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Carl Zimmer Hears the Sound

December 30, 2006
Intelligent Design
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Carl Zimmer hears the sound of taxonomy exploding. PZ Myers, in his haste to dismiss the notion that genotype and phenotype aren’t increasingly at odds in where to place different critters in the so-called Tree of Life, inadvertently refers to an article by his comrade-in-arms Carl Zimmer which backed up the very point I was making.

“But there are times, I must confess, when I feel like I am watching a blind fistfight.” -Carl Zimmer
Kaboom!

Zimmer’s impression of seeing a blind fistfight amongst biologists of different stripes (accurate imagery there Carl, way to go) is handily explained when one realizes they’re all working from a mistaken dogmatic core belief that evolution is the outcome of random mutation filtered by natural selection.

“The Genome: An Outsider’s View” by Carl Zimmer

The Buddha once told a story about a king who ordered a group of blind men to be presented with an elephant. Each man touched a different part of the animal. The king then asked them what an elephant is like.

The blind men who touched the elephant’s head replied, “An elephant, your majesty, is just like a water jar.” The blind men who touched its ear said, “An elephant, your majesty, is just like a winnowing basket.” The blind men who touched its tusk declared, “An elephant, your majesty, is just like a plowshare.” The ones who touched the trunk replied, “An elephant, your majesty, is just like a plow pole.” The blind men who touched the body replied, “An elephant, your majesty, is just like a storeroom.” The blind men who touched the foot replied, “An elephant, your majesty, is just like a post.” The blind men who touched the hindquarters replied, “An elephant, your majesty, is just like a mortar.” The blind men who touched the tail replied, “An elephant, your majesty, is just like a pestle.” And the blind men who touched the tuft at the end of the tail replied, “An elephant, your majesty, is just like a broom.”

The blind men fell into a fistfight, shouting, “An elephant is like this, an elephant is not like that! An elephant is not like this, an elephant is like that!” [1]

I am a science writer, and my chief passion is biology. I spend time with biologists of all stripes—computational biologists, paleontologists, biochemists, ecologists, and all the rest. It is a marvelous privilege. But there are times, I must confess, when I feel like I am watching a blind fistfight.

Read the rest of Zimmer’s paper at the PLoS: Computational Biology link above.

Comments
LOL! Preview First! Geaux Tigers!Michaels7
January 3, 2007
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Another explosion, unrelated to ID or issssssssssssss it... http://creationsafaris.com/crev200701.htm#20070103a “Ironstone bodies of the Barberton greenstone belt, South Africa: Products of a Cenozoic hydrological system, not Archean hydrothermal vents!” Geuax Tigers!Michaels7
January 3, 2007
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Jud, That is not my only point, but that Zimmer is relying on evidence that is still uncertain in my estimation and grows more uncertain by the day. We could see a broader redefinition. Or possibly the ToL shaken down eventually to its roots, with possible multiple origins scenarios. Least that is the way I'm starting to lean. I'm stating all the men are still blind. It is still largely a guessing game even with genetic information flying in at a rapid pace. In fact, it is the rapid pace of information coming in that has caused the Modern Synthesis to be "superceeded" as Dr. MacNeil admitted not long ago in this very forum. From an evolutionary, materialistic POV, it will always be that way because it is stated as unguided. Design looks for evidence of guidance within boundaries. I think we're still somewhere between ID proving it has merit as a theory and long held Evolutionary positions falling apart. EvoDevo will not save the materialist pov. Todd summed it up quite well I think with #4,6-7.Michaels7
January 3, 2007
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Michaels7 - Please understand that I was posting about what I think the Zimmer article is saying. I am not interested in making arguments or engaging in persuasion with regard to whale evolution, or evolution in general - we are all able to seek out information on those topics and entitled to evaluate it for ourselves. The link regarding the "fossil in question" appears in a footnote to Zimmer's article: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11567134&dopt=Abstract That's the abstract of the published article in Science magazine. The full version is available with free registration.Jud
January 2, 2007
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http://www.sciam.com/article.cfm?articleid=CF2AA0B2-E7F2-99DF-34CD01DE3E68F8ED Haven't seen this one posted on UD yet; sorry for the duplicate if I missed it. Just one more cross-connecting twig on the bush of life. Did you know your brain was like a sea slugs?dacook
January 2, 2007
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I think you missed a few cues in dave’s original post. 1. ‘inadvertently’ 2. Zimmer is identified as a ‘comrade-in-arms’ of Myers – we know before reading the story the author accepts the pseudo-mystical appeals to chance and parsimonious tautologies of neo-darwinism. 3. We therefore deduce whatever point dave is making by use of Zimmer is, in light of #1, not purposefully critical of the #2 appeals 4. The extended story of the blind men & elephant – an illustration of problems of perspective 5. Zimmer was applying #4 to all stripes of biologists – he used the examples you quoted to show two perspectives, pheno- and geno- 6. The #4 analogy ‘is handily explained when one realizes they’re all working from a mistaken dogmatic core belief’ 7. The men are blinded by #6 mistaken dogma – The analogy is therefore apt Hope that helps!todd
January 2, 2007
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Jud, I have not seen the fossil in question that links a hippo to a whale. As I asked, can you refer to the link? I think there is way to much sympathy for one point of view when DNA, Non-coded regions and regulatory functions are undermined by the examples of Voles. What is being reported more recently is that we cannot always trust DNA in morphology or in representing a tree as well. The voles are a great example that even molecular science is still guessing what is going on between species that cannot be deteceted by the naked eye. Again, show the fossil links to the hippo. Common Design is just as much a factor here as any other "imaginative" scienctific assumption. Reading thru this link still shows a bunch of guessing including the 30 my Gap amid other assumptions. "Furthermore, Boisserie et al. (2005) examined 80 morphological characteristics of extant and extinct cetartiodactyls and determined that hippos evolved from a group known as the anthracotheres, and that this hippos-anthracothere clade appears to be sister to Cetacea. An anthracothere origin for Hippopotamidae would fill in the 30 million year gap in the fossil record between the origin of whales in the Eocene and the origin of hippos in the Miocene. (Boisserie, Lihoreau, and Brunet, 2005; Thewissen, Williams, and Hussain, 2001) quote from SuperOrder "Cetartiodactyla" http://animaldiversity.ummz.umich.edu/site/accounts/information/Cetartiodactyla.html Cetacea and Artiodactyla, "traditionally classified" as monophyletic orders. None of this is fact. There's a lot of imagination. Yet you talk as if it is fully proven as fact.Michaels7
January 2, 2007
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DaveScot said: "Comparative genomics is making a mess out of phenotype classifications. I’ve brought up a number of articles in the past 30 days which attest to this." I hope this continues to happen, since that's how science functions - new knowledge replacing old hypotheses. (Though as I felt Zimmer pointed out in his article, the "old" sciences - paleontology, natural history, etc. - can continue to contribute to this "new" knowledge in order to create a more complete picture.)Jud
January 2, 2007
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Well then I guess we agree to disagree. Comparative genomics is making a mess out of phenotype classifications. I've brought up a number of articles in the past 30 days which attest to this. You've done nothing but put your own spin on one of them.DaveScot
January 2, 2007
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DaveScot, You're correct that in concentrating on the whale discussion, I did not respond with regard to the part of the article discussing the coelacanth. Let me turn to that now. I look at Zimmer's article as being divided, like Gaul under Caesar, into 3 parts. The first part, from which you quoted extensively in your original post, describes a situation where paleontologists, concentrating on phenotype, often disputed the conclusions of molecular biologists (including computational molecular biologists, for whom Zimmer wrote the article), who concentrated on genotype. The second part of the article, from which I quoted extensively, describes how the champions of phenotype eventually arrived at agreement with the champions of genotype regarding whale ancestry. Here Zimmer is describing to his audience how paleontologists came to recognize the value of the work done by computational biologists. In the third part of the article, regarding the coelacanth, Zimmer (IMO) tells his audience of computational biologists not to rest on their laurels, and to recognize that the real lesson of the whale story is that paleontologists, natural historians and computational biologists can all inform each other's work. Zimmer describes the coelacanth paper as "remarkable" for showing that humans share 80% of certain coelacanth genetic sequences in a non-protein-coding region, despite the more than 400 million years separating their ancestors. The fascinating question is why these sequences have been so well preserved over such a long period of time. In his conclusion, Zimmer tells computational biologists that consideration of information from other disciplines, including natural history, may help to provide answers: "If one thinks about the coelacanth's natural history as well as its genome, a new set of questions arises. Transposons are prone to mutations, which can take away their ability to insert new copies in a genome. These coelacanth transposons have been replicating for 400 million years, and now probably take up a significant fraction of the coelacanth genome. And yet they still have not diverged very much in all that time. Is natural selection conserving them? Is natural selection acting on the transposon or the coelacanth? How do these proliferating transposons affect the physiology of the coelacanth? Do they act like pathogens, or are they providing some benefit we don't yet understand? Does their expansion play any role in the ecology of living coelacanths? "None of these questions would even arise without the invaluable work of computational biologists. But if all the blind men [computational biologists, paleontologists, natural historians, etc.] gather together around the coelacanth, perhaps they can better understand just what this creature is." Turning then to DaveScot's statement that Zimmer's article shows genotype and phenotype are increasingly at odds, I must continue to respectfully disagree. My take on what Zimmer is telling his computational biologist audience is that paleontological evidence of phenotype, as well as environmental information from natural history, can help them use genotypic information to obtain a more complete picture of the "Tree of Life."Jud
January 2, 2007
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bdelloid I suggest you look at the cartoon and think about it real hard. Read all the captions and look them up if necessary.DaveScot
January 1, 2007
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DS, But you do agree, though, that this whale example is a striking demonstration of how genotype actually PREDICTED a phenotypic discovery ? Prior to the discovery of the double pulley joint whale ancestor, this would have been a prime example of "genotype-phenotype discordance". But in the end, it wasn't. So I agree with jud here, the primary argument being made by Zimmer in that article is that while we often feel like blind men describing the elephant, in the end, things tend to fall in place when the blind men sit down and hash things out with one another.bdelloid
January 1, 2007
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jud You completely ignored my point that Zimmer used other examples of genotype and phenotype in disagreement including one from 2006. In fact the example from 2006 (coelacanth) was the subject of a blog article by me here and was the reason Myers mentioned Zimmer in the first place.DaveScot
January 1, 2007
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DaveScot said that Carl Zimmer's article supported the notion that genotype and phenotype are "increasingly at odds" with regard to proper characterization of the ancestry of various animals. I disagreed, noting Zimmer's article actually illustrated the coming together in agreement of biologists championing phenotype with those researching primarily in the area of genotype. DaveScot quoted a portion of Zimmer's article in support of his statement. In support of my interpretation of what the article says, let me quote another segment of it. Apologies for the length, but I feel it's necessary: "At the time, molecular phylogenies were still a novelty. The computational methods for calculating them were relatively new, and scientists could only use them to compare a few gene sequences of whales and other mammals. But the conclusions from these few studies were the same: the closest living cousins of whales are hippos. "This may not seem like a big deal. It certainly didn't seem to bother the scientists who carried out the studies. They were just analyzing digital code, abstracted from the animals that carried it. The results spoke for themselves. Nevertheless, they gave paleontologists and mammalian systematists conniptions. "Here's why. Hippos are artiodactyls (also known as even-toed ungulates). Other artiodactyls include cows, camels, and pigs, and goats. Zoologists have long recognized a number of anatomical features that unite artiodactyls in their own group, distinct from other hoofed mammals such as horses and rhinos. One of the most obvious hallmarks was a bone in the ankle, the astragalus. The artiodactyl astragalus has a unique double-pulley shape that allows the artiodactyl hoof to swing back and forth in a distinctive way. "In the 1990s paleontologists found a number of spectacular early whale fossils, but they had yet to find bones from the whale ankle. The bones and teeth they did find suggested that the closest relatives of whales were an extinct group of mammals called mesonychids. Mesonychids were hoofed mammals, but they did not have a double-pulley astragalus. Therefore, paleontologists concluded, they were probably not artiodactyls. And if mesonychids were not artiodactyls, then whales could not be either. And that meant that the whale–hippo link had to be wrong." * * * "Subsequent studies on mammal DNA continued to support the whale–hippo link. And meanwhile paleontologists discovered more fossils of ancient walking whales. In 2001 Phil Gingerich and his colleagues from the University of Michigan and from Pakistan described a skeleton of the seal-like species Rodhocetus. Among its bones, they found an astragulus—the first whale astragulus ever discovered. And lo and behold, the astragalus had a double-pulley shape [citation omitted]. The DNA, it seems, had been right all along." So biologists started out in disagreement - DNA indicated artiodactyls, the fossils seemed to point to mesonychids. However, later fossil finds confirmed whale ancestors were artiodactyls, the same line from which hippos came. Thus, Zimmer's article points out that phenotype was found to agree with genotype. Therefore, I can't agree that Zimmer's article supports the notion that genotype and phenotype are "increasingly at odds."Jud
January 1, 2007
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JUd, we should see csome 50,000+ transitionals in the whale lineage alone. Yet all we can muster are a handful of speculative choices.Joseph
December 31, 2006
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have preview and forget to use it, "their" not there. Dave, thanks for the article and I think it shines light on the current process. It is an interesting read.Michaels7
December 30, 2006
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Jud, Do you have any actual pictures of the ancestoral fossil record or a link that we may see and judge for ourselves instead of stressing it as an unchallenged fact? I tried looking up taxa here: http://animaldiversity.ummz.umich.edu/site/accounts/classification/Artiodactyla.html And what I find is Cetartiodactyla as a SuperOrder which contains the whale. The "artiodactyla" order contains a hippo and water buffalo, but no whales or sea mamals. Are there records out of date? I am skeptical of the entire process. Tomorrow they may change the order yet again. It is still largely a guessing game. BTW, its a fairly good link for all to have as an online reference.Michaels7
December 30, 2006
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jud No, that's not right. Zimmer's paper was published just yesterday and he gives an example from 2006 (the coelacanth). The whale tale was merely the first example he chose.DaveScot
December 30, 2006
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With respect, I must say that the portion of Zimmer's paper that you quoted is the "before" picture from years ago, and that the paper goes on to show the current situation of agreement between the former "fistfighters" - specifically, that the whale genotype showing descent from the same ancestors as hippos was eventually backed up by the discovery of fossils of a whale ancestor with a phenotypic feature characteristic of hippos (artiodactyly).Jud
December 30, 2006
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