To explain ID, *don’t* look up the homologies

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William 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?

128 Comments

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…

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.

I fixed the link, thanks.

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.

““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.

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

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

Pim as usual your comments and link are completely irrelevant.

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.

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.

Here’s a project for you, Nelson.…

What?! Actual research. What a novel idea.

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?

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..

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.

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.

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.

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.

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.

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?

Lenny: Nelson refers to Nelson Alonso not Paul Nelson

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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?

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.

“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_[…]_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.

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.

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

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.

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

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 . … .

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This page contains a single entry by Nick Matzke published on June 12, 2005 3:03 PM.

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