Wednesday, December 07, 2011

Fishing for Creationists

Fishing for creationists is not a sport. All you need to do is dangle a bit of bait and dozens of creationists will fight for the right to impale themselves on the hook. The latest victim is Jonathan McLatchie who responded to criticism of Phillip Johnson [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance]. I'm sure the other bloggers on Evolution News & Views don't see him as a fishy victim, they probably think of him as the designated hitter. (You could use "sacrificial lamb" if you want a Biblical metaphor.)

Jonathan M, as he prefers to be known, is studying in Scotland for a Master's degree in evolutionary biology. He's upset with Jeffrey Shallit for criticizing Phillip Johnson's 1993 video (see This Video Should Be Shown to all Biology Students). He's also upset with my critiques of the same video (see Phillip Johnson, One of the Very Best Intelligent Design Creationists).

Jeffrey and I pointed out the obvious; namely, that Phillip Johnson doesn't understand evolution. He has a nineteenth century view of evolution where natural selection is the only mechanism. Jonathan M responds,
This is the type of condescending rhetoric that is so prevalent in anti-ID writings. Does Shallit really think that we haven't heard of processes such as genetic drift and endosymbiosis?
Jeffrey responds at: A Discovery Institute Flack Responds. My own response is similar. It's possibly true that Jonathan M understands evolution, although the evidence is sparse, but we're talking about Phillip Johnson in 1993 not Jonathan M in 2011. Nobody listening to that video could ever mistake Phillip Johnson for an expert on evolution.

The fact that Phillip Johnson and the other IDiots use "Darwinism" to describe their opponents tells us a lot about their level of understanding. Jonathan M says,
I think it is legitimate to use the word "Darwinism" provided that one is clear on what one means by it. Like the words "evolution" and "creationism," "Darwinism" can be construed to mean a variety of different things. Most ID proponents use the term to refer to the common scientific view that all of life is explicable by mechanisms of unguided chance and necessity. The most frequently cited examples of such processes are random mutations and natural selections -- but we recognize that there are other mechanisms at play as well (such as symbiosis and genetic drift). The key point is that the mechanisms undergirding the evolution of life, according to Darwinism, are non-intelligent.
Nonsense. Most IDiots do not understand the mechanisms of evolution and they make that abundantly clear every time they open their mouths. We know why they refer to us as "Darwinists" and it's not because they need a word to describe materialism or metaphysical naturalism. Jonathan M is telling a fib.
Phillip Johnson is trained as a lawyer. He's got a very sharp mind for analytic philosophy and the evaluation of the logical structure of arguments. Indeed, many philosophers have become involved in this debate, many of whom take the Darwinian side (e.g., Michael Ruse, Daniel Dennett) -- are they out of their element as well?
Yes, Michael Ruse and Daniel Dennett are also ignorant of basic evolutionary biology and they have demonstrated that many times in their books and public talks. That's why you will never see evolutionary biologists making a big fuss on the 20th anniversary of the publication of Darwin's Dangerous Idea. And that's why you have prominent evolutionary biologists attacking the views of Ruse and Dennett. Jonathan M is probably too young to remember someone named Stephen Jay Gould. Dennett and Gould didn't exactly agree on most things [see Darwinian Fundamentalism, The Pleasures of Pluralism].

Are there any Intelligent Design Creationists who dare to criticize Phillip Johnson for his incorrect views on evolution? Why not?

We agree that Philip Johnson's understanding of evolution is no better than that of Michael Ruse and Daniel Dennett. In fact, it's much worse.
With the advent of the Internet age and readily accessible print media, it is now possible to train oneself to master a discipline without formal academic training simply by reading textbooks and the relevant primary literature. One can be a well-educated layperson in an area, even if lacking in professional expertise, and I would place Phillip Johnson into this category.
Earth to Johnathan M ... the video was from 1993. Back when Phillip Johnson became famous as one of the best Intelligent Design Creationists, the World Wide Web was still in its infancy. Besides, we can clearly demonstrate that Johnson was NOT well-educated in evolutionary biology so the point is moot.

Not only that, the idea that you can master a discipline by reading on your own and searching the internet is absurd. Not only is it impossible, but if it were true then we would expect to see many IDiots who were experts on evolution. Instead we see Casey Luskin, Jonathan Wells, Paul Nelson, David Berlinski, Stephen Meyer, Bill Dembski, David Klinghoffer, Cornelius Hunter, Guillermo Gonzalez, and Denyse O'Leary. Oops!

Jonathan M has more to say in defense of Johnson's knowledge of evolution but it doesn't get any better.

Finally Jonathan M turns his attention to my posting.
Such rhetoric -- pervasive in Moran's writings in general -- continues throughout the duration of his comments. He repeatedly makes assertions such as that Johnson "is way out of his element," calling him an "IDiot." But he does not provide any real substantive scientific or philosophical rebuttal to Johnson's stated position.
I posted the video for everyone to see. It speaks for itself. There's no need to point out each and every statement that betrays Phillip Johnson's ignorance of evolutionary biology.

Here are a couple of quotations from the video. Phillip Johnson is talking about the history of life and the evidence for evolution (about 20 minutes into the video).
The features that create the classification, such as hair or fur in mammals, are called homologies. They're supposed to be inherited from a common ancestor. But, in fact, in a great many cases the "homologies" are traceable to different parts in the embryo and to different genes. So, in short, the animals get them by an entirely different route and this is strongly inconsistent with the common ancestor hypothesis to explain them.

It's also a well-known fact among embryologists but it never comes out to the general public because, well, it's so unpalatable a fact and so difficult to explain under Darwinian theory.
Johnson is clearly talking about the kind of homology used in taxonomy, or the kind used to construct phylogenetic trees. Here's the definition of that kind of homology from Wikipedia,
Homologous[Etymology 1] traits of organisms are due to sharing a common ancestor, and such traits often have similar embryological origins and development. This is contrasted with analogous traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately.
You'll find similar definitions in all the textbooks on evolutionary biology. Thus, when two structures are homologous they are, by definition, descended from common ancestral genes and share the same embryological history. If they do not share the same ancestral genes then they are not homologous for the purposes of classification. Insect wings, for example, are not homologous to the wings of birds.

Johnson doesn't know what he's talking about, but why should he? He's not an expert in evolution. He's a lawyer.

At about 22 minutes Johnson starts talking about the fossil record. He claims that the fossil record hasn't gotten any better since Darwin's time. He then goes on to explain his view of the fossil record ...
What we found in the 1980s was that the fossil record was still characterized by two important features: one is sudden appearance, when new things appear they appear just as they are, there's no visible history of step-by-step development from earlier forms. And then after they have appeared they stay the same, that's called stasis in the jargon of the trade.

So that once you get the shark, or the horseshoe crab or anything else into existence it stays the same throughout its tenure on Earth—there's variation within that type but no step-by-step development into something different, no directional change of the Darwinian kind.

And this, I might add, is not the absence of evidence, it is positively documented, And so you see the fossil record is, and remains, on the whole completely different from the picture that you would expect from the Darwinian ideology.
Johnson has heard of punctuated equilibria but, like most IDiots, he hasn't got a clue what it means. And he seems to be completely ignorant of excellent examples like the evolution of horses and the evolution of hominids (to name just two) that were well-known in 1993.
ID critics like Shallit and Moran have grown very fond of the routine ridicule and insults. But just look below the surface, at the actual content of their argument. As you'll see, it reveals that their grounds for dismissing ID are fundamentally lacking in scientific substance. Their rhetoric may be impressive to some, but for those of us who are earnest seekers of truth, the repeated substance-free name calling and insults of many members of the anti-ID lobby will continue to confirm the merit of the ID enterprise.
I have spent decades documenting the bad science of the Intelligent Design Creationists. So has Jeffrey Shallit and dozens of other defenders of science.

My most recent attempts to teach Intelligent Design Creationists have focused on junk DNA and Jonathan Wells' book The Myth of Junk DNA. None of the "big guns" in the movement have responded to those scientific arguments. Those of us who are earnest seekers of truth find it astonishing that Intelligent Design Creationists are so demonstrably ignorant of the very subject they attack and we're not afraid to publicize that fact.

It would be every easy for the IDiots to show that we are wrong. For example, Jonathan M has just tried to prove that Phillip Johnson actually understands the science he describes in the video. How did he do?


36 comments :

  1. And he seems to be completely ignorant of excellent examples like the evolution of horses and the evolution of hominids (to name just two) that were well-known in 1993.

    Not to mention the evolution of whales. It was IDiot Michael Behe who claimed in his tome, "Darwin's Black Box," that the notion that the whales and dolphins are descended from a hoofed wolf-like land animal is unsupported by any intermediates. Since the publication of that pile of manure, fossils of at least a dozen intermediates have been found (Pakicetus, Ambulocetus, Basilosaurus, etc. anyone). In fact, Mr. Behe was forced to admit in his Dover testimony that he now accepts common descent, thus repudiating his position in the aforementioned tome.

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  2. How does his professor feel about his creationist views? I am surprised he was even allowed to pursue a master's degree in evolutionary biology. But it should be interesting if he tries to make a career out of it.

    Btw, the ID movement accepts an Old Earth and a broad common descent (even if it does include notable YECs as well). It disputes the Darwinian mechanism of evolutionary change.

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  3. Recent Phillip Johnson blather shows no more intelligence regarding evolution than did his past blithering:

    Wilson calls his example “evolution,” but in fact it is merely adaptive variation, not something that could produce a new kind of creature. Species have the ability to vary in some characteristics to cope with a temporary environmental crisis, and then to go back to their original form when the crisis is past. Natural selection in this sense is a conservative force that allows a species to thrive in different environments without undergoing any basic change, and thus to avoid extinction. As a witty critic explained the point, despite its title, Darwin’s Origin of Species​ explained the survival of species, not the arrival of species.

    http://www.touchstonemag.com/archives/article.php?id=24-06-015-c#ixzz1ftg0nmxA

    Rather than dealing with the work that has been done in evolutionary science he just says that adaptation isn't evolution, and that it's only conservative anyway (technically true, but meaningfully false).

    He tells disgusting lies about biologists:

    The theory of biological evolution does not in itself explain how the first living organism emerged from a soup of non-living chemicals, but evolutionary biologists are so encouraged by their supposed success in explaining the entire history of life after the mysterious appearance of the first organism, that they claim to know for sure that the ultimate origin of life also occurred by some combination of chance and chemical law, without the need for any participating intelligence. When knowledgeable critics are about, Darwinists sometimes pretend that the origin of life is not part of their theory, but when they think the coast is clear, they once again claim that the problem was solved in principle long ago.

    Ibid.


    Utterly dishonest. Evolution is not the same as abiogenesis, at least not initially. And no one pretends that abiogenesis has been solved ("in principle"? What's that supposed to mean, that we insist on evidence, not claims of magic?). He's still conflating very different things, in order to prop up his earlier false claims.

    The assumption that science knows of a naturalistic, mindless mechanism that could and did take life all the way from lifeless chemicals to Homo sapiens is so important that I concluded that critical analysis should, for the time being, put aside such distracting issues as the authority of the Bible or the age of the earth, so all attention could be focused on the naturalistic mechanism of biological creation.

    Ibid.


    Of course he didn't go through those thought processes, he instead decided that he could smear everyone involved in legitimate science without paying any attention to the lack of honest science on their side. And he did achieve a charlatan's success in that way, but nothing else.

    And once again, no knowledgeable person has claimed that evolution explains everything from "lifeless chemicals" and on, nor even that evolution "explains everything." It explains the sort of hereditary derivation that would be absurd for any intelligence to produce, and which unintelligent evolution entails.

    So why's that IDiot McLatchie lying as if Johnson were somehow less of a smear monger and purveyor of misrepresentations than he used to be? Or that any of the IDiots are less mendacious and intent on misrepresenting science and scientists than that video? Misrepresentation is all that they have, and they definitely use it.

    Glen Davidson

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  4. I would note that Jonathan M's arguments are literally unanswerable; like many (or most) IDists, he does not allow comments on his article.

    I find that this is a most consistent difference between ID proponents and actual scientists.

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  5. (I'm reposting as it seems the comment did not get through the system due to 'internet ununderstandables')

    Is there any evidence that Jonathan McLatchie studies evolutionary biology? Where? At what university?

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  6. With the advent of the Internet age and readily accessible print media, it is now possible to train oneself to master a discipline without formal academic training simply by reading textbooks and the relevant primary literature. One can be a well-educated layperson in an area, even if lacking in professional expertise, and I would place Phillip Johnson into this category.

    It's a shame that even with the advent of the internet, and the benefits of studying for a masters degree, Jonathan remains so clueless about biology.

    Jonathan has taken the same approach to some articles at my blog criticising Meyer. He cross-posts the opening paragraphs of most of them to the blog at CrossExamined where you can see the full range of his worldview, and leave comments.

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  7. I'd mention as an excellent example of homology substantiated by the fossil record the evolution of the definitive mammalian middle ear. Gould published an essay about this in 1990: "An Earful of Jaw" (reprinted in his 1993 collection "Eight Little Piggies").

    TomS

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  8. Atheistoclast said...

    Btw, the ID movement... disputes the Darwinian mechanism of evolutionary change.

    And proposes what as an alternative explanation? Magic?

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  9. While Johnson is simply a lawyer blathering about biology, JonathanM is expected to know better. If he werent an IDiot he would have nothing to do with Johnson's caricature of abiogenesis or the formation of the biomolecules. Sometime last year I caught one of Jonathan's icons and his fellow IDiot Paul Nelson here quote mining on the subject of Miller-Urey synthesis and abiogenesis. Nelson was simply pulling quotes from a proponent of inorganic clay initiated synthesis, a scientist who in no way supports Nelson's crackpottery. But that is the way of IDiots, to mine quotes from any side of the many debates among scientists and offer it up as disproof. IDiots themselves like to pass themselves off as the scientists they aren't. So someone like Wells who hasn't stepped into a lab since his PhD or a charlatan like Dave Berlinski who isn't a scientist in any sense of the term or a known dissembler like Behe are their icons. Jonathan unfortunately is earnest but an earnest rube to fall for their line.

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  10. Larry Moran wrote:

    "Thus, when two structures are homologous they are, by definition, descended from common ancestral genes and share the same embryological history. If they do not share the same ancestral genes then they are not homologous for the purposes of classification."

    Wrong.

    The disconnect between classical anatomical homology and its genetic and developmental basis has been one of the main topics of analysis in evo-devo over the past 15-20 years. As an introduction to the relevant literature, see Gunther Wagner, "The developmental genetics of homology," Nature Reviews Genetics 8 (2007):473-479. Wagner writes:

    "Intuitively, one would expect that the historical continuity of morphological characters is underpinned by the continuity of the genes that govern the development of these characters. However, things are not so simple: one of the most important results of the past 15 years of molecular developmental genetics is the realization that homologous characters can have different genetic and developmental bases. This seems paradoxical, because the historical continuity of morphological characters implies continuity of the (genetic) information about the characters." (p. 473; emphasis added)

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  11. It was IDiot Michael Behe who claimed in his tome, "Darwin's Black Box," that the notion that the whales and dolphins are descended from a hoofed wolf-like land animal is unsupported by any intermediates.

    I think both Behe and Johnson got that from Michael Denton's 1986 book Evolution: A Theory in Crisis; chapter 8, The Fossil Record.

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  12. Dr. Moran writes:

    Not only that, the idea that you can master a discipline by reading on your own and searching the internet is absurd. Not only is it impossible, but if it were true then we would expect to see many IDiots who were experts on evolution.

    Well, I don't know that I'd say the concept of mastery is "absurd." It might be possible for folks smarter than I am.

    But for most of us, even if we cannot be experts, we can inform ourselves sufficiently to have some idea of how much we don't know, and to have a decent chance of not getting things horribly wrong when we do speak.

    To allow one's strongly - one might say "religiously" - held preconceptions to negate any possibility of learning, though, takes an IDiot.

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  13. Paul Nelson writes,

    Wrong.

    The disconnect between classical anatomical homology and its genetic and developmental basis has been one of the main topics of analysis in evo-devo over the past 15-20 years. As an introduction to the relevant literature, see Gunther Wagner, "The developmental genetics of homology," Nature Reviews Genetics 8 (2007):473-479. Wagner writes:


    Paul, you are being disingenuous at best (I don't want to mention the other alternative).

    There's a long history of debating the meaning of homology (see Donogue, M.J. (1992) "Homology" in Keywords in Evolutionary Biology, E.F. Keller and E.A. Lloyd eds.). The modern meaning, and the only one that's relevant when discussing phylogeny and classification, is that true homologous structures are those that share a common ancestor.

    That's the definition used in the paper by Günter Wagner in the paper you quote.

    Characters found in different species are homologous if they are derived from the same character in their most recent common ancestor (MRCA), regardless of similarity in form or function.

    Thus, the wings of birds and the flippers of seals are homologous. They share the same structural genes and the same embryological development.

    The eyes of insects and the eyes of mammals are NOT homologous. They arose independently.

    But here's the rub. Insect eyes and mammalian eyes are built using different genes but those genes are regulated by a similar protein called Pax6 in vertebrates and ey in Drosophila. The genes are homologues, that is they are similar enough in sequence to conclude that they evolved from a common ancestor.

    Wagner goes through a lot to mental gymnastics to try and save the word "homology" for morphological structures in cases like this. He talks about the conservation of networks of transcriptional activators.

    It doesn't work. No taxonomist is going to group insects and mammals on the grounds that their eyes are homologous. You are misleading your followers if you tell them that homologous structures can be built from very different genes.

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  14. Paul Nelson quotes an article that says, in part:

    one of the most important results of the past 15 years of molecular developmental genetics is the realization that homologous characters can have different genetic and developmental bases.

    This does not show a "disconnect" between genotype and phenotype. It simply shows a more sophisticated understanding of the relationship between the two. Has this more sophisticated understanding overturned most of the morphology-based biological classifications developed over past decades, or have these been largely confirmed? The latter. It wasn't as if biologists thought whales descended from fish before genetics came along, because in the main they did a good, careful job with their morphology.

    So now we've got two independent confirming trains of evidence for evolution from common ancestors. As the owner of an inquiring mind, I'm sure this pleases you.

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  15. Larry wrote:

    "You are misleading your followers if you tell them that homologous structures can be built from very different genes."

    My "followers," so to speak, have nothing to do with this. Many structures that would be homologous (meaning, sharing common ancestry) on almost any view of evolution, appear not to arise from common developmental or genetic bases.

    This is a well-established puzzle in evo-devo. Your fellow Canadian, Brian Hall (at Dalhousie), has written extensively on the question. See, for instance, his paper "Homology and Embryonic Development," Evolutionary Biology 28 (1995):1-37. Hall observes, after several pages of examples of lack of congruence between anatomy, development, and genes, that

    "...homologous structures often arise from embryological origins that are not common and/or involve different developmental (often inductive) mechanisms. A logical corollary of these cases is that homologous structures need not have a common genetic basis." (p. 23, emphasis added)

    The concept of homology once had a clear (textbook) meaning in evolutionary biology, which now -- after 20 years of perplexing discoveries in evo-devo -- has been entirely scrambled. At the end of her long discussion of the topic in Developmental Plasticity and Evolution (Oxford, 2003), Mary Jane West-Eberhard throws up her hands, and says, "In fact, evolution makes a mess of homology" (p. 497).

    We could do a joint post on this at Evolution New and Views: you give your view, I'll give mine. The data will support me.

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  16. The concept of homology in phylogeny and taxonomy is not controversial. You'll find the same definition in most evolutionary biology textbooks.

    Here's the definition from Evolution (2009) by Douglas Futuyma.

    Under the phylogenetic concept of homology, which is fundamental to all of comparative biology and systematics, homologous features are those that have been inherited, with more or less modification, from a common ancestor in which the feature first evolved. That is, homologous structures are synapomorphies.

    Futuyma then goes on to describe the situation where similar regulatory genes might be involved in the development of otherwise non-homologous structures. This is the "biological homology concept" promoted by some developmental biologists like Günter Wagner.

    After discussing several examples, Futuyma continues with ...

    Conflicts between phylogenetic and biological homology can also occur when phylogenetically homologous traits have different developmental and genetic foundations.

    This is the partly the issue raised by Paul Nelson, although he is clearly confused about the whole topic. The classic example is the lens crystallins in vertebrates. The fact that all eyes have a crystalline lens is an example of morphological homology but the protein that forms the crystal can be very different in different species.

    This is a trivial exception to the general rule and it is wrong of the creationists to exploit it to discredit evolution.

    The more common conflict is ...

    Conversely, developmentally and functionally similar structures in different taxa may not be phylogenitically homologous. In perhaps the best example, animal eyes evolved indepentently in several taxa, but in all of these taxa, a highly conserved transcription factor, Pax6, controls eye development.

    Creationists exploit these differing definitions of homology to create confusion among their followers. When they deliberately talk about the problems with the "biological homology concept" while discussing taxonomy and phylogeny, as Phillip Johnson does in the video, they are either ignorant or lying.

    When I cal them IDiots, I'm giving them the benefit of the doubt.

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  17. Larry wrote:

    "The classic example is the lens crystallins in vertebrates. The fact that all eyes have a crystalline lens is an example of morphological homology but the protein that forms the crystal can be very different in different species.

    This is a trivial exception to the general rule and it is wrong of the creationists to exploit it to discredit evolution."

    Nonsense. The anomalies extend to such fundamental features as modes of gastrulation, origin of germ cells, and formation of the alimentary canal. And that's strictly within the vertebrates. As one moves out into the Metazoa, lack of congruence is the rule, not the exception.

    I repeat my offer of a semi-formal blog debate on this topic, at Evolution News and Views.

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  18. Paul,
    This is the second I have caught you quote mining at Sandwalk. Last year, remember this thread? http://sandwalk.blogspot.com/2010/12/iconic-delusions.html
    You mined Cairns-Smith in a discussion on related to Miller-Urey and pompously referred to some Science article. I caught you on that one and reproduced a large extract from the article to call your bluff. Today I have caught you quoting Gunther Wagner. Be my guest.

    Nature Reviews Genetics 8, 473-479 (June 2007) | doi:10.1038/nrg2099
    The developmental genetics of homology, Günter P. Wagner
    Homology is an essential idea of biology, referring to the historical continuity of characters, but it is also conceptually highly elusive. The main difficulty is the apparently loose relationship between morphological characters and their genetic basis. Here I propose that it is the historical continuity of gene regulatory networks rather than the expression of individual homologous genes that underlies the homology of morphological characters. These networks, here referred to as 'character identity networks', enable the execution of a character-specific developmental programme...
    In this paper, I propose that this capability is underwritten by GRNs of co-adapted transcription factor genes.


    It's a long paper that discusses GRNs, analogous features, functionally similar features and a lot else.

    Paul Nelson, last time I had posted this,

    So painting a complete picture requires Paul Nelson, Jon Wells, Casey Luskin and other liars of the IDiot Institute to say thus,
    I used to blabber "The accurate answer to that question is an unequivocal No. Most of what such experiments produce is material suitable for paving roads, not building organisms." But now I will be honest. I quoted Graham Cairns-Smith selectively to imply that he rules out any possibility of a Miller-Urey like history of early biochemical molecules. What he is actually talking about is the possibility of an even earlier stage of inorganic molecules being subjected to NS. I lied. Sorry

    Of course you don't have to add that Cairns-Smith and every scientist (that does not include a an intellectual fraud like Behe) thinks you and your collaborators at the IDiot Institute are a bunch of liars and cheats for quote mining and misrepresentation.


    Substitute above for Homology and Gunther Wagner.
    Someone who quote mines the first time, and gets caught in the act, is an IDiot. Someone who repeats the act is a habitual liar.

    You have a problem with homology in evolutionary biology? Spend IDiot Institute money to produce some research.

    And besides you show no understanding of the vast scope of evolutionary biology. Sometime back Larry had posted the picture here that helped me understand vastly how many more questions there are in evolutionary biology than homology or the latest hobby horse you IDiots blather about.
    http://sandwalk.blogspot.com/2011/02/problems-with-eukaryotic-tree-of-life.html

    By using the same shtick of quote mining, building up strawman allies out of scientists (you said you admire Gould) and posting references in the naive/sly belief that your readers wont bother to check the paper in full, over and over again, you show up yourself as a pathetic excuse for anything respectable.

    Truti

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  19. Paul Nelson writes,

    This is a well-established puzzle in evo-devo. Your fellow Canadian, Brian Hall (at Dalhousie), has written extensively on the question. See, for instance, his paper "Homology and Embryonic Development," Evolutionary Biology 28 (1995):1-37. Hall observes, after several pages of examples of lack of congruence between anatomy, development, and genes, that

    "...homologous structures often arise from embryological origins that are not common and/or involve different developmental (often inductive) mechanisms. A logical corollary of these cases is that homologous structures need not have a common genetic basis." (p. 23, emphasis added)


    Paul, do you think that quotation truly represents Hall's recent views on the subject or the consensus view among evolutionary biologists? Do you guys take classes on how to use selected quotations to advance your cause?

    It's true that Brian Hall struggled with the concept of homology, especially as it is is being misused among developmental biologists.

    Let's look at his paper from 2007 (Hall. B. (2007) "Homoplasy and homology: Dichotomy or continuum?" J. Hum. Evol. 52, 473-479). In this paper Hall distinguished between phylogenetic homology (=homology) and many of the more controversial examples (=homeoplasy).

    Here's an example.

    Animals share basic regulatory genes that can be traced to distant ancestors and/or be used in animals that do not share a recent common ancestor. Thus, homoplasy could involve the same (homologous) genes as those used in far distant groups (Hall, 1994, 1998, 2003; Dickinson, 1995; Abouheif et al., 1997; Meyer, 1999).

    A paradigmatic example that has emerged in the last few years is Pax-6, a gene that initiates the development of light sensitive cells, including the eyes, in many animal phyla. Ectopic expression of Pax-6 in Drosophila imaginal discs destined to form wings or legs, initiates eye formation in the wings and legs that develop from those discs (Halder et al., 1995). Pax-6 has been sufficiently conserved over such very long periods of evolutionary history that Pax-6 from Drosophila will initiate eye development in Xenopus, even though fruit flies are evolutionarily very distant from frogs (Altmann et al., 1997). Pax-6 is homologous across the animal phyla, but the eyes initiated by Pax-6 in flies and frogs are homoplasies. It has been argued that only if Pax-6 functioned to initiate eye development in a common ancestor of Drosophila and the vertebrates would their eyes be considered homologous (Dickinson, 1995). However, even this would not render the eyes homologous because the homoplasy of frog and fly eyes rests on much more than this single gene. The arguments raised (in various forms) by Spemann (1915), de Beer (1971), Hall (1995, 1998, 2003), Abouheif (1997), Abouheif et al. (1997), Meyer (1999), Laubichler (2000), and others concerning homologous genes initiating nonhomologous structures make a strong case for homoplasy reflecting shared, deep ancestry and retention of gene-signaling function.


    You've been talking to Jonathan Wells, haven't you? His ideas suffer from two problems: (1) they are out-of-date and (2) they are wrong [Homology in Biology: A Problem for Naturalistic Science from 1997].

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  20. Larry, exactly what does Hall say in the 2007 JHE article that contradicts his 1996 publication? The example you cite (the role of Pax-6 homologs in eye development in diverse phyla) does not contradict what Hall argued in 1996, but rather supports it.

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  21. Let me just say that the genetic (or chemical) basis for morphogenesis is absolute nonsense: transcripton factors, morphogens, cis-regulatory elements and RNAs don't even come close to explaining why a pig is so different in form to that of a closely related fellow-artiodactyl in the giraffe.

    Evo-devo is sheer pseudoscience. It should be disbanded.

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  22. The other problem with what Paul Nelson is saying is that even if there is non-homologous morphology coming from homologous genetics or vice versa (apologies to everyone for doing a bit of violence to a precise definition of "homologous" in order to get closer to Nelson-speak), it wouldn't negate the basis for evolution at all. In other words, yes, Nelson has made an invalid argument based on quote mining (if he even understands enough of what he quotes to realize what he's doing), but even if Nelson were right, so what? As Dr. Moran quotes:

    The arguments raised (in various forms) by [lots of folks] concerning homologous genes initiating nonhomologous structures make a strong case for homoplasy reflecting shared, deep ancestry and retention of gene-signaling function. [Emphasis added.]

    It reminds me of the great commotion amongst IDiots when the fact of bacterial genetic exchange made a Tree of Life a less good metaphor for evolution, at least among microbes. Conceptually, it might be pictured as more of a web. One would have thought Jesus himself had showed up to carve into the Ten Commandments at the Texas State Capitol an Eleventh Commandment: "Thou shalt not believe in evolution." Over an old metaphor, fer goshsakes!

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  23. Larry Moran will undoubtedly jump on me, but Paul Nelson is right in that homology of structure does not imply identical genetic pathways or identical development in present-day organisms.

    To define homology as identical by descend is muddling the point of homology: homology is evidence for identity by descent. The continuity of gene regulatory networks follows from the observations in molecular development, and is evidence for common descent.

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  24. http://bcseweb.org.uk/index.php/Main/MichaelBeheInBritainPart2
    calls Jonathan McLatchie “a forensic science student”.

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  25. Paul,

    Are you so stupid that you think Larry can't pick up the phone and talk to Hall? Or do you think you are so smart that Larry won't know who Hall is?

    Here's quoting from a guest editorial by Hall,
    Comparative embryology undertaken in a strict phylogenetic framework is on the upswing.
    • Genes that control major developmental processes—establishment of body plans, formation of appendages, formation of sense organs—have been shown to be shared across the animal kingdom and to have arisen early in metazoan evolution.
    • New knowledge of developmental mechanisms underlying the formation of organs or such major body parts as tetrapod limbs has contributed to an understanding of the mechanisms involved in their origin from structures in ancestral organisms (e.g., tetrapod limbs from fish fins).
    • We are beginning to understand how developmental processes are modified when organs are lost (e.g., limb loss in snakes). We now appreciate that loss of adult organs does not imply loss of the developmental potential to form those organs.
    • We are beginning to understand that life history stages (embryos, larvae, adults) can develop and evolve separately (e.g., loss of larvae in direct-developing echinoderms) and that such a change can provide opportunities to modify and modulate embryonic development, for specialization or diversification of adult structure, and for the evolution of novel structures.
    • Homology is now seen as hierarchical, with homologous genes initiating development of structures that are not homologous (Pax-6 and arthropod and vertebrate eyes) and homologous structures developing by processes that are not homologous.


    Do you have any idea of the work of Mary Jane Eberhard-West?
    Here's one reviewer on her "Developmental Plasticity and Evolution."

    Is macroevolution then best be taken as a gradualistic extrapolation of microevolutionary steps, the gradualism view? Certainly not, since under this concept, macroevolution always means genotype-phenotype divergence above species level, whereas microevolution is primarily an issue of intraspecific, populational differentiation. West-Eberhard elegantly connects this apparent paradox to alternative phenotypes, which represent major phenotypic change within a species. And this, again, connects macroevolution to developmental plasticity, that is, major phenotypic change can occur without the need to appeal to macromutation hypotheses. It is in this perspective that West-Eberhard reiterates the statement of Eldredge and Gould (1972) when they proposed the speciational punctuated equilibrium hypothesis that "the expectations of theory color perception to such a degree that new notions seldom arise from facts collected under the influence of old pictures of the world", and she concludes with the bold statement that the plasticity hypothesis proclaimed in the present book "is the only evolutionary hypothesis that proposes an explicit and testable mechanism (changes in degree of plasticity or developmental versatility) as an alternative to speciation to explain both morphological stasis and punctuated change in terms of natural selection".

    As usual blather, bluff and bluster. Paul biology isn't quote mining. Not in this age of the internet. That's a game you will surely lose. You have no idea what West-Ebrhard studies, what her hypothesis is about and what her conclusions are. Likewise for Hall. But some of us do, and guys like Larry who have worked v.hard to study and then publish and train cohorts of scientists are not like your ignorant audiences.

    Truti

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  26. heleen says,

    Larry Moran will undoubtedly jump on me, but Paul Nelson is right in that homology of structure does not imply identical genetic pathways or identical development in present-day organisms.

    You're darn right I'm going to jump on you!

    Two structures may be similar (e.g. insect wings and bat wings) but they are only homologous in the phylogenetic sense if they share common structural genes and a common developmental pathway.

    There are some bioogists who would like to use the word "homology" to describe the similarities in insect wings and bat wings but no taxonomist or evolutionary biologist would confuse that with the phylogenetic definition of homology. Many biologists use other words, like homeoplasy, to describe those similarities.

    The creationists like Phillip Johnson imply that there's a problem with the phylogenetic concept of homology. The one that's used to classify organisms and construct phylogenetic trees. They usually do this because they don't understand enough biology to recognize the differnece between the various definitions and concepts.

    To define homology as identical by descend is muddling the point of homology: homology is evidence for identity by descent. The continuity of gene regulatory networks follows from the observations in molecular development, and is evidence for common descent.

    Hmmm ... that's the argument that Jonathan Wells makes in Icons of Evolution. My second year students are quite adept at seeing the logical flaws in that argument.

    Homologous structures have a common ancestor. "Homology" is a conclusion based on evidence. The evidence is based on significant structural, or sequence, similarity, shared developmental pathways, and shared genes.

    The easiest way to see this is to think about how you decide whether two genes are homologous or not. You use evidence like sequence similarity to reach the conclusion that two genes are homologous. Homology is not evidence of descent, similarity is evidence of descent.

    Evolution is the explanation for why structures (or genes) are homologous. I assume that Intelligent Design Creationists have a different explanation for homologous structures, such as the wings of bats and the flippers of whales. I just can't remember what it is right now. I think it has something to do with understanding the motives of the intelligent designer.

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  27. Biologic analogies are something like what you'd expect from intelligent designers. The homologies underlying those analogies and practically everything else in biology point to derivation alone.

    Or is McLatchie going to tell other forensics specialists that DNA similarities might be due to "design," and that similarities in handwriting and wording in written evidence are due to magic or some such thing?

    Nelson's blustering about trying to detract attention from Johnson's failure, his failure, and McLatchie's failure to show that homologies somehow fail when one reaches the undetectable level of "macroevolution" (in the IDiot sense of that word), even though they accept it for "microevolution."

    Let's see, the nested hierarchies exist for what "design reason"? Why are most eukaryotes apparently derived almost entirely from ancestors, while prokaryotes appear to be derived as well from horizontal transfers? That would make sense on the "microevolutionary" level for IDiots, but it explains nothing of why the same pattern extends into "macroevolution."

    As usual, the IDiots merely whine about evolution, misrepresent the issues, and explain exactly nothing in biology. They'd have died from shame by now, were they capable of caring about scientific integrity, rather than saying anything and everything to save their religious dogmas.

    Glen Davidson

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  28. Larry: "Michael Ruse and Daniel Dennett are also ignorant of basic evolutionary biology and they have demonstrated that many times in their books and public talks."

    So, Larry, would you refer to Ruse and Dennett as "idiots" (small id)?

    I'm curious: which popular books on evolution would you recommend for us lay readers?

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  29. Bilbo,

    Speaking for myself. Michael Ruse is an IDiot enabler, but may actually doing us scientophiles a service. By parroting his "atheist" credentials and mangled biology he provides IDiots a false sense of security. IDiots in turn lug his arguments over here and to other science forums and get walloped. Dennett? I ain't sure.

    You can learn a lot by reading Larry tearing up pompous IDiots.

    Truti

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  30. "I'm curious: which popular books on evolution would you recommend for us lay readers?"

    Dr.Moran has recommended Jerry Coyne's Why Evolution Is True, despite having some disagreements with Coyne. He also frequently cites work by Stephen Jay Gould, but not Gould's work aimed at lay readers as far as I can recall, though he may have and I haven't seen or don't recall it. My personal favorite of Gould's books aimed at laypeople is Wonderful Life. I also think David Quammen's Song of the Dodo is carefully written and utterly fascinating, not an easy combination to bring off, but I don't know whether Dr. Moran has even read it, much less whether he recommends it.

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  31. For lay readers, on the topic of homologies, I recommend:

    Neil Shubin
    Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body
    New York: Pantheon Books, 2008
    ISBN 9780375424472

    It doesn't cover the whole subject, but it does present several instances of homologies of the human body with structures found in fish.

    TomS

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  32. (heleen): To define homology as identical by descend is muddling the point of homology: homology is evidence for identity by descent. The continuity of gene regulatory networks follows from the observations in molecular development, and is evidence for common descent.

    (Larry Moran):Hmmm ... that's the argument that Jonathan Wells makes in Icons of Evolution. My second year students are quite adept at seeing the logical flaws in that argument.

    Homologous structures have a common ancestor. "Homology" is a conclusion based on evidence. The evidence is based on significant structural, or sequence, similarity, shared developmental pathways, and shared genes.


    Quite: Larry Moran got as far as realizing homology is a conclusion based on evidence of far-going structural similarity. This implies that to define homology as identical by descend is muddling the point of homology: homology is evidence for identity by descent

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  33. @Larry Moran:
    The easiest way to see this is to think about how you decide whether two genes are homologous or not. You use evidence like sequence similarity to reach the conclusion that two genes are homologous. Homology is not evidence of descent, similarity is evidence of descent.
    Get to a good understanding of homology, and see when and why similarity is evidence for homology, and thereafter homology is evidence of descent. Similarity by itself is not sufficient evidence of homology. Only after the similarity has been assessed as homologous is it judged to be evidence for common descend.

    As old as the world:
    That gut enzyme lysozyme is similar in fore-gut segmenters due to selection: so there the interesting similarity is not homologous. (There is a homology level below that).

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  34. Dear Heleen:
    Larry Moran got as far as realizing homology is a conclusion based on evidence of far-going structural similarity. This implies that to define homology as identical by descend is muddling the point of homology: homology is evidence for identity by descent

    No, only ONCE you have prior independent evidence that a similatity is due to common descent you can claim "homology".

    Calling a similarity "homology" from the beginning and afterwards look for evidence of (or lack of) common descent is what drives to confusion. Once you have, others not.

    When you read a sentence like "homology is evidence of common descent" it implies that the embriological, developmental evidence has been already found and is well known. It doesn't mean that the mere morphological or functional similarity is evidence of such a thing.

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  35. @Enrique
    No, only ONCE you have prior independent evidence that a similatity is due to common descent you can claim "homology".
    NO.
    Don't confuse definition with explanation.
    Homology is defined as position similarity, where one knows a lot about position. The explanation of homology is common descent.

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  36. heleen, that's the point. That's YOUR definition of "homology", a similarity in position. But that usage is only yours, nobody else. Thus, such a use of language is counter-communicative: impedes communication with fellows.

    Everyone else do recognize morphological or functional similarities, and find them interesting. After studying them, if the similarities are backed by common development, embryology, physiology, genetic backgroud, etc, only then you call it "homology", otherwise it's mere similarity or "homoplasy".

    Thath's the usage accepted by people in the field. Changing meanings is only creating confusion.

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