Why Were So Many Darwin Defenders No-Shows at the World’s Premier Evolutionary Conference?

_{Thomas Cudworth
July 9, 2011

Intelligent Design

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Intelligent Design}

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I have often wondered whether the loudness and aggressiveness of many culture-war defenders of neo-Darwinian evolution bears any relationship at all to the actual scientific contributions of those defenders to the field of evolutionary biology. As it happens, we have at hand some evidence, albeit of a rough and ready kind, relevant to that question.

From June 17 to June 21, 2011, at the University of Oklahoma (Norman) campus, the conference “Evolution 2011” was in session. It was co-sponsored by three scientific societies – The Society for the Study of Evolution, The Society of Systematic Biologists, and the American Society of Naturalists. It was billed by its promoters as “the premier annual international conference of evolutionary biologists on the planet.”

That billing may be somewhat hyperbolic, yet two things are clear: the conference was huge, with an expected turnout of 1400-1500 people; and many of the big names of evolutionary biology were to be there. Jerry Coyne was to give an address; H. Allen Orr was to chair a session; and Gunter Wagner and Sergey Gavrilets, cutting-edge biologists from the famed 2008 Altenberg conference, were to be there as well. Hundreds of papers were scheduled, and the research contributors to the various papers and presentations, according to the index for the conference, numbered something like 2,000.

It is interesting to make a mental list of the Darwin-defenders who have been most active in the culture wars, whether by publishing popular books defending Darwin, by appearing as witnesses against school boards in court cases, by working for the NCSE, by running pro-Darwinian blog sites, or by attacking Darwin critics throughout cyberspace, and to see which of them either read papers or at least contributed to the research and writing of papers for this premier conference.

Let’s start with those Darwin defenders who are actively anti-religious or show contempt for religion in their writings and internet remarks. Conspicuously absent from the list of conference contributors were evolutionary champions Richard Dawkins, P. Z. Myers, Larry Moran, and Eugenie Scott.

Among those who have not attacked religious belief, but have violently bashed ID and/or passionately upheld neo-Darwinian theory, Paul Gross (co-author of Creationism’s Trojan Horse) and plant scientist Arthur Hunt (who has debated ID people live and on the internet) were not listed as contributors to any of the papers.

Among those who were active in the Dover ID trial, as witnesses for the plaintiffs, the no-shows include Kevin Padian, Robert Pennock, and Brian Alters.

Among the prominent Christian Darwinists, i.e., theistic evolutionists/evolutionary creationists, only Ken Miller was going to be there, and not to read a scientific paper, but to issue a cultural manifesto on why evolution matters in America today. The leading figures of Biologos – Darrel Falk, Dennis Venema, Kathryn Applegate, David Ussery, David Kerk, Denis Lamoureux – who have so often been presented, explicitly or implicitly, as experts on evolutionary biology – produced no papers for this conference. British scientists Oliver Barclay and Denis Alexander, who have posted several guest columns on Biologos, are not mentioned. The frequent UD commenter and Quaker TE Allan MacNeill, who has penned hundreds of thousands of words on UD and on his own blogs, apparently couldn’t manage 5,000 or so words for an original research paper for the conference, nor could the belligerent Calvinist TE and almost as prolific anti-ID blogger Steve Matheson.

Now of course statistics of this sort don’t prove anything about the competence or incompetence of any particular individual. There are all kinds of good reasons why a competent evolutionary theorist might not contribute to a particular evolutionary conference. Maybe some of these people elected to attend another evolutionary conference later this year, or early next year, or maybe their travel budget was exhausted. Maybe personal matters prevented them from going. Maybe some of them attended the conference, to keep up with the field, even though they contributed no paper. But one wonders why such a large number of rabid pro-Darwinists would be non-contributors at the premier evolution conference in the world, if they are as competent in the field of evolutionary biology as they make out. Could it be that most of these people, though possessing degrees in the life sciences, are in fact not trained specifically in evolutionary biology, and therefore had no original work to contribute?

I would be interested in hearing from readers about this. Of the people I’ve named, how many have read a paper at, or at least co-written a technical paper for, any secular conference on evolutionary biology in the past ten years? Or published a peer-reviewed paper specifically on evolutionary biology in a secular scientific journal in the past ten years? Are many of the loudest defenders of neo-Darwinian orthodoxy in fact unqualified to talk at an expert level about the latest theoretical and experimental work in evolutionary biology? And if so, why do they set themselves up as the world’s teachers when it comes to evolution? Why do they write so many blogs, post so many comments, put up so many nasty book reviews on Amazon, participate in so many anti-ID debates on the Darwinist side, if they aren’t experts in the field? Why don’t they let the real experts in evolutionary biology – the Coynes and Orrs and Sean Carrolls – do the public cheerleading and debating for evolutionary biology, and stick quietly to their own specialties of cell biology, genetics, developmental biology, etc.?

In most scientific areas, non-experts don’t pretend to stand in for experts. You don’t see solid-state physicists rushing onto the blogosphere to defend the latest view on black holes from Stephen Hawking. They leave the defense of cosmology to the cosmologists. But for some reason every medical geneticist, soil scientist, biochemist, developmental biologist, cell biologist, anthropologist, part-time first-year biology instructor, undergrad biology teacher at a Christian college, etc., thinks himself or herself an expert on evolutionary theory, and competent to debate it with anyone, any time. Normal professional humility goes out the window when defending Darwinian theory is concerned. That’s why I think it’s important to ask the question: how many of the self-appointed defenders of Darwinian evolution have demonstrated competence, proved by research and publication, in the field of evolutionary biology?

Comments

junkdnaforlife -- you aren't being particularly clear about what your argument is, but I think you are trying to say that after 50,000 generations E. coli is still E. coli, therefore we shouldn't think it is possible for humans and chimps to share a common ancestor. The answer: 1. Humans and chimps are connected by about 600,000 generations, not 50,000 (6 million years * 2 lineages / 20 years per generation). 2. Primates are sexual species with large genomes, E. coli is not. Sexual species can maintain a lot more variability and produce beneficial combinations of traits much more quickly than asexual species. 3. Primates have relatively low population size. This means selection is less effective when selection coefficients are very small (whether positive or negative). This also promotes genetic diversity and enhances chances for recombination and evolution of genome complexity. See the work of Michael Lynch. 4. Lab E. coli are kept in a simple, constant selective environment. They have selective pressure to adapt to basically one thing. They will tend to find that optimum and sit there. Humans, on the other hand, evolved in a complex, constantly changing environment. Constantly changing environment = more change than in a simple constant environment. 5. It's a fallacy to equate bacterial taxonomy and primate taxonomy. In many ways, the E. coli "species" is much more different than humans and chimps. E.g., in terms of sequence divergence, genome composition, etc. Some E. coli have 50% more genes than others. And no, you can't just brush this off with "they're all just E. coli." There are huge ecological differences between these strains. E.g. some are helpful gut bacteria, others are deadly specialized diseases. So I think your argument fails on multiple levels.NickMatzke_UD_{July 14, 2011
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Nick: I see you’ve turned tail again, refusing to answer my decisive rebuttal regarding the meaning of “creationism”. That’s not surprising. The rhetorical position you and the NCSE have staked out depends on promoting the willful, conscious lie that ID is creationism. You have repeatedly been shown irrefutable evidence that ID is not creationism, and you know in your heart that this is right (i.e., you know that neither Dembski nor Behe nor Meyer ever makes use of any argument in their technical ID works that requires the assumption of Christian faith or the literal truth of Genesis), yet you push the connection, as a propaganda tool.
The "creation scientists" said *exactly* the same thing in the 1980s. They said it in defense of the "creation science" laws. Bradley, Kenyon, etc., said that in defense of the "creation science" laws. Yet you and everyone else now acknowledge that that stuff was creationism. Even the arguments, as far as biology goes, are basically the same then as they are now. Irreducible complexity, random-assembly-is-impossible (never mind that evolution isn't random assembly), etc. And, heck, *you yourself* admitted:
OF PANDAS AND PEOPLE WAS NOT AN ID BOOK. IT WAS A CREATIONIST BOOK. IT HAS NO STATUS, ABSOLUTELY NONE, AMONG SERIOUS ID THEORISTS.
...and yet, the Pandas authors and producers, and Behe (on the stand!), and the DI, and most ID fans today all claim Pandas was totally definitely ID and definitely not no-way creationism. It's not my evil bias that connects ID to creationism, it is hard and undeniable historical facts. Any neutral observer will see it.
Neither you nor Eugenie cares about the true definition of ID in the slightest. Nor are you interested in an impartial investigation into questions of origins (or you would keep all options open, including those that don’t appeal to your religious views). All that you care about is victory for your materialist world view, and any means, fair or foul, will do. You should be ashamed of yourselves. If you don’t agree with ID, fine. But don’t lie about what it is. It isn’t creationism, and you know that it isn’t creationism, and you are willfully dishonest to keep insisting that it is. You’re hardly going to be a model for young scientists if your career starts out with a lie. Why not retract the lie now, and give yourself a clean start? Just say this: “ID is not creationism. I apologize for my willful misrepresentation of ID over the past several years.” If you do that, my respect for you will go up from negative 100 to zero, and then maybe you can start building up some positive credit by doing some real science instead of atheist/materialist ideology.
First, I'm not an atheist. Second, if I started ignoring what I know about the actual history of the ID movement, I would be abandoning my intellectual integrity. I won't do that. You don't get to put on rosy-colored glasses and ignore all the inconvenient parts of the history.NickMatzke_UD_{July 14, 2011
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If one aligns FliM with CheC (using Tcoffee) one will find that most of the similar residues between the two sequences are located in the “right half” of FliM (~70% of residues that are similar between FliM and CheC are located in the area around FliM’s C-terminus). Now, if one aligns FliM with FliN, one will find, again, that most of the similar residues between the two sequences are located in the area around FliM’s C-terminus (~60% of residues that are similar between FliM and FliN are located in the “right half” of FliM). This information, by itself, is not very interesting because fusion proteins are not always formed by two whole proteins fusing together (i.e., if FliM is the result of FliN and CheC simply fusing together – say FliN’s C-terminus fusing with CheC’s N-terminus – then we would expect that FliN would share more similar residues in FliM’s N-terminus, while CheC would share more similar residues in FliM’s C-terminus). But it does refute the notion that FliM is the result of a single fusion event of CheC and FliN. So, what evidence do you have that FliM is the result of a fusion of a FliN domain and a CheC domain?
I'm pretty sure your analysis is incorrect and/or whatever proteins you pulled out of the database are incomplete or unusual in some way (proteins are sometimes mislabeled by automatic annotation software, particularly when they are homologous to two or more proteins, e.g. FliM can return hits to both CheC and FliN, even though CheC and FliN are not themselves homologous to each other). This is the standard paper on the FliM/CheC question: Kirby et al. (2001). "CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis." Molecular Microbiology, Volume 42, Issue 3, pages 573–585, November 2001 DOI: 10.1046/j.1365-2958.2001.02581.x http://scholar.google.com/scholar?q=%22CheC+is+related+to+the+family+of+flagellar+switch+proteins+and+acts+independently+from+CheD+to+control+chemotaxis+in+Bacillus+subtilis.%22&hl=en&btnG=Search&as_sdt=1%2C5 See Figure 8. FliM isn't even universally found in flagella, IIRC. As I wrote back in, let's see, 2003:
Explaining the origin of the switch complex, which couples the chemotaxis system to flagellar rotation, requires an examination of the domain structure and interactions of the switch proteins. FliN and FliM, which make up the C-ring, are partially homologous. FliN is homologous to the C-terminal domain of FliM, and as a result the two proteins probably occupy similar positions in the C-ring, perhaps alternating in a 3 FliN:1 FliM pattern, which approximately matches their stoichiometry (Mathews et al., 1998; see also Figure 2, this paper). FliM also has a N-terminal domain with no counterpart in FliN that is the actual CheY-P receptor. CheY-P binds to the receptor domain, increasing the probability of a switch to CW rotation (Eisenbach, 2000) via an unknown mechanism involving interactions between FliM/N and FliG (Mathews et al., 1998). The receptor domain is homologous to the single-domain chemotaxis protein CheC of Bacillus subtilis (Kirby et al., 2001). CheC binds reversibly to the Bacillus C-ring, and is released when it binds to CheY-P. CheC has not been found in E. coli, but homologs are found in many early-branching bacteria, as well as archaea. A cladogram generated for CheC and the FliM CheC-like domain shows that CheC is phylogenetically basal (Kirby et al., 2001). A pre-existing sensory transduction system could be coupled to flagellar rotation in a single step on the hypothesis that a FliN-like protein existed for some nonflagellar cellular response purpose, serving as a receptor for CheC. The exact function of modern CheC is not known, but it appears to interact with CheA, CheD, and McpB, which form a receptor complex (Kirby et al., 2001). CheC may also have a FliM-like function via interaction with the C-ring (Szurmant et al., 2003). The ancestor of FliN might therefore be found among the other proteins that CheC interacts with. On the model, a mutation in this FliN-like protein created a proto-FliN that bound to FliG, slowing or jamming the motor. The reversible binding of CheC to proto-FliN, however, happened to alleviate this effect by changing the conformation of proto-FliN. CheY-P binding to CheC would result in the dephosphorylation of CheY-P and the release of CheC from proto-FliN, resulting in the slowed-rotation behavior. Chemotactic behavior would thereby originate by a single mutation (all other interactions would be inherited), which could then be followed by gradual improvements in the initial crude function. This hypothesis is more economical than supposing that FliN originated for some role in structural support or enhancing export, and was later coopted to a switching function via the binding of CheC, although this remains a possibility as FliN homologs are retained in type III virulence systems for some purpose. The first hypothesis suggests that the homolog of FliN will be found within sensory transduction systems as one of the proteins that CheC or a CheC homolog interacts with; it is difficult to know where to look with the latter hypothesis. The considerable variations in the C-ring of bacteria may yield further hints, as major variations on chemotaxis and the switch complex are known; for example, Aquifex aeolicus lacks the traditional chemotaxis system as well as FliM; Bacillus spp. have FliY (a FliM-FliN fusion protein; Bischoff and Ordal, 1992; Celandroni et al., 2000) rather than FliN. In any case, the fusion of CheC-like and FliN-like proteins would produce the FliM seen in most bacteria.
http://www.talkdesign.org/faqs/flagellum.html#chemoNickMatzke_UD_{July 14, 2011
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Nick: "Ah, typical creationist tactics too" What part of "does the mut/sel observed in the 50000+ generations of adapting e-coli show sufficient mechanism? don't you understand. Liz jumped in and created a distraction. My question was to you. Nowhere did I suggests that the e-coli speciate. My question was about observed mut/sel: Again, from the top:
Is this consistent with the observable evidence of mut/sel in the e-coli study of the 50,000+ generations? Does the direct evidence of the adapting 50,000 e-coli generations provide us with enough confidence that mut/sel administers sufficient horsepower for a chimp diverge from common ancestor, and from common ancestor to the bi-pedal ardi in the same 50,000+ or so generations? From Pre-cambriam to Cambrian body plans?
These are yes or no answers.junkdnaforlife_{July 13, 2011
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I appreicate Dr Cudworth's thought, but he is spitting in the wind. Nick is not a scientist, he is a culture warrior. He will use Dr Cudworth's appeal only to hit it again. It's simply the nature of his identity.Upright BiPed_{July 13, 2011
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I second Dr Cudworth's motion.kairosfocus_{July 13, 2011
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Nick: I see you've turned tail again, refusing to answer my decisive rebuttal regarding the meaning of "creationism". That's not surprising. The rhetorical position you and the NCSE have staked out depends on promoting the willful, conscious lie that ID is creationism. You have repeatedly been shown irrefutable evidence that ID is not creationism, and you know in your heart that this is right (i.e., you know that neither Dembski nor Behe nor Meyer ever makes use of any argument in their technical ID works that requires the assumption of Christian faith or the literal truth of Genesis), yet you push the connection, as a propaganda tool. Neither you nor Eugenie cares about the true definition of ID in the slightest. Nor are you interested in an impartial investigation into questions of origins (or you would keep all options open, including those that don't appeal to your religious views). All that you care about is victory for your materialist world view, and any means, fair or foul, will do. You should be ashamed of yourselves. If you don't agree with ID, fine. But don't lie about what it is. It isn't creationism, and you know that it isn't creationism, and you are willfully dishonest to keep insisting that it is. You're hardly going to be a model for young scientists if your career starts out with a lie. Why not retract the lie now, and give yourself a clean start? Just say this: "ID is not creationism. I apologize for my willful misrepresentation of ID over the past several years." If you do that, my respect for you will go up from negative 100 to zero, and then maybe you can start building up some positive credit by doing some real science instead of atheist/materialist ideology.Thomas Cudworth_{July 13, 2011
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Nick Matzke: FliM is indeed basically a fusion of a CheC-domain and a FliN domain. A domain? You mean just one FliN domain and one CheC domain fused to form FliM? I think the entirety of those two proteins would be needed to form the number of amino acid residues present in FliM. But that in itself it just a touch irrelevant. Based on a sequence analysis of FliM, FliN, and CheC I have to disagree with the view that FliM is basically a fusion of CheC and FliN. If one aligns FliM with CheC (using Tcoffee) one will find that most of the similar residues between the two sequences are located in the “right half” of FliM (~70% of residues that are similar between FliM and CheC are located in the area around FliM’s C-terminus). Now, if one aligns FliM with FliN, one will find, again, that most of the similar residues between the two sequences are located in the area around FliM’s C-terminus (~60% of residues that are similar between FliM and FliN are located in the “right half” of FliM). This information, by itself, is not very interesting because fusion proteins are not always formed by two whole proteins fusing together (i.e., if FliM is the result of FliN and CheC simply fusing together – say FliN’s C-terminus fusing with CheC’s N-terminus – then we would expect that FliN would share more similar residues in FliM’s N-terminus, while CheC would share more similar residues in FliM’s C-terminus). But it does refute the notion that FliM is the result of a single fusion event of CheC and FliN. So, what evidence do you have that FliM is the result of a fusion of a FliN domain and a CheC domain? But note that once you are arguing about issues like statistical significance of homology matches, ID has basically already lost, because there are a bunch of homology matches that no one doubts, and if homology is conceded, then we have agreed there is direct evidence of evolutionary history between flagellar and nonflagellar proteins. The problem is that Darwinian evolution is not the only explanation for homology. As I said earlier – and just for the record, I don’t think you replied to this – if one, for example, aligns the un-evolved sequences designed by Fisher et al., one will find a very high level of sequence similarity. This is because human designers often take an already-existing protein and then modify the amino acid sequence to produce another protein, but since the original amino acid sequence is rarely modified to an extreme amount, there is often a fairly significant level of sequence similarity between two designed proteins. In other words, homology in itself is not evidence that a given protein system arose via purely mindless processes.LivingstoneMorford_{July 13, 2011
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Namecalling, instead of dealing with the merits. What part of bottom up vs top down, and gateway does the above not understand? Methinks, very little. But, it is soooo convenient to shout "creationist in a cheap tuxedo" Utterly telling.kairosfocus_{July 13, 2011
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Ah, typical creationist tactics too -- when you lose on PunkEek for reasons of complete misunderstanding, switch to the Cambrian, a completely different issue. This sort of stuff many fool lay audiences, but it will never, ever get credibility with the serious people in academia, and this is why ID will never deserve a place in universities or schools where serious people who know the science firsthand hang out.NickMatzke_UD_{July 13, 2011
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PPS: Recall, DNA exhibits codes in accord with linguistic rules, to specify functional proteins sand to regulate how they are given effect in building and operating a body plan. That is going to put you into islands of quite specific function. PPPS: Sternberg of course is an expert in evolutionary biology, and is here making a presentation in light of that expertise. But notice how he points out reasonably easily accessible or check-able facts on whale anatomy, the background knowledge that testes need to be at a proper, lower temp range than the rest of the body [why they hang in those little bags in most mammals . . . ], reasonable or generous scenarios and standard models accessible in textbooks.kairosfocus_{July 13, 2011
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PS: Please watch this clip by Sternberg [as was linked earlier], to see the limitations of darwinist mechanisms on pop genetics and mutation fixation in the context of body plan origination.kairosfocus_{July 13, 2011
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Dr Liddle: Thanks for the thoughts. I am very aware of the claims. On my physics background, I tend to take the implications of say 10^57 atoms, 5 - 12 BY, 10^45 or so Planck-time quantum states [PTQS] [10^30 of which are needed for the fastest chem reactions] fairly seriously as constraining what can happen on the gamut of our solar system in our galaxy. The above makes 10^102 a reasonable upper bound on number of PTQS events in our solar system. Just 500 bits of functionally specific complex information specifies some 10^150 configurational possibilities. So, the PTQS resources of our solar system -- our practical universe -- could not sample 1 in 10^48 of the space. Now a sample like that will be fine for getting to typical states in the space, but it is going to be way too small to have a reasonable chance of picking up UN-representative needle in the haystack FSCI clusters. A look at this will show that body plan level origin, where the evidence is that starting from a unicellular organism we need 10 - 100 mn bases worth of complex new info [you were shown linked data on that in an earlier thread but IIRC never came back to it], in a context where the embryological development program that gives it effect is KNOWN to be exquisitely vulnerable to breakdown on blind tampering by mutations, will be severely challenged on search space grounds. Such is BTW the same basic analysis that grounds the 2nd LOT. E.g. if all the O2 molecules in a room are seen at one end, that is so utterly unlikely on chance plus necessity that if we say such a room -- say with an asphyxiated dead man at one end and the O2 at the other -- we have prima facie grounds to infer murder, even if we do not have a clue how that was done. Maybe that demon raised in another thread recently dunit. So, as of right now, there is need for those who propose unlimited, smooth variation across body plans to show some direct observational evidence for their claims. There has been a lot of huffing and puffing, smoke, mirrrors and handwaving in front of exhibits that show a lot less than this or even have been in some cases outright frauds. But what has not been done is to actually demonstrate as fact that we observe body plan origination or what can credibly lead up to it. BTW, horizontal gene transfer, drift of near neutral mutations and the like do not answer to the info origination challenge. Giving the reduced form of the Chi equation, we have abundant evidence on observation, that where we directly see the cause, info beyond the FSCI threshold is an excellent index of design as cause: Chi_500 = I*S - 500, bits beyond the solar system threshold. And, if you want to thing at cosmos scale, simply doubling that number of bits to 1,000 puts the challenge way beyond the resources of our observed cosmos. If you believe that chance and necessity are sufficient to generate FSCI, instead of simply being an illustration of how searches that are intelligently designed will in specific cases outperform chance based random walks in the task of finding target zones, within which hill-climbing mechanisms have differential function to work off. GEM of TKIkairosfocus_{July 13, 2011
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Liz: junkdnaforlife – remember that bacteria (including e-coli) do not speciate. The oldest known life found in the universe was bacteria or archaea so I was told. From LUCA, rumor has it, that everything from a flagellum motor to the human brain has sprouted. All I am concerned with now is if the 50,000+ generations of adapting e-coli bacteria has shown sufficient mechanism.junkdnaforlife_{July 13, 2011
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kf:
The body plan origination and embryological feasibility of mutations required to effect it challenges have of course never been met. Instead, we have been told that macro-evo is simply accumulated micro evo, as though there is not a major informational threshold issue at work.
Couple of points: Yes, that is the issue - "evolutionists" do dispute the existence of a "major informational threshold". So that is probably what we should be talking about. They certainly dispute it as occuring between "macro" and "micro"! Secondly - depends what you mean by macro and micro - if macro means speciation - lateral divergence, then yes, macro isn't simply more micro, there is another ingredient which is population divergence I'd put it this way: micro-evolution is, essentially, adaptation, down any one lineage. And it has no obvious longitudinal limits. Speciation is independent adaptation down two divergent lineages. Again, it has no obvious longitudinal limits, but once the point of hybridisation is passed, there are clear lateral limits - an adaptive innovation in one lineage cannot be transferred to another. Bird lungs will not be transferred to mammals; however, both bird lungs and mammal lungs can continue to adapt down their separate lineages. If there is an unsolved "leap" - an informational threshold, if you like, it's from non-replication to replication - that's abiogenesis. But it isn't relevant to evolution, once started, nor to speciation. Or, at least, I do not see that a convincing case has yet been made that it is :)Elizabeth Liddle_{July 13, 2011
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Re Dr Matzke:
using that Gould quote outside of context of what it really means is a classic cheap creation-science trick. There, Gould is talking about species-to-species transitions in the fossil record . . .
Of course, this -- sadly -- is yet another misleading talking point, further poisoned by namecalling; all intended to carry us further and further from the main issue in the thread, while poisoning the atmosphere. All, further revelatory on the underlying rhetorical games that are afoot. What was not acknowledged above is that in the usual darwinist scheme, species to species transitions are held to be the basis for all else, so if these are systematically missing in action -- and they should be the most numerous of all, everything else above in the taxonomic pattern will be problematic. So the attempted deflection actually implies far more problems than is suggested by the smoothly poisonous way it is done. But in fact the fossil transitions problems are much bigger than this. For in fact right from the days of Darwin the three of life has been stood on its head -- top down not bottom up, and with transitions all across the scale notoriously generally missing in action [never mind the rare exceptions that as Gould points out are headlined, in a context where the implied admission of data cutting across the expectations, is a serious challenge to the pretension to be scientific] -- when confronting the evidence of the actual fossils. Meyer's PBSW summary -- which BTW (despite attempts to smear it and expel the editor for in effect being open minded) passed proper peer review by "renowned" scientists -- aptly sums up with the most significant case, right from the top. In so doing Meyer exposes the key issue that is unaccounted for in the Darwinist scheme, which underlies the informational challenge (which thanks to the informational view of thermodynamics is linked directly to thermodynamics issues on the credible source of functionally specific complex information) that design theory has highlighted:
The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information . . . . In order to explain the origin of the Cambrian animals [an issue of origin of dozens of phyla and sub-phyla, not bottom up from speciation but top down from the highest levels of body plan organisation], one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [NB: For the open-minded, the video discussion of Cichlid variability patterns here and of origin of the whale body plan in light of pop genetics issues here will be interesting. As will this video that brings out more details on the Cambrian life problem. The problem is much broader and deeper than is usually admitted by evo mat advocates as they make their talking points.]
The body plan origination and embryological feasibility of mutations required to effect it challenges have of course never been met. Instead, we have been told that macro-evo is simply accumulated micro evo, as though there is not a major informational threshold issue at work. And, ironically, what is a species is an unanswered question so that North American Elk and Red Deer are seen as interbreeding in New Zealand, Grizzlies and Polar bears can mate and form similarly fertile offspring, and in the Galapagos, birds have been seen happily breeding across species lines. There is plainly a lot of adaptation and variation within the body plan "island of function" level but that is where the issue just highlighted kicks in: where do body plans come from and how can the huge jump in FSCI to explain that new "wiring diagram" come from given the problem of traversing huge config spaces to find narrow target zones of function that are UNREPRESENTATIVE of the physically possible configs. Chance and necessity without intelligence do not provide a feasible, plausible answer; unless the deck is subtly stacked in favour of a priori Lewontinian materialism. Getting back to the main issue raised by Dr Cudworth, it is plain that a serious double-standard is at work, and there is a selectively hyperskeptical game afoot, centred on fallacies of distraction, distortion and denigration by namecalling. (Notice the creationism in a cheap tuxedo distortion point is simply being reiterated again and again on various talking points, without warrant. FYI Dr Matzke, I am a biological origins deep past reconstruction agnostic, save on the point that it is patent that FSCI has to be properly accounted for and its most credible answer is intelligence, so if the cosmological evidence that there has been deep time and origin in a big bang 13.7 BYA speaks true -- and that has a lot better, less circular empirical warrant -- then it is at minimum a credible option that the cosmos is a work of design, and in that light one of the best candidate explanations of origin of life and body plans is design working with intelligently built in evolutionary adaptation capacity to fill niches based on robust, flexible body plans. Worse, even had my cite above been truly out of context -- and plainly, it was only a gateway pointing to a much broader problem that was in turn being diverted from by atmosphere poisoning tactics, and was not indicative of wider and wider problems as we go, quoting out of context is not a specifically "creationist" problem. So, there is an unwarranted snide inference here. But to tag any and all questioning of the evolutionary materialist agenda as "creationist" where that stands in for "ignorant, stupid, insane or wicked" IS patently a serious problem with the ruthless, amoral evo mat factionism that has been exposed at one level or another since Plato. Cho man, do betta dan dat! [Let me be a bit more explicit: If you continue to try to force-fit me into a handy strawman caricature in the teeth of an explicit summary as above, all that will tell me is that you are more interested in pushing ideology than in truth or fairness. In light of the internet thuggery I have been recently subjected to, to the cheers of too many on your side, that will be utterly revealing on the significance, current relevance and force of Plato's grim warning in The Laws, Bk X.) Surely, there is a better way, to actually teach people about what science is historically (especially in modern times) and what it tries to do, acknowledging the limitations of scientific and broader empirical warrant and especially those of attempts to reconstruct a deep, unobserved past: we were not there and we cannot directly observe the true state of the deep past, so we should not project an unwarranted confidence, especially one driven by ideological imposition of a priori materialism. In that context, the major historic and recent approaches to origins views can be presented on a true and fair view basis [Wikipedia style distortions and trashing will not do], in the context of that history and the strengths and limitations of evidence, inference and reasoning can be assessed, with an eye to the issues of institutional politics and rhetoric. To do less than that -- as we are, sadly, plainly seeing at the hands of the evolutionary materialist establishment -- is to resort to mind closing indoctrination, not sound education. Which would be a failure in duties of care. We can and must do better than that. GEM of TKIkairosfocus_{July 13, 2011
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junkdnaforlife - remember that bacteria (including e-coli) do not speciate.Elizabeth Liddle_{July 13, 2011
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Nick: "In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond" Is this consistent with the observable evidence of mut/sel in the e-coli study of the 50,000+ generations? Does the direct evidence of the adapting 50,000 e-coli generations provide us with enough confidence that mut/sel administers sufficient horsepower for a chimp diverge to common ancestor, and from common ancestor to the bi-pedal ardi in the same 50,000 or so generations? From Pre-cambriam to Cambrian body plans?junkdnaforlife_{July 12, 2011
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LOL, using that Gould quote outside of context of what it really means is a classic cheap creation-science trick. There, Gould is talking about species-to-species transitions in the fossil record, which is what his "Punctuated Equilibrium" model was about. He is talking about the transitions between *very similar* and *very closely related* species -- things like horses and zebras. At that very fine scale -- differences much smaller than the differences within what creationists usually call "created kinds", which creationists usually put at the genus or family level (or even higher) -- we don't have very many gradual transitions. Punk Eek suggests that this is because speciation is rapid and often takes thousands of years instead of millions (whereas the fossil record usually has a time-resolution of only hundreds-of-thousands or millions of years). Gould could be right or wrong about this, it's still debated. But either way, larger changes than species-to-species transitions, e.g. reptiles to mammals, dinosaurs to birds, etc. have *lots of transitional fossils*. As Gould himself said, specifically to rebut creationist abuse of exactly that quote! Decades ago!! ======== [T]ransitions are often found in the fossil record. Preserved transitions are not common -- and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. [He then discusses two examples: therapsid intermediaries between reptiles and mammals, and the half-dozen human species - found as of 1981 - that appear in an unbroken temporal sequence of progressively more modern features.] Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am -- for I have become a major target of these practices. I count myself among the evolutionists who argue for a jerky, or episodic, rather than a smoothly gradual, pace of change. In 1972 my colleague Niles Eldredge and I developed the theory of punctuated equilibrium. We argued that two outstanding facts of the fossil record -- geologically "sudden" origin of new species and failure to change thereafter (stasis) -- reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond . . . Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. - Gould, Stephen Jay 1983. "Evolution as Fact and Theory" in Hens Teeth and Horse's Toes: Further Reflections in Natural History. New York: W. W. Norton & Co., p. 258-260. ======== http://www.talkorigins.org/faqs/quotes/mine/part3.html This kind of thing is exactly why ID proponents don't get no respect from scientists, and until this kind of thing stops, they won't deserve it. PS: If you think Gould and Prothero -- both famous paleontologists -- are too biased to be believed about transitional fossils, have a look at what YEC paleontologist Kurt Wise says: http://pandasthumb.org/archives/2009/01/honest-creation.html ========== [p. 218] In various macroevolutionary models, stratomorphic intermediates might be expected to be any one or more of several different forms: – (a) inter-specific stratomorphic intermediates; (b) stratomorphic intermediate species; (c} higher-taxon stratomorphic intermediates; and (d) stratomorphic [intermediate] series. As an example (and to provide informal definitions), if predictions from Darwin’s theory were re-stated in these terms, one would expect to find: – (a) numerous stratomorphic intermediates between any ancestor-descendent species pair (numerous interspecific stratomorphic intermediates); (b) species which were stratomorphic intermediates between larger groups (stratomorphic intermediate species); (c} taxonomic groups above the level of species which were stratomorphic intermediates between other pairs of groups (higher-taxon stratomorphic intermediates); and (d) a sequence of species or higher taxa in a sequence where each taxon is a stratomorphic intermediate between the taxa stratigraphically below and above it (stratomorphic series). With this vocabulary as a beginning, the traditional transitional forms issue can be gradually transformed into a non-traditional form, more suitable to the creationist researcher. It is a Very Good Evolutionary Argument Of Darwinism’s four stratomorphic intermediate expectations, that of the commonness of inter-specific stratomorphic intermediates has been the most disappointing for classical Darwinists. The current lack of any certain inter-specific stratomorphic intermediates has, of course, led to the development and increased acceptance of punctuated equilibrium theory. Evidences for Darwin’s second expectation - of stratomorphic intermediate species - include such species as Baragwanathia27 (between rhyniophytes and lycopods), Pikaia28 (between echinoderms and chordates), Purgatorius29 (between the tree shrews and the primates), and Proconsul30 (between the non-hominoid primates and the hominoids). Darwin’s third expectation - of higher-taxon stratomorphic intermediates - has been confirmed by such examples as the mammal-like reptile groups31 between the reptiles and the mammals, and the phenacdontids32 between the horses and their presumed ancestors. Darwin’s fourth expectation - of stratomorphic series - has been confirmed by such examples as the early bird series,33 the tetrapod series,34,35 the whale series,36 the various mammal series of the Cenozoic37 (for example, the horse series, the camel series, the elephant series, the pig series, the titanothere series, etc.), the Cantius and [p. 219] Plesiadapus primate series,38 and the hominid series.39 Evidence for not just one but for all three of the species level and above types of stratomorphic intermediates expected by macroevolutionary theory is surely strong evidence for macroevolutionary theory. Creationists therefore need to accept this fact. It certainly CANNOT said that traditional creation theory expected (predicted) any of these fossil finds. ==========NickMatzke_UD_{July 12, 2011
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PS: Mr Roache -- being plainly enamoured of the talking points of objectors who are at minimum careless of facts -- seems unaware of this, on the EF applied to biological objects. He should pay particular attention to the examples as given since April in response to challenges, from the 35 protein families addressed by Durston et al.kairosfocus_{July 12, 2011
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Gould's summary of the actual as opposed to headlined state of the fossil evidence, which continues to today after 1/4 million and more fossil species and many millions of fossils:
"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:
The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps [[ . . . . ] He who rejects these views on the nature of the geological record will rightly reject my whole theory.[[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9.]
Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks. Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.]
For more at the first level, cf here. Design theory, as Behe -- and even Wallace, co-founder of the theory of evolution -- will point out, is compatible with common descent, up to and including universal common descent. However, it should be noted that there is here a common distortion of the actual overall state of the fossil evidence that tells much, and none of it good for the promoters of Darwinism.kairosfocus_{July 12, 2011
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Right. And you said Darwin’s book. And Nick recommended a book on fossils. And Darwin said the fossil record could be urged as a valid objection against his theory.
For the love of the IDer, that was 152 years ago, it's illegitimate to quote it without even considering what has happened since then. We've discovered rather a lot of transitional fossils since then. The main point of Prothero's book is that Darwin's statement back then is no longer true.NickMatzke_UD_{July 12, 2011
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128 Mung 07/12/2011 2:05 pm p.s. I was really hoping for more than just fossils though. I meant the big case. All the evidence. Including molecular, etc. The best case for common descent is a book on fossils?
It discusses phylogenetics and some of the other arguments as well. But it has lots of fossils. Lots and lots of *transitional* fossils. I think this is a more direct argument than many of the other arguments, which are more statistical in nature and thus more abstract. And, I did give you the link to the huge 29+ Evidences website, which is book-length and discusses all of the issues, fossil, molecular, etc., in more detail, starting from the basics, than you'll find anywhere else. And it's free!NickMatzke_UD_{July 12, 2011
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FliM is indeed basically a fusion of a CheC-domain and a FliN domain. IIRC YscQ and other T3SS FliN homologs have only the region homologous to FliN, so a score based on comparing to FliM is inappropriate. IIRC if you start a standard PSI-BLAST search on FliN you will easily retrieve YscQ and homologs without difficulty and without lots of random sequences. Re: homology -- it is a common mistake to say 2 proteins are "20% homologous". Except in cases like domain shuffling, two proteins are either homologous or not. 20% sequence similarity is evidence that helps us determine which is the case. Typically 25% or more amino acid sequence similarity makes homology a "sure thing", and 10-20% similarity is the "twilight zone" where you can't be sure just from the sequence similarity number. But if the shared similarities are spread out over an alignment, not eliminated by a low-complexity filter, etc., the e-values will still indicate statistically significant similarity well beyond what is expected from random matches in the database. In many, many cases homology has been concluded from this sort of analysis, and has later been supported by linking intermediate sequences, strongly similar structures, etc. Every paper you will read on flagellum/T3SS acknowledges the FliN/YscQ homology, it's one of the classic "10 shared proteins" you always hear about. The FliG/MgtE one is admittedly less certain (although I think it's likely as I get it in PSI-BLAST searches), having been proposed in only 1 paper by Pallen and colleagues. But note that once you are arguing about issues like statistical significance of homology matches, ID has basically already lost, because there are a bunch of homology matches that no one doubts, and if homology is conceded, then we have agreed there is direct evidence of evolutionary history between flagellar and nonflagellar proteins.NickMatzke_UD_{July 12, 2011
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You asked for a book that laid out the case for common descent.
Right. And you said Darwin's book. And Nick recommended a book on fossils. And Darwin said the fossil record could be urged as a valid objection against his theory.Mung_{July 12, 2011
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Nick Matzke: “In actual fact, phylogenetically we have, as further and further out sister groups…” Two points here: firstly, I don’t think you’ve presented any evidence so far that indicates that “a T3SS-like common ancestor preceded the flagellum and the modern T3SS.” Secondly, you cite several examples of ‘sub-parts’ of the flagellum, and functions that contain some flagellar homologues. However, one of my concerns here is the low level of homology between flagellar proteins and their non-flagellar homologues. For example, last time I checked the flagellar switch complex protein FliG shares only 20% homology with its non-flagellar counterpart, MgtE. And the alignment score that results from a ClustalW alignment of FliM (accession no. P06974) and YscQ (accession no. A9R9I6) is a whopping 7. If one aligns a randomly-generated string of amino acid letters with another randomly-generated string of amino acid letters, the ClustalW score will be somewhere around 6-8. So the homology between FliM and YscQ is unimpressive, to say the least. In the case of the bacterial flagellum, I have never been impressed by the cited homologues, one reason being the fairly low level of homology present. So, where do you think FliM, for example, came from, and what evidence can you cite in favor of your hypothesis? Back in 2003 I believe you argued that a proto-FliN/CheC fusion formed FliM, but I’m not sure if you still hold to that idea.LivingstoneMorford_{July 12, 2011
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Re WR: Copying of gross and distorting errors -- in the teeth of direct and undeniable evidence in open court -- is "standard practice" for judges? Bad news, that.kairosfocus_{July 12, 2011
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KF
And if Judge Jones’ blind copying of NCSE/ACLU submissions, gross errors and all, is anything to go by, under current circumstances, too many judges may not be neutral observers in the relevant sense.
What Judge Jones did is standard practice. It's funny how you are not complaining about how it happens day in, day out because it is. It's just this one specific example you have a problem with of the completely logical situation where a Judge who has been persuaded by one side uses that sides own data, word for word in some cases, in his verdict.
Tag and dismiss tactics — which you (sadly, predictably) used — do not answer to that.
Hardly. The way I see it is that Nick is taking time out from doing more productive work to explain his work to you to prevent, as much as possible, misunderstanding. If you have a problem with what Nick is saying then perhaps you should collect your evidence and publish! As I suggested to Upright. Publish or perish KF! Links to an angelfire website (are they really still going) might as well be to the timecube guy for all the difference it's going to make. The guy you are arguing with cannot lose here, he wins, he wins. He loses, well, it's only you that's seen it. And according to you and everybody else he loses every time anyway so who's to know it's different this time? So, save your energy and publish in the only venue that matters! The only venue where you have a chance of persuading others of the validity of your point of view! A Nobel awaits for the first worked example of the Explanatory filter for a biological object, I'm sure!WilliamRoache_{July 12, 2011
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Mung:
Elizabeth Liddle:
Mung – there’s always Darwin’s
Do you’ve changed your mind? Darwin’s book did contain a theory of common descent?
You asked for a book that laid out the case for common descent. Darwin wrote one - that's why the title is "On The Origin of Species". However, the mechanism he is famous for proposing - natural selection acting on variation - can be applied even to the animals coming off the Ark. The proposed mechanism does not, in itself, depend on Common Descent being true. However, Darwin argued that the mechanism he proposed could account for common descent of all living species from "few forms...or one", and thus for the nested hierarchies identified by Linnaeus, and laid out the case in his book.Elizabeth Liddle_{July 12, 2011
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p.s. I was really hoping for more than just fossils though. I meant the big case. All the evidence. Including molecular, etc. The best case for common descent is a book on fossils?Mung_{July 12, 2011
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