Nick Matzke posted Entry 1139 on June 12, 2005 03:03 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/1137

http://www.arn.org/docs/mm/flag_dithani.gifWilliam Dembski has just blogged about a short comment I made this morning on The Thumb answering someone’s question about whether or not a detailed evolutionary model for the bacterial flagellum would deserve a Nobel Prize.  In that comment, I pointed to this long web article I wrote on the evolution of the bacterial flagellum (which is already badly in need of an update), but I said that, no, such a model would clearly not deserve a Nobel, because it would be entirely routine and conventional — simply the application of the current paradigm (modern evolutionary theory) to fill in one more little gap in our knowledge of evolutionary history.  Although creationists don’t realize it, discoveries showing how complex system evolved come out all the time in the scientific literature.  (A number of examples are linked from my comment here.)

Dembski’s post in reply is entitled “To Explain the Flagellum � Just Look Up All the Homologies.”  There are numerous dubious assertions in Dembski’s short post that would take all day to write up, but I just want to focus on one limited point for the moment.  Will the ID advocates admit that they made a mistake in asserting that, except for the 10 proteins of the Type III secretion system, they other 30-40 parts of the flagellum were “unique”?

Dembski first mischaracterizes the evolutionary argument for a complex system like the flagellum as merely looking up related (homologous) proteins. 

This is wrong: Taking my flagellum evolution essay as an example, in addition to reviewing the homologies (something no IDist has ever done — they regularly show their ignorance of the literature on flagellum homologies, see below), it also includes a review of relevant biological analogies, a quantitative analysis of passive and active bacterial dispersal, a step-by-step analysis of function at each stage and the transitions between the stages, and a review of the literature on the types of molecular steps that would be involved in the transitions — origin of new genes with new functions, origin of new protein-protein binding sites, origin of multiple-proteins-required systems, etc.  By showing that all of these micro-processes have been observed to occur in the lab and/or in the wild, and showing that the origin of the flagellum can be broken down into a series of such micro-processes, and showing that function is continuously maintained throughout, I showed that a reasonably detailed model for the evolutionary origin of the bacterial flagellum was perfectly plausible. 

I invite readers to check out Dembski’s hilarious 2003 reply to my essay — he mostly does a page-count analysis, and then chokes out the latest last-ditch, if-all-else-fails ID argument, “Not…detailed…enough!” (This is often soon followed by, “And we’re not going to give you any detail at all about our ID hypothesis, either!”)

Dembski also concludes today’s post with the emergency backup IC argument:

The problem is not a matter of identifying similar parts, but of coordinating them into novel, functional wholes. No literature search of preexisting components will resolve this problem.

(Dembski, "To Explain the Flagellum � Just Look Up All the Homologies")

This is yet another instance of IDists making an unacknowledged retreat (here is another recent example, from Behe) from the original irreducible complexity argument. 

IDists originally claimed that IC systems that were missing parts would have no function, and therefore partial systems would be unselectable by natural selection, and therefore gradual evolution couldn�t produce such systems. This is precisely why Dembski himself, just back in 2003, highlighted what he thought was a great argument against Ken Miller’s essay on evolution of the bacterial flagellum:

It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.

(Dembski (2003), "The Flagellum Unspun")

Dembski is not the only one to make this argument.  In 2004, DI Fellows Scott Minnich and Stephen C. Meyer wrote in an allegedly peer-reviewed article (see my analysis) for a conference proceedings volume,

Natural selection can preserve the motor once it has been assembled, but it cannot detect anything to preserve until the motor has been assembled and performs a function. If there is no function, there is nothing to select. Given that the flagellum requires ca. 50 genes to function, how did these arise?

[…]

Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?

(Minnich & Meyer )

Both of these essays are late enough in the history of ID that they have included backup arguments just in case those protein parts are found (many of the homologies are documented in the big flagellum essay, and although I’m pretty well convinced that most of the IDists never read the essay in any detail, perhaps the general idea reached Minnich and Meyer).  Regardless of the emergency backup argument, both Dembski and Minnich and Meyer thought that “look at all those unique parts” was a pretty spiffy argument.

Behe (1997) shows an example of the original IC argument, in bold form, and shorn of emergency backup arguments:

Without any one of a number of parts, the flagellum does not merely work less efficiently; it does not work at all. Like a mousetrap it is irreducibly complex and therefore cannot have arisen gradually.

(Behe (1997))

It is clear that IDists have tacitly given up on this simple version of the IC argument for the intelligent design of the bacterial flagellum.  They have not, however, ever admitted that they were wrong about the original argument, “flagellum = multiple-required-parts = subset of parts can’t function = no selection = can’t evolve.”  Questions like, “do subsets of flagellar parts have other functions, or not?” are the kinds of simple factual questions that are easily checked, and IDist errors on these questions are common, widely copied, and easily explained.  On the flagellum, the ID people should have found the homologies out for themselves years ago, before the ID critics got around to doing it for them, forcing the ID advocates to drag the goalposts further back.  This kind of basic, endlessly copied mistake, easily explained to anyone willing to pay close attention, is why ID has no chance in science, with well-informed science teachers, or in a real courtroom (the Kansas Kangaroo Court was, of course, something entirely different).

To conclude, I would just like to get the answer to one simple question from Dembski.  Dr. Dembski: do you now concede that your 2003 statement, “The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique” was incorrect, and that, in fact, systems homologous to flagellum subsystems (in addition to the T3SS) are known which do have selectable function?

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Comment #34892

Posted by PvM on June 12, 2005 4:20 PM (e)

Great job Nick at exposing the scientific vacuity of Intelligent Design. ID is retreating quickly into its gaps and front loading now that their ‘Icons’ have come crumbling down. No wonder Dembski is ‘returning to theology’, there is no future in science for his arguments.
I can’t wait for Intelligent Design to be placed on the witness stand. Is Dembski not one of the planned expert witnesses in the Kitzmuller case?
He is becoming a liability I would say…

Comment #34895

Posted by Jon Fleming on June 12, 2005 4:50 PM (e)

Both of these essays are late enough in the history of ID that they have included backup arguments just in case those protein parts are found (many of the homologies are documented in the big flagellum essay, and although I’m pretty well convinced that most of the IDists never read the essay in any detail, perhaps the general idea reached Minnich and Meyer).

This instance of the “big flagellum essay” link is broke.

Comment #34896

Posted by Nick (Matzke) on June 12, 2005 5:01 PM (e)

I fixed the link, thanks.

Comment #34897

Posted by Mike Klymkowsky on June 12, 2005 5:02 PM (e)

Unfortunately, given that ID creationists are not scientists, but rather anti-scientists, it is clear that they feel no allegiance to the standards of honesty, rigor, objectivity, testability or self-criticism to which the scientific community is committed.

(I reflect with some melancholy at the number of beautiful hypotheses I have had to discard, because of annoying experimental results).

First and foremost, they see no need to be critical of the evidence for their own hypothesis (which is surprising, since they appear to have only one). They clearly do not feel that they have to make useful predications about the natural world (which is lucky for them, since it might well end up with them espousing atheism).

Science’s cultural acceptance is due in large measure to its ability to produce tangible, testable, and useful insights and results.

Perhaps we might suggest that they return to the debate when they have developed a prayer-based antibiotic with a cure rate approaching that of atheistic- (that is science-based) drugs. Or maybe a race, to see which approach first leads to a reproducible cure for cancer (oops, I believe they may have already lost that one).

While I firmly believe that arguing with creationists is a futile, I applaud your diligence at not letting such drivel go unanswered.

Comment #34909

Posted by Guts on June 12, 2005 6:28 PM (e)

““The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique” was incorrect, and that, in fact, systems homologous to flagellum subsystems (in addition to the T3SS) are known which do have selectable function?”

Nick, you are forgetting that your essay is riddled with errors when it comes to homology. For example, you look at similar sequences of E. coli FliH (sequence NP_416450) it looks like there is a sequence that has overlapping hits to both FliH (domain COG1317) and to F0F1-type ATP synthase, subunit b, (domain COG0711). But this is most likely a random occurrence, as the FliH hit has a high evalue of 0.01.

Comment #34910

Posted by PvM on June 12, 2005 6:58 PM (e)

Yawn… Nelson, you’re missing the point. Even if you contest a few of the homologies under the argument ‘your essay is riddled with errors’, Dembski’s retreat is really the topic. See this link for homology data

Comment #34917

Posted by Alex Merz on June 12, 2005 7:57 PM (e)

What’s up with that idiotic flagellum animation? How is it that the motor’s rotor is rotating, but the hook is not?

Comment #34921

Posted by Guts on June 12, 2005 8:22 PM (e)

Pim as usual your comments and link are completely irrelevant.

Comment #34923

Posted by Nick (Matzke) on June 12, 2005 8:25 PM (e)

Actually, Nelson, recent research findings seem to have vindicated my contention that FliH is probably homologous to the F0-b subunit of the F1F0-ATPase.

YscL is a member of the FliH family of proteins. In flagellar systems, FliH binds to and regulates the activity of the ATPase FliI [57], and YscL is also known to bind to YscN [54]. PSI-BLAST searches across the NCBI’s non-redundant database with YscL fail to identify any homologue in the LEE system, because of contamination with low-complexity eukaryotic proteins. However, if the PSI-BLAST search is restricted to bacterial proteins, after one iteration, YscL appears in the results list (15% identity 29/184 residues; e value 0.002). After two iterations, several more FliH homologues are found. Furthermore, consistent with the recent suggestion that the YscL-YscN interaction mirrors similar interactions in other ATPases [54], weak similarity is also reported between Orf5 and several F0 ATPase b subunits (data not shown). A multiple alignment confirms the presence of conserved residues within FliH, YscL and Orf5 (Figure 5). It thus seems likely that Orf5 is a homologue of YscL and FliH, plays a similar role (Table1, Figure 1) and should be re-named EscL.

[…]

54. Jackson MW, Plano GV: Interactions between type III secretion apparatus components from Yersinia pestis detected using the yeast two-hybrid system. FEMS Microbiol Lett 2000, 186:85-90.

(Pallen et al. 2005, “Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.” BMC Microbiology, 5:9.)

The point goes to Matzke on FliH, it appears. (And I do believe I cited Jackson and Plano (2000) myself, so it wasn’t even a novel idea.)

Like I said in the essay, the case for flagellum-ATPase homology is strongest for FliI and F1-alpha/beta, then FliH and F0-b, then FliQ and FliR with F0-c and F0-a, respectively. Mike Gene makes a convincing case that there is no reason to favor homology for F1-gamma, -delta, and -epsilon, with flagellum proteins, but I made it clear in the essay that homology for these last three proteins was particularly speculative. Gene’s case against all the others is not convincing, and the unexpected discovery last year that the T3SS uses proton motive force in protein export (!!!) makes the whole question of homology between T3SS and the F1F0-ATPase much more interesting. Based on the hypothesis of homology between F0-c and FliQ, I will stick my neck out and predict that FliQ is the proton channel in the T3SS. We’ll see how things turn out, I guess.

Here’s a project for you, Nelson: go through the 50 or so flagellum proteins in the “canonical” E. coli flagellum and tell me how many of the proteins are both (a) required for flagellum function in all bacteria, and (b) “unique”, with no evidence of homology to nonflagellar proteins published in the peer-reviewed literature. Hint: it’s a low number.

Comment #34926

Posted by Steve on June 12, 2005 8:44 PM (e)

Here’s a project for you, Nelson….

What?! Actual research. What a novel idea.

Comment #34929

Posted by PvM on June 12, 2005 8:57 PM (e)

Nelson without Mike Gene’s “hand holding” seems to be somewhat of a fish out of the water :-)
My links were as relevant as your comments my dear friend and I also addressed your confusion as to the topic of the thread.
Of course, Matzke has shown that his prediction seems to have found supporting evidence. Perhaps you can take up the project Nick has suggested to you?

Comment #34939

Posted by Stuart Weinstein on June 12, 2005 10:29 PM (e)

Alex writes: What’s up with that idiotic flagellum animation? How is it that the motor’s rotor is rotating, but the hook is not?

If what you mean by the “hook” is what I think you mean, the “hook” from which the flagella is extended may be a “protein” sheath or some such thing. It doesn’t have to rotate with the “gears” or the flaglella..

Course, I’m just a geophysicist, and feel free to tell me to mind my own business..

Comment #34940

Posted by Timothy Scriven on June 12, 2005 10:32 PM (e)

I would still maintain that such a discovery would be worth a nobel prize on the grounds that it would perhaps be the most detailed and meticilous model of evolution in action so farproduced. It’s true it would have little practial import on the rest of microbiology but it would have much value as a inspiration for further research.

A detailed explanation of the fallgela would hence be valuable as a archetype, a plan for further plans of a similar sort, I would hold that it would be on those grounds deserving of a nobel prize. I am not a microbiologist, in fact I am a high school student, so please don’t take my comments too seriously.

Comment #34949

Posted by Timothy Scriven on June 13, 2005 12:35 AM (e)

this is probably the closest I’ll ever get to celebrity so I might as well put down my thoughts on my comments. Firstly I’d like to respond to that “Pastor” guy who attacked my spelling. The post was written at 10:30 at night, for the medium of a blog, by a 17 year old whose not even doing biology as a subject, give me a break!

Secondly I’d like to respond to his claim that the problem has already been solved. Yes the basic fragments have been created by they still need to be synthesised. In addition a lot more detail would need to be added. Mr Pastor also claimed ( to my memory) that such solutions are everyday. They probably are in other areas of biology but I’ve been led to believe by no less a rationalist authority then Daniel Dennet that such explanations are rare in microbiology. I think the good pastor fails to understand what I suggesting, not just a brief basic solution but a meticulously detailed minute step by minute step analysis.

To my very limited knowledge nothing like this exists in the literature. Indeed I’ve heard a lot of you guy’s at panda’s thumb claim that such a thing is impossible and that creationists are unrealistic to demand it, raise the bar for yourselves! I think it could be done. There would be no guarantee that the outlined path was the one the flagella actually took but as a theoretically demonstration of the conceptual failure of “Irreducible complexity” it would be priceless, science education would be saved, at every school board hearing it could be presented in slide show form. As I understand it the rules of the Nobel prize mean that it would not be eligible to actually win ( and besides, as Nick reminded me there is no Nobel prize in biology) but I never said that such a explanation of the flagella would have a chance of winning, only that it would deserve to win.

Comment #34959

Posted by Alex Merz on June 13, 2005 1:49 AM (e)

Stuart, the hook rotates. The first experimental demonstration that the flagellar motor is rotary was obtained when a mutant bacterium with the hook but without the flagellum was attached to a glass slide by anti-hook antibodies. The attached bacteria rotated with respect to the slide.

If the motor is turning, the hook is rotating. The animation is completely wrong.

Comment #34962

Posted by Alex Merz on June 13, 2005 2:42 AM (e)

To be clear: someone clearly put a lot of effort into the flagellum animation, but apparently could not be bothered to take a little time to get the biology consistent with what was known thirty years ago.

Comment #34967

Posted by Pastor Bentonit on June 13, 2005 6:01 AM (e)

TScriven wrote:

this is probably the closest I’ll ever get to celebrity so I might as well put down my thoughts on my comments. Firstly I’d like to respond to that “Pastor” guy who attacked my spelling. The post was written at 10:30 at night, for the medium of a blog, by a 17 year old whose not even doing biology as a subject, give me a break!

Please accept my apologies.

such explanations are rare in microbiology. I think the good pastor fails to understand what I suggesting, not just a brief basic solution but a meticulously detailed minute step by minute step analysis.

To my very limited knowledge nothing like this exists in the literature. Indeed I’ve heard a lot of you guy’s at panda’s thumb claim that such a thing is impossible and that creationists are unrealistic to demand it, raise the bar for yourselves! I think it could be done.

Agreed, the more scientific progress, the more detailed explanations can be expected. However, the “La la la I can´t hear you”-crowd (ID as well as “ordinary” creationists) will likely never be impressionable (see below). Although, I guess there is a real problem “winning” the general public on matters of science. Alas, I´m from Sweden where we have practically no political impact from creationists as school (science) curricula are firmly reality/reason-based over here. I am truly sorry for you in the U.S.A, you have an anti-enlightenment movement on the roll, as is evident from daily perusal of PT comments and news items. I wish you good luck!

There would be no guarantee that the outlined path was the one the flagella actually took but as a theoretically demonstration of the conceptual failure of “Irreducible complexity” it would be priceless, science education would be saved, at every school board hearing it could be presented in slide show form.

Sadly, school board officials touting ID stickers and whatnot, are unlikely to accept neither any current evolutionary explanation of biological observations; nor any future (possibly improved) explanations, that are in conflict with their religious views. In fact, we can be reasonably sure that they would not know a sufficiently detailed “evolutionary path to the flagellum” if it jumped up and bit them on the…nose. This is painfully obvious from numerous posts here on PT.

Comment #34971

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 7:14 AM (e)

Hey Paul, are you ever going to answer my questions? Why is the ID movement called the ID movement if, as you say, there isn’t any ID theory?

Where can we see a public repudiation by Ahmanson of any of the nutty extremist ideas he’s held for the past 20 years? What parts has he repudiated, according to you, and why. More importantly, what parts has he NOT repudiated, according to you, and why NOT?

Comment #34985

Posted by PvM on June 13, 2005 10:29 AM (e)

Lenny: Nelson refers to Nelson Alonso not Paul Nelson

Comment #34991

Posted by Glen Davidson on June 13, 2005 11:41 AM (e)

Dembski (with Nelson) demonstrates his obtuseness and ignorance yet again. Well gee, “designers” do use “design components” in fairly novel productions. Of course they do, dim, dim Dembski, which is why we don’t just say that something was “designed by humans”, rather we attempt judicial, psychological, and scientific explanations for “human design”, instead of simply believing that “intelligence” is the cause of “design”.

Dembski’s mindlessness begins long before his resort to “ID” for biological organisms, in that he has not a clue that “design” is not really a scientific explanation per se, but that “design” is a placeholder for what we don’t yet know about how and “why” certain organisms produce certain things. That is to say, Dembski’s essentially in the scholastic tradition throughout, who thinks that shortcut words like “intelligence” and “design” are answers to questions, which is why the obtuse fellow doesn’t even have any curiosity about intelligence and its evolution. To be sure, he might “want” intelligence to be a “Ding an sich” (to use Kant’s phrase), or he might simply not be sophisticated enough to recognize what science and philosophy do. Either way, though, it’s the same in the end, that he’s too ignorant to ask why humans copy designs. And evidently he is both too prejudiced and ignorant to ask why God would stupidly co-opt “designs” that are not obviously suited to become the new “design”. Again, if I were religious I think I’d take his view of God as the most offensive of all his thuddingly idiotic claims.

This is a different sort of projection than the usual psychological projection–Dembski wants to force his lack of understanding onto society. It is in this way that the mindless one could become the Newton of information science–by dumbing down everything and everyone else to his level.

Of course Dembski’s too dishonest and/or ignorant to consider homologies properly. Contrasting with homologies found in organisms, intelligent folk know why languages (at least European languages) have a much broader range of sharing of “design traits” than do typically genomes, which is because minds can transfer useful and/or intriguing words between languages. Horizontal gene flow is much more restricted than is word flow in the typical case.

Something as obtuse as Dembski’s “understanding” of biology is, cannot follow the meaning of homologies, however. Designers of limited intelligence (like humans) use designs without regard for origin (aside from copyright law, custom, etc.), while evolution is restricted to using inherited information plus a limited amount of variation and horizontal transfer.

How does anyone even as ignorant as Dembski know that anyone quoting or even paraphrasing Isaiah 7:14 is ultimately dependent on the Bible for that string of words? This is because, in spite of all his prejudice and lack of scientific understanding, Dembski knows that something with as many specific points of correspondence as a Bible verse has derive from the original source. This is true even of “human designs”, that in fact it requires a sort of “evolution” for there to be even a derivative line of text that shares a considerable correspondence with Isaiah 7:14.

This is also true of even 10 proteins of the flagellum, as well as the ones that Dembski appears to be ignorant of (why doesn’t anyone ever write of what Dembski shows that he knows? Surely he must know some things, but clearly he’s mostly blithering in areas where he evidently knows nothing of note). They must have derived from the apparent source with which they share many specific correspondences (the true story behind “specified complexity”), and this would be so even for a “designer” kludging together a system.

The trouble is that the appallingly ill-educated Dembski doesn’t have the slightest evidence that some homologies, like those of Death Valley pupfish, are due to evolution, while others are due to some “designer” who is far more limited in scope than are even human designers.

Of course he needs this idiot savant “designer” to “explain” why the doofus is both so very intelligent as to be able to “design” a working flagellum, while being far too unintelligent and/or perceptive to use new parts and designs, or even to borrow “designs” outside of the bacterial lineage, in order to do so. Note again the likely projection of Dembski’s very narrow education and intelligence and near-total lack of imagination onto his “God”. His “God” fits into his almost complete lack of understanding of science, thus he invokes this “God” without any regard for science or for the likelihood that a real God might surpass Dembski’s prejudice and ignorance.

But anyhow, even Dembski probably would admit that pupfish share so much genetic information because of their relatedness to each other. Dembski turns around and claims that flagella share data with other protein complexes due to a “designer”, without a smidgeon of evidence that the same explanation doesn’t apply across the genomes of organisms.

That he doesn’t feel the need to validate his different interpretation of data from the same source indicates his utter lack of regard for science and its careful treatment and interpretation of data. To him, similarities mean one thing in pupfish morphology, quite another thing in the flagellum. As such he’s pseudoscientist of the first order.

Comment #35028

Posted by Ronald Newland on June 13, 2005 2:22 PM (e)

I am a strong advocate of evolutionary biology and its teaching and consider myself a secular humanist. I say this to assure you that I have a sincere question.

I have been reading Ernst Mayr’s recent book “Toward a New Philosophy of Biology: Observations of an Evolutionist”. Possibly spurred by this a thought occurred to me that was new to me. It concerns the irreducible complexity bogus issue and how to argue against it.

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either. I refer to human designed and created artifacts. Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins? We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

All this is by way of preface to the problem that occurred to me. I ask this sincerely as one who is a natural materialist and atheist. How does one counter an argument put forward by intelligent design advocates that goes as follows?

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I await your refutation anxiously,

Ronald Newland

Comment #35029

Posted by Wislu Plethora on June 13, 2005 2:37 PM (e)

Ronald wrote:

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

Why would you want to compare living and nonliving things in this regard? Both the brain and the comb give the appearance of having been designed, but no one ever saw a pair of combs reproduce.

Comment #35031

Posted by Glen Davidson on June 13, 2005 3:00 PM (e)

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either. I refer to human designed and created artifacts.

No, that is not right. Human designed artifacts are indeed considered to be a part of the evolution of matter/energy, as is “biological evolution”. We split the various areas of study up for our convenience, not because we are not a part of the “evolution of matter”.

Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins?

See, this is why I have to at least wonder if you are what you say you are. How is “regularity” supposed to be evidence for “design”? Regularity can be the opposite evidence, evidence for nondesign, as we might see in a “perfect crystal”. Which means that I’m not sure what you’re getting at.

Is a seeming spear point regular enough to put it outside the possibility of natural, non-human origins? What does that mean? Archeology often enough has difficulty distinguishing between crude human artifacts and “natural objects”. In fact there was a cave found in France that was thought to have been the abode of tool-making Homo species, which from various evidences was later discovered almost certainly not to be. The “tools” were merely broken rocks, having “regularity” for little reason other than the fact that the internal structure of many rocks is fairly uniform, cleaving, or otherwise fracturing along a fairly consistent surface.

We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

Yes, generally we make rather simpler artifacts than one would expect of evolution. And why are you saying that an anthropologist would attribute a comb to “human intelligent design”? That’s not really the issue (though an anthropologist might indeed say it, since what “intelligence is” does not belong to anthropology) for science has to deal with questions of what “intelligence” is rather than simply crediting “intelligence”. Btw, I covered enough of that in my own post, which I have to wonder isn’t the source of these “questions”. I answered some of what you asked, and you responded by using terms and “science” in a manner that simply shows that you don’t understand science.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I await your refutation anxiously,

Yeah, sure, what a troll! Anyway, I did refute it, and though I can see that you didn’t understand a good intelligent refutation, here is part of it again:

Designers of limited intelligence (like humans) use designs without regard for origin (aside from copyright law, custom, etc.), while evolution is restricted to using inherited information plus a limited amount of variation and horizontal transfer.

How does anyone even as ignorant as Dembski know that anyone quoting or even paraphrasing Isaiah 7:14 is ultimately dependent on the Bible for that string of words? This is because, in spite of all his prejudice and lack of scientific understanding, Dembski knows that something with as many specific points of correspondence as a Bible verse has derive from the original source. This is true even of “human designs”, that in fact it requires a sort of “evolution” for there to be even a derivative line of text that shares a considerable correspondence with Isaiah 7:14.

This is also true of even 10 proteins of the flagellum, as well as the ones that Dembski appears to be ignorant of (why doesn’t anyone ever write of what Dembski shows that he knows? Surely he must know some things, but clearly he’s mostly blithering in areas where he evidently knows nothing of note). They must have derived from the apparent source with which they share many specific correspondences (the true story behind “specified complexity”), and this would be so even for a “designer” kludging together a system.

The trouble is that the appallingly ill-educated Dembski doesn’t have the slightest evidence that some homologies, like those of Death Valley pupfish, are due to evolution, while others are due to some “designer” who is far more limited in scope than are even human designers.

Of course he needs this idiot savant “designer” to “explain” why the doofus is both so very intelligent as to be able to “design” a working flagellum, while being far too unintelligent and/or perceptive to use new parts and designs, or even to borrow “designs” outside of the bacterial lineage, in order to do so. Note again the likely projection of Dembski’s very narrow education and intelligence and near-total lack of imagination onto his “God”. His “God” fits into his almost complete lack of understanding of science, thus he invokes this “God” without any regard for science or for the likelihood that a real God might surpass Dembski’s prejudice and ignorance.

But anyhow, even Dembski probably would admit that pupfish share so much genetic information because of their relatedness to each other. Dembski turns around and claims that flagella share data with other protein complexes due to a “designer”, without a smidgeon of evidence that the same explanation doesn’t apply across the genomes of organisms.

The fact is that there is no single factor distinguishing between designed and evolved objects, rather there is science and getting down to working with the evidence. The reason you’re so unbelievable as a sock puppet for someone else is that you appear not to know the slightest bit about science and the “natural materialism” you claim. And that you apparently asked all that stupid uncomprehending nonsense after I had just answered most of it.

Comment #35032

Posted by Flint on June 13, 2005 3:06 PM (e)

I think Ronald Newland asks a good question. So once again, I suggest that if Dembski (or I) were to land on an alien world where we saw nothing familiar, we would have no database of experience against which we could decide if any particular thing we saw were designed, natural, or something else. We might very well not be able to identify the proper boundaries of the thing either. The question of whether we could even identify an alien, much less distinguish one of their artifacts from whatever might be natural on that planet, is probably unanswerwable. We would probably march right up to the nearest zorrgle and try to communicate, while the actual aliens did the equivalent of rolling on the floor laughing.

Even watching zorrgles reproduce might not be sufficient. Plenty of inorganic things reproduce in various ways. And so I would expect we’d need to answer Ronald’s question the hard way: By having thousands of specialists collect millions of data for decades, to build the base of knowledge necessary to generate best-fit explanations with a high likelihood of being correct.

And incidentally, this is why Dembski has never even tried to apply his Explanatory Filter to anything remotely ambiguous, nor has anyone else. Dembski’s Filter works ONLY when the answer is already known (on the basis of substantial evidence if by scientists, on the basis of declared religious doctrine if by Dembski), and not before. Indeed, there are objects archaeologists exhume fairly commonly, which may or may not be artificial. Was this rock a tool? A tool to do what?

So there is no glib answer to Ronald’s question. We know the comb is artificial because of specific knowledge we have about combs. We know the brain evolved because of specific knowledge we have about the evolution of brains. We do NOT know about zorrgles for lack of any specific knowledge about them at all.

Comment #35033

Posted by Steve Reuland on June 13, 2005 3:09 PM (e)

Ronald Newland wrote:

nthropology uses the regularity of found objects as proof of human, as opposed to natural, origins.

I don’t think this is quite the case. On some occasions, we may use the presence of achaeological artifacts as evidence for the presence of humans, but for the most part, evidence of their human origins is independent. We know that humans exist and we can discover the precise mechanisms by which they create certain artifacts. We don’t attribute intelligent design to a spear point because we can’t think of any natural means by which they may have come about (things that look like spear points can be created by natural weathering, afterall) but because we already know how they come about.

If we were to find some putative “designed” object in a place where we know that humans could never have been (such as in strata that’s a hundred million years old) then we would not immediately jump to the conclusion of “intelligent design”. We would probably prefer some other hypothesis until such a time as a “design” hypothesis could be substantiated. There are many examples of things that look designed at first glance but actually aren’t. We blogged about some of these previously.

The way things work in the real world is that we compare competing hypotheses. Any design hypothesis must have some sort of evidence in favor of it or else it’s no better than some natural hypothesis that relies on mysterious, hitherto unseen forces. What it really comes down to is that ID cannot be substantiated by trying (and failing) to rule out natural hypotheses. In order to be acceptable, ID must present a better hypothesis with its own independent evidence. Only then can it be compared to competing hypotheses and (possibly) found to be superior. This is something that ID advocates have been either unwilling or unable to do, preferring instead to use a purely negative approach by which they argue against evolution, and then claim ID true by default.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I wouldn’t maintain that a pencil or a comb are evidence of “intelligent design”. If I were to find such objects without any prior knowledge of what they were or where they came from, I would consider them an unexplained mystery until such a time as I was able to test hypotheses about their origin. Knowing that humans use them – and that humans built them – kind of makes it a no-brainer. But it’s different for something whose origin goes back millions of years and has no identifiable designer.

Here is something that is often overlooked: We know for a fact that individual brains are not designed. We know this because we see them develop and arise spontaneously within biological organisms. Organisms and their components don’t come from a deity’s manufacturing plant, they come from their parents’ genes. The only way in which we know that biological organisms arise is through birth.

So what exactly is being “designed”? It’s never really clear. I know that I wasn’t personally designed. But was my species somehow designed? Some of our ancestral genes? Maybe a primordial unicellular organism was designed and then everything evolved naturally since then. All of these notions and more have been put forth by ID advocates, but they are inconsistent.

Given that we lack anything resembling a coherent theory of ID, there’s just nothing to compare to the already successful and well-evidenced hypotheses that we do have.

Comment #35035

Posted by harold on June 13, 2005 3:17 PM (e)

Ronald -

“How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?”

I don’t understand your logic. There’s no limit on how simple a human designed object can be. Are you seriously suggesting that we take the most simple possible human designed objects (which would be far, far less complex than pencils and combs) and conclude that everything more “complex” must have been magically “designed”?

Why do you think that something “complex” had to be “designed” in the first place? Can’t you think of complex things that clearly arise spontaneously? Since human designed objects are not necessarily characterized by greater “complexity” than natural objects, why do you use “complexity” as a test for “design” at all?

How do you measure complexity in this regard? What is the threshold of complexity at which you conclude that something was “designed”? Who is the designer? How does he or she design? How can we test your answers? If you use terms like “specificity”, “complexity”, “organized”, or “ordered”, please define these traits and explain how to quantify them.

Comment #35036

Posted by Steve Reuland on June 13, 2005 3:18 PM (e)

Ronald Newland wrote:

nthropology uses the regularity of found objects as proof of human, as opposed to natural, origins.

I don’t think this is quite the case. On some occasions, we may use the presence of achaeological artifacts as evidence for the presence of humans, but for the most part, evidence of their human origins is independent. We know that humans exist and we can discover the precise mechanisms by which they create certain artifacts. We don’t attribute intelligent design to a spear point because we can’t think of any natural means by which they may have come about (things that look like spear points can be created by natural weathering, afterall) but because we already know how they come about.

If we were to find some putative “designed” object in a place where we know that humans could never have been (such as in strata that’s a hundred million years old) then we would not immediately jump to the conclusion of “intelligent design”. We would probably prefer some other hypothesis until such a time as a “design” hypothesis could be substantiated. There are many examples of things that look designed at first glance but actually aren’t. We blogged about some of these previously.

The way things work in the real world is that we compare competing hypotheses. Any design hypothesis must have some sort of evidence in favor of it or else it’s no better than some natural hypothesis that relies on mysterious, hitherto unseen forces. What it really comes down to is that ID cannot be substantiated by trying (and failing) to rule out natural hypotheses. In order to be acceptable, ID must present a better hypothesis with its own independent evidence. Only then can it be compared to competing hypotheses and (possibly) found to be superior. This is something that ID advocates have been either unwilling or unable to do, preferring instead to use a purely negative approach by which they argue against evolution, and then claim ID true by default.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

I wouldn’t maintain that a pencil or a comb are evidence of “intelligent design”. If I were to find such objects without any prior knowledge of what they were or where they came from, I would consider them an unexplained mystery until such a time as I was able to test hypotheses about their origin. Knowing that humans use them – and that humans built them – kind of makes it a no-brainer. But it’s different for something whose origin goes back millions of years and has no identifiable designer.

Here is something that is often overlooked: We know for a fact that individual brains are not designed. We know this because we see them develop and arise spontaneously within biological organisms. Organisms and their components don’t come from a deity’s manufacturing plant, they come from their parents’ genes. Living things are different than human-made objects, and therefore analogies between them don’t work very well.

So what exactly is being “designed”? It’s never really clear. I know that I wasn’t personally designed. But was my species somehow designed? Some of our ancestral genes? Maybe a primordial unicellular organism was designed and then everything evolved naturally since then. All of these notions and more have been put forth by ID advocates, but they are inconsistent, and never well developed.

Given that we lack anything resembling a coherent theory of ID, there’s just nothing to compare to the already successful and well-evidenced hypotheses that we do have.

Comment #35037

Posted by Glen Davidson on June 13, 2005 3:26 PM (e)

I tend to believe that many alien objects would be identifiable as “designed”.

There is one very crucial factor in identifying design, however, and it is one that the IDists attempt to obscure. And this is that we can identify design only where we don’t have a non-design explanation for something. Take a cube, for instance.

Suppose we find a nearly perfect cube made out of limestone just sitting in the desert. I mean a chunk like those being used in fine Egyptian palaces. Do we believe that it was designed? Certainly so, and if it was a large block of genuine limestone found on glorph, we would have good reason to suspect that it was “designed” as well.

But suppose I find a nearly perfect cube of iron pyrite? Do I have any reason to suspect that it was designed? In fact it could have been, and yet if the tool marks have been rubbed off one could not tell the difference.

With life it’s different, though, because we have the strong genetic evidence for evolution by natural selection (as good as textual evidence between Biblical manuscripts), and we have no evidence that life can be designed. It’s the method that is known to produce new forms of life that IDists oppose, only hoping to replace it with a “method” not know to be capable of producing life out of other life at all.

That is to say, we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines. We can distinguish distinct “intelligently made” artifacts from evolution quite readily. We never look at fish bones from the archeological record that retain cellular level complexity with having been designed. So our “Newland” troll is misusing his analogy, in that we have no problem differentiating between life and design at the present human level.

Maybe highly advanced aliens could make life indistinguishable from evolved life. First, I’d like to know why they’d bother, but maybe they would. Secondly, it would be nothing fundamentally different from our making cubes as good as the cubes sometimes found as “natural crystals”–it would just be much better mimickry than we are now capable of effecting.

Comment #35040

Posted by Ronald Newland on June 13, 2005 3:39 PM (e)

Thanks you both for your replies. I am indeed as I described and am not a troll. I haven’t read any posts by anyone else here and I apologize for that. I know it is proper etiquette to read before posting.
I really meant my question a a simple one and not with hidden traps of any kind.

My comment about anthropologist was not meant to be obtuse. It is a common scientific problem in this field to try to decide if an artifact was created by man or not. Another way of asking that is, “does it exhibit any features that are not likely to have been caused by non human forces?”

I did misspeak at least one place as was pointed out. Of course, science views all matter and objects as ultimately being caused by the Big Bang and subsequent evolution of the cosmos. But, it is common to divide the cosmos into living and non-living, the living being created by organic evolution. I was just pointing out that another way of dividing the matter of the cosmos is into non-human designed, organically evolved and human desiigned. These are three mutually exclusive and exhaustive categories.

One comment said that we know the comb is artificial. But this is just another word for human designed. I think that supporters of evolution should be a little more precise in their description of the types of “things” in the universe so as not to allow for attacks by IDers such as I tried to describe.

Ron Newland

Comment #35045

Posted by Flint on June 13, 2005 4:19 PM (e)

Glen Davidson:

we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines.

Permit me to disagree very strongly. The ONLY basis we have for such identification is our own experience. So you are saying “An alien planet would be sufficiently similar to our own experiences so as to support qualified judgment.” But my point was that this hypothetical alien planet had NO OVERLAP with ANYTHING in our experience.

And I insist that until we accumulated some relevant knowledge, we could do no better than random in guessing which are the aliens, which are the artifacts, and what might be natural.

This is an important point. IF we had intimate knowledge of the Designer and His methods, and if that knowledge indicated that He gets his kicks creating life as we know it, we would surely change our minds and find that we are intelligently designed after all. So if you are arguing that we could reliably identify alien organisms on the basis of no prior experience, I suggest you are simply wrong.

Comment #35046

Posted by Glen Davidson on June 13, 2005 4:40 PM (e)

Well, Ron, I’ll tentatively take you at your word (in spite of the oddly IDist sounding language) and apologize for writing that you’re a troll. Trouble is, “Simon” has been lurking, and it seemed strange that you’d be leaping from simple regularities to complex brains without any reasonable linkage between the two, much as IDists do. But hey, can happen.

One comment said that we know the comb is artificial. But this is just another word for human designed. I think that supporters of evolution should be a little more precise in their description of the types of “things” in the universe so as not to allow for attacks by IDers such as I tried to describe.

No, I think the point was that we know that the comb is made by humans. Where I don’t agree with Flint, for instance is that we can identify artificiality without knowing the source, much as we would probably recognize a trap-door spider’s lair as having been produced by life. What we would not know is if it was “intelligent” in the sense that we ordinarily mean it, another reason why I thought you sounded IDist. That is to say, we really don’t know if something as complex as a trap-door spider’s burrow was made by intelligence, but only know that it was made by life (other items could be identified as being made by “intelligent life”, but in many archeological artifacts this would not be so. Some “tools” are identified as such only because they are smooth stones that fit well into the human hand, and have been transported away from a streambed–which means that we’re identifying “intelligence” which is much less sophisticated than the trap-door spider’s burrow).

With a comb it might be difficult, because if they weren’t associated with dwellings and the like, how would we really know that it wasn’t produced by “non-intelligent” life. Sure, we’d probably be able to say that it was made by life, but by intelligent life as you wrote? I’m not so sure, unless of course we could show tool marks, or that the material of the comb was made by nickel catalysts or something of the sort. A comb is so simple and conceivably of use to some hypothetical organism that we’d just have to work through the problem, and not be certain just on the basis of one comb that it was made by “intelligent life”–unless, again, specific design characteristics could be seen.

One thing we certainly can do on earth is to distinguish between the turtleshell that an antique comb might be made of, and the work that made the comb itself. The turtleshell has the marks of life in it, including the complexity that goes beyond that of design that we know, while the comb may be made using sophisticated techniques, while not being anywhere near the complexity of life. While designers might be able to make objects as complex as life someday, it will require a long evolution of “designer knowledge” to get to this point.

Comment #35047

Posted by Henry J on June 13, 2005 4:54 PM (e)

Re “Why is the ID movement called the ID movement if, as you say, there isn’t any ID theory?”

Cause if they called it something else, adding the “-iot” suffix wouldn’t have the same effect?

Comment #35048

Posted by Flint on June 13, 2005 4:55 PM (e)

Well, allow me to reiterate my disagreement with Glen Davidson. We can NOT identify artificiality without a lifetime of experience with our environment, its nature and its constraints. Consider a newborn human child, just old enough to focus its eyes (itself a learned ability). Put something in front of the child, and the child sees it. Move the object to one side, and the child *does not follow it*. Even the recognition that the object is a “separate thing” is learned knowledge.

We recognize that a comb is artificial and man-made for one reason and one reason only: because we know that men make combs, and that no other known process, either organic or inorganic, produces combs of that type. I emphasize: know other KNOWN process.

So what Glen Davidson is talking about is our ability to distinguish natural from designed (in the sense of an intelligent designing agent) within the very well-understood context of our own environment, with which we have all of recorded history to use as a database of comparison. And I agree that backed with this ample body of knowledge, our ability to avoid false positive and false negative identification errors is impressively good. But it’s good ONLY because we know the context so very intimately.

I’m beating away at this dead horse because our knowledge of the nature (supernature?), purposes, methods and techniques, and goals of the “intelligent designer” are as unknown to us as my hypothetical totally alien planet, and perhaps even unknowable to us in principle. And on the basis of ignorance this broad and deep, we can make no statements whatsoever about that that Designer may have done or might be doing.

And it’s this sheer ignorance that permits “theistic evolution” to exist. Anything no conceivable evidence might exist to support or refute, permits any belief about it at all.

Comment #35053

Posted by Glen Davidson on June 13, 2005 5:24 PM (e)

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Comment #35055

Posted by Glen Davidson on June 13, 2005 5:58 PM (e)

We can NOT identify artificiality without a lifetime of experience with our environment, its nature and its constraints.

The trouble is that you are treating alien environments as if they were not “part of our environment”. They are, which is why we understand them, why we can land on them and study them using the physics that we presently understand. 2LoT will come into play and make any evolved life very complex indeed, and as such we will be capable of recognizing the difference between life and any sort of machine made similarly to the way we design machines.

Now if you were talking about life on neutron stars, or something as alien as that, I might agree that we could have difficulty knowing what was designed and what was evolved. I thought of mentioning this way back, but you seemed to be using few enough scientific constraints even with your “planet” that I didn’t get around to it (whatever the causes). And sure, neutron stars are part of our environment, but they are so very alien compared to planets that studying anything on them would be extremely difficult practically, and the criteria for identifying evolution, while still holding, might not be within our range of perception and thought.

Again, though, we were talking planet, not the extremely alien environment. I just don’t know how the typical planet could be so difficult to study biologically as Flint proposes it would be.

Move the object to one side, and the child *does not follow it*. Even the recognition that the object is a “separate thing” is learned knowledge.

You were writing this while I was composing my post, and I’ll just repeat what I suggested there, that we have indeed learned to deal with “physical environments”, and it should be rather easier to recognize design and evolution on Mars than it was to initially identify these on earth.

It’s not clear that we really “learn” that an object is a “separate thing”. I suspect that we more or less inherit these abilities, and are “learned” only through experience (depends on what is meant by “learn”, certainly). Where we draw the line is learned culturally, at least in part, since there is nothing that inherently “is object”, and nothing that inherently tells us that dreams are “not real” and waking experience is real. (I was just going to repeat and then leave off, but then this “phenomenology” and psychology are right down my lane).

Regardless, we are fortunate that any “normal planet” is unlikely to be beyond our recognition (Venus’ atmosphere’s high refraction will take some getting used to, but that’s about it). It’s what we inherited from Galileo, and I’m sticking with it.

because we know that men make combs, and that no other known process, either organic or inorganic, produces combs of that type. I emphasize: know other KNOWN process

Sure, we know that. And how do archeologists know that an abstract symbol “carved in bone” was made by humans? It’s really more difficult to say, but basically it comes down to facts like that we know what humans are capable of doing, and what animals are capable of doing. Yet we know humans are really animals, the distinction is artificial, and that we couldn’t say that spider webs and trap-door spider burrows weren’t “intelligently designed” without simply knowing what sorts of objects spiders make (silken, for one criterion) and what sorts of objects humans make.

But we don’t know what “intelligence” is in any non-relative sense. We know something about what life makes, just not this “intelligence”. Or do IDists think that an intelligent machine might have made life? Well, they can’t rule it out from their espoused standpoint.

So what Glen Davidson is talking about is our ability to distinguish natural from designed (in the sense of an intelligent designing agent) within the very well-understood context of our own environment, with which we have all of recorded history to use as a database of comparison.

No, I am not, for I would never understand natural as being different from human.

Additionally, we can distinguish “designs” that sea creatures make, and what we ourselves make without much difficulty in the majority of cases. This is part of our “database”, but then so is evolution and physics, and what these entail for any alien evolution similar to our own.

And I agree that backed with this ample body of knowledge, our ability to avoid false positive and false negative identification errors is impressively good. But it’s good ONLY because we know the context so very intimately.

Yes, Flint, we’re studying the planets and stars today. Or is this beyond our ability to do?

I’m beating away at this dead horse because our knowledge of the nature (supernature?), purposes, methods and techniques, and goals of the “intelligent designer” are as unknown to us as my hypothetical totally alien planet, and perhaps even unknowable to us in principle. And on the basis of ignorance this broad and deep, we can make no statements whatsoever about that that Designer may have done or might be doing.

Well the original question was not about this unknown planet, or even about an unknowable “designer”. Naturally I’m not interested in discussing anything as meaningless as the “unknown Designer” or “totally alien planet”, rather I was discussing what we know and how we can know it.

And it’s this sheer ignorance that permits “theistic evolution” to exist. Anything no conceivable evidence might exist to support or refute, permits any belief about it at all.

Well you certainly moved the goalposts beyond anything I was discussing. I was discussing what we can tell in our environment known through physics and 2LoT, and Flint is discussing something that is by definition unknowable. It certainly is not going to resolve matters related to the question that Ron asked.

Comment #35056

Posted by Henry J on June 13, 2005 5:59 PM (e)

I wonder if “made by life” might be a more basic concept than “made by an intelligence”? After all, anything made by humans was made by life.

Then again, since an evolving gene pool has some of the attributes of intelligence (it can try different things, react to its environment, and remember results of previous trials), would it be too much of a stretch to say that an evolved species was designed - by the gene pool of its ancestors?

Henry

Comment #35057

Posted by Henry J on June 13, 2005 6:08 PM (e)

Re “2LoT will come into play and make any evolved life very complex indeed,”
Why would 2LoT be a cause of life becoming complex?

Henry

Comment #35058

Posted by Guts on June 13, 2005 6:08 PM (e)

Nic writes:

Actually, Nelson, recent research findings seem to have vindicated my contention that FliH is probably homologous to the F0-b subunit of the F1F0-ATPase.

Huh? That recent research just repeats what I said about weak similarity.

weak similarity is also reported between Orf5 and several F0 ATPase b subunits (data not shown).

The similarity of YscL (Yersinia T3SS homolog of FliH), in the Plano paper to the ATP synthase component was found by a blast search, but was pretty far down the list. The similarity was certainly not high enough to call them homologs.

A blast with E. Coli FliH you’ll see the alignment is less than half the length of the query sequence. Psi-BLAST brought back only a few apparently ATP-related sequences. The first round of Psi-BLAST is actually a BLAST search, and is probably less reliable than the next iterations. The reverse search did not find significant numbers of flagellar proteins but did find many ATP-related proteins, suggesting that the sequence found is not mislabeled. Thus it is most likely that the similarity here coincidence rather than homology. You could make a case for convergence givent that they both bind an atpase, but event that would be shaky.

[block]
Gene’s case against all the others is not convincing,
[/block]

Well actually I think Gene makes a good case for all the homologs that he discussed, (and he also gives other reasons for thinking that FliH and Fob aren’t homologs that go beyond the weak sequence similarity). But you can discuss that with Gene if you’d like. But I’m not here to defend other people’s statements.
I’m here to remind you that you need to get the homologies right first then accuse other people of being incorrect.

Comment #35063

Posted by Flint on June 13, 2005 6:33 PM (e)

Glen,

We are talking entirely past one another. I don’t know how to get us on the same page. All I can say is, I do not share your optimism that our current general understandings can be accurately extrapolated in detail. I confess that if I were to find Paley’s watch on Pluto, I sincerely would not be able to identify its history. I would guess it was a manufactured item, because on Earth this would be obvious. So I would be extrapolating my Earthly experience and hoping it applied closely enough.

But if I confronted you with a zorrgle and asked you to identify whether it was life, or created by life, or neither, I think you would be mostly guessing, and your probability of guessing correctly wouldn’t be as high as you prefer to think. I may be wrong.

Comment #35064

Posted by Glen Davidson on June 13, 2005 6:42 PM (e)

Why would 2LoT be a cause of life becoming complex?

Technically, 2LoT isn’t a “cause” of anything, being merely a description of what happens. With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction). Of course one could simply be appealing to probability theory or some such thing, but either way, life is going to increase in complexity without some major event constricting it, or holding it down to very simple levels.

It was written in a specific context in the first (or nearly first) place:

That is to say, we can predict from 2LoT and other physical considerations that life will be complex, and, in any reasonably undisturbed environment, that life will become diverse, exhibit “nested hierarchies”, and be very complex due to neutral and near-neutral mutations.

I needed to be careful here, for life could conceivably be reduced to a non-complex state by frequent destruction or the like. One may always increase complexity enough in complex organisms that they cease to live, while the simple survive. However, in absence of any such scenario, life will become more complex, and it will be explainable via 2LoT (the caveat that 2LoT only applies to energy is moot at any temperature above absolute zero).

I thought about getting into whether or not I meant that organisms would become more complex, or if life as a whole would become more complex, but didn’t know if it would matter. I meant the latter far more than the former, in fact, though the increase in overall complexity tends to make larger organisms also become more complex over time. It is in the overall increase in life’s complexity that we really see 2LoT come into play, because 2LoT says that entropy (essentially information) will either be preserved or will increase. Without extreme extinction, some of this increase in entropy/information will be preserved by the splitting lines of life.

It’s all context, of course, since life can be reduced down to extreme simplicity (in all probability) or fully destroyed by circumstances. However, 2LoT predicts that the overall complexity of two splitting lines will increase in the areas of the DNA where neutral mutations may occur, barring any mechanism that prevents this from happening. While we don’t understand all preserved segments, certainly most obviously randomized sections of evidently unselected DNA are predictable through evolutionary considerations, as are neutral and near-neutral randomization of coding DNA.

Of course I’m not using 2LoT in any hard and fast manner, however the increase in overall complexity of life remains a fulfilled prediction of evolution, while it isn’t a prediction of any sort of design. In fact of the designs that we know about, the predictions are that such randomization will not occur. The IDists, however, don’t really have a Designer, but only a word “Designer”, thus they have no predictions, and will not accept falsification based on what we know about tangible “designers”.

Comment #35067

Posted by Glen Davidson on June 13, 2005 6:52 PM (e)

I confess that if I were to find Paley’s watch on Pluto, I sincerely would not be able to identify its history. I would guess it was a manufactured item, because on Earth this would be obvious. So I would be extrapolating my Earthly experience and hoping it applied closely enough.

Certainly we’re talking past each other, but I don’t know how, other than following my own line of reasoning, to discuss how we really can identify designed objects.

I would expect you to believe that a watch on Pluto was designed and made (if not exactly “manufactured”), because it shows apparent purpose and a lack of a natural means of producing it.

The crux is the predictions that evolution makes. We best know that life was not designed because it shows only evidence of being evolved, and we lack any means of distinguishing the evidence of evolution from some proposed “design”. That is to say, we know that life can evolve, at least to some degree, and fully lack any evidence that the genomes that we see are or can be made by any reasonably understandable designer.

We might have some sympathy for Paley’s nevertheless unsupported assertion if we did not know that life shows evidence of “natural” evolution. It the evidence of evolution that which moves us beyond mere skepticism to full-blown denial that life was designed. And it is the predictions of evolution that make it science here or on any other planet that we are capable of investigating.

Comment #35068

Posted by steve on June 13, 2005 7:06 PM (e)

With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction).

No it doesn’t. Such a duplication may be unreasonably unlikely, but 2LoT doesn’t have anything to do with it.

Comment #35071

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 7:25 PM (e)

Lenny: Nelson refers to Nelson Alonso not Paul Nelson

Oh, darn.

Oh well, if Paul is out there, maybe he’d like to answer my questions anyway. :>

Comment #35072

Posted by Flint on June 13, 2005 7:34 PM (e)

Glen:

You may be right, but I can’t escape the suspicion that There are more things in heaven and earth, Than are dreamt of in your philosophy. You remind me of the proclamation someone once made (which I could remember, I think the president of some university) that science had basically completed the skeleton and fleshed out all there was to be known. All that remained for scientists to do was to grind out the details. Ironically, this speech was made only a year or two before the Year of Einstein, 1905.

Is it necessarily the case that given conditions more or less as we’re familiar with them, natural processes will produce more or less comparable results given enough time? How far can these results vary in the “less” direction before we could not properly identify them without some considerable study? While I don’t wish to denigrate what we have learned with so much effort, I can’t help but consider it local knowledge. The universe presents us with an endless supply of surprises, some quite totally unexpected, and I expect this to continue. I lack your confidence that our local knowledge will be all that portable.

Comment #35073

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 7:35 PM (e)

I am a strong advocate of evolutionary biology and its teaching and consider myself a secular humanist. I say this to assure you that I have a sincere question.

Not sure what difference your beliefs (whatever they are) make. Science is science. Makes no differnce if you are atheist or saint, Baptist or Buddhist, Taoist or Tantric, Christian or Quetzalcoatlian.

It occurred to me that evolutionary science readily admits that there are objects in the universe that were not created by the physical evolution of matter initiated by the Big Bang and that were not created by biological evolutionary development either.

Huh?

I refer to human designed and created artifacts.

Humans are the product of the Big Bang. Human brains and hands are the product of evolution. Anything produced by those human brains and hands is, by definition, products of biological evolutionary development.

Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins. For example, is a seeming spear point regular enough to put it outside the possibility of natural, non human, origins? We are, of course surrounded by objects that could not exist without intelligent design by humans and they are all much simpler, less complex, than life, usually by a very wide margin. For example, the comb I carry in my pocket, if found by an anthropologist, would unhesitatingly be attributed to human intelligent design.

That is only because we see the designer and see it at work.

All this is by way of preface to the problem that occurred to me. I ask this sincerely as one who is a natural materialist and atheist.

I’m not an atheist, and I don’t know what the heck you mean by a “natural materialist”. But as I said before, I fail utterly to understand why your beliefs (assuming you’re not just bullshitting us) have anything to do with the matter at hand. Science is science. No matter WHAT religious beliefs you have or don’t have.

How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?

Um, combs don’t reproduce, mutate and reproduce their mutations.

The human brain does.

I await your refutation anxiously,

No offense intended, but I’m awfully skeptical of your too-much-vaunted “atheism”. First, it’s utterly irrelevant to science and the only ones I ever hear bring it up are fundies. Second, I’ve seen this movie before, ad nauseum. I wish I had a dollar for everyone who told me “I’m not a creationist IDer, but I have a question to ask”, and then go on to parrot all the standard DI boilerplate — usually just before they scream “you’re all going to hell !!!!!!” and run away. apparently, IDers don’t feel themselves bound by that commandment-thingie against “bearing false witness” …. .

Comment #35074

Posted by 'Rev Dr' Lenny Flank on June 13, 2005 7:39 PM (e)

My comment about anthropologist was not meant to be obtuse. It is a common scientific problem in this field to try to decide if an artifact was created by man or not. Another way of asking that is, “does it exhibit any features that are not likely to have been caused by non human forces?”

More the opposite, actually. In deciding whether a stone flake was the product of human tool-making or natural fracturing, for instance, it is precisely the unmistakable sings of human design that are searched for —- human-produced flakes have distinctive percussion bulbs that natural fractures don’t have. So the question asked is not “does this have features that couldn’t form naturally?” but “does this have the features that we know are indicative of human activity?”

Comment #35090

Posted by Nick (Matzke) on June 13, 2005 9:50 PM (e)

Nelson/Guts,

Well, I’ll take the published alignment in Figure 5 of Pallen et al.’s article over your unsubstantiated assertions. Or perhaps Pallen et al. is “riddled with errors” also?

The alignment and BLAST hits, plus the fact that both F0-b and FliH are extended dimers, plus the fact that both are membrane-associated, plus that both associate with homologous ATPase hexamers (a hexameric nature, let us not forget, that you once denied with scorn because it was inferred from homology, until experimental confirming evidence was found, at which point you totally changed your tune and denied your previous scorn), all make for a reasonable case for homology between FliH and F0-b. The features that Mike Gene points out that distinguish F0-b actually vary among different F0-b proteins – e.g., they can have 0, 1, or 2 membrane-spanning helices.

Your failure to be able to come up with any proteins both universally required in flagella, and unique to the flagellum, is noted. There might be one or two, but it is a short list at best.

Comment #35094

Posted by Guts on June 13, 2005 10:45 PM (e)

Nick:

Well, I’ll take the published alignment in Figure 5 of Pallen et al.’s article over your unsubstantiated assertions. Or perhaps Pallen et al. is “riddled with errors” also?

No, I see where he gets the “weak similarity” from in that figure as well.

(a hexameric nature, let us not forget, that you once denied with scorn because it was inferred from homology, until experimental confirming evidence was found, at which point you totally changed your tune and denied your previous scorn),

Thats a bizarre accusation. I didn’t “deny” anything with scorn. I simply pointed out that there’s a difference between an experimentally confirmed prediction and an imaginary model that seems to fit.

The features that Mike Gene points out that distinguish F0-b actually vary among different F0-b proteins — e.g., they can have 0, 1, or 2 membrane-spanning helices.

The differences he points to are:

F0b has an N-terminal transmembrane region, a weak dimerization domain, and a C-terminal region that interacts with both F1delta and F1alpha (as part of a heterohexamer). FliH has no N-terminal transmembrane region, a strong dimerization domain, and a unique C-terminal region that interacts with a flagellum-specific N-terminal portion of the FliI monomer. When the lack of sequence similarity is added to these differences, the analogy (thus homology inference) looks very weak.

Nick:

Your failure to be able to come up with any proteins both universally required in flagella, and unique to the flagellum, is noted. There might be one or two, but it is a short list at best.

There is no way you could accuse me of “failing” something I did not attempt to do. I don’t attempt it because I believe:

1. There are many, many examples of common design throughout life.

2. The flagellum is an IC system that is made up of many sub-IC systems.

Comment #35095

Posted by Guts on June 13, 2005 11:10 PM (e)

Actually I should apologize for saying that Matzke’s article is “riddled with errors”. There is a lot that I would call errors and a lot that I disagree with, but it isn’t fair that I throw those words out there without myself being an expert in genetics or flagella (not yet anyway) and because there is a lot in the article that is quite useful to anyone studying these systems.

Comment #35096

Posted by Raven on June 13, 2005 11:13 PM (e)

There is no way you could accuse me of “failing” something I did not attempt to do. I don’t attempt it because I believe:

2. The flagellum is an IC system that is made up of many sub-IC systems.

What does “sub-IC” mean? I thought “irreducibly complex” meant that you couldn’t break it up into subsystems.

Comment #35097

Posted by Guts on June 13, 2005 11:20 PM (e)

Raven:

What does “sub-IC” mean? I thought “irreducibly complex” meant that you couldn’t break it up into subsystems.

IC means you can’t break it up into subsystems and still retain the same function as the “whole” system. Since this leaves open the possibility that you can have systems with different functions (e.g. secretion), those systems may be IC themselves.

Comment #35098

Posted by Raven on June 13, 2005 11:30 PM (e)

IC means you can’t break it up into subsystems and still retain the same function as the “whole” system. Since this leaves open the possibility that you can have systems with different functions (e.g. secretion), those systems may be IC themselves.

Ok, but doesn’t your argument invalidate the “what good is half an eye?” argument ID advocates use against evolution? If half an eye (or half a wing or whatever) can serve some sub-function as you describe, doesn’t that answer the “what good is…?” objection?

Comment #35100

Posted by Guts on June 13, 2005 11:37 PM (e)

Raven:

Ok, but doesn’t your argument invalidate the “what good is half an eye?” argument ID advocates use against evolution? If half an eye (or half a wing or whatever) can serve some sub-function as you describe, doesn’t that answer the “what good is … ?” objection?

Yes, if you are correct that an ID advocate has used that argument against evolution. Behe himself never said that sub-systems to IC can’t have other functions or that the parts are unique to a particular system. In fact, he noted that the spring in a mousetrap can be used in clocks, for instance. The problem here is that there is a sea of nonfunctionality that small, step by step evolution can’t surpass.

Comment #35107

Posted by Russell on June 14, 2005 12:39 AM (e)

The problem here is that there is a sea of nonfunctionality that small, step by step evolution can’t surpass.

Correction: “…there is a sea of unknown functionality that I, with my limited imagination - and even more limited will to exercise it - can’t see how to surpass.”

Comment #35116

Posted by bcpmoon on June 14, 2005 4:17 AM (e)

Yes, if you are correct that an ID advocate has used that argument against evolution. Behe himself never said that sub-systems to IC can’t have other functions or that the parts are unique to a particular system.

Where was that thread about “jumping the shark”?
What is left of IC if it allows to be split in ever smaller, fully functional sub-systems? Nothing! And this is what critics have always said…
It reminds me of a soap bubble: At first it is brightly coloured, but as the shell gets thinner, the colours vanish until only a invisible shell is left which silently goes…pop.

Comment #35117

Posted by Toby on June 14, 2005 4:24 AM (e)

I’m fairly new round here - how exactly is the current IC argument any different from any other argument from ignorance?

I mean, I know sod all about flagella, but I know a bit about logic. Assuming something didn’t evolve because you can’t understand how it did is a logical fallacy. Biology doesn’t even enter into it.

Comment #35123

Posted by 'Rev Dr' Lenny Flank on June 14, 2005 7:03 AM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #35131

Posted by Flint on June 14, 2005 8:00 AM (e)

Toby:

I mean, I know sod all about flagella, but I know a bit about logic. Assuming something didn’t evolve because you can’t understand how it did is a logical fallacy. Biology doesn’t even enter into it.

Your knowledge of logic has led you astray, I’m afraid. Behe doesn’t assume a form didn’t evolve, he knows it didn’t evolve. It is a foregone conclusion. I would bet serious money that Behe understands perfectly well how his forms may have evolved: he’s been provided with no shortage of explanations and analyses assuming he may even have needed them. But Behe’s faith says these things CANNOT have evolved, because this omits Behe’s god.

But this raises a procedural problem: Behe can’t SAY this, because doing so would instantly doff the trappings of science, leaving naked religion. Lenny Flank tirelessly (if a bit monotonously) attempts to put our ID proponents in a position where they have only two choices: admit that their position is based on pure religious faith and science is window dressing, or ignore his questions. Most do the latter. Some pretend to answer by producing nonresponsive sermons, which they later point to and say “I answered your question” when in fact they did not.

This does, however, have the effect of obliging dishonest people to attest to their faith by pretending their faith is not involved. Instead, they look illogical and often somewhat retarded. I wonder if, each night just before going to sleep, they tell themselves “I’m doing this to save souls, I’m doing this to save souls…”

Comment #35132

Posted by mrwizard on June 14, 2005 8:10 AM (e)

“Anthropology uses the regularity of found objects as proof of human, as opposed to natural, origins.” Ronald Newland

Um. Sort of. Long ago and far away I was an English Lit/Anthro major. (i.e. unemployment) There was a cautionary tale one instructor used to illustrate the danger of this very assumption. In the ‘70’s (or maybe 60’s) a North American location was found which seemed to be covered with tools very similar to those being found by the Leakeys in Africa. Speculation immediately led to the possibility of very early humans on this continent.

Until someone took a closer look at what happens when you scatter a lot of the right types of rocks of the right size around the surface of a pasture and let cattle tromp all over them for maybe a century…

The appearance of human origins should be supported with more than just regularity.

Comment #35133

Posted by Toby on June 14, 2005 8:20 AM (e)

I do agree that if you are Behe, and unencumbered by such inconveniences as critical thought, you can ignore all the logical fallacies you want.

And I applaud Lenny Flank for repeating those questions, because if any IDer ever claims to do science those questions are key. Without a testable theory of ID, any further discussion of biology from an ID perspective is hand-waving.

Comment #35134

Posted by Flint on June 14, 2005 8:39 AM (e)

Toby:

Granted there is no science involved with ID. But ID has been defined not in the hopes that people will learn anything new, but rather in the hopes that people will adopt the “right” set of religious beliefs.

The main purpose of science is probably to satisfy human curiosity. We are a curious species. Granted, we can turn our understandings into labor saving (and life enhancing) technology, but mostly we’re just curious. The main purpose of religion is to calm our fears, and this is much more primary. It’s also much more indirect: our fears are not calmed if we only pretend to believe in special protection through the magic dispensed by a Sky Daddy, because we’d know better and the pretense wouldn’t hold. Instead, we’d more likely shake our heads at the comical childishness of this notion.

And this in turn means we must internalize these beliefs deeply and indelibly, so that we are so entirely sincere that we can lie through our teeth and never see any need to admit it to ourselves. And to do this, we recognize that we must start the process as young as possible. While it’s true that such training does not always “take” perfectly, those exposed young enough very often go through a rebellious period but later in life get “born again”, while most of those who attempt to acquire belief later can never quite eliminate all doubt that their doctrine is, well, basically silly.

And THIS means the religious perspective must be reinforced in public schools, and the most corrosive knowledge neutralized or hidden, because most children attend public schools where they are rapt (or at least present) minds ready to Hear the Good News. So ID isn’t scientific hand-waving at all, it is religious doctrine reworded in an attempt to co-opt the reputation of science in the service of God. And this means it does not matter if everything they say is a deliberate lie, provided that the lies are believed during those years when indelible faith gets hardwired into our neurons. Once the child is old and experienced enough to realize they are lies, it’s too late. They CAN’T be lies! God says so!

Comment #35135

Posted by Flint on June 14, 2005 8:44 AM (e)

Toby:

Granted there is no science involved with ID. But ID has been defined not in the hopes that people will learn anything new, but rather in the hopes that people will adopt the “right” set of religious beliefs.

The main purpose of science is probably to satisfy human curiosity. We are a curious species. Granted, we can turn our understandings into labor saving (and life enhancing) technology, but mostly we’re just curious. The main purpose of religion is to calm our fears, and this is much more primary. It’s also much more indirect: our fears are not calmed if we only pretend to believe in special protection through the magic dispensed by a Sky Daddy, because we’d know better and the pretense wouldn’t hold. Instead, we’d more likely shake our heads at the comical childishness of this notion.

And this in turn means we must internalize these beliefs deeply and indelibly, so that we are so entirely sincere that we can lie through our teeth and never see any need to admit it to ourselves. And to do this, we recognize that we must start the process as young as possible. While it’s true that such training does not always “take” perfectly, those exposed young enough very often go through a rebellious period but later in life get “born again”, while most of those who attempt to acquire belief later can never quite eliminate all doubt that their doctrine is, well, basically silly.

And THIS means the religious perspective must be reinforced in public schools, and the most corrosive knowledge neutralized or hidden, because most children attend public schools where they are rapt (or at least present) minds ready to Hear the Good News. So ID isn’t scientific hand-waving at all, it is religious doctrine reworded in an attempt to co-opt the reputation of science in the service of God. And this means it does not matter if everything they say is a deliberate lie, provided that the lies are believed during those years when indelible faith gets hardwired into our neurons. Once the child is old and experienced enough to realize they are lies, it’s too late. They CAN’T be lies! God says so!

Comment #35146

Posted by Glen Davidson on June 14, 2005 10:16 AM (e)

With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction).

No it doesn’t. Such a duplication may be unreasonably unlikely, but 2LoT doesn’t have anything to do with it.

Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

Comment #35149

Posted by Glen Davidson on June 14, 2005 10:25 AM (e)

I can’t escape the suspicion that There are more things in heaven and earth, Than are dreamt of in your philosophy. You remind me of the proclamation someone once made (which I could remember, I think the president of some university) that science had basically completed the skeleton and fleshed out all there was to be known.

What a lame accusation by someone who won’t deal with the fact that evolution does make predictions. Nothing like the old pseudoscience favorite, out-of-context Shakespeare quote. I’m not going to discuss your sci-fi world as a “hypothetical”, and if you want to ignore the actual science of evolution when discussing hypotheticals, go ahead. But you’re on the wrong side there, about as profound as Steve’s uninformed comments on 2LoT.

I can’t help but consider it local knowledge. The universe presents us with an endless supply of surprises, some quite totally unexpected, and I expect this to continue. I lack your confidence that our local knowledge will be all that portable.

Science is not local knowledge.

Comment #35155

Posted by steve on June 14, 2005 10:57 AM (e)

Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

Entropy, defined in an Information Theory sense, might increase according to some IT law analogous to SLOT, it’s not SLOT, which is a statement about the entropy of a thermally isolated system.

Comment #35158

Posted by Flint on June 14, 2005 11:07 AM (e)

Glen:

What you lack in depth, you more than make up for in hostility. Do you really think you “win” when you dismiss others’ points by labeling them “lame” and “won’t deal with facts” and “pseudoscience” and “out of context” (that’s a howler, since the context was dead-on accurate), and “sci-fi” and “ignores science” and “uninformed” – wow, what an impressive list. You are a master at the game of “let’s have a discussion.” We can play “Let’s disagree with Glen and watch his mind slam shut.”

Meanwhile, you have completely missed what I was driving at, not surprising if your goal is to dismiss and insult first, and think never. I didn’t say science was local knowledge, I consider the actual outcomes of understood forces and processes to be local results. I agree that science as a method would help us understand how alreadly-known processes could (and surely would) produce unexpected effects. My claim is that initially, and before any study, those effects might not be readily identifiable. Our intuition is informed by lifelong experience with a set of known effects. But evolutionary processes are contingent, and as Dawkins and others have demonstrated, very little of potential morphospace is occupied. Probably very early forms set up a bias. The earliest experiments that “worked” would necessarily set up a bias. That bias may well be very different every time it occurs.

There is a very good reason why Dembski refuses to apply his explanatory filter to any useful real-world example. The range of what is possible dwarfs the range of what has actually occurred within our experience. A world may not need to be as totally alien as I described, to produce objects unidentifiable within the categories so far presented: produced by life, or produced by nonliving forces. Indeed, (consider viruses), our definition of life is itself hazy: to the best of my knowledge, nobody has ever defined life such that someone else can’t point to what is obviously NOT life, but that meets the definition exactly. And this has interesting implications: it’s easily possible to imagine processes entirely consistent with science, where opinion as to whether they are living processes would be split 50-50. And the mechanisms of evolution themselves require conditions not guaranteed to occur everywhere.

Prediction can be a slippery idea. Given our knowledge of meteorology, would we have predicted tornados? Sure, AFTER we observe them, and AFTER a great deal of analysis and computer modeling, we can understand that our theory does not DISallow them. And in this sense, we can say that our knowledge “predicts” them. But we’d never have anticipated them. And in fact, tornados occur only very rarely, only under ideal conditions, and only in small parts of the planet. It wouldn’t take much of a change (which may happen, the climate being so variable in the longer term) to eliminate them altogether.

So imagine that you had never seen a tornado and didn’t know they were even possible (there’s a great deal our climate and weather models does not disallow that doesn’t actually occur). You go to another planet, and you see a tornado. Is it alive? Is it an artifact of conditions deliberately created for the purpose by alien intelligences? Would your science really answer these questions?

Comment #35159

Posted by steve on June 14, 2005 11:12 AM (e)

But you’re on the wrong side there, about as profound as Steve’s uninformed comments on 2LoT.

Okay, forget it, I’ll leave it to someone else with a physics background to explain this to you.

Comment #35162

Posted by Glen Davidson on June 14, 2005 11:19 AM (e)

Entropy, defined in an Information Theory sense, might increase according to some IT law analogous to SLOT, it’s not SLOT, which is a statement about the entropy of a thermally isolated system.

You obviously haven’t had much of a physics course in your lifetime. That anyone would even claim that the “laws” apply only to “thermally isolated systems” only gets back to the ill-considered claims that science is local. Anyway, here’s just one of the many websites that discusses SLOT in open systems:

http://www.tim-thompson.com/entropy3.html

http://www.tim-thompson.com/entropy2.html

One crucial consequence of 2LoT in open systems is that heat flows in only one direction. From the second link:

The asymmetrical 2nd law forces them to flow always in one direction, but not the other. But gravity asymmetrically forces water, for instance, to always flow down hill. So the asymmetry of the 2nd law, and the need to pump heat or entropy “uphill”, as one would for water, don’t seem like a fundamental problem.

The fact is that I have discussed matters intelligently, and you haven’t even begun to deal with proper science. If you could respond with any sort of scientific knowledge we could begin to discuss things, but as long as you’re using your lack of knowledge as a blunt instrument you’re doing science and the fight against ID no good at all.

Comment #35163

Posted by Glen Davidson on June 14, 2005 11:23 AM (e)

But you’re on the wrong side there, about as profound as Steve’s uninformed comments on 2LoT.

Okay, forget it, I’ll leave it to someone else with a physics background to explain this to you.

They already did, Dembski-like “scientist”. Try to learn honesty along with physics, and then you might begin to be able to deal with actual science, and not the prejudices that you prefer to learning.

Comment #35168

Posted by Glen Davidson on June 14, 2005 11:33 AM (e)

What you lack in depth, you more than make up for in hostility. Do you really think you “win” when you dismiss others’ points by labeling them “lame” and “won’t deal with facts” and “pseudoscience” and “out of context” (that’s a howler, since the context was dead-on accurate), and “sci-fi” and “ignores science” and “uninformed” — wow, what an impressive list. You are a master at the game of “let’s have a discussion.” We can play “Let’s disagree with Glen and watch his mind slam shut.”

Flint, you show yourself unworthy to discuss science as usual. I discussed matters at length, you simply attacked me with your short, uninformed comments and personal attacks. I finally responded to your unscientific frame of mind by returning the favor, and you showed your inability even to address evolutionary issues once more.

Neither you or Steve are capable of addressing the matters that I raised, thus the blunt, uneducated attacks in response to nuanced and informed discussion on my part. The fact is that you both bring disrepute on science and lend credence to the IDist attacks on the closed minds of those who won’t even begin to address orthodox science when I discuss it.

I really don’t have much point in going further in dealing with you who won’t deal with evolutionary issues in a scientific manner when discussing hypothetical aliens, or the even worse nonsense that Steve brings up in his near-total ignorance of 2LoT.

I don’t have any reason to put up with mindless attacks and pseudoscience from our side any more than from IDists. And btw, I know that you blame me for “hostility” no matter that you had to attack me for not going along with unscientific “hypotheticals”, however I haven’t met with anything but hostility and unscientific attitudes since I first got into this mess. One gets tired of meaningless nonsense being used in response to legitimate science.

Comment #35169

Posted by Glen Davidson on June 14, 2005 11:42 AM (e)

One minor correction. I meant as usual on this thread your “science” has been “unworthy”, Flint, which is a shame since you typically do better. Unfortunately you appear unwilling to concede anything to evolutionary prediction when I bring it up, though, hence the bad blood at present.

Steve may be better usually, too, but I really am appalled at what he wrote about SLOT. If one doesn’t know about a subject one does best to not start making statements against someone who does.

Comment #35173

Posted by Aaron on June 14, 2005 11:58 AM (e)

“How can you maintain that such simple uncomplicated objects as my pocket comb or a pencil, among multiple thousands of other examples, are evidence of intelligent design when you deny that the many orders of magnitude more complex object called the human brain does not require intelligent design to account for it?”

IMO, combs and pencils are no more (and no less) intelligently designed than beaver dams, coral reefs, and stromatolites. If one posits that human thought is a purely materialistic process capable of “designing” art, architecture, and household appliances, doesn’t it become reasonable to believe that evolution is a purely materialistic process capable of “designing” ecosystems, organisms, and biospheres?

Comment #35174

Posted by Glen Davidson on June 14, 2005 11:59 AM (e)

Meanwhile, you have completely missed what I was driving at, not surprising if your goal is to dismiss and insult first, and think never.

Cheap shot, something you’ve kept up throughout. While I discuss evolutionary prediction, you bring up unscientific “examples” and meaningless “hypotheticals”. Course, what else can you say when you don’t and seemingly can’t address the issues I bring up, and must cling to your original position no matter how inappropriate?

This is why I revisited your post again, however:

I didn’t say science was local knowledge, I consider the actual outcomes of understood forces and processes to be local results.

What you wrote was:

I lack your confidence that our local knowledge will be all that portable.

Granting that you evidently never read anything I wrote well, I was discussing science, not local knowledge. As in every case where I brought up evolutionary predictions, you brought up “local knowledge”. Well if you were claiming to be answering me, then you would be claiming that my resort to science is a resort to “local knowledge”, since in fact I was discussing science. If you were simply setting up a straw man, then indeed you might have been discussing “local knowledge”, but that’s hardly an honest answer to what I had been discussing. To be sure, I have yet to receive a really proper reply to what I’ve written on this thread from you.

You claim that I was missing what you were writing about, when you had no right to suggest that I was ever discussing local effects, and appear to have done so to avoid the scientific issues I raised.

As for the rest of your post, it’s more avoidance of every scientific issue I brought up related to evolution. More attempt to avoid the science while you discuss the “local knowledge” that I was never discussing from the beginning on down. In fact it wasn’t so much that we were talking past each other as that you were forever talking past me and my points and attacking strawmen like your “local effects”.

Comment #35178

Posted by Ron Newland on June 14, 2005 12:11 PM (e)

Lenny Flank obviously has much to learn about evolutionary theory. He made this statement:

Humans are the product of the Big Bang. Human brains and hands are the product of evolution. Anything produced by those human brains and hands is, by definition, products of biological evolutionary development.

How confused can one person be. Evolution produces living matter. My comb is not living matter. It was designed by a human.

My point in a nut shell was this. There are objects that cannot be produced any other way, that science knows of, than by intelligent design. My pocket comb is one of millions of such objects. I was trying to enlarge the arena of refutations that those who defend evolution can use against IDers. A defender of evolution, which really does not need defending in the community of clear thinking people, but alas there are other types of people that have power and need enlightening, could say that yes we admit that ID must be invoked to explain certain objects. But that does not prove the divine origin of ID. We know that humans designed and created many objects and we a certainly not divine or supernatural.

Ron Newland

Comment #35179

Posted by SEF on June 14, 2005 12:34 PM (e)

But gravity asymmetrically forces water, for instance, to always flow down hill.

False. Tidal bores are one anomalous example.

Comment #35182

Posted by Flint on June 14, 2005 12:41 PM (e)

Glen:

There, there, I hope you feel better now. Don’t cry, everything will be all right. Mommy still loves you.

Comment #35183

Posted by Glen Davidson on June 14, 2005 12:41 PM (e)

You could have read the next sentence, SEF: “So the asymmetry of the 2nd law, and the need to pump heat or entropy “uphill”, as one would for water”.

Yes, the author of the site knows that water can move uphill. Slight mis-statement that some would pounce on notwithstanding.

Comment #35184

Posted by Seething Pool on June 14, 2005 12:46 PM (e)

Hi Ron,

Might I recommend Dawkins’s “Extended Phenotype” before jumping to any conclusions regarding who is confused as to the “products” of “biological evolution”. Certainly, natural selection operates upon far more than the morphology of a living organims: their behaviours, endeavours, and constructions are also fair game, and these therefore can be properly considered “products” of evolution as well. Though it is perhaps a bit abstract (although I wouldn’t say it is indirect), it isn’t too difficult to see how selection acts upon the “design” of beaver dams, spider webs, bowers, etc. ad nauseum (are these products of ‘intelligent design’ like your comb?). The comb might take a bit of a broader perspective, unless perhaps one considers a human population riddled with lice, or, likely more applicably, one in which one sex really dug the coiffed look in a mate. ;)

Comment #35186

Posted by Glen Davidson on June 14, 2005 12:50 PM (e)

Glen:

There, there, I hope you feel better now. Don’t cry, everything will be all right. Mommy still loves you.

Still can’t deal with the science, eh Flint? Whatever insults it takes to cover up your ignorant responses and lack of evolutionary analysis is all right with you.

I hope the IDists enjoy this wretched display of closed minds and unintelligent strawman attacks that you launched as I defended evolution as a science against your statements that we couldn’t distinguish evolved life from machines on an alien planet. You’ve really shown your mettle, Flint, in refusing even to consider legitimate science that went against your incorrect statements.

Obviously you have nothing intelligent to say on the matter, simply a repetition of your inability to recognize the soundness of evolutionary prediction, and out of the blue stupid remarks like your last one.

Comment #35193

Posted by Ron Newland on June 14, 2005 2:02 PM (e)

Thanks for your reply Seething Pool. Certainly there is a sense in which what you say is true. But, I was speaking of the theory of biological evolution. It involves, of course, living matter, chance mutations of the genome, and differential reproductive success depending upon the ecological niche the living matter is in.

This says it far better than I can:
“The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection; that most adaptive genetic variants have individually slight phenotypic effects so that phenotypic changes are gradual (although some alleles with discrete effects may be advantageous, as in certain color polymorphisms); that diversification comes about by speciation, which normally entails the gradual evolution of reproductive isolation among populations; and that these processes, continued for sufficiently long, give rise to changes of such great magnitude as to warrant the designation of higher taxonomic levels (genera, families, and so forth).”
- Futuyma, D.J. in Evolutionary Biology, Sinauer Associates, 1986; p.12

The artifacts that humans, or, of course, any other beings that evolve, make are a result of them applying their intelligence to a particular design. They are a result of the intelligent design of humans. They (the artifacts) did not evolve.

Ron Newland

Comment #35199

Posted by Alex Merz on June 14, 2005 2:12 PM (e)

Glen Davidson types:

Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

Golly, Glen. My P-chem textbook has a lot to say about the 2nd law, but it doesn’t seem to mention information anywhere. Let alone “terrestrial processes.”

I suppose you’d be willing to explain exactly what you mean?

I’m looking forward to your definition of “information,” your explanation of how this definition relates to entropy, and your description of how “terrestrial processes” differ from other processes.

Comment #35201

Posted by Seething Pool on June 14, 2005 2:21 PM (e)

Ron: Of course, based on the definition you provide, you are technically correct. But I don’t think it helps the categorization scheme you are attempting to craft, not to mention the entire thrust of your argument as I see it. If you are proposing that “Intelligent Design” includes ANY non-living construct formed by the natural biological processes of all living organisms, shaped through extensive and varied iterative “trial and error” attempts, and honed by selection to arrive at better local solutions through known natural processes, then your purported aim (i.e., to help defend against proffered ID arguments) is of rather limited use: no self-respecting proponent of “Intelligent Design” would posit (has posited) a “Designer” with the mental faculties of a spider, barnacle or amoeba, not to mention one whose creations are directly selected by purely natural phenomenon, since we already have a name for THAT theory (hint: they don’t like it).

Comment #35204

Posted by Wislu Plethora on June 14, 2005 2:28 PM (e)

OMG, here we go with the 2LoT confusion. The law can be expressed quite simply, and in one short sentence: Entropy will never decrease in a closed thermodynamic system. In this sense of the word, “entropy” is defined as the amount of thermal energy present in a closed thermodynamic system that is not available to do work. “Entropy” was sloppily co-opted by information scientists who thought they saw a parallel, but, like most humans, didn’t understand 2LoT or thermodynamics in general.

Comment #35207

Posted by Glen Davidson on June 14, 2005 2:51 PM (e)

Golly, Glen. My P-chem textbook has a lot to say about the 2nd law, but it doesn’t seem to mention information anywhere. Let alone “terrestrial processes.”

Golly, possessor of a P-chem book, you’re one smarmy little ignoramus. I really don’t care what your P-chem book says, I suggest that you learn something outside of your narrow little educational realm. My chemistry texts weren’t exactly complete either. Here’s some real science, also for Plethora who also thinks that he’s an authority who can properly dismiss ongoing science:

http://www.logic.univie.ac.at/cgi-bin/abstract/show.pl?week=030202

Of course it’s not simple, and I don’t claim to understand it all. But you guys seem to think that you’re experts on all of this, so I’d say it’s up to you to finally learn something.

I’m looking forward to your definition of “information,” your explanation of how this definition relates to entropy

There are various definitions of information, not all of which correspond with “entropy”. I couldn’t discuss all the ramifications before, nor do I have the space (or full expertise) to do so now. And it is up to you to quit laughing where someone disagrees with your paltry knowledge, and obtain a scientific attitude. Or even just a decent attitude if you can’t bring yourself to actually be open-minded.

and your description of how “terrestrial processes” differ from other processes.

The little know-it-all demands a description of what I never claimed. I simply wrote:

Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

I had been discussing evolution, when Steve made his incorrect remarks. I mentioned “terrestrial processes” simply to bring it in line with evolutionary issues. It takes a real smarmy fool to turn this into the strawman that Merz did. But obviously he lacks reading ability almost as much as he does physics knowledge.

Comment #35209

Posted by Seething Pool on June 14, 2005 2:59 PM (e)

A follow-up to Ron: I guess I really don’t understand what you’re getting at. Isn’t your goal to nest the “biologically evolved” category within either the “designed” or “non-designed” categories, or at least recognize that others try to do so? You seem to acknowledge that IDists try to craft the argument as follows: we have an in-group of known “intelligently designed” artifacts (but outside of contemporary human-designed technology, they aren’t specific, though you would seem to include spider webs, beaver dams, various animal nests/dens and presumably snail ‘love-darts’, to name a few) and an out-group of non-“intelligently”-designed artifacts (but here they REALLY aren’t specific, and I get the feeling most of them really don’t believe this out-group exists – EVERYTHING was designed), and when we compare living organisms against these groups, they more closely resemble the undefined (and exhaustive by any mealy-mouthed definition of ‘complexity’) “intelligently designed” in-group as opposed to the undefined (also exhaustive in terms of complexity, but possibly non-existent to most IDers) “not designed” out-group. Do you really believe we need a “better” defense to this “argument”?

Comment #35211

Posted by Glen Davidson on June 14, 2005 3:04 PM (e)

For those who do care about learning, this link covers some of the issues of entropy and information briefly, and links to something by Elsberry and Shallit:

http://www.talkorigins.org/indexcc/CI/CI010.html

Comment #35212

Posted by Wislu Plethora on June 14, 2005 3:05 PM (e)

Try this: Entropy, Disorder and Life. It’s very simple, and even Glen should be able to understand it.

Comment #35213

Posted by qetzal on June 14, 2005 3:20 PM (e)

Glen,

I’ve been reading your exchanges with Flint, steve, SEF, etc.

FWIW, as someone who hasn’t been part of the conversation, I also think your tone and word choice have seemed unduly harsh, and have detracted from your arguments.

Just by way of example:

In #35155, steve wrote:

…it’s not SLOT, which is a statement about the entropy of a thermally isolated system.

To which you replied (#35162):

You obviously haven’t had much of a physics course in your lifetime. That anyone would even claim that the “laws” apply only to “thermally isolated systems” only gets back to the ill-considered claims that science is local. Anyway, here’s just one of the many websites that discusses SLOT in open systems:

http://www.tim-thompson.com/entropy3.html

http://www.tim-thompson.com/entropy2.html

And further commented on (#35169):

Steve may be better usually, too, but I really am appalled at what he wrote about SLOT. If one doesn’t know about a subject one does best to not start making statements against someone who does.

I thought you sounded unnecessarily belittling, but decided to check out your links before judging.

The fourth sentence of your second link says this:

As we saw in the previous chapter, the 2nd law of thermodynamics applies only to isolated systems in thermodynamic equilibrium. (emphasis in original)

Maybe you should reconsider your reply to steve? ;^)

In any case, it’s not my intent to attack you. Just to let you know that I think you have sounded very antagonistic (even before things deteriorated to their current state), and I’m not even the object of your comments. If you care about convincing others of your points, you might want to tone it down.

Or not. JMHO. Feel free to ignore or flame on me if you prefer.

Comment #35215

Posted by Glen Davidson on June 14, 2005 3:27 PM (e)

Apparently it is not dumbed-down enough for the mindless Wislu Plethora, since of course the article has no mention of information whatsoever. It could be that he, like many creationists and IDists, confuses order with information, but then he’s obviously too ignorant to be mucking around in these matters.

Couldn’t deal with Shannon information, little uneducated one? Just made a meaningless link that you didn’t understand, while of course not responding to my sources or considered knowledge. You’d make a good IDist, Wislu, you’re so incapable of discussing science.

Comment #35218

Posted by Glen Davidson on June 14, 2005 3:41 PM (e)

Look, quetzal, you come in here not understanding and you make a personal attack. I wrote a great number of well-considered posts, received nothing but strawman attacks in return, and didn’t see why I should have to put up with them. I was defending evolution as science, while Flint keeps insisting that we can’t distinguish between evolved organisms and “designs” on some hypothetical planet. If that’s the case, we have no basis for understanding evolution here.

Well, what do you care about justice, you’ll just attack without consideration of the issues.

The fourth sentence of your second link says this:

As we saw in the previous chapter, the 2nd law of thermodynamics applies only to isolated systems in thermodynamic equilibrium. (emphasis in original)

And why did you rip it from context? The next couple of sentences change the meaning hugely. The next sentence says:

There are ways to use the 2nd law, in systems that don’t meet these fundamental criteria, and we will look at those here.

Again, you are being completely unjust in your intimation here, and it perhaps is time for you to consider what is true and just instead of simply attacking the one who knows science. Your post is antagonistic, and lacks the careful regard for science and proper discussion that exist in my posts.

Comment #35221

Posted by Alex Merz on June 14, 2005 4:01 PM (e)

Glen D. typed:

Golly, possessor of a P-chem book, you’re one smarmy little ignoramus. I really don’t care what your P-chem book says, I suggest that you learn something outside of your narrow little educational realm. My chemistry texts weren’t exactly complete either. Here’s some real science, also for Plethora who also thinks that he’s an authority who can properly dismiss ongoing science:

http://www.logic.univie.ac.at/cgi-bin/abstract/show.pl?week=030202

Of course it’s not simple, and I don’t claim to understand it all. But you guys seem to think that you’re experts on all of this, so I’d say it’s up to you to finally learn something.

Sigh. Such anger. I did not claim to be an expert; I simply asked you to define your terms, and you now have refused to do so. This strongly suggests that you are talking nonsense.

There are various definitions of information, not all of which correspond with “entropy”. I couldn’t discuss all the ramifications before, nor do I have the space (or full expertise) to do so now.

So I’ll ask again: which definition are you using, Glen?

And it is up to you to quit laughing where someone disagrees with your paltry knowledge, and obtain a scientific attitude.

You haven’t the slightest idea what I do or don’t know, and consequently are in no position to disagree with me.

Or even just a decent attitude if you can’t bring yourself to actually be open-minded.

I did not understand what you were saying (and, frankly, suspected that you might not know what you were saying), so I asked you to define your terms. You have now refused to do so; I conclude that you are talking nonsense.

(…)

I had been discussing evolution, when Steve made his incorrect remarks. I mentioned “terrestrial processes” simply to bring it in line with evolutionary issues. It takes a real smarmy fool to turn this into the strawman that Merz did.

What strawman? You used the adjective. I assumed you did do for a reason, and I asked what the reason was. My, but you are one thin-skinned nonsense-talker.

Comment #35222

Posted by Flint on June 14, 2005 4:02 PM (e)

Your post is antagonistic, and lacks the careful regard for science and proper discussion that exist in my posts.

I guess it’s impossible to parody some anti-creationists as well. I’m not entirely convinced that JAD hasn’t found a way into this thread.

Anyway, just to try once again to clarify if anyone is interested:

Flint keeps insisting that we can’t distinguish between evolved organisms and “designs” on some hypothetical planet. If that’s the case, we have no basis for understanding evolution here.

If that had been what I’d been arguing, Glen would be correct. My point was, we could not make this distinction until we knew something about what we were looking at. I happily agreed that we would quickly accumulate the necessary knowledge. Until that time, we would have only our intuition to work with, and that intuition is the cumulative experience in a different environment. It would probably do us more harm than good.

One more example for the road here. If we find some ivory with some runes carved into it, we can accurately presume we have a human artifact. In an unfamiliar environment, we find a block of *something* (not yet identified) with a visible pattern on the surface. Is the pattern natural or was it put there by some life form, and if so, was that life form intelligent? Would Glen presume to guess? I imagine we would need more information. I never said we could not get it, I said that initially we do not have it. And if we never find the relevant information (that cows trampled it for 100 years, or that it had been heated and heat brings out such patterns, or whatever) then we’d remain ignorant.

Remember that the original question was: How could we tell whether an ordinary pocket comb was an artifact of intelligent design. My response was that we could not do so, pending the accumulation of the knowedge necessary to make an informed judgment. I think Glen is arguing that we possess the tools necessary to accumulate that knowledge, and I agree that we do. But that there is nothing inherent in that comb, absent any and all context, that tells us it’s the product of intelligent design. So my “alien world” was an attempt to deprive an object of its context, in the hopes of illustrating that nothing can be identified as designed or not designed outside of its context. “Designedness” is never an inherent quality of anything.

Comment #35223

Posted by Glen Davidson on June 14, 2005 4:08 PM (e)

Sure, Merz, those were honest questions. Having shown that you’re ignorant, you try to salvage your pride by insisting on definition of terms that did not and do not need defining in science as normally understood. Learn something instead of only whining and continuing on with your smarmy indolence and ignorance.

Comment #35232

Posted by CD318 on June 14, 2005 4:47 PM (e)

Glen D.–

You yourself say there are multiple definitions of information. Which one are you using? Answer or continue to talk nonsense. Your call.

Comment #35233

Posted by Glen Davidson on June 14, 2005 4:48 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #35235

Posted by Glen Davidson on June 14, 2005 4:52 PM (e)

You yourself say there are multiple definitions of information. Which one are you using? Answer or continue to talk nonsense. Your call.

I used the term properly in context, and you simply seek to defame because you were too stupid to understand. I don’t take orders from the mindless who want only to obfuscate. Deal with the sources I gave if you’re not too stupid to learn anything.

Comment #35239

Posted by Alex Merz on June 14, 2005 5:01 PM (e)

Which definition of information are you using, Glen?

Comment #35252

Posted by qetzal on June 14, 2005 6:04 PM (e)

Glen,

I most sincerely did not mean my previous post as a personal attack. I said that explicitly, but I realize that tone of voice doesn’t communicate well over the internet. I apologize for not wording it better, since it obviously sounded like an attack to you.

My point was simply this. In reading your responses to Flint, steve, etc., I got a strong sense of condescension and ridicule that didn’t seem warranted.

Since it seemed unwarranted to me, I assumed it wasn’t really intentional. But I wasn’t surprised that others took it that way. Thinks devolved from there, and the theme of the thread became ridicule not reason. I thought that was a shame, so I tried to politely suggest that maybe your phraseology was giving people the wrong impression. Again, all in my opinion.

I know I was taking sides on a subjective matter that didn’t involve me, which was bad form and was probably a mistake to begin with. Apologies for that. I hope the above clarifies a bit, but I won’t pursue it any further.

I will, however, follow up on your comment that I took that one sentence out of context.

As you say, the point of the article is how the 2nd law can still be used in open systems. But I disagree that the sentence I quoted it out of context.

Here’s the entire introduction (note - this is actually from the first link Glen listed, not the second as I mistakenly said earlier):

Introduction

In our two preceding chapters, we have seen The Definitions of Entropy, and The Second Law of Thermodynamics. In this 3rd chapter, we will enlarge the discussion to open, or nonequilibrium, systems. You should read both of the prior chapters, before trying to cover this one.

As we saw in the previous chapter, the 2nd law of thermodynamics applies only to isolated systems in thermodynamic equilibrium. There are ways to use the 2nd law, in systems that don’t meet these fundamental criteria, and we will look at those here. But it must be emphasized that you cannot take the 2nd law off the shelf, and apply it “as is”, without regard to the isolated or equilibrium state of the system.

(again, emphasis in original)

That’s the entire introduction. It’s followed by a section explaining what temperature really means in a system composed of atoms and molecules. That’s followed by a section defining and explaining open, closed, and isolated systems.

Next comes the real meat of the chapter, which starts like this:

The 2nd Law in Nonequilibrium Systems

So, with all the stress on equilibrium and isolated, how does one use the 2nd law in systems that don’t measure up? There’s really only one answer: Fake it. In this case, the “fake” is to take your nonequilibrium system, and carve it up (Mathematically, not physically) into smaller subdomains, each of which has a fairly constant temperature throughout.

(all emphasis in original)

That’s followed by about eight sentences that go into greater detail on how one “fakes” the 2nd Law in open systems.

The whole chapter concludes with this single-sentence paragraph:

In this way, you can apply the essential spirit of the 2nd law, even in the case of a system that is neither in equilibrium, nor isolated.

So there’s the full context from the link you posted in rebuttal to steve’s claim that the 2nd law is a statement about the entropy of thermally isolated systems.

I don’t see where the full context proves steve’s claim wrong. I certainly don’t see where it supports your suggestion that steve’s statement was ‘appalling.’ Based on the full context of this link, steve’s claim is quite defensible. At worst, you can say that his claim is only formally correct, but ignores that fact that there are useful ways to employ the 2nd Law even in open systems.

In summary, I don’t think I quoted that sentence out of context at all. Or, at least, not unfairly so.

Comment #35257

Posted by 'Rev Dr' Lenny Flank on June 14, 2005 6:23 PM (e)

Lenny Flank obviously has much to learn about evolutionary theory. He made this statement:

Humans are the product of the Big Bang. Human brains and hands are the product of evolution. Anything produced by those human brains and hands is, by definition, products of biological evolutionary development.

How confused can one person be. Evolution produces living matter. My comb is not living matter. It was designed by a human.

And that human came from …… ?

Oh, and can you think of any NON-living matter that the IDer aare harping about “design”?

My point in a nut shell was this. There are objects that cannot be produced any other way, that science knows of, than by intelligent design. My pocket comb is one of millions of such objects.

Trivial. We already know that humans can design objects.

What IDers need to show is that some NON-human thing designed … well … anything. Anything at all.

Anyone care to give it a go?

I was trying to enlarge the arena of refutations that those who defend evolution can use against IDers. A defender of evolution, which really does not need defending in the community of clear thinking people, but alas there are other types of people that have power and need enlightening, could say that yes we admit that ID must be invoked to explain certain objects. But that does not prove the divine origin of ID. We know that humans designed and created many objects and we a certainly not divine or supernatural.

No kidding. Alas, it is not HUMAN design that IDers are concerned with. It is NON-human design.

Unless, of course, they think the bacterial flagellum was designed by time-travelling human biochemists …. ….

Comment #35262

Posted by steve on June 14, 2005 6:36 PM (e)

Qetzal, using a relationship like

ds = dQ/dt

and others, depending on what’s applicable, you can easily use SLOT with open systems as long as you track the movement of the relevant variables across the system boundary. Glen’s problem was he was claiming SLOT when he should have just said something was statistically extremely improbable.

Comment #35268

Posted by steve on June 14, 2005 6:54 PM (e)

To anybody else who’s watching, and doesn’t know what the hell is going on, Glen said a long stretch of DNA would not randomly mutate to become identical to another gene, according to SLOT. Now the fact is, it won’t mutate to become identical, because the odds against that are enormous, via simple statistics. You can use thermodynamics on the system under certain circumstances, for instance, you can calculate the dS (change in entropy) under certain changes to the sequence, if you know the dU (energy change) per sequence change. But if you want to use SLOT, you need to state a little more about the system, such as establishing some kind of boundary, and knowing what sort of equilibrium the system is in, what the dQ (influx/outflux of heat) is, or the PdV and VdP (pressure and volume change), or in quantum systems, what items are indistinguishable and obey different statistics, etc.

Comment #35269

Posted by steve on June 14, 2005 7:01 PM (e)

But you should, I suppose, take my comments with a grain of salt, because according to Glen I

obviously haven’t had much of a physics course in your lifetime.

Not sure which of the twelve he was talking about, though.

Comment #35271

Posted by steve on June 14, 2005 7:07 PM (e)

Sorry, make that 13. Forgot about that dinky 300-level astro class last fall. Damn technical electives.

Comment #35282

Posted by qetzal on June 14, 2005 8:04 PM (e)

steve,

Thanks. In fact, I understood that point when you first made it.

Comment #35283

Posted by steve on June 14, 2005 8:12 PM (e)

Sorry. I have a tendency to sound pedantic at times. I was a math tutor for a few years to pay for school, and I am now programmed to explain things from the basics.

Comment #35284

Posted by steve on June 14, 2005 8:17 PM (e)

BTW, one result of tutoring is, I understand that it is pointless to explain things to people who don’t want to understand them. i see with creationists all the time, it’s no use to debate them, to try to explain things to them, because if they don’t want to understand it, they won’t. Take those several exchanges with Heddle over the last 10 months. He knows, somewhere, that you can’t get a probability estimate without some info about the distribution. You can’t gauge the unlikeliness of a result in an interval, merely from the size of the interval in some arbitrary measurement system. He knows that. But he refuses to understand it w/r/t his ID arguments, because it undermines his beliefs.

Comment #35313

Posted by Guts on June 15, 2005 2:19 AM (e)

how exactly is the current IC argument any different from any other argument from ignorance?

Ignorance of what?

Comment #35317

Posted by SEF on June 15, 2005 4:18 AM (e)

'Rev Dr' Lenny Flank wrote:

What IDers need to show is that some NON-human thing designed … well … anything.

Well there are bower birds, ant hills and gorillas who paint. Although those are not in the direction intended by the IDers (ie the artists are regarded as more stupid than human and the artifacts as less intentionally designed) it would be interesting to see how the supposed (ie bogus) ID filter handles them. I’d also include in the test some modern human “art” which I regard as being rubbish. :-D

We should be able to put such things on a continuum of intelligently designedness, with any possible UFO and its aliens likely to be somewhere above humans and human design. Of course that’s actually what scientists have effectively been doing all along - long before the creationists created their ID cover story. What we see is that natural things from atoms to rocks and life-forms show the signs of iterative unintelligent processes and not the signs of one-off planned design or designs incorporating successful elements from disparate precursors. Hence Evolution not Creation.

It would still be nice to force the IDers to display the vacuousness of their version again though.

Comment #35320

Posted by Pastor Bentonit on June 15, 2005 5:53 AM (e)

Guts wrote:

(how exactly is the current IC argument any different from any other argument from ignorance?)

Ignorance of what?

Painfully obvious, yes…

Comment #35346

Posted by Glen Davidson on June 15, 2005 10:51 AM (e)

So I guess Steve pointed out how wrong you are once again, quetzal. Apparently you believe him, because he’s not me, showing your bias one more time. Steve has mightily changed his tune, for he wrote earlier:

Entropy, defined in an Information Theory sense, might increase according to some IT law analogous to SLOT, it’s not SLOT, which is a statement about the entropy of a thermally isolated system.

Later he writes:

you can easily use SLOT with open systems as long as you track the movement of the relevant variables across the system boundary. Glen’s problem was he was claiming SLOT when he should have just said something was statistically extremely improbable.

Does it bother you that he wrote the wrong thing previously, quetzal, or is it all just going to be one-sided as usual? True, Steve neglects to mention that I did mention probabilities–as well as changing his position here. I had written, before he got into the discussion:

2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction). Of course one could simply be appealing to probability theory or some such thing, but either way, life is going to increase in complexity without some major event constricting it

Steve leaves out the caveats, the mention of probabilities, and clings to the notion that I was wrong somehow. What I had written in response to Henry J had many caveats throughout, and no one who responded to me cared that a simple and wrong statement was all that I received in response.

Why don’t you actually revisit the actual discussion where it turned bad, quetzal, and try to find out how improper blaming me for “antagonism” is? The “discussion” declined after I wrote a reasonably polite response, this (minus the quoted text):

Certainly we’re talking past each other, but I don’t know how, other than following my own line of reasoning, to discuss how we really can identify designed objects.

I would expect you to believe that a watch on Pluto was designed and made (if not exactly “manufactured”), because it shows apparent purpose and a lack of a natural means of producing it.

The crux is the predictions that evolution makes. We best know that life was not designed because it shows only evidence of being evolved, and we lack any means of distinguishing the evidence of evolution from some proposed “design”. That is to say, we know that life can evolve, at least to some degree, and fully lack any evidence that the genomes that we see are or can be made by any reasonably understandable designer.

We might have some sympathy for Paley’s nevertheless unsupported assertion if we did not know that life shows evidence of “natural” evolution. It the evidence of evolution that which moves us beyond mere skepticism to full-blown denial that life was designed. And it is the predictions of evolution that make it science here or on any other planet that we are capable of investigating.

And then Flint attacked me quite unfairly and without addressing evolutionary issues. Here it is in its entirety:

You may be right, but I can’t escape the suspicion that There are more things in heaven and earth, Than are dreamt of in your philosophy. You remind me of the proclamation someone once made (which I could remember, I think the president of some university) that science had basically completed the skeleton and fleshed out all there was to be known. All that remained for scientists to do was to grind out the details. Ironically, this speech was made only a year or two before the Year of Einstein, 1905.

Is it necessarily the case that given conditions more or less as we’re familiar with them, natural processes will produce more or less comparable results given enough time? How far can these results vary in the “less” direction before we could not properly identify them without some considerable study? While I don’t wish to denigrate what we have learned with so much effort, I can’t help but consider it local knowledge. The universe presents us with an endless supply of surprises, some quite totally unexpected, and I expect this to continue. I lack your confidence that our local knowledge will be all that portable.

There he dredges up a questionable anecdote and simply attacks me with it, sans proper discussion, any evidence, or any regard for decency. Not your problem quetzal? Apparently it isn’t, rather you keep up your attacks however unwarranted until Steve makes a 180 and reverses what he had erroneously stated previously. Well I’m glad that he had the decency to do that.

I do agree with this by Steve:

You can use thermodynamics on the system under certain circumstances, for instance, you can calculate the dS (change in entropy) under certain changes to the sequence, if you know the dU (energy change) per sequence change. But if you want to use SLOT, you need to state a little more about the system, such as establishing some kind of boundary, and knowing what sort of equilibrium the system is in, what the dQ (influx/outflux of heat) is, or the PdV and VdP (pressure and volume change), or in quantum systems, what items are indistinguishable and obey different statistics, etc.

However, he’s really arguing about what is calculable under SLOT, not what SLOT actually implies about systems, which is that they tend to disorder unless there is some sort of entropy-reduction “mechanism” operating. That is to say, he’s being rather pedantic yet again, and trying to disallow my legitimate usage of SLOT (which I also mentioned could be considered via probabilities) by noting that one cannot “use” SLOT except by understanding and/or controlling the circumstances in great detail.

As it happens, SLOT and entropy may well be considered as probabilities within thermodynamic systems, and they often are. Steve is not correct either in ignoring the many caveats I made, including the probability matter, nor in sticking to a SLOT that must be calculable. I wrote an intelligent qualified piece in response to Henry J, and there is no excuse for ignoring nearly everything I wrote and responding to a strawman.

obviously haven’t had much of a physics course in your lifetime.

Not sure which of the twelve he was talking about, though.

Then you certainly did poorly in responding to me previously.

But now you’ve shown up quetzal, who incomprehensibly claims to have understood you the first time. Evidently he really understands very little in this discussion, and simply fakes it, while reserving his antagonisms for one person no matter what.

Boltzmann connected entropy issues, SLOT, and probabilities, and I made no mistakes in discussing SLOT (given that I wasn’t pretending any technical discussion of SLOT). I was in fact very careful to point out conditions under which SLOT would predict randomization of DNA information, while never claiming in the least that it was a calculable SLOT problem as Steve appears to suggest it must be. It really wouldn’t matter if I had first argued probabilities and then related them to SLOT, or if I had written them in the order which appeared, at least not with regard to actual science.

Regardless, Steve, apparently you do understand SLOT reasonably well in the later instantiations, and I have little to argue with this time around, in fact. That you shot down quetzal’s prejudiced and incorrect attacks over SLOT make things much better in my view.

Comment #35350

Posted by Glen Davidson on June 15, 2005 11:09 AM (e)

Just a bit about Boltzmann, probabilities, and open systems:

http://www.schuelers.com/ChaosPsyche/part_1_9.htm

One of the more important sections, IMO, not only re what I was discussing previously, but also with regard to evolution and the origin of life:

The theory of statistical mechanics, invented at the end of the last century, is one way of dealing with such subsystems. In this view, the system itself functions on the averages or probabalistic actions of its subsystems. For example, this is true for dissipative structures that are also autopoietic or self-organizing structures, which is to say, for living systems. Living systems maintain their dissipative structure by dissipating entropy before it has a chance to build up. Statistical entropy was created by the Austrian physicist, Ludwig Boltzmann. His equation is usually given as

S = -k E pi loge pi

where S is the entropy, pi is the probability of accessible states, and k is the Boltzmann Constant.

The higher the pi, the higher the entropy (Çambel, 1993). Boltzmann’s Entropy indicates that entropy will always tend towards a state of maximum probability (Lebowitz, 1993). In order to apply this equation, all of the accessible states must have the same probability of occurring (Fast, 1962).

When we view entropy as a measure of chaos, we can say that the probability of accessible states for any complex system is a measure of that system’s uncertainty. Ludwig Boltzmann was the first to note that entropy is a measure of molecular disorder and he concluded that increasing entropy implied increasing disorder (Prigogine, 1980).

I don’t vouch for it all, but the more basic issues agree with what I learned in physics. I happen to like the last part, since in many cases, though not all, it is not improper to treat entropy as disorder.

Of course, “molecular disorder” relates well to what I had written long ago in innocence, if with careful caveats, about DNA.

Comment #35354

Posted by Flint on June 15, 2005 11:30 AM (e)

Glen wrote:

I would expect you to believe that a watch on Pluto was designed and made (if not exactly “manufactured”), because it shows apparent purpose and a lack of a natural means of producing it.

If we disagree anywhere, it is here. My contention is that we cannot reasonably conclude anything about the history of an object when we lack any appropriate context. There is no “inherent designedness” in any specific item that we can determine in a vacuum of knowledge.

The watch on pluto “shows an apparent purpose and lack of a natural means” only because our context identifies it as a watch, and we already know about watches. If we did not, we would have no way of sensing an “apparent purpose”. If we didn’t know how natural forces work on Pluto, we could not guarantee any “lack of natural means”. Instead, we are applying our existing knowledge about Pluto.

Now, I may be misunderstanding, but I think Glen is saying that there IS something we might call “desigedness” intrinsic to an otherwise unidentifiable object. And if he’s saying this, we disagree. We can never determine if something is designed if we lack the appropriate external context science can provide. Designedness lies in the history of the object, not the nature of the object.

Comment #35357

Posted by Glen Davidson on June 15, 2005 12:05 PM (e)

One thing that made the discussion go sour from the beginning is that I was comparing evolved life with a disputed “design”, while Flint was actually discussing something fairly different. Flint and I were not differing much at all about more or less having to eliminate non-life processes, plus having to have some evidence for a “designer” in some manner or other (I believe that I’m rather more expansive in allowing for evidence of a “designer”, however).

My position is and has been for long that life does not look designed, and particularly does not look like machines. Rarely has anyone had difficulty in distinguishing between life and design, and only after Newton did “design” of life in the modern sense become much of a belief (not that suggestive statements from before that don’t exist, yet mostly they didn’t really believe in “design” as in instantiation or reproduction as being “God’s method”). It makes sense to IDists that life is made up of machines, but this is primarily an industrial age bias that they haven’t questioned.

So I really went straight to the life vs. machine issue in responding to Newland, as I have never been confident that he was aiming at anything else but an ID position. I wrote:

That is to say, we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines. We can distinguish distinct “intelligently made” artifacts from evolution quite readily. We never look at fish bones from the archeological record that retain cellular level complexity with having been designed.

I did make this caveat:

Maybe highly advanced aliens could make life indistinguishable from evolved life.

Obviously I can only speak of the differences between life and non-life that are visible now. But the fact is that life is very complex, often even in gross morphology–much more complex than human designs of a couple centuries ago (arguably more so than today’s computer chips). Certainly anything the size of a tree is far more complex, typically, if it is made by life than if made by humans. This is just one aspect by which we should be able to tell life and machines apart–at stages of technological evolution similar to our own, of course.

Flint made this post (barely modified):

[Glen wrote] we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines.

[Flint]Permit me to disagree very strongly. The ONLY basis we have for such identification is our own experience. So you are saying “An alien planet would be sufficiently similar to our own experiences so as to support qualified judgment.” But my point was that this hypothetical alien planet had NO OVERLAP with ANYTHING in our experience.

And I insist that until we accumulated some relevant knowledge, we could do no better than random in guessing which are the aliens, which are the artifacts, and what might be natural.

This is an important point. IF we had intimate knowledge of the Designer and His methods, and if that knowledge indicated that He gets his kicks creating life as we know it, we would surely change our minds and find that we are intelligently designed after all. So if you are arguing that we could reliably identify alien organisms on the basis of no prior experience, I suggest you are simply wrong.

I was discussing “design” specifically in contrast with life, and Flint was discussing “design” as produced by some unknown “designer”. I’m going to try to do now what I probably should have done previously, point out that I was simply discussing the elimination of life from the “design category”, which I do expect we should be able to do reasonably well for most macroscopic alien life with minimal study. Flint may disagree, but I don’t think that this issue is really what he cares about, in fact. It’s the other eliminations that he appears to be targeting, not so much our minor disagreements about identifying life.

but I think Glen is saying that there IS something we might call “desigedness” intrinsic to an otherwise unidentifiable object.

I really don’t know where Flint got that idea, but if there is any doubt, of course I do not think that in the least. I had written early on (#35046) this:

With a comb it might be difficult, because if they weren’t associated with dwellings and the like, how would we really know that it wasn’t produced by “non-intelligent” life. Sure, we’d probably be able to say that it was made by life, but by intelligent life as you wrote? I’m not so sure, unless of course we could show tool marks, or that the material of the comb was made by nickel catalysts or something of the sort. A comb is so simple and conceivably of use to some hypothetical organism that we’d just have to work through the problem, and not be certain just on the basis of one comb that it was made by “intelligent life”—unless, again, specific design characteristics could be seen.

One thing we certainly can do on earth is to distinguish between the turtleshell that an antique comb might be made of, and the work that made the comb itself. The turtleshell has the marks of life in it, including the complexity that goes beyond that of design that we know, while the comb may be made using sophisticated techniques, while not being anywhere near the complexity of life. While designers might be able to make objects as complex as life someday, it will require a long evolution of “designer knowledge” to get to this point.

I should have written “tortoiseshell” instead of “turtleshell”. Regardless, Flint and I were remarkably close together on what we wrote about the comb.

And that perhaps can come close to wrapping up this tempest in a teapot.

Comment #35364

Posted by Flint on June 15, 2005 1:15 PM (e)

Glen:

You write this:

the fact is that life is very complex, often even in gross morphology—much more complex than human designs of a couple centuries ago (arguably more so than today’s computer chips). Certainly anything the size of a tree is far more complex, typically, if it is made by life than if made by humans. This is just one aspect by which we should be able to tell life and machines apart.

Now, my reading of this statement is that given object X, we can tell whether or not it is life by its degree of complexity, as a fairly reliable indicator. You seem to be saying that anything sufficiently complex (whatever that means) is probably life.

But then you say

I really don’t know where Flint got that idea [that I consider designedness intrinsic], but if there is any doubt, of course I do not think that in the least.

This is confusing, because comlexity however designed IS intrinsic to the object, independent of any context. And my understanding of Dembski’s “specified complexity” is that if we define complexity in a certain way (that is, how we specify it) we can reliably tell “intelligent design” from “evolved gradually”.

I personally don’t think we can describe any arragement of molecules as being more “life-type-complex” than any other arrangement, except within the context of life as we know it: we can identify DNA, for example, and know that DNA is invariably an indicator of life as we know it.

The problem here as I see it is that Dembski’s specification is post facto - he’s taking what he has already decided was purposefully designed, and using its properties to craft his specification. And I think we can agree this is quite backwards, but from my perspective what you seem to be doing is similar: taking one type of complexity and post-specifying that pattern as an intrinsic indicator of life. If this is what you are doing, I don’t think it’s entirely justified. We may very well someday encounter what we agree is life, but which is based on entirely different patterns. I don’t think that “lifeness” is intrinsic either, it also requires a context.

Comment #35368

Posted by Glen Davidson on June 15, 2005 1:47 PM (e)

Flint wrote”

And I think we can agree this is quite backwards, but from my perspective what you seem to be doing is similar: taking one type of complexity and post-specifying that pattern as an intrinsic indicator of life. If this is what you are doing, I don’t think it’s entirely justified

I wrote:

Certainly anything the size of a tree is far more complex, typically, if it is made by life than if made by humans. This is just one aspect by which we should be able to tell life and machines apart. [bolding added]

Previously I had mentioned these other aspects:

This is because, in spite of all his prejudice and lack of scientific understanding, Dembski knows that something with as many specific points of correspondence as a Bible verse has derive from the original source. This is true even of “human designs”, that in fact it requires a sort of “evolution” for there to be even a derivative line of text that shares a considerable correspondence with Isaiah 7:14.

This is also true of even 10 proteins of the flagellum, as well as the ones that Dembski appears to be ignorant of (why doesn’t anyone ever write of what Dembski shows that he knows? Surely he must know some things, but clearly he’s mostly blithering in areas where he evidently knows nothing of note). They must have derived from the apparent source with which they share many specific correspondences (the true story behind “specified complexity”), and this would be so even for a “designer” kludging together a system.

The trouble is that the appallingly ill-educated Dembski doesn’t have the slightest evidence that some homologies, like those of Death Valley pupfish, are due to evolution, while others are due to some “designer” who is far more limited in scope than are even human designers.

Of course he needs this idiot savant “designer” to “explain” why the doofus is both so very intelligent as to be able to “design” a working flagellum, while being far too unintelligent and/or perceptive to use new parts and designs, or even to borrow “designs” outside of the bacterial lineage, in order to do so. Note again the likely projection of Dembski’s very narrow education and intelligence and near-total lack of imagination onto his “God”. His “God” fits into his almost complete lack of understanding of science, thus he invokes this “God” without any regard for science or for the likelihood that a real God might surpass Dembski’s prejudice and ignorance.

But anyhow, even Dembski probably would admit that pupfish share so much genetic information because of their relatedness to each other. Dembski turns around and claims that flagella share data with other protein complexes due to a “designer”, without a smidgeon of evidence that the same explanation doesn’t apply across the genomes of organisms.

And I wrote:

That is to say, we can predict from 2LoT and other physical considerations that life will be complex, and, in any reasonably undisturbed environment, that life will become diverse, exhibit “nested hierarchies”, and be very complex due to neutral and near-neutral mutations. This will not happen in any reasonable design scenario, and this is how we recognize that life has evolved and not been produced by God or aliens (barring Gods or aliens who deliberately mimic evolutionary evidence).

I also wrote:

My point (“we almost certainly could tell if organisms on another planet were indeed organisms which have evolved, or if they were mere machines”) necessarily holds, I think, not only because evolution leaves tell-tale marks, but also because organisms are quite unlike machines in “purpose” and in form. That is to say, from the fact that some things just live and apparently open surfaces to the sun, the fact that they (some at least) aren’t serving obvious other-oriented purposed, and show similarities which exist beyond functional reasons, we could at least tentatively distinguish many such life forms from alien productions. Any sort of genetic study would be so much the better.

Flint, you’re still not dealing with evolutionary prediction or even the normal matters of life that would betray to us what life is at least in some cases. And you’re still attributing to me simplistic positions that are entirely incorrect. I am afraid that I am not likely to really get across to you the complexity that is unavoidable in life, and particularly the complexity predicted by evolution that should not be too difficult to discover on most planets inhabited by macroscopic organisms.

Comment #35371

Posted by qetzal on June 15, 2005 2:11 PM (e)

Glen,

As I already said, and will say again, it was never my intention to attack you. I bent over backward to emphasize that in my second post, and went further to apologize for giving you the impression that I was attacking.

Your response, in #35346, was rather less than gracious. I am not surprised.

Regarding your suggestion that I revisit the actual discussion where it turned bad, I did. The first unambiguously perjorative comment, in my opinion, is yours - #35149. I realize that in your opinion, you were attacked first, but it didn’t read that way to me at the time, and it still doesn’t.

Regarding the thing with steve, I was never trying to argue the accuracy of any of steve’s comments on 2LoT, precisely because it’s not a subject I’m expert in.

I also didn’t say I agreed (or disagreed) with his comments. I can understand his points (or at least believe that I do), even if my subject knowledge isn’t strong enough to judge whether he’s correct.

My whole point with steve’s comment was that you ridiculed it, and then cited a link which contained the same statement, almost word for word. Your attitude was, how could anyone even say such a thing? How appalling!

Well, if your own link says such a thing, I think it’s going a bit far to say it’s appalling. Even though the link does, in fact, go on to explain a way around the issue. (And even then, it uses language that repeatedly reinforces the point about the formal limits of 2LoT.)

Don’t you think it might have been more conducive to polite discussion to simply say (to steve), “Your comment is only formally true. You should know there are ways to apply 2LoT to open systems. If you don’t, try this link.”

Again, my comments were not directed to the merits of anyone’s arguments. I think you came off sounding like a rude jerk when there was no call to do so. I think you continue to sound that way in your recent reply to me. I think you are quick to take unwarranted offense at others, loathe to consider whether you over-reacted or misunderstood, and disinclined to give others the benefit of the doubt. And I think it obscures the merits of your arguments.

But that’s all I will likely say on the matter. I agree with you that it’s a good idea to bring this to a close. You are welcome to have the last word if you wish.

Comment #35372

Posted by Flint on June 15, 2005 2:16 PM (e)

Glen:

I am afraid that I am not likely to really get across to you the complexity that is unavoidable in life, and particularly the complexity predicted by evolution that should not be too difficult to discover on most planets inhabited by macroscopic organisms.

I’m afraid this is probably true. I’m not a biologist. My reading is, you have a concept of the complex specification life must meet to BE life, and that anything within hollering distance of this specification is almost surely alive (or was once living). You assume that macroscopic organisms on other planets fall within this distance, and certainly we have no evidence by which to either agree or disagree with this position.

You speak of “Gods…who deliberately mimic evolutionary evidence” and I admit this strikes me oddly. My understanding is that theistic evolutionists include those who believe their god uses supernatural means to inform and direct the evolutionary process, which would not be possible without Divine guidance in some way. I do appreciate that sufficiently advanced aliens can hypothetically construct things that would fool our heuristics. My contention is that your assessment that some otherwise-unidentified object was “life” is a probabilistic statement. You and I might disagree only on your odds of getting it right the first time.

Comment #35382

Posted by Glen Davidson on June 15, 2005 3:04 PM (e)

I bent over backward to emphasize that in my second post, and went further to apologize for giving you the impression that I was attacking.

Saying it isn’t an attack doesn’t make it not one. I know psychology, and I’m particularly unlikely to accept disclaimers from someone who has never dealt properly with the evidence from the beginning of his attacks. If you convince yourself that they’re not attacks, fine, but I wouldn’t be even in the ballpark of understanding humanity if I were simplistic enough to accept such statements.

Your response, in #35346, was rather less than gracious. I am not surprised.

Of course you’re not surprised, you were prejudiced from the start. That’s why I’m not gracious with you.

The first unambiguously perjorative comment, in my opinion, is yours - #35149. I realize that in your opinion, you were attacked first, but it didn’t read that way to me at the time, and it still doesn’t.

Oh, first “unambiguous attack” as judged by this guy who can’t even read remarks in context properly. Like I said, it’s time you think about truth and justice, and not merely attacking while denying same.

My whole point with steve’s comment was that you ridiculed it, and then cited a link which contained the same statement, almost word for word. Your attitude was, how could anyone even say such a thing? How appalling!

Well, if your own link says such a thing,

It doesn’t, only you are so incompetent at reading that you think that even in context it says what you first said it did. In fact I can’t argue down someone who can’t read physics material, as it’s more like trying to get across to you that two plus one does not equal two.

I guess that you feel justified in distorting and falsifying what the link says, simply because you’re too inept even to know what they mean by “we fake it”. The fact is that NO SYSTEMS ARE ENTIRELY CLOSED, so that if SLOT only referred to completely closed and equilibrated systems (which actually is an odd statement, IMO), then it would refer to nothing at all. But since you’re not capable of understanding these matters you pretend that you do.

I quoted part of the following from one of my links (same site for both, of course):

The 2nd law is no different in statistical mechanics than it is in classical thermodynmics. It remains a fact that S 0, as previously derived by the founders of classical mechanics. But in classical thermodynamics, heat and entropy are treated like fluids that flow from one system to another. The asymmetrical 2nd law forces them to flow always in one direction, but not the other. But gravity asymmetrically forces water, for instance, to always flow down hill. So the asymmetry of the 2nd law, and the need to pump heat or entropy “uphill”, as one would for water, don’t seem like a fundamental problem.

But the transition to statistical mechanics, and the idea that a gas is made up of moving particles creates a large, fundamental problem. The motion of the particles is controlled by Newton’s equations, and they are all time symmetrical, they work just as well “backwards” as they do “forwards”. Indeed, there is no intrinsic difference between the two at all. That means that a gas should be able to run “backwards” as well as “forwards”, and entropy, as a state variable for a gas system should be able to do likewise. But the 2nd law forbids it, setting up a fundamental conflict. Why should an essentially Newtonian system not be time symmetric? The problem has earned a name: The Paradox of Irreversibility.

This is dealing with SLOT issues in open (as well as closed) systems, and you totally ignored it and misunderstood the first link. I’m not surprised, you didn’t even refer to the correct link when you brought up your out-of-context quote, indicating that you’re either sloppy or incompetent.

I included the second link partly because the first is a bit ambiguous. Still, it does discuss how SLOT applies to open systems, it’s just that you don’t understand and would rather present false charges against me than to deal honestly with the whole situation.

I think it’s going a bit far to say it’s appalling. Even though the link does, in fact, go on to explain a way around the issue. (And even then, it uses language that repeatedly reinforces the point about the formal limits of 2LoT.)

It is in fact like I said in the first place, SLOT tells us why heat flows in one direction only (unaided). It actually has to do with the entropy of the system, wherein a reasonably closed system (mentioned for the sake of simplicity) must either conserve entropy (no heat flow) or increase entropy, which means equalization of temperature. The same equations also tell us that heat must flow from hot to cold (in any ordinary conducting situation) in open systems, and the equations are related to SLOT ([delta]S>=0) Instead of dealing with what I quoted you started in with your incompetent out-of-context quotes and attacks that are hidden as attacks only from the obtuse.

Had you dealt with what I specifically pointed to in a competent manner, you’d have understood the other link better (though to be fair to both SEF and quetzal, the writer of the links is not a particularly good one, or especially careful).

Don’t you think it might have been more conducive to polite discussion to simply say (to steve), “Your comment is only formally true. You should know there are ways to apply 2LoT to open systems. If you don’t, try this link.”

I made a reasonably polite comment at first, and received nothing but a blank and erroneous statement in reply:

[Glen wrote]Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

[Flint]Entropy, defined in an Information Theory sense, might increase according to some IT law analogous to SLOT, it’s not SLOT, which is a statement about the entropy of a thermally isolated system.

I can’t discuss matters when the issues have been closed off by erroneous statements, much as you are incapable of discussing your attacks in a psychologically competent manner. And again you don’t bother to be fair or competent, you just attack. You have yet to begin to reach the standards that you enjoin upon me in your hypocrisy.

Again, my comments were not directed to the merits of anyone’s arguments. I think you came off sounding like a rude jerk when there was no call to do so.

You have to continue your falsehoods in order to justify your name-calling. You have been nothing but dishonest with me, and even if you’re unable to understand anything being said here (as it seems), you still have the responsibility to deal honestly with people. Since you can’t deal with the issues you simply attack, and only you (if any) are fooled by your claims that these aren’t attacks.

I think you are quick to take unwarranted offense at others, loathe to consider whether you over-reacted or misunderstood, and disinclined to give others the benefit of the doubt. And I think it obscures the merits of your arguments.

You haven’t bothered to justify any of your claims, except for the inept attempt to reclaim your out-of-context remarks. I think that speaks volumes for your rudeness and lack of regard for others. One thing I don’t do is hide my attacks with thinly veils of denial, for I believe in being honest with people. Another thing I don’t do is come along with out-of-context quotes and false claims while acting like a pompous lord who thinks his incompetence is truth.

That is to say, I have every right to take offense at anyone who posts as rudely and dishonestly as you have, quetzal. It’s one thing to be justified in one’s comments, quite another to blather away without competence or knowledge while pretending that one is better than the actually competent and honest.

And the only way one can get one’s arguments across is by standing up to people like quetzal who counsel “politeness” which apparently is modeled on his lack of having anything of value to say (at least not in this matter, that’s for sure).

Comment #35383

Posted by Glen Davidson on June 15, 2005 3:07 PM (e)

My contention is that your assessment that some otherwise-unidentified object was “life” is a probabilistic statement. You and I might disagree only on your odds of getting it right the first time.

Could be. I’ll only add, good post.

Comment #35384

Posted by steve on June 15, 2005 3:07 PM (e)

“Your comment is only formally true. You should know there are ways to apply 2LoT to open systems. If you don’t, try this link.”

My problem wasn’t that the system wasn’t closed, it was that it was so wide open that you can’t dream of using SLOT. People use SLOT when they really just mean that something’s getting disordered or that a certain outcome is very unlikely. A good example is that architecture guy, (Kunstler?) who tries to drag it into social policy discussions. SLOT is pure physics. The T stands for Thermodynamics, not information Theory, though there are sometimes analogous situations, and occasional intersections (like the entropy of physical bits).

Comment #35385

Posted by steve on June 15, 2005 3:15 PM (e)

But now let’s talk about something interesting. Flint speaks of heuristics. If someone asked me for the 10¢ explanation of the truth of ID, I would use that word. I would say,

“We have some heuristics which help us recognize things other humans produce. They are rules of thumb. A few religiously motivated people look at living things and those heuristics suggest design. The heuristics are imperfect rules of thumb, which can’t be made into a perfect algorithm. The appearance of design is sometimes just an appearance. Evolution can produce that appearance, and that’s one thing that makes it so shocking and beautiful. In the last decade or so some people have tried to make those rules of thumb into a perfect algorithm, and failed badly. The scientific community thinks they’re cranks, when it thinks of them at all.”

Comments?

Comment #35389

Posted by Flint on June 15, 2005 3:27 PM (e)

steve:

I would change the emphasis a bit. Religiously motivated people have it on the Word of God that life is designed. Genesis is not ambiguous about it. The claim that evolution can produce the appearance of design is not very relevant. Evolution does not happen according to this doctrine, and “produces the appearance of design” for the simple reason that it IS design. God said so.

So the change of emphasis is away from conceding this appearance, in the direction of ID *using* that appearance in an effort to dress their religious doctrine in the trappings of science. And the algorithm for detecting design in life works so perfectly there’s no reason ever to apply it.

My “alien world” was an effort to illustrate the limitations of our heuristics; how heavily they depend on experience taken so fully for granted we forget we even apply it.

Comment #35391

Posted by Glen Davidson on June 15, 2005 3:31 PM (e)

“Your comment is only formally true. You should know there are ways to apply 2LoT to open systems. If you don’t, try this link.”

My problem wasn’t that the system wasn’t closed, it was that it was so wide open that you can’t dream of using SLOT.

Don’t take quetzal’s word for mine, though I’m not saying you were. I wasn’t talking about “applying SLOT” in the sense you mean at all, and I said so. That’s one reason I mentioned probability theory, because I know that it’s not going to be “using SLOT” in the sense that you mean, Steve.

It’s this again (from an earlier quote):

When we view entropy as a measure of chaos, we can say that the probability of accessible states for any complex system is a measure of that system’s uncertainty. Ludwig Boltzmann was the first to note that entropy is a measure of molecular disorder and he concluded that increasing entropy implied increasing disorder

Of course I do know that one need barely consider SLOT in calculating entropy, nevertheless it is the typical “law” invoked to inform people that entropy will increase, which in molecules will generally mean that disorder increases. Any number of processes can prevent this in DNA, and they do, too. However, in some portions it seems that SLOT is reasonable to invoke.

The fact is that I mentioned 2LoT first, rather than simple probabilities, because the laws of thermodynamics have to be broken for ID or creationism to be “true”. It is what I argued with Berlinski in Commentary (pp. 16-17):

http://www.defenddemocracy.org/usr_doc/Letters_from_Readers.pdf

It just seems so hypocritical for IDists to complain about evolutionary probabilities, when they have to actually break the laws of thermodynamics to get their designer to do his “designing”.

Then in the genetic evidence, we actually see what we’d roughly expect if entropy and natural selection were battling it out, namely conserved genetic material which nevertheless differs more or less randomly in the neutral and near-neutral aspects of the genes.

I like using 2LoT instead of probabilities because IDists and their sort like to invoke “laws”, yet will flout them to make way for their miracles. That’s my little story.

Comment #35420

Posted by Alex Merz on June 15, 2005 8:28 PM (e)

It really does appear that there are several people talking past one another on this thread. I’m not happy to say that I added smoke but not light myself. Glen Davidson wrote the following, which set me off a bit.

Glen:

With that minor caveat gone, 2LoT prevents (or “prevents”) the duplication of long, highly specific genetic sequences through simply random processes (i.e., sans reproduction).

Steve:

No it doesn’t. Such a duplication may be unreasonably unlikely, but 2LoT doesn’t have anything to do with it.

Glen:

Yes, it does. Or do you suppose that 2LoT doesn’t predict randomization in such circumstances? [duplication of a DNA sequence] Does 2LoT predict a general increase in information during terrestrial processes or doesn’t it?

Me, snarkily:

Golly, Glen. My P-chem textbook has a lot to say about the 2nd law, but it doesn’t seem to mention information anywhere. Let alone “terrestrial processes.”

I suppose you’d be willing to explain exactly what you mean?

I’m looking forward to your definition of “information,” your explanation of how this definition relates to entropy, and your description of how “terrestrial processes” differ from other processes.

In post #35064 (which I somehow missed, and which is really essential to all that follows) Glen discusses the relationship that I’d asked for, between entropy and information. I’m not delighted with that post but it’s far closer to what I had in mind than any of the other posts here. I’m well aware of the description of information as (neg)entropy, and I’m well aware of its application to biology by (among many others, but perhaps especially) Manfred Eigen.

Nevertheless, the question posed about duplication of a DNA sequence was essentially biochemical, and from that perspective 2LoT is hardly necessary where the law of mass action will suffice. One can invoke entropy here, but as Steve in effect points out, that’s using a Howitzer to pop a balloon.

Anyway. Glen proceeded to get rather pissed off ( #35207). Did I attempt to calm things down? Of course not. But I should have, and I apologize for not doing so. And I don’t expect that Glen and I would find a great deal to disagree about if we were to sit down over a cup of tea or a fermented yeast beverage.

I do suspect that his argument about entropy is not as well thought-out as perhaps he thinks that it is; or at the very least, not as well-explained.

Comment #35429

Posted by Henry J on June 15, 2005 10:00 PM (e)

Re “Evolution does not happen according to this doctrine, and “produces the appearance of design” for the simple reason that it IS design. God said so.”

There’s also the point that saying evolution (or some part of it) is impossible contradicts the view that God can do anything he/she/it wants. (And I am under the impression that this view of God is typical of Creationists.)

Henry

Comment #35435

Posted by Flint on June 16, 2005 7:53 AM (e)

Henry,

Yes and no. God can indeed do anything He wants, but this doesn’t imply He wants to do everything possible. He said in so many words how He did it. Evolution doesn’t contradict what God CAN do, but rather what God told us He DID do.

Comment #35455

Posted by Henry J on June 16, 2005 1:44 PM (e)

Flint,
Or what the writers of those parts of the Bible told us God told them.

I don’t see that the Bible said “how” any of it was done though, just in what order. And it’s way oversimplified if it were meant as anything like a technical description.

Henry

Comment #35469

Posted by 'Rev Dr' Lenny Flank on June 16, 2005 5:58 PM (e)

Evolution doesn’t contradict what God CAN do, but rather what God told us He DID do.

No it doesn’t. The Bible says that God “caused the earth to bring forth” life.

Exactly as evolutionary biology discovered.

Anyway, the Bible wasn’t written by God. It’s not what God told us — it’s what some humans said God told THEM.

And as Charlie Manson and David Koresh demonstrate, God apparently tells some people, uh, some pretty strange things …. .