in earnest, to read about Evolution for real. Given the rapid advance of science, what 3 books would PT regulars recommend?

Rapid advance of science or not, I’d recommend the Origin of Species, maybe 6th edition. Obviously it’s outdated in all sorts of respects, but it’s extremely lucid, written for the layman, and necessarily intended to explain the evidence for evolution to someone 150 years behind our current level of knowledge. It has the side effect of demonstrating that Darwin a) was not in fact advocating Satanism and b) has been horribly quote-mined by creationists.

Perhaps also Campbell, Reece & Mitchell’s Biology textbook. Of course many people wouldn’t want to read it cover to cover, but much of the post-Darwin evidence for evolution would be difficult to appreciate without such a reference. It has nice sections on population genetics and a detailed look at the evolutionary tree.

I’m not sure what else…a paleontology primer of some sort? One of Gould’s essay collections?

Comment #97045

Posted by Anton Mates on April 17, 2006 9:52 PM (e)

Oh, and another vote for “The Demon-Haunted World.” Sagan’s “The Dragons of Eden” is more directly concerned with evolution, but also a bit outdated. Still, for the fundamentalist or ex-fundamentalist who’s wondering about the mental status of humanity vs. the rest of creation, it’s a valuable read.

Comment #97046

Posted by 'Rev Dr' Lenny Flank on April 17, 2006 9:55 PM (e)

I think Zimmer’s “Evolution” would have to find a place in the bookshelf, too.

Comment #97047

Posted by Glen Davidson on April 17, 2006 10:05 PM (e)

Read your claims again … no wonder you don’t comprehend what others say, you’re not even aware of what YOU say.

Sal’s latest only punctuates what Don wrote above:

We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly process involving the principle of prefabrication and modular construction.

In fact so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.

Sal has the perpetual incapacity to understand that we know the ID claims, and find them to be ridiculous based on our knowledge of biology. Nothing in biology is like what humans make, until one reduces the components down to an unreasonable level. So Denton rattles on about the “analogues” of our machines within cells–the fact is that as a discipline biology, including evolutionary biology, is busy studying how different cells are from our own machines. For one thing, biology tends not to compartmentalize what we consider to be “functions”, and for another thing, biology is highly derivative in a way that human machines are not.

Sal conveniently does not understand these things, and accepts the absurd analogies that Denton makes between biology and machines. There is, of course, value in the reductionism that Denton engages in, and indeed, I recall reading fairly closely an article in Nature which dealt with the syntax and semantics of DNA. But of course this is only a model of DNA coding which is applied for our convenience, and not because we ever once invented anything like DNA informatics. This is why I later qualified my original question:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

The qualification was this (it should be refined, but my point is that the complexity of the systems and/or organs must be included):

Btw, quite obviously my question is about the totality of design, not the overlap between design and evolution which is possible in some cases. Tacitly you admit that you have not achieved this starting point essential to ID every time that you fail to adequately answer the question.

I added that because I know how reductively IDists typically think, reducing biological systems down to concepts, along with the reduction of human productions down to concepts, then equating the two concepts. There is nothing wrong with the first question when it is posed to people who understand biology, but for IDists it opens up opportunities for their faulty analogies and their lack of concern for the actual complexity of evolved structures.

One thing that does amaze me about IDists is, certainly, their lack of regard for real complexity, as they reduce organisms down to conceptions that fit their limited knowledge. It’s all just machines, “artificial languages”, bits and pieces here and there made by the ideal counterpart of themselves, the “great designer”. The kinds of complexity effected by evolution bypass them as they suppose that DNA is simply an artificial language system, and not a highly complex interplay of physics, chemistry, stochastic processes, evolutionarily produced redundancies, apparently evolved mechanisms for protection and correction of broken and miscopied DNA, direct templating of RNA, and widely evident relatedness found across the taxa–to mention just some of the complexity.

We see how simplistically Sal thinks about biology when he reduces DNA’s complexities down to one conceptual aspect, instead of concerning himself with the biology, physics, chemistry, and evolution of DNA, all in order to make the ludicrous claim that his reductive simplicity shows that intelligence makes something like what we see in organisms. It is his misunderstanding of the very limited extent to which something (that is not highly reduced) biological is “like” something that humans have made that underlies his conceptual difficulties with evolution vs. ID.

Sal hasn’t come close to showing that anything made by humans is actually “like” what exists in biology, except via an absurd reductionism. It’s odd that IDCists like to present biology as being so very complex “that it couldn’t evolve”, yet they are forced to reduce biology conceptually down to the simplicity of designed entities in order to produce their faulty analogies with “complex designs”.

You’d think that Sal might recognize that lurking beneath my question was the fact that life in fact is rather more complex than anything that we have designed. This is the high absurdity underlying ID, that no intelligent “designer” has ever designed anything nearly as complex as the human body, yet they use analogies with designed objects to argue that “life must be designed”. There are many other absurdities, including their apparent belief that the “designer” must have used only evolutionary algorithms to “design” (actually, they probably don’t deal with the evolutionary evidence in DNA at all in this way, but we may for convenience infer it when we try to give ID some coherence), but the analogy with human designs for something quite unlike anything humans have ever made up to this point is absurdity enough. They have no candidates whatsoever for an “intelligent designer” which could handle the complexity of biology, let alone any that might account for the derivative nature of biology’s information.

It’s not surprising that Sal would “answer” a question about whether or not any intelligent designers have made anything like the forms and “machines” that we see in biology with entirely irrelevant “analogies” between human creations and the very different biological adaptations. His lack of biological knowledge again prevents him from even understanding a relevant question made from within a biological context, and he again resorts to distorting simplifications and reductions to conceptually change the biological into the equivalent of very different designed structures. This is the only meaningful fact that appears with virtually every post by Sal, while he never manages to learn anything from those who understand biology better than he does.

Glen D
http:tinyurl.com/b8ykm

Comment #97048

Posted by PvM on April 17, 2006 10:26 PM (e)

The only usefulness of his password analogy is to show that when trying to calculate the probability of an event you can’t just make assumptions, you have to have data to back up those assumptions. Probabilities used to “prove” specified complexity or whatever suffer from false premises in the same way, as has been detailed by many people on many occasions.

Hear hear. ID activists often fall victim of their own ‘cleverness’. Remember Behe/Snoke or Dembski who used unreasonable scenarios to ‘model evolution’ to show that evolution would be impossible. Of course, anyone can inflate the probabilites to make something impossible, scientists however make things more probable by doing hard work, proposing hypotheses and perform countless testing.

ID is more the lazy type…

Comment #97054

Posted by Freelurker on April 17, 2006 10:52 PM (e)

Glen D said:

This is the only meaningful fact that appears with virtually every post by Sal, while he never manages to learn anything from those who understand biology better than he does.

Salvador made it clear from the beginning that he had no interest in counter-arguments.

Salvador wrote:

Ungresigtered wrote:
Sal must not be aware of the reverse ordination refutation.

I am not aware of it. If you can present where the refutation can be found, that would be helpful to the people here at PT trying to combat my claims.
So, for their sake, not mine, please provide more information.

He completely dismissed an argument of which he had never heard.

Comment #97058

Posted by Freelurker on April 17, 2006 11:54 PM (e)

But thank you, Glen D and the rest, for attempting to converse with Salvador. At least you are educating some lurkers like me.

Comment #97059

Posted by dons on April 17, 2006 11:59 PM (e)

I’m pretty gassed that Salvador used the work “architected”. Wierding the language like that might gall some people but it really sexy’s things for me. It’s funny enough when people circular their logic, but verbing one’s nouns just ices it.

Comment #97060

Posted by fnxtr on April 18, 2006 12:04 AM (e)

My questions to the ID camp are the following:

If ID is not about religion, and

since the theory of evolution has been so successful, predictive, and, most importantly, useful for the past 150 years or so, then

why spend so much time and effort to undermine the current theory, without ever offering something equally effective, predictive, and, most importantly, useful???

What, exactly, is the problem with current evolutionary theory, that you believe can be fixed or improved by “Poof!”???

How does “Poof!” help us understand and predict the world, currently and historically, better than the prevailing theory???

As the giant children said in H.G.Wells’ Food Of The Gods: “What’s it all for?”

fnxtr

Comment #97070

Posted by Frank J on April 18, 2006 5:18 AM (e)

fnxtr wrote:

evolution has been so successful, predictive, and, most importantly, useful for the past 150 years or so, then

why spend so much time and effort to undermine the current theory, without ever offering something equally effective, predictive, and, most importantly, useful???

Not just not “offering something equally effective…” but increasingly covering up the flaws and contradictions in the few pathetic attempts to do so.

Let me tell you what no IDer, and few fellow critics of ID will: ID (or neo-creationism, or designer-free phony critical analysis, whatever you want to call it) is a game. The chief goal of the game is to get critics to either defend evolution, or argue against design in general. That neatly deflects the argument away from the fact that the anti-evolutionist has no clue as to what takes place other than “macroevolution,” let alone how to support it. Unfortunately, IDers usually win the game because they see are very mindful of the target audience and how to manipulate them, while too many critics get trapped into an “us vs. the ‘creationists’” mentality.

Comment #97071

Posted by Michael J on April 18, 2006 5:34 AM (e)

For any Aussies out there. SBS has a show by Horizon on ID. It has just started

Comment #97072

Posted by KL on April 18, 2006 6:21 AM (e)

“I’m not sure what else…a paleontology primer of some sort? One of Gould’s essay collections?”

A nice read is Earth Time by Douglas Palmer.

Comment #97078

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 7:14 AM (e)

Let me tell you what no IDer, and few fellow critics of ID will: ID (or neo-creationism, or designer-free phony critical analysis, whatever you want to call it) is a game. The chief goal of the game is to get critics to either defend evolution, or argue against design in general. That neatly deflects the argument away from the fact that the anti-evolutionist has no clue as to what takes place other than “macroevolution,” let alone how to support it. Unfortunately, IDers usually win the game because they see are very mindful of the target audience and how to manipulate them, while too many critics get trapped into an “us vs. the ‘creationists’” mentality.

Indeed, the primary aim of creationism/ID has always been simply to poke as many holes as they think they can in evolutionary theory, while at the same time carefully and deliberately avoiding the necessity of presenting, defining or testing anything of their own. After all, they CANNOT present anything of their own, since all they have is religious doctrine, and that would be instant death in a courtroom.

It’s why there is not, has never been, and never will be, any scientific theory of ID or creationism.

Comment #97083

Posted by AV on April 18, 2006 8:16 AM (e)

For any Aussies out there. SBS has a show by Horizon on ID. It has just started

Indeed. Details here.

Comment #97087

Posted by fnxtr on April 18, 2006 9:37 AM (e)

Lenny wrote:

It’s why there is not, has never been, and never will be, any scientific theory of ID or creationism.

Lenny, am I coming across as incredibly dense?

I knew what the answer from the scientific community would be. I want the IDiots to defend themselves. I know they can’t, I just wanted to see them try.

Comment #97091

Posted by Don Baccus on April 18, 2006 10:09 AM (e)

PvM wrote:

Hear hear. ID activists often fall victim of their own ‘cleverness’. Remember Behe/Snoke or Dembski who used unreasonable scenarios to ‘model evolution’ to show that evolution would be impossible.

What really annoys me is that engineers, computer scientists and the like should be more aware of the need to verify the correctness of one’s assumptions than just about anyone. They build systems that in many cases kill or otherwise harm people when they fail.

I’ve mentioned two different approaches to quickly breaking passwords that were surprising in each case to professional software engineers, who had failed to think creatively (the VAX/VMS example wasn’t due to a bug, strictly speaking, and dictionary attacks are based on our knowledge of human behavior, not engineering).

The space shuttle program has had two spectacularly fatal accidents based on faulty assumptions leading to a belief that certain kinds of failures were extremely unlikely to cause problems.

The airplane industry’s full of examples, frequently fatal examples.

And the original application of fault-tree analysis (a probabilistic approach) to nuclear power plants made many assumptions that turned out to be way off the mark.

Yet a large percentage of IDers who claim to know more about biology than biologists are engineers who parrot the most absurd probabilistic arguments based on obviously false assumptions.

They should know better. They’re trained to know better.

Comment #97094

Posted by Rilke's Granddaughter on April 18, 2006 10:44 AM (e)

Perhaps you are right. But the problem is that Salvador isn’t an engineer: he’s a fundie with some engineering background. There’s a major difference, and it produces Salvador’s most characteristic technique: he long ago abandoned any actual understanding or interest in science in favor of using scientific language and ‘tricks’ to create creationist arguments.

And frankly, I don’t care what his religious beliefs are (unlike Lenny); I just object to his gross ignorance of science and logic, and his perversion of that ignorance in service of his religious beliefs.

Comment #97102

Posted by harold on April 18, 2006 11:11 AM (e)

Don Bacchus -

I agree. It’s unprofessional for engineers to parrot transparently wrong pseudoscience. Their training may not be in evolutionary biology, but it should be good enough to make ID transparet. Why do some do it?

1) Politics. Some people have a cultish attachment to what they perceive as a “conservative movement” (this is NOT intended as a general swipe at “conservatives”). The necessary implicit position for this movement is “pro-ID” (and “anti-global warming” and even “anti-HIV causes AIDS” when they can get away with it). They will argue these positions no matter what the facts and no matter what their training.

2) Ego. Older engineers, who were trained before the molecular biology era, may bolster big fragile egos with the idea that they are “smarter than biologists”. (They are presumably unaware of population genetics and so on, the many highly mathematical approaches of the pre-molecular era.) The silly idea that all biomedical scientists (many of whom are cross-trained in engineering, math, or the physcial sciences) could be wrong about an elementary idea has appeal to the over-inflated yet defensive ego.

3) Religion? All “movement conservatives” proclaim themselves to be morally outraged followers of some strict religious philosophy (usually Protestant fundamentalism, sometimes conservative Catholocism or Judaism). However, this needs to be taken with a grain of salt. Often, at least if private behavior is an indication, the authoritarian political fantasies come first and the “religion” is adopted as an enabling device. Having said that, there may be some engineers who are genuinely tormented by spiritual doubts, and who, instead of taking a constructive path, respond by self-destructively attacking science.

I would venture to predict that any ID-loving engineer has at least two of these motivations.

Comment #97103

Posted by Frank J on April 18, 2006 11:12 AM (e)

'Rev Dr' Lenny Flank wrote:

After all, they CANNOT present anything of their own, since all they have is religious doctrine, and that would be instant death in a courtroom.

Even if they privately think that the “religious doctrine” is bogus (but necessary for “the masses”), what gives them the edge in the court of public opinion, if ironically not in real courtrooms, is that they never stop thinking like lawyers. Critics tend to think like teachers, constantly reminding the “jury” to look at the cold and dry evidence, while the “lawyers” dazzle them with a misleading, but persuasive speech.

Comment #97105

Posted by harold on April 18, 2006 11:23 AM (e)

Afdave -

You asked for a five step description of the theory of evolution. That may be doable, in a severely superficial yet relatively accurate way. But first I need to establish where you’re starting from. I’m going to list some key terms, and you tell me what you think they mean. “I don’t know” is a perfectly acceptable answer, but be as complete as possible. I can’t explain the theory of evolution, even in a very succinct and compressed way, without using at least some of these terms, and the more of them you understand the better. Some of them may look deceptively familiar, but be careful. Don’t copy definitions from some internet source, either. I need to know how much you actually understand. This isn’t a “test”, it’s establishing where you are. Ready?

Cell, eukaryote, prokaryote, organelle, chromosome, unicellular, multicellular, haploid, diploid, polyploid, germ cell, somatic cell, germline mutation, somatic mutation, allele, gene, DNA, RNA, protein, amino acid, genetic code, enzyme. We may run into some others along the way.

You claim to be an engineer, so I’ll assume familiarity with basic chemistry and physics.

However, I suspect that either a) you’re DaveScot in disguise or b) you aren’t really an engineer. Forgive me if I’m wrong. Am I?

Comment #97108

Posted by improvius on April 18, 2006 11:46 AM (e)

harold -

You left out “money”. How much money was Behe making from book sales and speaking engagements before he wrote Black Box?

Comment #97110

Posted by Don Baccus on April 18, 2006 12:02 PM (e)

Rilke's Granddaughter wrote:

But the problem is that Salvador isn’t an engineer: he’s a fundie with some engineering background.

Oh, I wasn’t thinking of Salvador in particular, but making a more general observation.

Salvador’s properly described as being “ethically challenged”, I think :)

Comment #97111

Posted by Salvador T. Cordova on April 18, 2006 12:05 PM (e)

Flank asked:

Is God dead?

I don’t think so. You may find out some day, so it may be a moot point then.

I don’t know what your beliefs are Reverend Flank, but Panda’s thumb has a lot of Atheists. There are of course theists here like PvM, and for that I am grateful.

Seems you all have a hard time getting the message out. Ken Miller points where he thinks much problems lie with promoting Darwinism (not that it is necessarily my position, but since he is so reverenced here, I figured I’d quote mine him):

…much of the problem lies with atheists…

Ken Miller, Finding Darwin’s God

Ouch! Awfully nasty of him to be taking a swipe at atheists. Shame on the guy.

And here is Reverend Ken Miller admonishing the faithful. A YEC could hardly say it better:

….
Genesis 1:26 tells us something very different. We are assured that our efforts to understand nature are valid, because our hearts and minds are fashioned in the likeness of God. Our senses, the ultimate sources of scientific knowledge, are imperfect, but they are not deceitful. Nature does not give up her secrets easily, and our first explanations are not always correct. Nonetheless, if we persist, if we apply the tools of reason and the power of the human mind, the world will yield its secrets; and so it has. The God in whom believers put their trust may surpass our understanding, but the assurance that we are made in His image means that He and His world are accessible to our best efforts…..

grace is as real as the presence of God Himself….I would argue that any scientist who believes in God possesses the faith that we were given our unique imaginative powers not only to find God, but also to discover as much of His universe as we could. In other words, to a religious person, science can be a pathway towards God, not away from Him, an additional and sometimes even an amzing source of grace.

Ken Miller, Finding Darwin’s God

Comment #97113

Posted by Rilke's Granddaughter on April 18, 2006 12:17 PM (e)

Don wrote:

Salvador’s properly described as being “ethically challenged”, I think :)

Yes. He lies in the service of God. Why fundies insist on violating their own moral code baffles me.

Comment #97116

Posted by Moses on April 18, 2006 12:26 PM (e)

Comment #97087

Posted by fnxtr on April 18, 2006 09:37 AM (e)

Lenny wrote:

It’s why there is not, has never been, and never will be, any scientific theory of ID or creationism.

Lenny, am I coming across as incredibly dense?

I knew what the answer from the scientific community would be. I want the IDiots to defend themselves. I know they can’t, I just wanted to see them try.

Not only “can’t” but “won’t.” Rather: attack, quote-mine, avoid, befuddle and obfuscate.

Comment #97117

Posted by harold on April 18, 2006 12:36 PM (e)

Salvador Cordova -

Lenny Flank recommended a popular book by Ken Miller. Everyone knows that Ken Miller is a religious Catholic and that part of his public personna is the defense of the theory of evolution from that perspective. Even if they didn’t, the title of the book kind of gives it away.

Yet bizarrely, you seem to think that you’re scoring points on Lenny Flank by finding something religious in the book.

For the record, Miller would never include religious writing in his technical publications. That book is intended for lay people. It’s especially intended for religious lay people, obviously, but works as a good lay explanation of evolution for anyone can handle the presence of a few religious parts.

Perhaps you can read the book, realize that the theory of evolution has nothing to do with religion or politics, learn something, at least at a layperson’s level, about the theory of evolution, and drop all this ID nonsense.

Comment #97118

Posted by harold on April 18, 2006 12:56 PM (e)

Improvius -

“You left out “money”. How much money was Behe making from book sales and speaking engagements before he wrote Black Box?”

Good point, but I was talking about the parrots. How much money does DaveScot make from ID?

Comment #97119

Posted by Tyrannosaurus on April 18, 2006 1:07 PM (e)

You see every time I read or see IDiots basking on the “mathematical evidence” for ID and against ToE, I remind myself of the old story about how it was mathematically proved that bumble bees cannot fly!!!!
Dumbski is doing the same argument; using pseudo mathematical jargon to obfuscate arguments that he perfectly well know are baseless. At least it can give these arguments to the “faithfull” with a scientifiqy-sounding cover.
Facts have no place in the make believe world of ID. Just wave the magic wand of mathematics and viola those pesky facts disappear.

Comment #97120

Posted by ivy privy on April 18, 2006 1:07 PM (e)

Afdave -
You asked for a five step description of the theory of evolution….

Hmmm, that sounds like “Dave Hawkins” from this thread.

Claims Air Force connnection (=”af”).
Asks for top 5 list of evidence.
Is an engineer.

Comment #97121

Posted by Raging Bee on April 18, 2006 1:10 PM (e)

Nice bit of quote-mining, Sal. Let’s look at a few sentences from those paragraphs, shall we?

Nature does not give up her secrets easily, and our first explanations are not always correct.

I couldn’t have said it better myself. So why are so many creationists clinging so desperately, and so dishonestly, to their “first explanation” of the origin of the species we see today?

…I would argue that any scientist who believes in God possesses the faith that we were given our unique imaginative powers not only to find God, but also to discover as much of His universe as we could.

Notice that, in these paragraphs at least, the author doesn’t actually say that science can prove the existence of God, or that God intervened at this or that moment in the Earth’s history – we still have to posess faith. The author also says nothing about actually closing off any avenue of scientific inquiry, as the “cdesign proponentsists” have explicitly called on us to do (i.e., by “inferring design” while ruling out all discussion about the “designer” him/her/itself). Quite the contrary – we’re supposed to ask questions and “discover as much of His universe as we could.” Which, in fact, is what the Catholic and Lutheran hierarchies have endorsed as well, while explicitly rejecting creationism and ID: honest science, not just saying “Goddidit so stop asking questions!”

Oh, and check this out: the call to “discover as much of His universe as we could” rather strongly implies that the answers aren’t all prepackaged in the Bible, doesn’t it?

Comment #97122

Posted by improvius on April 18, 2006 1:18 PM (e)

Good point, but I was talking about the parrots. How much money does DaveScot make from ID?

Sorry, I missed that qualification. But now that I think about it, this could seem like a viable career path to some people. You’ll never go poor telling people what they want to hear.

Comment #97123

Posted by Salvador T. Cordova on April 18, 2006 1:24 PM (e)

Don wrote:

The false premise here is that people chose random passwords. They don’t.

No. The even more false premise by Don was that the passwords were created by peoples choices. Some passwords, particularly long ones are generated on behalf of people by a machine in certain applications (such as an enabling key for a software upgrade).

Any way, Don is focusing on peripheral issues. The password analogy was an illustration to help readers understand that the problem IC poses for evolution is the exponentially rising difficulty of evolution for finding certain functional structures which require several well matched interacting parts. Note, I didn’t say it was impossible to create IC, but I’m simply pointing out the challenges it poses, and they are substantial.

harold wrote:
None of this has anything to do with the theory of evolution; it’s just an irrelevant discussion of passwords and computer programs. In fact, the real point of my post was that this analogy, used by Sal, reveals a profound misunderstanding of the theory of evolution, as well as of genetics and molecular biology.

No, I do understand what the theory of evolution claims, and I’m challenging that empirical reality and serious theoretical examination shows there are some serious flaws in it’s claims. Evolutionary theory is justified through affirmation of the consequent and circular reasoning. But by and large, “nothing in evolution makes sense in the light of biology.”

For starters, it assumes the some of the very things it claims to prove, namely, that most large scale biological innovation can be reached through step-wise incremental improvements. IC is a serious barrier to that, and password illustration was to help the reader see the way IDists view certain biological structures like the Flagellum or a biological Turing Machine.

To say that evolutionary theory doesn’t view the world a certain way is really an admission that it may not be rooted in reality.

The issue of the evolvability in stepwise fashion of every known protein is still open, and the growth of knowledge in theses areas ain’t promising for Darwinian evolution.

Comment #97126

Posted by Don Baccus on April 18, 2006 1:28 PM (e)

Sal wrote:

No. The even more false premise by Don was that the passwords were created by peoples choices. Some passwords, particularly long ones are generated on behalf of people by a machine in certain applications (such as an enabling key for a software upgrade)

I made no premise, false or true.

My point is that you can’t compute probabilities based on unwarranted assumptions not supported by data. In your computation you ASSUMED passwords made of letters chosen at random. In many case (I never said all cases) this assumption is false. Just as IDers do when computing the probability of various evolutionary events taking place.

You can’t possibly be as dumb as this, can you, Sal?

Comment #97127

Posted by Raging Bee on April 18, 2006 1:34 PM (e)

The issue of the evolvability in stepwise fashion of every known protein is still open, and the growth of knowledge in theses areas ain’t promising for Darwinian evolution.

Really, Sal? Are you implying that there’s a growing number of peer-reviewed papers (which is, I’m guessing, where such “knowledge” can be found) citing observations and/or experiments refuting a basic tenet of the theory of evolution? Pray tell us where we can find such papers!

Comment #97129

Posted by wamba on April 18, 2006 1:44 PM (e)

The issue of the evolvability in stepwise fashion of every known protein is still open, and the growth of knowledge in theses areas ain’t promising for Darwinian evolution.

That’s right folks, Sal demands not just that natural selection be proven in principle, but that every step-by-step pathway in the history of life on this planet be provided in detail. That’s a pretty steep demand.

Meanwhile, here’s a complete list of details elucidated by ID “theory”:

Comment #97130

Posted by Don Baccus on April 18, 2006 1:51 PM (e)

HeWhoShootsSelfInFoot wrote:

The issue of the evolvability in stepwise fashion…

Heh. Hey, Sal, it’s this step-by-step series of events that blows the naive ID calculations of probability to bits in the first place!

You’ve just admitted that the assumption that everything comes together poof! at random and is therefore improbable beyond belief is a false one.

Heh. Heh. Heh.

Comment #97131

Posted by Don Baccus on April 18, 2006 2:00 PM (e)

Sal wrote:

The password analogy was an illustration to help readers understand that the problem IC poses for evolution is the exponentially rising difficulty of evolution for finding certain functional structures which require several well matched interacting parts.

Still not getting it, are you, Sal? The “exponentially rising difficulty of evolution” you mention is based on unsubstantiated assumptions, just as your password analogy did.

Let’s try a different tack …

State your assumptions that underpin the computed probability of some particular aspect of evolution rising exponentially and then give us the real-world observational data that backs those assumptions.

Without doing so you’re just handwaving, just as you did in your password example.

Comment #97133

Posted by Steverino on April 18, 2006 2:43 PM (e)

Sal,

Irreducible Complexity is not a valid scientific concept. AT BEST…It’s a concocted assumption in an effort to give credence to a pseudo-science.

If it were truly a valid scientific concept, it would have useful applications in other areas of science…but, alas….

Comment #97134

Posted by Rilke's Granddaughter on April 18, 2006 2:44 PM (e)

Sal wrote:

No. The even more false premise by Don was that the passwords were created by peoples choices. Some passwords, particularly long ones are generated on behalf of people by a machine in certain applications (such as an enabling key for a software upgrade).

The usual song-n’ dance from Sal. Some were, but some weren’t. Don’t pretend to knowledge you don’t have Sal, it makes you look like an idiot. And we’ve enough of those around here.

Any way, Don is focusing on peripheral issues.

Then why are you wasting so much time replying to it, when you’ve not offered anything substantive on the ID topic? ID has no theory, no research, no scientific credibility. It is gaining no traction in the scientific community, and it’s a laughing stock among those with even a smattering of knowledge of biology. Given all that, you waste your time on internet forums inaccurately rebutting arguments about passwords? A bit OCD, are we?

The password analogy was an illustration to help readers understand that the problem IC poses for evolution is the exponentially rising difficulty of evolution for finding certain functional structures which require several well matched interacting parts.

But evolution has no problems whatever with IC. Behe even says as much in D BB.

Note, I didn’t say it was impossible to create IC, but I’m simply pointing out the challenges it poses, and they are substantial.

Detail them. Use math. Be specific for a change.

Harold wrote:

None of this has anything to do with the theory of evolution; it’s just an irrelevant discussion of passwords and computer programs. In fact, the real point of my post was that this analogy, used by Sal, reveals a profound misunderstanding of the theory of evolution, as well as of genetics and molecular biology.

Sal wrote:

No, I do understand what the theory of evolution claims, and I’m challenging that empirical reality and serious theoretical examination shows there are some serious flaws in it’s claims.

But to do that you’d have to actually show those flaws. And you haven’t. And based on the stuff you post on ARN, you’ve no clue what evolution actually says.

Evolutionary theory is justified through affirmation of the consequent and circular reasoning.

As I said - you don’t understand evolution in the slightest. What ‘circular reasoning’ for example?

But by and large, “nothing in evolution makes sense in the light of biology.”

Overblown rhetoric is the last refuge of the intellectually bankrupt.

For starters, it assumes the some of the very things it claims to prove, namely, that most large scale biological innovation can be reached through step-wise incremental improvements.

Nope. It doesn’t assume this, it concludes this. Sal, you must learn to reason. I realize that you didn’t pick this up in your undergraduate work; see if you can squeeze in a class in basic logic for your doctorate.

IC is a serious barrier to that,

How?

and password illustration was to help the reader see the way IDists view certain biological structures like the Flagellum or a biological Turing Machine.

How? There are no biological Turing Machines. As usual, you’ve picked up some clever idea and tried to use it as an argument - without realizing that it’s meaningless.

To say that evolutionary theory doesn’t view the world a certain way is really an admission that it may not be rooted in reality.

This is an apparently meaningless statement. Perhaps you should translate it.

The issue of the evolvability in stepwise fashion of every known protein is still open, and the growth of knowledge in theses areas ain’t promising for Darwinian evolution.

What a good thing that we’ve moved beyond Darwin, then? And what a good thing that we’ve got 140 years of research to indicate that you’re wrong.

Your theological bias makes you look like a fool, Sal - especially when you mangle science in the name of your faith.

Don’t lie for God - it just turns people off.

Comment #97135

Posted by Rilke's Granddaughter on April 18, 2006 2:52 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #97138

Posted by fnxtr on April 18, 2006 3:12 PM (e)

Here’s an interesting thing I learned from a marine biologist on a whale-watching tour last summer:

On the west coast of Canada, there are three populations of orcas (killer whales): the northern population, around Hyder/Queen Charlottes area, has as its diet, primarily mammals (seals, mostly); the southern population, just up from Seattle, eats fish; the western population, on the seaward side of Vancouver Island, is presumed from teeth and stomach contents to eat rays, skates, and sharks.

The populations don’t interbreed. I’m told it’s because they’re songs have diverged too much for them to recognize each other as potential mates, though I suppose geography has something to do with it.

The interesting part will be the examination of their genetic divergence, and how long it will be before they are truly speciated.

Or maybe “Poof!” and they’ll be three different species. Could happen…

Comment #97139

Posted by fnxtr on April 18, 2006 3:18 PM (e)

Oops. “Their songs”, not “they’re songs”. Apologies.

Comment #97140

Posted by Bill Gascoyne on April 18, 2006 3:30 PM (e)

Tyrannosaurus in Comment 97119 wrote:

You see every time I read or see IDiots basking on the “mathematical evidence” for ID and against ToE, I remind myself of the old story about how it was mathematically proved that bumble bees cannot fly!!!!
Dumbski is doing the same argument; using pseudo mathematical jargon to obfuscate arguments that he perfectly well know are baseless.

Nit pick: I disagree that it’s the same argument. First of all, the whole “mathematical bumblebee” problem was not that they shouldn’t be able to fly, it was that they should have been aerodynamically unstable, and the problem was solved by a better understanding of small scale vortexes. Second, the point was to show that there was something wrong with the mathematics (in this case, of aerodynamics at small scales), not that (as Wild Bill would have us believe) the math is divinely inspired and there are actually angels holding up the bumblebees.

Comment #97142

Posted by Mythos on April 18, 2006 3:35 PM (e)

Glen Davidson wrote:

Nothing in biology is like what humans make, until one reduces the components down to an unreasonable level. So Denton rattles on about the “analogues” of our machines within cells—the fact is that as a discipline biology, including evolutionary biology, is busy studying how different cells are from our own machines. For one thing, biology tends not to compartmentalize what we consider to be “functions”, and for another thing, biology is highly derivative in a way that human machines are not.

What gripe, in particular, do you have with functional analysis? It seems to me that functionalism has worked rather well in psychology. Is there any scientific principle I should be made aware of that prohibits it there and elsewhere, say in biology?

Comment #97143

Posted by Steviepinhead on April 18, 2006 3:35 PM (e)

Heck, forget about Sal verbing his nouns. The real question is, how does he arrive at his decisions to apostrophize or not?

the passwords were created by peoples choices

there are some serious flaws in it’s claims

The first refuge of the ID “statistician”–coin flipping?

Stay tuned for the answers to these even more-exciting questions:

Will Sal ever learn to write?

Will Sal ever learn to read?

Will Sal ever learn to think before foaming over at the mouth?

(Of course, these really might be exciting questions if there were just some element of suspense involved…)

Comment #97144

Posted by harold on April 18, 2006 3:37 PM (e)

Salvador Cordova wrote -

“No, I do understand what the theory of evolution claims,”

Obviously, the next logical step here would be to provide some sort of evidence to back up this assertion. After all, anyone can say this. And Sal isn’t just claiming to know a little about evolution. As a would-be serious critic, it is imperative that he understand what he criticizes. In fact, I already made the point that further dwelling on irrelevant computer analogies would be evidence of evasion on Sal’s part.

But instead, Sal moved on to say…

“and I’m challenging that empirical reality and serious theoretical examination shows there are some serious flaws in it’s claims.”, and repeat some computer nonsense.

But he hasn’t come close to doing what he claimed. He hasn’t said a single word about empirical data, other than to make the trivial assertion that a complete step-by step evolutionary history of every protein that exists isn’t available. This is akin do denying gravity by arguing that every apple that ever came off a tree hasn’t been accounted for.

On the theoretical level, all Sal has offered is an extremely inapt analogy of a code-breaking algorythm. It is this very “theoretical” argument that convinces me that Sal doesn’t grasp the theory of evolution. Although he disdainfully refers to “step by step” processes, his argument merely makes the obvious point that an incredibly improbable set of simultaneous events is unlikely to occur at one time.

Amazingly, astoundingly, Sal doesn’t make reference to even one of the existing computer or mathematical models of evolutionary processes, not even to the decades old work of Sewell Wright. Nor does he make any reference to the theoretical work on DNA computers of about a decade or so ago.

The “password” analogy fails on so many levels it’s hard to list them all.

1) The theory of evolution doesn’t propose single generation leaps from one distantly related organism to another.
2) The theory of evolution doesn’t propose that evolutionary steps are taken in pursuit of an ultimate goal. (Science-accepting theistic evolution positions would tend to argue that a supreme being “intended” evolution to ultimately produce consciousness, but would agree that from a human perspective, evolution is best studied as a non-magical process.)
3) Don gave an example of an algorythm which could solve passwords one step at a time (albeit due to a security flaw). This is a great deal closer to how evolution actually works, but still a far cry from it.

Computer models of evolution work on the principles of random variation, usually limited, followed by preferential selection of some variants.

I’m not even sure that Sal’s arguments qualify as “straw man” arguments. Literally all he does is say “the cell is a Turing machine”, without offering the slightest justification for this extraordinary claim (or even clarifying whether he means an honest-to-goodness theoretical Turing machine or merely a contemporary computer with a hard drive, RAM, keyboard, and output device). We all agree that DNA encodes information, Sal, but that doesn’t mean that an amoeba is the same thing as your laptop.

Personally, I don’t think that a PhD in “evolution denial” should be given out to anyone who can’t first demonstrate a PhD level understanding of the theory of evolution.

Sal, I give up. You just want to repeat buzzwords, not to acknowledge anyone else’s points or defend your own assertions. Just answer Lenny’s 31 questions, TELL ME IF HIV CAUSES AIDS, and I’ll move on.

Comment #97146

Posted by Don Baccus on April 18, 2006 3:57 PM (e)

Sal wrote:

[the] password illustration was to help the reader see the way IDists view certain biological structures like the Flagellum or a biological Turing Machine.

We know this, Sal. You used the illustration help the reader see the way IDists view certain biological structures. Everyone now sees that IDists incorrectly conclude they could not’ve evolved because they compute nonsenical probabilities based on provably false assumptions. Just as you did with your password example.

Thanks!

Comment #97147

Posted by AC on April 18, 2006 3:59 PM (e)

Snake Oil Sal wrote:

For starters, [evolution] assumes the some of the very things it claims to prove, namely, that most large scale biological innovation can be reached through step-wise incremental improvements.

Sal, you’re trying so hard to shoehorn evolution into this logical fallacy that your pants have fallen down. Evolution doesn’t claim to prove anything. It is an explanation for the origin and diversity of life on Earth based on the observed fact that - to use your terminology - biological innovation can be reached through step-wise incremental improvements. There is no evidence that scale is a problem. If you contend that scale is a problem, prove it. Otherwise, continue to provide us your characteristic soap opera/train wreck level of entertainment by blustering ignorantly.

And, as a computer engineer, I’d like to hear afdave explain, in HIS OWN WORDS, not referring to a single outside source, what HIS theory of electronics is and WHY he “believes it” in 5 simple statements. For extra credit, he can also explain why the random aspects of evolution are a problem for him but those of quantum mechanics are not.

Comment #97148

Posted by RupertG on April 18, 2006 4:00 PM (e)

As for the question “why do they do it?” - well, Dembski and Behe have had a lot of book sales and TV appearances out of ID, but I doubt that’s it - although I’m sure it’s hard to walk away from. If I was shifting units like Dembski and had to battle with my doubts, I’m not at all sure I wouldn’t quietly smother them under a pillow in the dead of night.

At heart it’s good old primate hierarchy, and you too can be an alpha male if you make an elite from the ignorant.

It’s hard to get there through science – to be really something in science you have to know a _lot_ and be creative, and hold your own among an awful lot of other creative, bright, inquisitive. hard working and knowledgable people. Sometimes, you need the guts to prove everyone in your peer group wrong after years of derision (primate hierarchies not being exactly absent from science either). That’s hard, and most people can’t do it. I love science, and I’d make a crap scientist. No, not coproliths.

To be a bit of a noise in ID, what do you need? Well, Salvador and Dave and plenty of other people have it, so I guess you should ask them. ID is nice, because you don’t need to know a lot, it’s forbidden to ask difficult questions (otherwise not knowing a lot might becomes a disadvantage), but you get to be smarter than all those scientists anyway! What’s not to like? Plus, you get to Think Of The Children and Save Mankind From Sin – oops, sorry, not sin. Bad thinking, perhaps, not sin. And you get a community, and the love of the President, and eternal life. No, no, sorry, not eternal life. That’s… oh, what’s the word, begins with an R, rhymes with real pigeon… sorry, lost it (a few years ago now).

Coming up with a theory and evidence and predictions (real ones, not ones that coincide with evolutionary predictions) and heated debate about details – you know, like what scientists do – would ruin the fun for everyone. You don’t want to let everyone down, do you?

R

Comment #97149

Posted by k.e. on April 18, 2006 4:00 PM (e)

Sal and F.L. Berlinski and all the others are not going to answer questions that reveal their ignorance or misrepresentation of the facts. (political death)

Their whole M.O. is to spout some nonsense and when called on it, click the remote and move to the next channel like someone with ADD.

Comment #97166

Posted by Stevaroni on April 18, 2006 4:56 PM (e)

Posted by afdave on April 17, 2006 06:58 PM (e)

… I have an idea for a simple, fun exercise. I’m an Electrical Engineer and business man and I used to fly AF jets. I like simple, uncomplicated arguments and I like people to cut to the chase … fast.

Oooh! I’ll play!

I’m also an electrical engineer and a small businessman. No, I didn’t fly jets (not that I didn’t want to, mind you, I was courted by the Air Force, but I didn’t have the eyesight, they did, however, offer to send me to medical school, and offer I should have accepted - but I digress) Anyhow, No, I didn’t fly jets but I did design them instead. Maybe even the ones you flew.

You don’t win this argument with slogans and bumper stickers.

I’ve spent most of my professional life with people trying to sell me things, so I’ve gotten pretty good at separating the shit from the shinola.

And if there’s one thing that consistently divides those peddling the two, it’s that the people selling the real deal want you to examine the merchandise. Closely.

They have nothing to hide. They’ll send you so much data that your mailman dreads the sight of your name. They want you to understand.

The other guys have glossy brochures and tell you how much they think of their product. But they won’t ever show you what’s in the box. They want you to believe

But those jets you’re so fond of don’t stay up in the sky because someone believes they will.

They stay up there because someone did the math.

They stay up there because the science says they will, even if its’ completely counter-intuitive.

I just flew back to Texas from Beijing. In a big metal tube with 400 of my closest friends. It was bigger than my block, weighed 10 times as much as my house, and moved me halfway around the earth in 12 hours. There’s just no way that should be possible

But it is, because the egghead scientists have spent 100 years figuring out how.

And that’s how evolution is.

In the last 150 years this goofy little theory has been hideously unpopular. Demonized and vilified by the biggest voices in the land. Subject to name calling and legal challenge from the very start, hundreds of thousands of smart people have attacked it for decades from every conceivable angle.

But it’s never been proven wrong.

November / Echo / Victor / Echo / Romeo.

Never.

It’s never even been so much as seriously challenged.

In all the mountains of bones and reams of data over the last 150 years I don’t know of a single piece of solid evidence that so much as strongly hints that something else is going on.

Yes, there are some fringe “scientists” out there who claim they have proof evolution is wrong. Hell, there are also fringe “scientists” who insist we never went to the moon, the earth is flat and the Russians paid the Cubans to hire the mafia to kill Kennedy.

If they could make their case, if they had something - anything - to put out on the table, they’d be as famous as Newton and Einstein; household names, which would make many of them happier than anything else in the world.

But if they’ve got that honest-to-goodness chunk of evidence, it’s pretty telling that they’ve decided they don’t need to show it. More people who want you to just believe.

It’s time to put up or shut up. One hand holds shinola, one hand holds the other stuff. All you have to do is sniff.

Comment #97167

Posted by Grey Wolf on April 18, 2006 4:58 PM (e)

My biggest problem with Sal’s password “example” of evolution is the fact that he assumes that there is only one correct password. I assume this is because he is utterly convinced that the universe exists to bring him forward and that he is, in fact, the crown of creation and that is why it is so impossible that evolution is true - because think about the chances of Salvador existing!

The example would work much better if all you wanted is access to a computer used by billions of people. Yes, each has a password of 40 characters, but they also all have maximum privileges so any of them will do. Now it is far easier, isn’t it? Particularly because if evolution is applied to this picture, all you need is to get successively closer - because you attempt thousands of combinations and select the ones that were closer to any of the solutions.

Yes, it is a pathetic example because evolution doesn’t work anywhere close to password cracking programs. Of course, Sal either is so stupid that he doesn’t understand the difference or is so immoral that does understand it but uses it anyway in the foolish hope that everyone else won’t.

To whit: only creationists believe that the entire genetic code appeared in one go, in complete disregard of all know facts of physics, when God breathed life into clay. And all their examples do is demonstrate that their belief is completely impossible without some higher power. But none of it has anything to do with evolution, or with the actual evidence of how life came to develop on this planet.

Hope that helps,

Grey Wolf

Comment #97169

Posted by Russell on April 18, 2006 5:04 PM (e)

Their whole M.O. is to spout some nonsense and when called on it, click the remote and move to the next channel like someone with ADD.

Excuse me, but isn’t it a little bit glib of you to associate these jerks with people who, through no fault of their own…

wait… what’s that shiny… I gotta go.

Comment #97170

Posted by Anton Mates on April 18, 2006 5:06 PM (e)

fnxtr wrote:

Here’s an interesting thing I learned from a marine biologist on a whale-watching tour last summer:

On the west coast of Canada, there are three populations of orcas (killer whales): the northern population, around Hyder/Queen Charlottes area, has as its diet, primarily mammals (seals, mostly); the southern population, just up from Seattle, eats fish; the western population, on the seaward side of Vancouver Island, is presumed from teeth and stomach contents to eat rays, skates, and sharks.

The populations don’t interbreed. I’m told it’s because they’re songs have diverged too much for them to recognize each other as potential mates, though I suppose geography has something to do with it.

Geography’s probably not a big deal, as whales from the populations often travel into each other’s territories; the transients in particular will pass through the residents’ territories but the pods will avoid contact. It seems to be more that orcas very rarely disperse out of their natal pod at adulthood, and due to massive cultural differences (movement patterns, acoustic signals as you mention, diet & foraging strategies) the resident (e.g. northern and southern) and transient (e.g. western) populations pretty much never exchange members.

The interesting part will be the examination of their genetic divergence, and how long it will be before they are truly speciated.

There isn’t much genetic difference between the various resident populations AFAIK; the most likely speciation event will be (or is already) between the transients and the residents. They may never be “truly speciated” in the sense of total reproductive incompatibility, though–I would imagine that they’ll remain as ready to hybridize as canids or rorqual whales are for a long time to come. Nature, unlike the Great Designer, doesn’t worry too much about distinguishing “kind” from “kind”…

A Durham University page on relevant work (thanks, Google!) is here.

Comment #97178

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 5:41 PM (e)

Lenny, am I coming across as incredibly dense?

Not at all. I’m simply poiting out that the evasion and misdirection that you describe is a deliberate, planned, political and legal strategy. It’s not just “a game” or a “debating tactic”.

I knew what the answer from the scientific community would be. I want the IDiots to defend themselves. I know they can’t, I just wanted to see them try.

Well heck, just sit back, pop open a beer, keep the popcorn handy. :>

Comment #97179

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 5:47 PM (e)

I don’t know what your beliefs are Reverend Flank, but Panda’s thumb has a lot of Atheists.

So f’ing what, Sal. I thought ID was ***science***, and was NOT, repeat NOT, as in N-O-T, just religious apologetics. Isn’t that what all your buddies told that judge in Pennsylvania? Or were they all just . . well . . LYINGto us about that?

Since ID is SCIENCE and is NOT religious apologeitcs, then what damn difference does it make if people here are atheist or zoroastrian or buddhist or worshippers of Quetzalcoatl or Odin or Amaterasu Omikami?

Thanks for making it so clear to everyone what ID’s real agenda is, Sal.

Now that you’ve demonstrated so clearly that (1) ID is nothing but religious apologetics, (2) IDers (like you) are just lying when they claim it isn’t, and (3) Judge Jones was entirely correct when he concluded it is – I’ve asked you a few questions that you seem not to have answered.

Wassamatter, coward. Cat got your tongue?

Comment #97180

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 5:55 PM (e)

Yet bizarrely, you seem to think that you’re scoring points on Lenny Flank by finding something religious in the book.

That’s because Sal, like most other IDers, is under the delusion that anyone who opposes ID is atheistic.

He’s demonstrably wrong about that. Most Christians, worldwide, think that his kindergarten science is just as silly as his kindergarten theology. Indeed, most Christians view ID/creationism as doing tremendous HARM to Christianity, by making it looks silly, stupid, medieval, intolerant, uneducated, dishonest and pig-ignorant. Every time some fruitcake like Sal screams “SCIENCE IS ATHEISTIC !!!! at the top of his lungs, he just reinforces the stereotype that most people have of fundies as uneducated redneck backwoods hicks who live in trailer parks in small southern towns and married a close relative in a ceremony led by Reverend Billy Joe Bob. (shrug)

All Sal does is drive educated people AWAY from Christianity.

Whether that is a good thing or a bad thing, I leave up to each reader to decide.

Comment #97181

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 5:59 PM (e)

I’m challenging that empirical reality and serious theoretical examination shows there are some serious flaws in it’s claims.

Blah blah blah. Tell it to the judge, Sal.

Oh wait, you already DID, didn’t you …. .

How’d that, uh, go for you guys, Sal …. . ?

By the way, coward, I’ve asked you a few questions that you keep running away from. Are you gonna answer them this time, or just run again.

Comment #97184

Posted by steve s on April 18, 2006 6:14 PM (e)

I’m also an electrical engineer and a small businessman. No, I didn’t fly jets (not that I didn’t want to, mind you, I was courted by the Air Force, but I didn’t have the eyesight, they did, however, offer to send me to medical school, and offer I should have accepted - but I digress)

Maybe you should have waited til MEPS. I did, in Jacksonville, in 1995, and they pretended I didn’t have 30 dB hearing loss in my left ear. My roommate was literally drunk when he went through MEPS, and while he was yanked out of the lineup for an hour or so, at some point he mysteriously reappeared behind me in line. Qualifications for the Air Force depend on how desperate they are for personnel. Right now, you could probably kill someone in the recruiter’s office, and they’d cover it up and waive you through. :-)

Comment #97185

Posted by k.e. on April 18, 2006 6:19 PM (e)

Sal found something shiny ….or he changed the channel.

Maybe he’s gone off on a Ark hunt or he’s seen the light and become a Scientologist (snicker) he likes a little fame. He could go on Oprah’s show and jump up and down on the couch and say he thinks Dembski is hot.

Comment #97187

Posted by Glen Davidson on April 18, 2006 6:24 PM (e)

What gripe, in particular, do you have with functional analysis? It seems to me that functionalism has worked rather well in psychology. Is there any scientific principle I should be made aware of that prohibits it there and elsewhere, say in biology?

And what in the following would suggest to you such an idiotic idea as that I have a “gripe” with functional analysis:

Nothing in biology is like what humans make, until one reduces the components down to an unreasonable level. So Denton rattles on about the “analogues” of our machines within cells—the fact is that as a discipline biology, including evolutionary biology, is busy studying how different cells are from our own machines. For one thing, biology tends not to compartmentalize what we consider to be “functions”, and for another thing, biology is highly derivative in a way that human machines are not.

I did, after all, write this as well:

There is, of course, value in the reductionism that Denton engages in, and indeed, I recall reading fairly closely an article in Nature which dealt with the syntax and semantics of DNA.

I guess you have problems with understanding normal English, much like Sal. I am more than a little aware of the value of functional analyses, and the various reductions which are made, it’s just ridiculous for Sal to treat functional analysis as if it treated with the range of aspects found in the actual physical systems. Too bad you can’t recognize the argument against taking the analysis as if it were the whole.

I’m never sure which side you’re on, Mythos. You don’t seem to be an IDist, yet you seem to carp about matters that you don’t understand, just like an IDist. Well, I guess we’re not going to be rid of ignorance on our side, either.

Glen D
http://tinyurl.com/b8ykm

PS. Oh, I remembered after posting that I had used “informatics” when I meant something like the “DNA information system” in this:

But of course this is only a model of DNA coding which is applied for our convenience, and not because we ever once invented anything like DNA informatics.

As in it should have been, “not because we ever once invented anything like the DNA information system.” (which may still not be the “proper jargon”, but gets the concept across well enough).

It didn’t seem worth another post, but I thought I’d mention it if I posted on this thread again.

Comment #97191

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 6:36 PM (e)

Qualifications for the Air Force depend on how desperate they are for personnel.

Ya know, I tried to join in 1979, after I got out of high school. Just wanted to learn to fly on Uncle Sam’s dime.

Alas, they told me that because I wear glasses, I could be a back-seat, but couldn’t drive.

Pfffft. No fun in THAT. (shrug)

The Marines, on the other hand, wanted me bigtime because I scored high on my SAT’s. They kept pestering and pestering me, until I told them I was a commie. Then they left me alone. :>

Comment #97196

Posted by Don Baccus on April 18, 2006 7:14 PM (e)

Glen wrote:

But of course this is only a model of DNA coding which is applied for our convenience, and not because we ever once invented anything like DNA information system.

Apparently Sal and friends seem to think that since you can mathematically describe something (in this case using formal grammars), that description IS the thing.

That’s just … weird.

Comment #97199

Posted by Bill Gascoyne on April 18, 2006 7:43 PM (e)

Apparently Sal and friends seem to think that since you can mathematically describe something (in this case using formal grammars), that description IS the thing.

I’ve always likened that mistake to going to Denny’s and eating the menu.

Comment #97206

Posted by Don Baccus on April 18, 2006 8:45 PM (e)

I’ve always likened that mistake to going to Denny’s and eating the menu.

Oh, that’s good …

Comment #97208

Posted by Bill Gascoyne on April 18, 2006 8:51 PM (e)

Glad you liked it. I would also compare the above to the question of how the electron “knows” when to act like a particle and when to act like a wave. The erroneous question is the result of thinking that the electron becomes a particle or a wave, instead of the truth, which is that the electron behaves like an electron, and it is we who describe it as “particle-like” or “wave-like.”

Comment #97220

Posted by AD on April 18, 2006 10:06 PM (e)

Since you are here, Sal…

Sal,

As an aside, while you are here, I asked for information on ID from another source in one of these threads (as I have repeatedly), and recieved deafening silence (as I have repeatedly). Perhaps you would be willing to step up to the plate for me? Namely:

http://en.wikipedia.org/wiki/Scientific_Method


1- Define the question
2- Gather information and resources
3- Form hypothesis
4- Perform experiment and collect data
5- Analyze data
6- Interpret data and draw conclusions that serve as a starting point for new hypotheses
7- Publish results

I’m sorry, but I seem to have missed some of the literature the ID scientists are putting out. I’m sure this is riveting stuff if you actually have a set of experiments refuting evolution. Could you please refer me to where I might find these, either on the internet and in print, and clearly explain what your hypothesis are and what the result of experimentation on those testable predictions were?

Thanks.

As it currently stands, I think the abject refusal of any member of the ID movement to adequately (or, to be blunt, at all) attempt to address these questions says everything we need to know about ID.

ID will become scientific the moment it starts doing science. It’s that black and white.

When you have answers, I will start listening. Until then, I just scroll past your text and move on with my life. I have better things to do than wade through babble when someone can’t pony up with results, Sal.

Show me the money, Sal.

Comment #97232

Posted by fnxtr on April 18, 2006 11:51 PM (e)

Thanks, Anton, for the link to the cetacean studies. Holy crap there’s a lot out there to learn. No wonder some folks run in terror and hide behind “Poof!”

fnxtr

Comment #97235

Posted by Bob O'H on April 19, 2006 12:17 AM (e)

Just wave the magic wand of mathematics and viola those pesky facts disappear.

Why would waving a viola around help? :-)

Oh wait, it means it’s not being played, which can only be a good thing.

Bob

Comment #97277

Posted by Raging Bee on April 19, 2006 7:54 AM (e)

Brave Cordova ran away
Bravely ran away, away
When reason reared its fright’ning head
He bravely turned his tail and fled
Brave, brave, brave, brave Cordova…

Comment #97300

Posted by Salvador T. Cordova on April 19, 2006 9:47 AM (e)

I would like to thank PvM for opening this thread. I feel so honored.

Here is something to consider with Protein Evolution, though I do not concur with sweeping statements that there are no protein-to-protein intermediates, the few “intermediates” are sketchy and one wonders if any real intermediates really exited. That is my only obejction to the paper.

This then poses a serious problem for evolution as the multi-component parts of a protein can be part of an IC barrier to Darwinian evolution:

Problems in Protein Evolution

Some very serious problems in the evolution of proteins threaten the theory of evolution, and appear to disprove it. A demonstration of the seriousness of these problems therefore constitutes a disproof of the theory of evolution. In particular, the evolution of proteins having significantly different shapes (tertiary structures) than previously existing proteins appears to be impossible.

Although there are other arguments against the theory of evolution, the present argument differs in several ways. Some arguments against evolution involve the improbability of abiogenesis, that is, the origin of the first life forms. These arguments are convincing, but biologists will say that some as yet undiscovered mechanism resulted in the first life forms. The biologists’ argument is hard to refute in a formal way. Other arguments point to the complexity of life, and the implausibility of such a complex system evolving. For example, Behe documents the complexity of flagella and argues that they are “irreducibly complex,” meaning that the system cannot function unless many parts appear, and all these parts could not have arisen at once by evolutionary processes. This is also a convincing argument, but it is hard to formalize because it does specify mathematical probabilities. Biologists will say that some as yet undiscovered mechanism resulted in the evolution of the flagellum and other structures that appear to be irreducibly complex. Other arguments involve the fact that information of the kind found in life forms does not appear by natural processes. However plausible this argument is, it does not have a formal mathematical justification. Similar comments apply to the lack of transitional forms in the fossil record, and many other arguments commonly used against the theory of evolution. The argument presented here is different, in that it involves existing genetic mechanisms, not hypothesized ones, and it involves the calculation of mathematical probabilities (or rather, improbabilities). This therefore appears to be the first argument that qualifies formally as a disproof of the theory of evolution.

This argument also involves redundancies in many of its aspects. That is, under several models, the change of shape of proteins is impossible, and each model has its own set of reasonable assumptions.

The difficulties presented here do not imply that proteins cannot acquire new functions by mutations; this can happen by mutations that do not significantly affect the shape of the protein. It is only the change of the shape of a protein that presents difficulties.

Grishin [Grishin 01] proposes some mechanisms for the evolution of new protein folds without an explicit computation of probabilities, but this process is still problematical. The difficulties in changing the shape of proteins by evolution involve both probabilities and laws of protein structure. The evolution of proteins of new shapes by point mutations is not possible, because the change of shape of a protein would require too many mutations. If the probability of a mutation is high enough to change the shape of the protein, then many other mutations will also occur that will essentially randomize the rest of the gene and cause the newly shaped protein to be harmful to the organism. One might argue that large scale changes to a gene could result in a protein of a new shape more readily than could point mutations. However, other arguments based on laws of protein structure prevent this. The kinds of amino acids that appear on the inside and the outside of a protein are different. There can only be a small number of insertions of a part of one protein into another that do not violate the distinction between the inside and outside of the protein, and the chance that any one of these will be beneficial, is very small.

The present argument is based on assumptions from the theory of evolution, according to which life began as a simple reproducing system that gradually developed into the life forms we see today. This system (or systems, if life developed multiple times) must have been very simple, because it had to originate without the benefit of evolution. In particular, it could only have had one or a very small number of proteins. From these few proteins, those in current life forms must have evolved.

Each protein is produced by one (or possibly several) genes. The evolution of new proteins must have occurred by mutations to these genes. Since genetic mechanisms in current life forms are strikingly uniform, with a few modifications, it is reasonable to assume that these mechanisms have been in operation for hundreds of millions or billions of years, in the accepted evolutionary scenario. Thus the evolution of many proteins from a few must have occurred by genetic mechanisms that are still in existence. Even if special mechanisms operated in the evolution of one-celled creatures, there are undoubtedly many proteins and shapes of proteins that only appear in multicellular organisms, and these must have evolved from others by currently existing genetic mechanisms. Furthermore, because all known one-celled organisms have similar genetic mechanisms, it is reasonable to assume that these mechanisms were operating for a considerable portion of the time that these one-celled organisms evolved from simpler organisms having many fewer proteins. During this time, proteins having new shapes must have appeared.

Each protein is composed of a sequence of amino acids that join together and are then called “residues.” The “side chains” of the residues determine their chemical properties. These side chains are joined together by the “backbone” of the protein. Some side chains are hydrophobic (oily) and tend to cluster together inside the protein. Others are hydrophilic (water loving) and tend to occur on the outside of the protein. Some proteins function in a hydrophobic environment, such as the cell membrane; these may have more hydrophobic residues on the outside. A given shape of a protein will tend to be associated with a particular sequence of hydrophobic and non-hydrophobic side chains. Changing the shape of the protein requires changing this sequence of side chains. Even if the shape of the protein is not changed, having too many hydrophobic side chains on the outside can cause proteins to stick together, interfering with their function, as happens in sickle cell anemia. This is caused by a single mutation replacing a hydrophilic side chain on the outside of hemoglobin with a hydrophobic side chain.

A protein can be in a folded or unfolded state, and if it is folded, it may fold into a variety of structures. The unfolded state is more flexible and less dense. In order to have a function in an organism, a protein must fold, and it must fold the same way sufficiently often. This means that the wild type fold (the one found in nature) must be significantly more stable than other possible folds. If the protein is modified, it may fold into a different structure, or simply not fold at all.

Proteins have “active sites” where they can interact with other proteins or other substances. The geometry and composition of these sites is very highly constrained, because in order for two proteins to interact, their active sites have to match very closely in their geometry and chemical properties.

A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.

I invite the unenlighted PandaThumbites to learn something for a change.

Let me remind you all of what Evolutionary Biologist Coyne said of his own field:

In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics.

Just remember evolution’s place in the pecking order is right down there near the bottom, not at the top, and that will give you better perspective in defending this worthless theory.

Comment #97303

Posted by Raging Bee on April 19, 2006 9:54 AM (e)

Sal quote-mined thusly:

In particular, the evolution of proteins having significantly different shapes (tertiary structures) than previously existing proteins appears to be impossible.

Um…isn’t Mad Cow Disease caused by a certain protein changing its shape, and thus its properties and function? So much for “appears to be impossible,” eh?

Comment #97306

Posted by Shirley Knott on April 19, 2006 10:08 AM (e)

Sal, honey, you got some ‘splainin to do.
Specifically, justify or retract your truly idiotic assertion that evolution is a worthless theory.
Do please be sure to take into account the billions of dollars it has earned the biopharmaceutical industries.

hugs,
Shirley Knott

Comment #97307

Posted by Salvador T. Cordova on April 19, 2006 10:09 AM (e)

Raging Bee said:

Sal quote-mined thusly:

In particular, the evolution of proteins having significantly different shapes (tertiary structures) than previously existing proteins appears to be impossible.

Um…isn’t Mad Cow Disease caused by a certain protein changing its shape, and thus its properties and function? So much for “appears to be impossible,” eh?

LOL! Just like a Darwinist to appeal to Mad Cow disease prions as a selective improvement. LOL! Prions are considered misfolded proteins, bub.

Mad Cow, Creation of a Prion

Summary: For the first time, an artificial prion, or misfolded protein, has been created that can, by itself, produce a deadly infectious disease in mice. This is thought to occur in mad cow disease. This research, if corroborated, would provide strong evidence for the protein-only hypothesis, the controversial concept that a protein alone, without the help of DNA or RNA, can cause infectious disease.

You said I run away, no, I love this place, just not enough time to hang out with you guys.

PvM, any refrences you can supply to “reverse ordination refutation”? You seemed familiar with it. Can you enlighten us?

Sal

Comment #97313

Posted by Raging Bee on April 19, 2006 10:21 AM (e)

Sal: you quoted a statement that proteins can’t change their shapes significantly. Mad Cow proves that statement wrong – the protein in question changed its shape significantly. And if such a thing can happen, it can happen with bad or good results. The credibility of the arguments you quote is therefore somewhat…diminished. And your insulting phony bravado only proves your insecurity, which is a result of knowing you’re in over your head and have no clue what you’re talking about.

Comment #97318

Posted by Raging Bee on April 19, 2006 10:35 AM (e)

The paper Sal quotes has this telling little howler:

The biologists’ argument is hard to refute in a formal way.

The “formal way” of refuting an argument is with facts, logic, research, testable hypotheses, and/or repeatable experiments. And, because they can’t refute evolution in a “formal way,” creationists are, often by their own admission, resorting to less “formal” ways – i.e., no facts, no logic, no testable hypotheses, no repeatable experiments, and no peer-reviewed papers anywhere.

The fact that the paper Sal quotes contains certain old – and discredited – objections to evolution, and pretends they’re not “really” discredited, because they “sound convincing,” but are just “hard to formalize,” only shows the author’s dishonesty.

Comment #97321

Posted by Salvador T. Cordova on April 19, 2006 10:47 AM (e)

Dear IDers reading this thread,

I should point out some comments regarding IC which our fearless leader, Casey Luskin pointed out:

Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum (Part I)

and

Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum (Continued–Part II)

I suggest the reader look at figure C in Part 2. Apt description for Ken Miller’s ideas:

Figure C in part 2

Ken Miller like many PTers is pathologically persisten in making an argument with logical fallacies like the “Strawman Argument”. There is even a guidebook on how to formulate such arguments, and Miller and friends would provide excellent illustrations for the guid book. The guide book can be found here:

The Swamp Battle Tactic Manual

Comment #97322

Posted by wamba on April 19, 2006 10:53 AM (e)

Just remember evolution’s place in the pecking order is right down there near the bottom, not at the top, and that will give you better perspective in defending this worthless theory.

ID on the other hand, is not science and therefore has no place at all in the pecking order.

Comment #97323

Posted by Salvador T. Cordova on April 19, 2006 10:56 AM (e)

Raging Bee:

you quoted a statement that proteins can’t change their shapes significantly. Mad Cow proves that statement wrong

A protein prior to being folded and then being folded is a “change of shape”, and that is not the kind of “change of shape” Plaisted was talking about. You are using Fallacy of Equivocation regarding the conception of “change of shape”.

Your use of “change of shape” is not the same as Plaisted.

Plaisted’s context of “change of shape” pertained to properly folded functional proteins which help the organism, not misfolded polymers which kill it. Kind of hard to evolve something that’s dead.

Comment #97324

Posted by Glen Davidson on April 19, 2006 10:57 AM (e)

I read in a recent Nature, I believe it was, that a recent study calls into question the prion shape-changing hypothesis. There seems to be a possibility that faulty prions are in fact being manufactured by the body instead of being shifted from the shape of “healthy prions” into the diseased ones. It’s all very tentative at present, of course, but the old model is perhaps not certain.

Moving on to other matters:

Science operates by making observations, then by coming up with hypotheses which generalize and explain sets of phenomena. This is what evolutionary biologists do, they observe the similarities of proteins in apparently closely related animals, plus the differences and similarities between ourselves and, say, yeasts, and come up with the very reasonable hypothesis that proteins have evolved in various ways, including in their gross morphology.

Of course major changes in the structures of proteins are indeed not readily effected, which is why we happen to have so many proteins in common with yeast (including prions, of all things), though none or virtually none are unchanged. Indeed, Sal has mentioned the probable reason why the evidence for the relatedness of all life is so abundant and inescapable, which is the difficulty in shifting proteins dramatically. To be sure, the usual absoluteness of the puritanical mind strikes, and it becomes in his claims “impossible” for proteins to evolve (indicating once again that Sal avoids the literature). I should add it is probably at least as much the complexity of life that conserves protein structure as does the difficulty in changing proteins by themselves. Regardless of the reasons, though, Sal has once again touched upon the powerful empirical data in favor of evolution, and managed to completely fail to make the intelligent inference–which is that life has evolved.

It’s like looking at Sal’s derivative remarks and being incapable of recognizing that he is wholly the product of selective “study” of mindless creationist/ID drivel. Is anyone here stupid enough to think that Sal thinks for himself? Then it must be recognized by those who do think that the similarities of proteins across life does have much to do with the difficulties in evolving proteins, while the changes that we actually do see (which in vertebrates are typically not all that great in most of the “basic proteins”, in the functional sense) cannot be due to anything other than evolution.

Btw, thanks much for the writings of a creationist, Sal. I treasure that BS like my own digestive tract had made it.

Actual scientists are learning to use evolution to change the structure and function evolutionarily, by mimicking nature. It’s what separates us from the apes, and other functionally illiterate primates. Here’s a decent summary of the thinking behind these evolutionary strategies, with a nice table summarizing some of the directed evolutions effected by researchers:

http://tinyurl.com/fr9on

This is source that one may actually have hopes of learning the real story. To be sure, even the creationist is cognizant of some of the actual problems in protein evolution, but the focused denial of the practicing pseudoscientist is of quite limited value.

Btw, Coyne can hardly be correct in his assessment and/or hyperbole regarding the pecking order in science. Physics doesn’t have the same exalted status that it once had, and indeed, it has turned some of its attentions toward biology–in which evolution is inescapable. This isn’t to say that biology and evolution are the higher-status parts of science, however the increasing rigor of biology and of evolution in this time of DNA analysis, coupled with the decline in the exaltation of physics, has tended to move the sciences closer to equality. Not that Sal’s swipe had anything to do with scientific relevance, but I have yet to see anything written by him that does.

My first question on this thread still demands a credible (and contextual) answer:

Has any intelligent designer ever been shown to produce designs that are like the forms and “machines” that we find in organisms?

Sal’s incompetence at answering such a basic ID question only demonstrates why ID not only is considered to be the equal of phrenology, but why it is likely to remain there for all time.

Glen D
http://tinyurl.com/b8ykm

Comment #97325

Posted by wamba on April 19, 2006 11:02 AM (e)


A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.

If proteins are so highly constrained, how is it that two versions of a protein can differ in hteor specific sequence at over 80% of their positions, and still share the same overall fold and the same function?

What about frame shift mutations? Are you saying that a gene for a protein could not undergo a frameshift mutation, resulting in something substantially different? If you need an example, how about those nylon-digesting proteins?

Comment #97330

Posted by Tracy P. Hamilton on April 19, 2006 11:11 AM (e)

Salvador Cordova wrote:

Here is something to consider with Protein Evolution, though I do not concur with sweeping statements that there are no protein-to-protein intermediates, the few “intermediates” are sketchy and one wonders if any real intermediates really exited. That is my only obejction to the paper.

This then poses a serious problem for evolution as the multi-component parts of a protein can be part of an IC barrier to Darwinian evolution:

Problems in Protein Evolution

Remainder of ridiculous essay snipped. So, you want to discuss protein evolution now, using “negative argument, hence ID is the alternate explanation”?

Perhaps you would like to explain why protein FOLDING is like a grammar. This way we can combine two topics you know nothing about to double our amusement.

Comment #97338

Posted by Salvador T. Cordova on April 19, 2006 11:45 AM (e)

Just to show that I do make attempts at being even handed with my opponents, I would like to take a moment to speak on behalf of Lenny Flank.

In this post: Pvm to Lenny

Pvm said:

So what have you done lately Lenny to help ID activists understand either the follies of their ideas or help them understand better evolutionary theory…..
Shape up or become part of the bathroom plaster…

I would say in defense of my friend (choke) Lenny Flank, that people like him give PT it’s distinctive character. He is someone that PT should uphold as an example of what PT is all about.

Salvador
PS
See Len, I put in a good word for ya. Where is Great White Wonder these days, I miss him (her?) here at PT.

Comment #97340

Posted by Raging Bee on April 19, 2006 12:01 PM (e)

Your use of “change of shape” is not the same as Plaisted.

This is how Noam Chomsky and his fawning fans respond whenever he’s caught lying: by insisting he actually meant something different from the statement his critics have just debunked or disproven.

It’s also a standard ID/creationist dodge: the ID argument that just got smacked down wasn’t the “real” “theory” of ID; and every refutation of ID only proves that ID is so, so horribly misunderstood.

Comment #97345

Posted by PvM on April 19, 2006 12:29 PM (e)

Sal wrote:

I would say in defense of my friend (choke) Lenny Flank, that people like him give PT it’s distinctive character. He is someone that PT should uphold as an example of what PT is all about.

Man… Sal and Len, separated at birth? So Sal, I hope you are not using Len as an excuse to stop your contributions to PT :-)

Comment #97349

Posted by AD on April 19, 2006 1:07 PM (e)

Sal,

Once again, you are not answering my question about where I can find all of the experimental studies and actual science ID is performing.

Can you expect to be a science if you either refuse to do such work or hide it from everyone? Where do I find this?

Comment #97356

Posted by Tracy P. Hamilton on April 19, 2006 2:18 PM (e)

More on Plaisted’s argument - i.e. calculate that something couldn’t have happened, ergo it didn’t happen and blissfully ignore it!

First let us use an estimate of how many “shapes” proteins have:

“Protein Eng. 1998 Aug;11(8):621-6. A re-estimation for the total numbers of protein folds and superfamilies.

Wang ZX.

National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, Peoples Republic of China.

The issue of the number of protein folds is steeped in controversy despite its significance for understanding evolution and predicting protein structure from amino acid sequence. Using various assumptions, several research groups have tackled this problem with very different results. In the present study, a more rigorous statistical approach is used to address this question. From three different data sets, the total number of protein folds is estimated to be about 650. A detailed theoretical analysis suggests that (i) a random sample of non-transmembrane protein families has been selected for crystallization and structural determination, (ii) except for about 40 folds, most protein folds occurring in nature contain about the same number of different protein families. With the estimation of the total number of protein folds, the number of naturally occurring superfamilies can then be estimated as 1150.”

OK, around a thousand. Based on this, how often does this mean a new fold protein gets made, by some unlikely
occurrence? 4,000,000,000 years by 1000 folds is
one every 4,000,000 years on the whole planet!

Clearly, not getting a new protein fold would not prevent speciation - that occurs much more frequently! There are millions of species today.

Now, I also wonder, are there any differences between
humans and chimps with respect to some new protein fold?
Maybe Salvador and Plaisted would accept that amount
of microevolution?

Finally, I would like to probe Salvador’s understanding of what is meant by “protein shape”, and how proteins evolve. Go to the web page http://www.unc.edu/~traut/EnzymeEvolution.htm and read part A about protein evolution being modular (hint: did Plaisted calculate the probability of new “shapes” using this mechanism?). What the hell, I’ll paste it here:

“A. Modules are structural and ligand-binding units

Several separate lines of data support a hypothesis that modules are small units of local structure, most commonly involved in binding specific ligands.

1. The subunit mass for many enzymes, when divided by the number of identified ligand-binding functions has a distribution around 4 - 7 kDa.

2. For the great majority of exons, the amount of polypetide coded has a distribution around 4 - 7 kDa.

3. The same modular elements are commonly used in many different proteins to form a specific type of ligand-binding site, as for ATP (next section).

The above support a hypothesis that exons code for small functional units of protein structure. Since exons may be shuffled within and between genes, both singly and in combinations, this leads to a model for protein evolution where established functional units may be used in completely novel protein environments by natural recombination and selection.

Our work has supported the above by compiling and analyzing relevant data sets for genes and for proteins.”

Comment #97359

Posted by Salvador T. Cordova on April 19, 2006 2:43 PM (e)

Wamba:

If proteins are so highly constrained, how is it that two versions of a protein can differ in hteor specific sequence at over 80% of their positions, and still share the same overall fold and the same function?

If the average protein has 366 positions (per PZ Myers), 20% implies 73 positions are constraining. A very crude approximation is 1 in 20^73 in terms of that constraint alone. That is substantial.

Further it may be true that in a protein like cytochrom-c that 70 of the 105 or so positions are “unconserved”. That is we find 70 of the positions have variations across species. It does not mean automatically however that these 70 positions can willy nilly be altered and the organism survive. There is a chance neutral theory is wrong in that regard, and that the organisms need to have the protein in that configuration.

Read:
Missense Meanderings

Taken as a whole, recent findings from biochemistry
and evolutionary biology indicate that our understandingof protein evolution is incomplete, if not fundamentally flawed.

Yeah, I’ll say.

Oh, but they have add yet another nasty constraint in addition to folding constraints.

In addition to functional properties, proteins have a wide range of biophysical characteristics, such as stability, propensity for aggregation and rate of degradation. These properties are at least as important as function for cellular and organismal fitness.

Proteins tolerate only narrow ranges of stability, aggregation propensity and degradation rate. Many individual missense mutations perturb these traits by amounts that are on the same order as the permissible range of values, and are consequently common causes of human genetic disease.

The narrow range of tolerance of deviations from optimum characteristics and the significant effects of mutations give rise to a substantial degree of epistasis for fitness. Moreover, mutations simultaneously affect function, stability, aggregation and degradation. For these reasons, mutations might be selectively beneficial on some genetic backgrounds and deleterious on others.

Mutations that change function often do so at the cost of protein stability and aggregation. Compensatory mutations therefore function by relieving the biophysical strain that is introduced by adaptive mutations.

NOTE: They propose a model to solve it, I don’t want to represent that they’re claiming the end of evolution. The model however is nothing more than an affirmation of the cosequent, a proof based on affirming that which one already believes. They simply “solve” one set of problems by displacing it to another set which may actually be even more an unlikely an explanation. I credit their determination however. One of the authors, Hartl, is author of my grad level Population Genetics book. He’s a good guy, though I disagree with him.

Comment #97369

Posted by Anton Mates on April 19, 2006 3:39 PM (e)

Salvador T. Cordova wrote:

Wamba:

If proteins are so highly constrained, how is it that two versions of a protein can differ in hteor specific sequence at over 80% of their positions, and still share the same overall fold and the same function?

If the average protein has 366 positions (per PZ Myers), 20% implies 73 positions are constraining. A very crude approximation is 1 in 20^73 in terms of that constraint alone. That is substantial.

A very crude approximation of what? I can’t see what you’re trying to calculate in the above.

Comment #97375

Posted by wamba on April 19, 2006 3:55 PM (e)

wamba wrote:

What about frame shift mutations? Are you saying that a gene for a protein could not undergo a frameshift mutation, resulting in something substantially different? If you need an example, how about those nylon-digesting proteins?

Salvador T. Cordova wrote:

blah blah blah

Call me an experimentalist if you will, but I’ll take one experimental proof of concept over a full page of hand-waving any day.

Comment #97378

Posted by J. Biggs on April 19, 2006 4:05 PM (e)

Hey Sal:

All you’ve done this entire time is attack evolution (quite poorly I might add). You have not produced one bit of scientific evidence that supports ID (or for that matter scientific evidence that refutes ToE). I for one would be interested in seeing ID “theory” stand on its own. If ID is truly superior to “Darwinism” then produce some research that shows that its a better explanation of observed phenomenon. You can try and refute evolution all you want, but it remains useful to Biologists, while ID apparently has no value whatever. If ID can be shown to be more useful in coming up with novel solutions to biological problems; Evolution will become less prominent. Get to work doing some useful ID research Sal, because disproving Evolution in no way proves your ID creationism true.

Comment #97379

Posted by wamba on April 19, 2006 4:06 PM (e)

If the average protein has 366 positions (per PZ Myers), 20% implies 73 positions are constraining. A very crude approximation is 1 in 20^73 in terms of that constraint alone. That is substantial.

Further it may be true that in a protein like cytochrom-c that 70 of the 105 or so positions are “unconserved”. That is we find 70 of the positions have variations across species. It does not mean automatically however that these 70 positions can willy nilly be altered and the organism survive. There is a chance neutral theory is wrong in that regard, and that the organisms need to have the protein in that configuration.

Wow, it’s got numbers in it, it must be science!

Let’s stick with the cytochrome C example. Suppose each of those unconstrained positions can accept a small number of substitutions, say 3. (Some will be more, some less, 3 seems like a pretty conservative estimate.) That means 70^3 different sequences that could successfully perform the function of cytochrome C. That’s not even accounting for insertions, deletions, etc. That kind of makes your computer password example, where you’re looking for a single solution, look pretty retarded.

Comment #97381

Posted by J. Biggs on April 19, 2006 4:13 PM (e)

That kind of makes your computer password example, where you’re looking for a single solution, look pretty retarded.

I agree, but I think I know of someone (Sal) who will disagree.

Comment #97382

Posted by wamba on April 19, 2006 4:19 PM (e)

That means 70^3 different sequences

Oops, I think that should be 3^70, which still gives a number >> 1.

Comment #97388

Posted by Salvador T. Cordova on April 19, 2006 4:44 PM (e)

Lenny boasts of his skill at persuasion

PVM asks: So what have you done lately Lenny to help ID activists understand either the follies of their ideas or help them understand better evolutionary theory.

Lenny Responds: Nothing. It is quite pointless. In my 20-plus years of anti-creationist organizing, I can count on the fingers of one hand the total number of ID/creationists I have seen actually “understand the folly of their ideas”.

Hey! I’m so glad to hear Lenny is totally useless to PandasThumb. Oops, check that, I mean, PT should do all it can to keep Lenny around. His persuasion skills are exceptional. Any IDist reading his posts will be really attracted to evoltutionary ideas.

Ah but to other matters:

Wamba wrote:

Oops, I think that should be 3^70, which still gives a number >> 1.

3^70 out of how many sequences though?

3^70 / 20^70 = 1 out of 4.72 * 10^57 which is remote and that’s on top of the 35 positions that are likely immutable (20-35 is are the numbers i’ve seen in literature). Oh, but I know, wamba can just refudge numbers to make it more palatable. Well done.

NOTE: I acknowledge up front that 20^X is a crude approximation, a better one is obtained by including considerations for synonymous codons. But the general point of improbability remains. Yockey I think explores the codon issues with the Shannon-MacMillan theorem. I haven’t looked at that in detail recently.

Comment #97399

Posted by Bruce Thompson GQ on April 19, 2006 5:24 PM (e)

So what have you done lately Lenny to help ID activists understand either the follies of their ideas or help them understand better evolutionary theory…..

Lenny correctly reminds us that the major thrust of the anti evolution movement is political and requires a political counter since all the major victories have been in the courts. But this is also a multi-faceted battle with many fronts. We each bring something unique to the discussion, political, legislative, scientific, and educational backgrounds are all needed to combat the growing misperceptions about evolutionary theory and science in general.

Blunting the cultural black lash requires better education which includes the involvement of the scientific community and educators. It requires commitment of legislators to provide the tools to educators and this will only happen with grass roots efforts from local communities. Grass roots organizations exist around the country and scientific organizations are now recognizing the growing threat of the anti evolution movement. But it still comes back to the courts and that’s where Lenny comes in, to remind the anti evolutionists (so they won’t forget) that every time they have tried to slip something in the back door the courts recognized the ploy and stopped them dead in their tracks.

Delta Pi Gamma (Scientia et Fermentum)

Comment #97410

Posted by Steviepinhead on April 19, 2006 5:43 PM (e)

Stated purposes of Panda’s Thumb:

The patrons gather to [1] discuss evolutionary theory, [2] critique the claims of the antievolution movement, [3] defend the integrity of both science and science education, and [4] share good conversation.

Lenny:

In my 20-plus years of anti-creationist organizing, I can count on the fingers of one hand the total number of ID/creationists I have seen actually “understand the folly of their ideas”.

While it would be nice to imagine, as PvM suggests, that Panda’s Thumb and its contributors and commentators, might on rare occasions be able

to help ID activists understand either the follies of their ideas or help them understand better* evolutionary theory,

achieving that idealistic goal is neither one of the stated purposes of PT, nor an objective which any of us would realistically expect to achieve on any regular basis.

A more-realistic objective is to help those unfamiliar with the scientific and political realities which underlie the phony “controversy” to more accurately understand the terms of the debate and the consequences of ignorance and inaction. This might occasionally include assisting those who have thus far been exposed only to the ID/creationist anti-evolutionary sloganeering to realize that there is WAY MORE to the full picture.

Sal’s own blithering butcherings of poorly-digested “scientific” and “mathematical” concepts–and his poorly-concealed religious biases–perfectly epitomize the difficulties involved in breaking down the mental barriers of the more-committed anti-evolutionary spear-carriers.

Lenny’s “20-plus years of anti-creationist organizing,” on the opposite end of the spectrum, certainly help advance PT goals [2] and [3] above. Lenny usually lets the scientific contributors focus on goal [1], though he not infrequently contributes in a pithy fashion to the scientific commentary. With regard to PT purpose [4] I, for one, find Lenny’s conversation far more direct, honest, and humorous than I do the disingenous posturings of the anti-evolutionary trolls.

Despite the consistent vacuity and circumlocution of Sal’s attempts at “scientific reasoning” and his constant failure to produce anything remotely resembling a “scientific theory of ID,” Sal is typically polite, and deserves some minimal courtesy in return. He is not, of course, entitled to any respect whatsoever for his unpersuasive ideas or his stick-in-the-mud ideology. He may arguably deserve some backhanded “credit” for serving as a negative example for lurkers and fence-sitters.

In terms of contribution to the site and its larger mission, therefore, Lenny deserves considerable credit, while Sal, at most, serves only as a flaccid foil.

One would hope the exemplary PvM did not mean to suggest anything to the contrary…

*(presumably “better understand” better expresses what Pim intended here)

Comment #97411

Posted by 'Rev Dr' Lenny Flank on April 19, 2006 5:44 PM (e)

Hey Sal, since you’re so talkative now and all, perhaps you’d like to take a crack at some simple questions for me?

*ahem*

What, precisely, about “evolution” is any more “materialistic” than weather forecasting, accident investigation, or medicine?

What did the designer do, specifically. What mechanisms did it use to do whatever the heck you think it did. Where can we see it using these mechanisms today to do … well … anything.

I can’t think of any scientific advance made in any area of science at any time in the past 25 years as the result of ID “research”. Why is that?

Hey Sal, why is it that all of DI’s funding comes from fundamentalist Christian political groups and Reconstructionist nutjobs?

You once said to me: “We do not see the Designer of life in opreation today as far as I know”.

Why not, Sal? Did it climb back aboard its flying saucer and go home?

Comment #97413

Posted by 'Rev Dr' Lenny Flank on April 19, 2006 5:51 PM (e)

But this is also a multi-faceted battle with many fronts. We each bring something unique to the discussion, political, legislative, scientific, and educational backgrounds are all needed to combat the growing misperceptions about evolutionary theory and science in general.

Yeah, verily.

The creationists are not concerned in the slightest about scientific questions, or about correctly interpreting data, or about forming better explanations and understanding of the natural world. Instead, creationism/ID is a wholly-owned subsidiary of the fundamentalist Religious Right – it is a religious and political movement, not a scientific one, and its goals are entirely religious and political, not scientific. The ID/creationists are a part of a larger political movement with radical theocratic aims, and their anti-evolution and anti-science efforts are, as they themselves declare, simply the “wedge issue” which they have chosen in order to gain entry for their wider anti-democratic political goals. Indeed, the most prominent “intelligent design” group in the United States today, the Seattle-based Discovery Institute, is largely funded by a single extremist Christian fundamentalist billionaire who, for 20 years, preached the Taliban-like idea that the US should repudiate the Constitution, dismantle the wall between church and state, and place the country completely under “Biblical law”, to include such Biblical imperatives as stoning sinners and executing unbelievers or heretics.

Many people have treated the evolution/creation controversy (if they think about it at all) as if it were a scientific dispute – as if the two viewpoints were merely differing ways of interpreting scientific data. (This, in fact, is precisely how the ID/creationists wish to present it.) Scientists in particular have tended to respond to the ID/creationist movement by first ignoring it in the hopes that it would go away, and then with long technical explanations of how the scientific conclusions of the ID/creationist arguments are unsupported, incomplete or just plain wrong. All of the scientific refutations of ID/creationism have not, however, lessened the conflict – if anything, they have heightened it. The reason for this is simple; ID/creationism is not science and it does not have scientific goals. Because of this, it will not be beaten by science or by scientific arguments — these are essentially irrelevant to the real goals of the ID/creationist movement. The ID/creationist movement is a political movement with political goals, and it must be beaten the same way that every other political movement is beaten – by out-organizing it.

I’m a firm beleiver in attacking on all fronts, wherever the ID/creationists are vulnerable – and there are lots of those. Most theologians reject the religious assumptions of the ID/creationists and their fundamentalist base. The IDers have no science to speak of. No one agrees with their political extremism. Many of the prominent IDers spout out things that are, quite frankly, nutty (such as Phillip Johnson’s denial that HIV causes AIDS). The ID movement’s funding comes mostly from fundamentalist extremists and, in the case of the Center for Science and Culture, largely from one single radical ayatollah-wanna-be. Internally, the ID movement’s supporters are an unsteady marriage of convenience between a variety of different religious zealots, most of whom would ordinarily be ready at the drop of a hat to wage Holy War on each other. Their most vocal “supporters” undermine their own legal strategy by preaching their religious opinions at every opportunity.

So attack them on every possible front. Don’t let up for a second, come at them from every possible direction, and don’t give them an instant’s rest. Above all, take the fight to the IDers. It’s not enough for us to be defensive and react to what the IDers do – we need to start setting the agenda and go on the offensive, introducing things that we want and forcing the other side to defend themselves against it.

The only thing that will beat ID/creationism (and all its future derivatives) is an informed public that makes it clear to everyone that it does not want a fundamentalist Christian theocracy, won’t support it, won’t allow it, and will do whatever it takes to prevent it.

Comment #97415

Posted by Lenny's Pizza Guy on April 19, 2006 5:58 PM (e)

Not to mention that, for whatever it’s worth, no Lenny would mean no, uh, ME.

Well, I mean, I’d still be here, but I wouldn’t be here

And, don’t forget, in another week or so, I won’t be here, but PIZZA WOMAN will be!

Comment #97430

Posted by 'Rev Dr' Lenny Flank on April 19, 2006 6:23 PM (e)

no Lenny would mean no, uh, ME.

And vice versa, since if you weren’t around, I would be forced to either (1) learn how to cook, or (2) starve.

;)

Comment #97436

Posted by steve s on April 19, 2006 6:33 PM (e)

http://goodmath.blogspot.com/

Sal, check out that link. That guy’s been wailing on Dembski lately. And that guy’s a computer scientist with a hankerin for math, so he’ll understand all those complicated things the poor dumb biologists don’t. I bet you two will have amus–uh interesting…conversations.

Comment #97515

Posted by Anton Mates on April 20, 2006 12:32 AM (e)

Salvador T. Cordova wrote:

Wamba wrote:

Oops, I think that should be 3^70, which still gives a number >> 1.

3^70 out of how many sequences though?

3^70 / 20^70 = 1 out of 4.72 * 10^57 which is remote and that’s on top of the 35 positions that are likely immutable (20-35 is are the numbers i’ve seen in literature). Oh, but I know, wamba can just refudge numbers to make it more palatable. Well done.

NOTE: I acknowledge up front that 20^X is a crude approximation, a better one is obtained by including considerations for synonymous codons. But the general point of improbability remains.

Sal, this makes no sense. We’re talking about evolvability of an extant functional protein, not random assembly of such a protein from scratch. The total number of sequences is irrelevant; what we want to know is the number of sequences which are close enough to the original to be attainable by one or two mutations, and how many of those retain their function. Sure, there’s a vastly larger set of sequences which are completely unlike the original and lack whatever we defined as its function. So what? A single mutation (barring some massive frameshift or something) isn’t going to give you any of them.

Making a crude approximation here is very simple. If roughly 80% of your protein’s positions can sustain an amino acid swap without loss of functionality, and if about 3 amino acids can be swapped in at each of those positions, then about 80% * 3/20 = 12% of possible single swaps will preserve functionality.

Needless to say, 12% is a whole lot bigger than 1 in 10^[much of anything].

Comment #97532

Posted by k.e. on April 20, 2006 4:10 AM (e)

geez Sal trapped in a corner and what do you do ?
Quite unseemly on your part don’t you think?
Sh*t or get off the pot.

Answer Lenny’s questions

And here are 2 more, how old is the earth 4.5Billion years or some wanky number dreamt up by a crackpot ?
Also do you accept Humans and Chimps have a common ancestor ?

Time to change hands Sal.

Comment #97577

Posted by J. Biggs on April 20, 2006 10:11 AM (e)

Sal wrote:

3^70 out of how many sequences though?

3^70 / 20^70 = 1 out of 4.72 * 10^57 which is remote and that’s on top of the 35 positions that are likely immutable (20-35 is are the numbers i’ve seen in literature). Oh, but I know, wamba can just refudge numbers to make it more palatable. Well done.(emphasis mine)

NOTE: I acknowledge up front that 20^X is a crude approximation, a better one is obtained by including considerations for synonymous codons. But the general point of improbability remains.

Point well taken Sal. And the truth is you can also refudge the numbers to support your Creationist assertions as well. And hence an unending battle of crappy math that has no bearing on what really happens. You talk about probabilities and how improbable it is that even a single protein came into existence by itself. How improbable is it that a God that is infinitely more complex came into existence by itself. Can your math calculate that probability. All this Creationist probability crap basically started after Emil Borel stated in Probability and Life:

When we stated the single law of chance, “events whose probability is sufficiently small never occur,” we did not conceal the lack of precision of the statement.

Meaning phenomena with a very small probability for all practical purposes don’t occur. And ever since Creationists have been trying to prove evolution is impossible using probabilities. However, Borel also states in Probability and Certainty, p. 124-126:

In conclusion, I feel it is necessary to say a few words regarding a question that does not really come within the scope of this book, but that certain readers might nevertheless reproach me for having entirely neglected. I mean the problem of the appearance of life on our planet (and eventually on other planets in the universe) and the probability that this appearance may have been due to chance. If this problem seems to me to lie outside our subject, this is because the probability in question is too complex for us to be able to calculate its order of magnitude. (emphasis mine). It is on this point that I wish to make several explanatory comments.

When we calculated the probability of reproducing by mere chance a work of literature, in one or more volumes, we certainly observed that, if this work was printed, it must have emanated from a human brain. Now the complexity of that brain must therefore have been even richer than the particular work to which it gave birth. Is it not possible to infer that the probability that this brain may have been produced by the blind forces of chance is even slighter than the probability of the typewriting miracle?

It is obviously the same as if we asked ourselves whether we could know if it was possible actually to create a human being by combining at random a certain number of simple bodies. But this is not the way that the problem of the origin of life presents itself: it is generally held that living beings are the result of a slow process of evolution, beginning with elementary organisms, and that this process of evolution involves certain properties of living matter that prevent us from asserting that the process was accomplished in accordance with the laws of chance. (emphasis mine)

Moreover, certain of these properties of living matter also belong to inanimate matter, when it takes certain forms, such as that of crystals. It does not seem possible to apply the laws of probability calculus to the phenomenon of the formation of a crystal in a more or less supersaturated solution. At least, it would not be possible to treat this as a problem of probability without taking account of certain properties of matter, properties that facilitate the formation of crystals and that we are certainly obliged to verify. We ought, it seems to me, to consider it likely that the formation of elementary living organisms, and the evolution of those organisms, are also governed by elementary properties of matter that we do not understand perfectly but whose existence we ought nevertheless admit. (emphasis mine)

Similar observations could be made regarding possible attempts to apply the probability calculus to cosmological problems. In this field, too, it does not seem that the conclusions we have could really be of great assistance.

So basically your probability calculations are useless since they don’t take into account all of the non-random factors predetermined by physics and chemistry. So keep on fudging the numbers, just realize they are meaningless as an argument against abiogenisis or evolution. (credit TOA)

Comment #97599

Posted by Stevaroni on April 20, 2006 11:43 AM (e)

Salvador T. Cordova Said…

LOL! Just like a Darwinist to appeal to Mad Cow disease prions as a selective improvement.

It would be difficult for you to miss the point by any wider margin. Of course mad cow proteins are an improvement - from the protein’s point of view.

This little protein has “figured out” how to reproduce! It couldn’t propagate itself before, now it can. That’s a huge improvement! (are those echos of an abiogenisis argument I hear off in the distance?)

That it kills off it’s host in the process is immaterial, at least as far as the protein is concerned.

You’re making the classic ID mistake that evolution has to somehow have some sort purpose, a higher calling, something to make it an intelligent agent, to be morally contrasted with God.

It doesn’t

It isn’t moral.

It isn’t ethical

It just is.

It doesn’t care if it’s product is pretty, or nasty, or good, or evil. Look at roaches, mosquitoes and bubonic plague. Parasites get just as much play in this game as little baptized babies in Easter bonnets. What matters is that they survive long enough to breed, and that’s the only criteria that evolution judges on.

Comment #97617

Posted by Don Baccus on April 20, 2006 1:53 PM (e)

Someone schooling Sal wrote:

We’re talking about evolvability of an extant functional protein, not random assembly of such a protein from scratch.

Sigh … Sal made THAT false assumption again?

Quit lying for God, Sal.

Comment #97633

Posted by Salvador T. Cordova on April 20, 2006 2:47 PM (e)

PvM wrote:

I agree, registered user, it will be quite a task for Sal or anyone else to address let alone rebut the reverse ordination refutation.

Is that because it’s hasn’t even been made clear what the “reverse ordination refutation” is? Do you know what it is, Pim?

Sal

Comment #97748

Posted by Anton Mates on April 21, 2006 1:41 AM (e)

Sal, just Google “reverse ordination refutation” and follow the link. It’s very straightforward.

Comment #97768

Posted by 'Rev Dr' Lenny Flank on April 21, 2006 7:29 AM (e)

Sal, uh, doesn’t do research.

He just brainlessly parrots whatever the Isaac Newton of Information Theory tells him.

Comment #97770

Posted by Rilke's Granddaughter on April 21, 2006 8:28 AM (e)

Anton Mates wrote:

Sal, just Google “reverse ordination refutation” and follow the link. It’s very straightforward.

True. It leads directly to this thread.

%:-p

Comment #97789

Posted by k.e. on April 21, 2006 10:46 AM (e)

Seriously Sal you are trying to refute the vacuity of ID and you don’t know what the reverse ordination refutation is?

Just admit it you do not have a clue.

Comment #97795

Posted by k.e. on April 21, 2006 11:12 AM (e)

Then of course there is the ridiculous stochastic heuristic fallacy that Heddle, Dembski and Berlinski all fall into.

As though numbers had thoughts or preconceived notions of their own existence.

Sal do Chimpanzees have a common ancestor with humans?

And how old is the earth?

For everyone around here you will note Sal is a very desperate religious apologist and has difficulty answering even the simplest questions

Comment #97796

Posted by Anton Mates on April 21, 2006 11:13 AM (e)

Rilke's Granddaughter wrote:

True. It leads directly to this thread.

Shush, you! We’re trying to educate Sal here.

Comment #97798

Posted by Salvador T. Cordova on April 21, 2006 11:14 AM (e)

Don wrote:

Someone schooling Sal wrote:

We’re talking about evolvability of an extant functional protein, not random assembly of such a protein from scratch.

Sigh … Sal made THAT false assumption again?

Evolvability from existing proteins? Haha. To illustrate DarLogic at it’s finest let’s consider evolving a given protein from something like say the insulin protein. What happens?

Change a few amino acids, oops, cripes the organism is dead. Kinda hard to evolve a dead creature. Oooh, and what if the protein is highly plieotropic (has many multiple functions, and will affect many systems in the critter). Not to mention the sensitivities to change based as described in DePristo’s paper on missense mutations. Ouch! Oh well kill that idea (pun intended). So what’s the recourse?

Duplicate the gene which codes the protein and mutate it and perhaps by chance the gene gets later activated (for no good reason except to rescue a failed theory) and then we hope some function evolves which can fix it in the population. Yeah, nothing like a just so story.

And then after that let’s hope the process can rinse and repeat to take one protein to become another. And thus the otherwise lethal pathway of evolving proteins is avoided by yet another more improbable set of events. Isn’t it wonderful what Natural Selection coupled with imagination can do? Did it ever occur to you guys that starting from scratch is actually a less laughable scenario than trying to evolve an existing protein to a radically different one? DarLogic at it’s finest.

Comment #97802

Posted by PvM on April 21, 2006 11:19 AM (e)

Sal wrote:

Duplicate the gene which codes the protein and mutate it and perhaps by chance the gene gets later activated (for no good reason except to rescue a failed theory) and then we hope some function evolves which can fix it in the population. Yeah, nothing like a just so story.

Is it not fascinating how what Sal considers ‘just so stories’ is actually observed in real nature?

Could Sal remind us of the ID ‘just so story’? Or is there none other than ridiculing science and revelling in one’s ignorance of science and scientific hypotheses?

Comment #97809

Posted by Anton Mates on April 21, 2006 11:28 AM (e)

Wow, that was fast. Sal’s attempts at mathematically supporting his claims vanished like fairy gold at sunrise.

Comment #97810

Posted by k.e. on April 21, 2006 11:33 AM (e)

Ah Sal DarLogic ?
Performing science again without science ?
Sal performs The Group attribution error
or succumbs to the the False consensus effect

These guys here have quite a collection
http://www.absoluteastronomy.com/reference/list_of_cognitive_biases

Comment #97811

Posted by PvM on April 21, 2006 11:36 AM (e)

Some interesting papers on Insulin evolution

Blundell TL, Wood SP. Is the evolution of insulin Darwinian or due to selectively neutral mutation? Nature. 1975 Sep 18;257(5523):197-203.

A model for the evolution of insulin mainly in terms of adaptive processes is discussed. The model depends critically on the relationship of sequence changes to the three-dimensional structure and the role of various parts of this structure in the conversion of the proinsulin molecule to the active form, the storage of insulin, its transport to the site of action and its interaction with a receptor.

Berg J, Willmann S, Lassig M. Adaptive evolution of transcription factor binding sites.
BMC Evol Biol. 2004 Oct 28;4(1):42.

The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. RESULTS: We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background) mutation rate, the selection coefficient, and the effective population size. CONCLUSIONS: The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

De Meyts P. Insulin and its receptor: structure, function and evolution. Bioessays. 2004 Dec;26(12):1351-62.

I present here a personal perspective on more than three decades of research into the structural biology of the insulin-receptor interaction. The solution of the three-dimensional structure of insulin in 1969 provided a detailed understanding of the insulin surfaces involved in self-assembly. In subsequent years, hundreds of insulin analogues were prepared by insulin chemists and molecular biologists, with the goal of relating the structure to the biological function of the molecule. The design of methods for direct receptor-binding studies in the 1970s, and the cloning of the receptor in the mid 1980s, provided the required tools for detailed structure-function studies. In the absence of a full three-dimensional structure of the insulin-receptor complex, I attempt to assemble the existing pieces of the puzzle generated by our and other laboratories, in order to generate a plausible mechanistic model of the insulin-receptor interaction that explains its kinetics and negative cooperativity. Copyright 2004 Wiley Periodicals, Inc.

Comment #97814

Posted by PvM on April 21, 2006 11:39 AM (e)

And a very timely one

Irwin DM. A second insulin gene in fish genomes. Gen Comp Endocrinol. 2004 Jan 1;135(1):150-8.

The recent characterization of diverse vertebrate genomes has revealed the importance of gene duplication in vertebrate evolution. Evidence suggests that a genome duplication event occurred on the lineage leading to teleost fish-species that are often used to understand human biology. The existence of a genome duplication event complicates the use of fish as a model for human diseases as there are often two fish homologues for a single copy human gene. Often the second homologue has not been recognized. Our searches of the near complete zebrafish and fugu fish genomes indicate that both species have two insulin genes. Phylogenetic analysis indicates that the two genes are likely the product of the fish-specific genome duplication. The maintenance of two insulin genes within the fish suggests that the two genes have different functions. Thus the well-characterized insulin genes in some fish species may not be complete homologues of the human insulin gene.

Comment #97817

Posted by PvM on April 21, 2006 11:51 AM (e)

And an oldie
Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Dev Suppl. 1994;:125-33.

All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates. Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

Comment #97818

Posted by PvM on April 21, 2006 11:55 AM (e)

And finally, the scientific literature is full of the ‘just so stories’ ROTFL

Genome Duplication-Driven Evolution of Gene Families: Insights from the Formation of the Insulin Family ROBERT PIOTR OLINSKI, LARS-GUSTAV LUNDIN and FINN HALLBÖÖK Ann. N.Y. Acad. Sci. 1040: 426–428 (2005).

In addition to the two complete genome duplication events, our results showed that subsequent local duplications, rearrangements, and gene losses corroded the regions in question. This corrosion might eventually disguise the paralogous patterns. For example, an analysis of regions flanking the INSL3 and RLN3 genes on human chromosome 19p revealed that additional duplication, together with rearrangements, contributed to the formation process. This duplication took place before the bony fishes diverged from the main vertebrate branch and, of course, after the suggested tetraploidization events. This finding provides support for the 2R hypothesis as compatible with duplications occurring either before or after the proposed genome duplications

Also McRory, J.E. & N.M. Sherwood. 1997. Ancient divergence of insulin and insulin-like growth factor. DNA Cell Biol. 16: 939-949

Studies on the evolutionary pathway of the insulin gene family suggest that insulin and insulin-like growth factor (IGF) became distinct molecules only after the vertebrates arose. A single molecule with identity to both insulin and IGF was reported in amphioxus. To study the origin of insulin, we selected tunicates because their ancestors are thought to be a nodal point in the evolution of vertebrates. This is the first report of separate insulin and IGF molecules from invertebrates. Two cDNAs were isolated from the tunicate Chelyosoma productum: One cDNA encodes a distinct preproinsulin with B, C, and A domains, whereas the other encodes tunicate preproIGF, including all five domains in their proper sequence. Both mRNAs are expressed in the nervous system, digestive tract, heart, and possibly the gonad but not in branchial basket or tunic. Hence, insulin and igf genes have similar expression patterns. In situ methods confirm the polymerase chain reaction evidence that tunicate insulin and igf mRNAs are expressed in cortical cells of the neural ganglion. We conclude that insulin and IGF have maintained separate gene lineages in both vertebrate and protochordate evolution and, thus, a distinct evolutionary history of more than 600 million years.

What has ID done for the diabetes research lately?

Comment #97878

Posted by deadman932 on April 21, 2006 6:42 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #97880

Posted by deadman932 on April 21, 2006 6:47 PM (e)

Hi there, Long-time listener, first-time caller.

Sal Says : “Evolvability from existing proteins? Haha… What happens? Change a few amino acids, oops, cripes the organism is dead. Kinda hard to evolve a dead creature…Did it ever occur to you guys that starting from scratch is actually a less laughable scenario than trying to evolve an existing protein to a radically different one? DarLogic at it’s finest.”

Since Mr. van Meurs has already shown you some interesting sights in the world of insulin evolution, I thought I might point out some other ,older faves. Here’s an oldie but goodie, Sal-baby, you wack-a-doo krazy kreashunist kat: http://www.pnas.org/cgi/content/full/94/8/3485

Chen et al. demonstrate that an Antifreeze Glycoprotein (AFGP) gene from the Antarctic notothenioid Dissostichus mawsoni derives from a gene encoding a pancreatic trypsinogen. There are now known at least four types of fish AFPs (antifreeze proteins) , all apparently unrelated to each other (AFPs types I, II, III, and AFGP). In the case of “type II” AFP’s, they are found in at least three fish: Atlantic herring , smelt , and sea ravens. These AFP’s arose from C-type lectin genes. (Eek! More …evilushuns!!!)

I found this interesting , not only because of the evolutionary implications, but also because protease zymogens like trypsinogen act as autocatalytic systems in organisms like me and you, Sal: Trypsinogen enters the small intestine, and gets a peptide bond cloven and breaks down into trypsin. Trypsin itself then cleaves lysine peptide bonds, and so, once a small amount of trypsin is generated, it participates in cleavage of its own zymogen, generating – more trypsin! Fascinating, eh, Sal?

Sal, really, now. Do you ever read anything other than Chick tracts? The literature is replete with such examples, as even a cursory search by a non-biologist like me shows. Get your bleedin’ head out of your bleedin’ bum and let your bloody brains breathe, Sal. P.S. Would you view this as an example of cooption? I mean, gosh , it kept the li’l fishies alive and all.

Comment #97889

Posted by 'Rev Dr' Lenny Flank on April 21, 2006 7:34 PM (e)

Hey Sal, if ID is science, then why does it get all its funding from fundamentalist Christian political groups and Reconstructionist wackos?

Thanks in advance for not answering my simple question.

Comment #98004

Posted by Don Baccus on April 22, 2006 6:10 PM (e)

Since Sal’s last shot knocked off his penis and lodged in his foot, I thought I’d let him reload and fire again…

me wrote:

Someone schooling Sal wrote:

We’re talking about evolvability of an extant functional protein, not random assembly of such a protein from scratch.

Sigh … Sal made THAT false assumption again?

Care to back up and try again, Sal? :)

Comment #98187

Posted by Salvador T. Cordova on April 24, 2006 2:22 PM (e)

Pvm cited in favor of gene duplication:

And an oldie
Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Dev Suppl. 1994;:125-33.

PvM,

These articles assume the very thing they wish to prove. We call that circular reasoning.

I’m afrraid your offerings only prove that Darwinists think circular reasoning is a valid mode of deduction.

Salvador

Comment #98192

Posted by PvM on April 24, 2006 2:37 PM (e)

Sal wrote:

Pvm cited in favor of gene duplication:

And an oldie

Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Dev Suppl. 1994;:125-33.

PvM,

These articles assume the very thing they wish to prove. We call that circular reasoning.

I’m afrraid your offerings only prove that Darwinists think circular reasoning is a valid mode of deduction.

Salvador

This is rich from an ID activist. It’s ID which calls something complex and thus designed without showing that it matches the complexity criterion.
On the other hand real science observes the fact of gene duplications, and understands how such duplications may find various fates. The fact that we find such exquisite examples of for instance hox gene duplications which explain the many ‘innovations’ in life show that rather than circular reasoning, these findings support an evolutionary paradigm. Sal may object that science is ‘circular’ in the sense that the data support the theory but that’s the power of real science.
Sal may doubt that natural selection is sufficient in explaining these data and I would agree, natural selection is one of various mechanisms which can cause variation to become (permanently) part of the genome. As science is uncovering neutral variations are another important contributor, also biology’s dark matter of cryptic genetic variation may play a role. Then we have selective sweeps were other alleles can become fixated because of a selective sweep elsewhere.

Perhaps Sal’s real problem is that he does not appreciate how real science works. After all being a YECer in spite of all the contrary evidence suggests that there may be some deeper issues here. Perhaps Sal can start by explaining what in these papers is circular and how such circularity affects the scientific nature.

And finally, Sal can provide us with the ID hypotheses in this area? Let him show how vacuous ID is compared to science.

Comment #98194

Posted by CJ O'Brien on April 24, 2006 2:43 PM (e)

These articles assume the very thing they wish to prove.
No, they don’t.
Do you ever get tired of saying the same things over and over? I swear Sal, if Nature hadn’t published that goofy picture of you, I’d take even odds that you did not in fact exist, and were a cut-rate chat-bot.

As it is, I’ll still take it at 3:1.

Comment #98196

Posted by Russell on April 24, 2006 2:50 PM (e)

Perhaps Sal can start by explaining what in these papers is circular and how such circularity affects the scientific nature.

Indeed. I’ve got my popcorn all popped, and got my comfortable computer chair all set. Let the show begin!

Comment #98206

Posted by Bruce Thompson GQ on April 24, 2006 4:55 PM (e)

If it’s cooption there’s some neat nifty goodies in that icon of design, the vertebrate eye. Lens crystalins come in a number of flavors, but there are some taxon specific lens crystallins that are specific to certain groups of organisms. Many taxon specific crystallins are encoded in a single gene which produce both an enzyme and the lens crystallin. The Zeta crystallin, quinone reductase, found in some mammals is transcribed from a lens specific promoter not present in other mammals. The recruitment of quinine reductase required the evolution of a new lens specific promoter allowing expression in the lens. The lens promoters in 2 distantly related species are both found in the same intron but in different places suggesting an independent origin.

In summary, our data indicate that recruitment of CRYZ by the lens was not the result of neutral evolution but rather derives from a selective mechanism. We would further suggest that a primary factor underlying this selective pressure may be the marked elevation in reduced pyridine nucleotides that occurs in the lens as a result
of high CRYZ expression. As has been shown previously, lenses with relatively low levels of reduced pyridine nucleotides appear to be more susceptible to UV radiationinduced oxidative damage than do lenses containing high concentrations of pyridine nucleotides (C. Rao and Zigler 1992). While the molecular mechanism of enzyme/ crystallin recruitment may vary, the fact that the large majority of recruited proteins bind pyridine nucleotides may be of paramount importance. We believe that
greater consideration should be given to the possibility that enzyme/crystallin recruitment is, in general, an adaptive process and that enzyme/crystallins may provide specific benefits to the lens.
Evidence for Independent Recruitment of &-crystallin/Quinone Reductase (CRYZ) as a Crystallin in Camelids and Hystricomorph Rodents
Pedro Gonzalez, P. Vasantha Rae, Susan B. Nun”ez,-t_a nd J. Samuel Zigler, Jr. Mol. Biol. Evol. 12(5):773-781. 1995 .

LDH B is another taxon specific crystallin that is found only in reptiles and birds and also exists as a single copy gene. It is expressed as a house keeping enzymatic activity and a lens crystallin.
The enzyme lactate dehydrogenase as a structural protein in avian and crocodilian lenses
Graeme J. Wistow, John W. M. Mulders & Wilfried W. de Jong
Nature 326, 622 - 624 (09 April 1987)

Duck lens e-crystallin and lactate dehydrogenase B4 are identical: A single-copy gene product with two distinct functions
WILJAN HENDRIKS, JOHN W. M. MULDERS, MICHAEL A. BIBB, CHRISTINE SLINGSB,
HANS BLOEMENDAL, AND WILFRIED W. DE JONG
Proc. Natl. Acad. Sci. USA Vol. 85, pp. 7114-7118, October 1988

Some taxon specific crystallins are the result of duplicated genes. ALDH is the most abundant crystallin in elephant shrews and some rodents. It exists as a duplicated gene with tissue specific expression and the lens crystalline still has enzymatic activity.

As has been suggested for other cases (1, 2), the primary selective pressure for this gene recruitment may have been the modification of the optical properties of the lens in an ancestor of elephant shrews, “diluting” the specialized g-crystallins, to help make a softer accommodating lens. Other benefits may have been protection against the toxic effects of aldehydes resulting from light-induced oxidation of lens components, or generalized anti-oxidant and UV-filtering effects though sequestration of NAD(H) or retinoids in the lens (1, 28, 43, 44). While there may have been selective advantages for the recruitment of ALDH1/h-crystallin in lens, there is no clear advantage to its collateral recruitment as the major ALDH1 expressed in other parts of the eye
A Retinaldehyde Dehydrogenase as a Structural Protein in a
Mammalian Eye Lens GENE RECRUITMENT OF h-CRYSTALLIN
Caroline Graham, Jason Hodin, and Graeme Wistow
Journal of Biological Chemistry Vol. 271, No. 26, Issue of June 28, pp. 15623–15628, 1996.

Then there’s gelsolin, glyceraldye 3 phosphate dehydrogenase, alpha enolase, argininosuccinate lyase, NADPH dependent reductase.

So there are examples of taxon specific crystallins that are recruited from metabolic enzymes by the addition of a lens specific promoter. Others are examples of duplicated genes encoding metabolic enzymes where the duplicate has been recruited to function as a crystallin.

These are all old references, there’s nothing new and cutting edge about this information. If ID has a better mechanism for the occurrence of the taxon specific crystallins and the implications of their distributions i.e. bird/reptile LDHB crystallin, then I would like to hear it. I would like to point out that the bird/reptile relationship extends to alpha and beta chains of alpha crystallin and rhodopsin.

Delta Pi Gamma (Scientia et Fermentum)

Comment #98212

Posted by deadman_932 on April 24, 2006 6:02 PM (e)

Sal says: “ These articles assume the very thing they wish to prove. We call that circular reasoning. I’m afrraid your offerings only prove that Darwinists think circular reasoning is a valid mode of deduction.”

Well, let’s look at the number of fallacies explicit or implicit in those two sentences , Sal-baby.

You mention one citation by PvM, then say “These articles” as if you adressed each example presented to you. You fail to show that even the one article you name contains circular reasoning. By implication, since you use the collective “these,” you are falsely implying that all PvM’s examples are invalid, but you haven’t shown that.

You leap from these fallacious claims to yet another one: That your assertion alone ( without evidence ) of “circularity” enables you to say you have “proven” something…when you have not shown anything at all. You then move from PVM to “Darwinists”, indicting a whole range of people without showing you have a basis for that indictment.

Now stand back and look at the collection of fallacies you used, Sal. To what purpose did you use them? Answer: To show that “Darwinists” argue illogically and ivalidly.

I count at least 5 distinct fallacies in two measly sentences comprising 32 words. And you never *really* address the actual articles cited – you wave your hands and hope they go away?

Comment #98214

Posted by deadman932 on April 24, 2006 6:13 PM (e)

I forgot to add: after you’ve substantively addressed Mr. van Meurs’ articles, you may address the one I cited. Please do so. (Oh, and in the previous post, it should be “invalidly”)

Comment #98226

Posted by 'Rev Dr' Lenny Flank on April 24, 2006 7:17 PM (e)

I’m afrraid your offerings only prove that Darwinists think circular reasoning is a valid mode of deduction.

(yawn) How dreadful.

Hey Sal, if ID is all about science and not religion, then, uh, why does all of its funding come from fundamentalist political groups and Christian Reconstructionist wackos?

Oh, and hey, what part of evolutionary biology is any more “materialistic” or “atheistic” than is, say, weather forecasting or accident investigation or the rules of baseball?

Thanks in advance, once again, for not answering any of my simple questions. I just want every lurker here to see that you are nothing but a loudmouthed coward.

Comment #98326

Posted by Russell on April 25, 2006 9:10 AM (e)

Perhaps Sal can start by explaining what in these papers is circular and how such circularity affects the scientific nature.

Indeed. I’ve got my popcorn all popped, and got my comfortable computer chair all set. Let the show begin!

Sal? Hello?… Sal?
My popcorn is getting stale.

Comment #98495

Posted by PvM on April 25, 2006 12:19 PM (e)

Sal, your audience is awaiting your presentation of data to support your claims. Or will ID remain scientifically vacuous yet once again?
Don’t worry, we have the patience… 10 years and more and counting….

Comment #98568

Posted by k.e. on April 25, 2006 1:41 PM (e)

only 10 years PvM
why not give them until the second coming?
2000 years plus whatever billions of years until its lights out for the universe of circular reasoning is sure to produce something?

Here is a tip Sal the one true test of circular reasoning is it produces mere words and nothing else useful EXACTLY like creationism.

The reason you (Sal) think that creationism is true and science is false is because you are functionally incapable of determining the truth and the reason for that is you believe a lie (creationism) to be true. The reason that lie is created, by religious cults, is to manipulate its followers for fun and profit…. no other reason,the one tried and true method used by priest’s since Adam was a boy.
You have heard of Jim Jones and Scientology and the other cults have you not?
In fact Sal all religions have a cult methodology to inculcate their followers. The way it is done is by manipulating the followers perception of reality, in short form their minds so that the cult determines what is real and what is not by means of social realism otherwise known as cultural engineering…but then you already know that (good christian soldier) Sal, don’t you?
You will do whatever HQ says with no questions asked, just like the good little soldier, salute and execute, no thinking required (or asked for in your case) Sal.
If you were able to think you would realize that practically everything the creo’s tell you is false about science, happens to be true in the real world.

Sal you not only have no idea what circular reasoning is, along with every other topic you have ever expounded on here at PT, I’m beginning to think you are genuinely stupid, your brains are practically useless for anything except saying yes Mr. Dembski.

Comment #98658

Posted by pvm on April 25, 2006 11:59 PM (e)

Keep down the insults and give Sal at least a chance to reply. Perhaps he may even surprise us.

Comment #98697

Posted by Russell on April 26, 2006 9:03 AM (e)

Keep down the insults and give Sal at least a chance to reply. Perhaps he may even surprise us.

Right. But that’s not to say we shouldn’t keep reminding him. Today, for those keeping track, is day 3 since Sal was asked to back up this:

Pvm cited in favor of gene duplication:
Holland PW, Garcia-Fernandez J, Williams NA, Sidow A.
Gene duplications and the origins of vertebrate development. Dev Suppl. 1994;:125-33.

These[sic] articles[sic] assume the very thing they wish to prove. We call that circular reasoning.
I’m afrraid your offerings only prove that Darwinists think circular reasoning is a valid mode of deduction.

Comment #98750

Posted by PvM on April 26, 2006 12:39 PM (e)

Today, for those keeping track, is day 3 since Sal was asked to back up this:

Well, since it took ID 10 years to come up with nothing, I’d wonder how long it will take Sal to come up with a response :-)

Comment #98763

Posted by CJ O'Brien on April 26, 2006 1:13 PM (e)

Maybe the chatbot software needed an upgrade:
TurboGoalposts v.3:16, now QuoteMine Enhanced!

Comment #99102

Posted by PvM on April 28, 2006 1:23 PM (e)

4 days and counting Sal. What better evidence to show that ID is scientifically vacuous as the silence from Sal…

Comment #100698

Posted by PvM on May 13, 2006 3:38 PM (e)

19 days and counting and still no response from Sal

This is rich from an ID activist. It’s ID which calls something complex and thus designed without showing that it matches the complexity criterion.
On the other hand real science observes the fact of gene duplications, and understands how such duplications may find various fates. The fact that we find such exquisite examples of for instance hox gene duplications which explain the many ‘innovations’ in life show that rather than circular reasoning, these findings support an evolutionary paradigm. Sal may object that science is ‘circular’ in the sense that the data support the theory but that’s the power of real science.
Sal may doubt that natural selection is sufficient in explaining these data and I would agree, natural selection is one of various mechanisms which can cause variation to become (permanently) part of the genome. As science is uncovering neutral variations are another important contributor, also biology’s dark matter of cryptic genetic variation may play a role. Then we have selective sweeps were other alleles can become fixated because of a selective sweep elsewhere.

Perhaps Sal’s real problem is that he does not appreciate how real science works. After all being a YECer in spite of all the contrary evidence suggests that there may be some deeper issues here. Perhaps Sal can start by explaining what in these papers is circular and how such circularity affects the scientific nature.

And finally, Sal can provide us with the ID hypotheses in this area? Let him show how vacuous ID is compared to science.

ID indeed seems to be quite vacuous…

Comment #100706

Posted by Henry J on May 13, 2006 5:16 PM (e)

Circular reasoning? That’s something that can happen in attempts at deductive reasoning. But support via evidence is not deductive reasoning, and so “circularity” doesn’t apply to it.

Henry

Comment #106839

Posted by Ricardo Azevedo on June 20, 2006 11:47 AM (e)

Jason Rosenhouse and I have returned to the topic of Salvador’s claims.