tag:blogger.com,1999:blog-37148773.post3989931551247099139..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Fishing for CreationistsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger36125tag:blogger.com,1999:blog-37148773.post-24606385499653682322011-12-12T02:36:20.318-05:002011-12-12T02:36:20.318-05:00heleen, that's the point. That's YOUR defi...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.<br /><br />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". <br /><br />Thath's the usage accepted by people in the field. Changing meanings is only creating confusion.Enriquenoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54254203623077908722011-12-11T10:28:24.677-05:002011-12-11T10:28:24.677-05:00@Enrique
No, only ONCE you have prior independent ...@Enrique<br /><i>No, only ONCE you have prior independent evidence that a similatity is due to common descent you can claim "homology".</i><br />NO.<br />Don't confuse definition with explanation.<br />Homology is defined as position similarity, where one knows a lot about position. The explanation of homology is common descent.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36947117328790259472011-12-10T19:24:54.053-05:002011-12-10T19:24:54.053-05:00Dear Heleen:
Larry Moran got as far as realizing h...Dear Heleen:<br /><i>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</i><br /><br />No, only ONCE you have prior independent evidence that a similatity is due to common descent you can claim "homology".<br /><br />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.<br /><br />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.Enriquenoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15469742200671034502011-12-10T04:21:33.021-05:002011-12-10T04:21:33.021-05:00@Larry Moran:
The easiest way to see this is to th...@Larry Moran:<br /><i>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.</i><br />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.<br /><br />As old as the world:<br />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).heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18385141811546751512011-12-10T04:08:49.055-05:002011-12-10T04:08:49.055-05:00(heleen): To define homology as identical by desce...<i>(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. <br /><br />(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.<br /><br />Homologous structures have a common ancestor. "Homology" is a <b>conclusion</b> based on evidence. The evidence is based on significant structural, or sequence, similarity, shared developmental pathways, and shared genes. </i><br /><br />Quite: Larry Moran got as far as realizing homology is a conclusion based on evidence of far-going structural similarity. This implies that to <b>define homology</b> as identical by descend is muddling the point of homology: homology is evidence for identity by descentheleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83953880218080164572011-12-09T06:24:47.281-05:002011-12-09T06:24:47.281-05:00For lay readers, on the topic of homologies, I rec...For lay readers, on the topic of homologies, I recommend:<br /><br />Neil Shubin<br />Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body<br />New York: Pantheon Books, 2008<br />ISBN 9780375424472<br /><br />It doesn't cover the whole subject, but it does present several instances of homologies of the human body with structures found in fish. <br /><br />TomSAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34453866497867903292011-12-08T20:58:50.218-05:002011-12-08T20:58:50.218-05:00"I'm curious: which popular books on evol..."I'm curious: which popular books on evolution would you recommend for us lay readers?"<br /><br />Dr.Moran has recommended Jerry Coyne's <i>Why Evolution Is True</i>, 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 <i>Wonderful Life</i>. I also think David Quammen's <i>Song of the Dodo</i> 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.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33233319828777330152011-12-08T18:02:53.776-05:002011-12-08T18:02:53.776-05:00Bilbo,
Speaking for myself. Michael Ruse is an ID...Bilbo,<br /><br />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.<br /><br />You can learn a lot by reading Larry tearing up pompous IDiots.<br /><br />TrutiAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68338589680985013602011-12-08T17:16:45.833-05:002011-12-08T17:16:45.833-05:00Larry: "Michael Ruse and Daniel Dennett are ...Larry: "<i>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.</i>"<br /><br />So, Larry, would you refer to Ruse and Dennett as "idiots" (small id)? <br /><br />I'm curious: which popular books on evolution would you recommend for us lay readers?Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69523826012825529292011-12-08T16:02:14.612-05:002011-12-08T16:02:14.612-05:00Biologic analogies are something like what you'...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.<br /><br />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?<br /><br />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." <br /><br />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."<br /><br />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.<br /><br /><a href="http://tinyurl.com/mxaa3p" rel="nofollow">Glen Davidson</a>Glen Davidsonhttp://electricconsciousness.tripod.comnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42847790406406199212011-12-08T15:46:08.451-05:002011-12-08T15:46:08.451-05:00heleen says,
Larry Moran will undoubtedly jump on...heleen says,<br /><br /><i>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.</i><br /><br />You're darn right I'm going to jump on you! <br /><br />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. <br /><br />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. <br /><br />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. <br /><br /><i>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. </i><br /><br />Hmmm ... that's the argument that Jonathan Wells makes in <i>Icons of Evolution</i>. My second year students are quite adept at seeing the logical flaws in that argument.<br /><br />Homologous structures have a common ancestor. "Homology" is a <b>conclusion</b> based on evidence. The evidence is based on significant structural, or sequence, similarity, shared developmental pathways, and shared genes. <br /><br />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.<br /><br />Evolution is the <b>explanation</b> 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.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46934445822945257092011-12-08T15:28:31.937-05:002011-12-08T15:28:31.937-05:00Paul,
Are you so stupid that you think Larry can&...Paul,<br /><br />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?<br /><br />Here's quoting from a guest editorial by Hall,<br /><i>Comparative embryology undertaken in a strict phylogenetic framework is on the upswing.<br />• 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.<br />• 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).<br />• 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.<br />• 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.<br />• 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.</i> <br /><br />Do you have any idea of the work of Mary Jane Eberhard-West?<br />Here's one reviewer on her "Developmental Plasticity and Evolution."<br /><br /><i>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".</i><br /><br />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.<br /><br />TrutiAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74358397723907098092011-12-08T14:35:04.060-05:002011-12-08T14:35:04.060-05:00http://bcseweb.org.uk/index.php/Main/MichaelBeheIn...http://bcseweb.org.uk/index.php/Main/MichaelBeheInBritainPart2<br />calls Jonathan McLatchie “a forensic science student”.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63740387557406259392011-12-08T14:33:13.556-05:002011-12-08T14:33:13.556-05:00Larry Moran will undoubtedly jump on me, but Paul ...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. <br /> <br />To <i>define</i> homology as identical by descend is muddling the point of homology: homology is <i>evidence</i> for identity by descent. The continuity of gene regulatory networks follows from the observations in molecular development, and is evidence for common descent.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71523839232544905552011-12-08T14:09:19.267-05:002011-12-08T14:09:19.267-05:00The other problem with what Paul Nelson is saying ...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:<br /><br /><i>The arguments raised (in various forms) by </i>[lots of folks]<i> concerning homologous genes initiating nonhomologous structures make a strong case for homoplasy <b>reflecting shared, deep ancestry and retention of gene-signaling function.</b></i> [Emphasis added.]<br /><br />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 <i>metaphor</i>, fer goshsakes!Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56492607528022356712011-12-08T14:07:15.603-05:002011-12-08T14:07:15.603-05:00Let me just say that the genetic (or chemical) bas...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.<br /><br />Evo-devo is sheer pseudoscience. It should be disbanded.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18231639757062797002011-12-08T13:21:39.522-05:002011-12-08T13:21:39.522-05:00Larry, exactly what does Hall say in the 2007 JHE ...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.Paul Nelsonhttps://www.blogger.com/profile/14127052026545950910noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43891360764366630162011-12-08T12:52:42.284-05:002011-12-08T12:52:42.284-05:00Paul Nelson writes,
This is a well-established pu...Paul Nelson writes,<br /><br /><i>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<br /><br />"...homologous structures often arise from embryological origins that are not common and/or involve different developmental (often inductive) mechanisms. <b>A logical corollary of these cases is that homologous structures need not have a common genetic basis.</b>" (p. 23, emphasis added)</i><br /><br />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?<br /><br />It's true that Brian Hall struggled with the concept of homology, especially as it is is being misused among developmental biologists.<br /><br />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).<br /><br />Here's an example.<br /><br /><i>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).<br /><br />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.</i><br /><br />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 [<a href="http://www.trueorigin.org/homology.asp" rel="nofollow">Homology in Biology: A Problem for Naturalistic Science</a> from 1997].Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48732466628134428072011-12-08T12:29:02.180-05:002011-12-08T12:29:02.180-05:00Paul,
This is the second I have caught you quote m...Paul,<br />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<br />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.<br /><br /><i>Nature Reviews Genetics 8, 473-479 (June 2007) | doi:10.1038/nrg2099<br />The developmental genetics of homology, Günter P. Wagner<br /><b>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...<br />In this paper, I propose that this capability is underwritten by GRNs of co-adapted transcription factor genes.</b></i><br /><br />It's a long paper that discusses GRNs, analogous features, functionally similar features and a lot else.<br /><br />Paul Nelson, last time I had posted this,<br /><br /><i>So painting a complete picture requires Paul Nelson, Jon Wells, Casey Luskin and other liars of the IDiot Institute to say thus,<b><br />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</b><br />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.</i><br /><br />Substitute above for Homology and Gunther Wagner.<br />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.<br /><br />You have a problem with homology in evolutionary biology? Spend IDiot Institute money to produce some research.<br /><br />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.<br />http://sandwalk.blogspot.com/2011/02/problems-with-eukaryotic-tree-of-life.html<br /><br />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.<br /><br />TrutiAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12652067187225602862011-12-08T12:21:30.378-05:002011-12-08T12:21:30.378-05:00Larry wrote:
"The classic example is the len...Larry wrote:<br /><br />"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.<br /><br />This is a trivial exception to the general rule and it is wrong of the creationists to exploit it to discredit evolution."<br /><br />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.<br /><br />I repeat my offer of a semi-formal blog debate on this topic, at Evolution News and Views.Paul Nelsonhttps://www.blogger.com/profile/14127052026545950910noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7606192079991134932011-12-08T12:02:53.890-05:002011-12-08T12:02:53.890-05:00The concept of homology in phylogeny and taxonomy ...The concept of homology in phylogeny and taxonomy is not controversial. You'll find the same definition in most evolutionary biology textbooks. <br /><br />Here's the definition from <i>Evolution</i> (2009) by Douglas Futuyma.<br /><br /><i>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.</i><br /><br />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.<br /><br />After discussing several examples, Futuyma continues with ...<br /><br /><i>Conflicts between phylogenetic and biological homology can also occur when phylogenetically homologous traits have different developmental and genetic foundations.</i><br /><br />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.<br /><br />This is a trivial exception to the general rule and it is wrong of the creationists to exploit it to discredit evolution.<br /><br />The more common conflict is ...<br /><br /><i>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.</i><br /><br />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.<br /><br />When I cal them IDiots, I'm giving them the benefit of the doubt.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11557470050706031372011-12-08T11:46:21.314-05:002011-12-08T11:46:21.314-05:00Larry wrote:
"You are misleading your follow...Larry wrote:<br /><br />"You are misleading your followers if you tell them that homologous structures can be built from very different genes."<br /><br />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.<br /><br />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," <i>Evolutionary Biology</i> 28 (1995):1-37. Hall observes, after several pages of examples of lack of congruence between anatomy, development, and genes, that<br /><br />"...homologous structures often arise from embryological origins that are not common and/or involve different developmental (often inductive) mechanisms. <b>A logical corollary of these cases is that homologous structures need not have a common genetic basis.</b>" (p. 23, emphasis added)<br /><br />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 <i>Developmental Plasticity and Evolution</i> (Oxford, 2003), Mary Jane West-Eberhard throws up her hands, and says, "In fact, evolution makes a mess of homology" (p. 497).<br /><br />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.Paul Nelsonhttps://www.blogger.com/profile/14127052026545950910noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28778308397022131032011-12-08T11:17:30.483-05:002011-12-08T11:17:30.483-05:00Paul Nelson quotes an article that says, in part:
...Paul Nelson quotes an article that says, in part:<br /><br /><i>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.</i><br /><br />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. <br /><br />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.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34715326761972865172011-12-08T11:14:12.049-05:002011-12-08T11:14:12.049-05:00Paul Nelson writes,
Wrong.
The disconnect betwe...Paul Nelson writes, <br /><br /><i>Wrong.<br /><br />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:</i><br /><br />Paul, you are being disingenuous at best (I don't want to mention the other alternative).<br /><br />There's a long history of debating the meaning of homology (see Donogue, M.J. (1992) "Homology" in <i>Keywords in Evolutionary Biology</i>, 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. <br /><br />That's the definition used in the paper by Günter Wagner in the paper you quote.<br /><br /><i>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.</i><br /><br />Thus, the wings of birds and the flippers of seals are homologous. They share the same structural genes and the same embryological development. <br /><br />The eyes of insects and the eyes of mammals are NOT homologous. They arose independently.<br /><br />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 <i>Pax6</i> in vertebrates and <i>ey</i> in <i>Drosophila</i>. The genes are homologues, that is they are similar enough in sequence to conclude that they evolved from a common ancestor.<br /><br />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. <br /><br />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.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76400752184495914652011-12-08T11:05:20.684-05:002011-12-08T11:05:20.684-05:00Dr. Moran writes:
Not only that, the idea that yo...Dr. Moran writes:<br /><br /><i>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.</i><br /><br />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. <br /><br />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.<br /><br />To allow one's strongly - one might say "religiously" - held preconceptions to negate any possibility of learning, though, takes an IDiot.Judnoreply@blogger.com