Uncommon Descent Serving The Intelligent Design Community

Of Mice, Men, and Coelacanths

December 11, 2006
Intelligent Design
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Alternate title: The Sound of the Tree of Life Exploding

Explosion
Comparing the sequence to other species also turned up a big surprise. When the researchers compared the human ultraconserved element to all the DNA sequences in the public database GenBank, the closest match was to DNA from the coelacanth…

Okay, so maybe it didn’t explode but some branches are bent and something is definitely fishy here. Rubin, Haussler, and Bejerano sure do turn up some interesting things. Our closest relative on the tree of life according to ultra-conserved DNA is a fish that’s been around unchanged for at least 360 million years.


Mobile DNA part of evolution’s toolbox
Thursday, May 4, 2006
Written by Howard Hughes Medical Institute

“The big question is whether this is a special case or whether it’s the tip of the iceberg,” says Haussler. A report on the research is published in the May 4, 2006, issue of the journal Nature.

Haussler and his colleagues were led to the discovery through their work on the ultraconserved elements of the genome. One ultraconserved element in particular caught their eye. “We were very interested in this sequence, because it had a number of copies elsewhere in the genome,” says postdoc Gill Bejerano, who is the first author of the study. Close copies of the sequence were ubiquitous in amphibians, birds, and mammals, indicating that it served an important function. “We found it in every species for which we have genomes, from frogs to humans,” says Bejerano.

Comparing the sequence to other species also turned up a big surprise. When the researchers compared the human ultraconserved element to all the DNA sequences in the public database GenBank, the closest match was to DNA from the coelacanth—an ancient fish thought to have gone extinct millions of years ago until a live specimen was caught in 1938 off the east coast of South Africa. The coelacanth is a descendant of the ancient marine organism that gave rise to the terrestrial vertebrates more than 360 million years ago. Humans are therefore separated from the coelacanth by hundreds of millions of years of evolution, yet the two organisms still share critical DNA sequences.

Read the whole article at the link above.

Comments
fallible The Nature article actually does confirm this but the HHMC quote might be misleading in that the ultraconserved element isn't the closest match. The ultraconserved element is a retrotransposon. It is ultraconserved amongst mammals and is also present (highly but not ultraconserved) in coelacanths. The retrotransposon in question inserts copies of itself into the genome of its host. There are many copies of it in all the organisms mentioned. Insertions of it that appear in the human genome are closer in sequence to some insertions in the coelacanth than they are even to other insertions in the human genome. Thus if you are comparing a copy of this retrotransposon in humans to copies in other organisms you get a closest match in the coelacanth. The only misleading part of the HHMC quote is that the copies are ultraconserved between human and coelacanth. Thanks for your interest but in regard to me making any correction in the blog post - there is nothing to correct. Anything misleading in regard to HHMC's use of "ultraconserved" has been addressed in the commentary.DaveScot
December 30, 2006
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The original article in Nature completely refutes your argument. It states in the abstract: "One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE ..." Nowhere in the Nature article do the authors claim that ultra-conserved DNA in the coelacanth is closer to Humans than is any other animal.TheFallibleFiend
December 29, 2006
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jehu, "bFast, I am not sure how you can tell the difference between convergence and horizontal gene transfer. To me it looks like common design." As genes are proported to undergo convergence, I am sure that sometimes the analysis of genes would create a situation where the evolutionary scientist would have a tough time telling the difference between the two. However, your example is of cells, not genes. In this case, I think it pretty clear that we are encountering convergence. I do, by the way, consider the rediculous extent of convergence to be excellent evidence in favor of intelligent design. I do not believe that MET can do a reasonable job of explaining it.bFast
December 14, 2006
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And it wouldn't be a rabbit anyway, it would be an interesting example of convergent evolution.Jehu
December 14, 2006
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Don't be silly. If a rock has a rabbit fossil in it then it is obviously not cambrian rock. [/sarcasm]StephenA
December 14, 2006
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bFast, I am not sure how you can tell the difference between convergence and horizontal gene transfer. To me it looks like common design. BTW, the prediction I made in post #53 has already come true - again. See this article in the New York Times:
“This was just totally out of nowhere, ,” Dr. Meng said in an interview at the museum this week, while pointing to the fossil’s telling features. In the journal report, Dr. Meng and colleagues wrote, “This discovery extends the earliest record of gliding flight for mammals at least 70 million years earlier in the geological history and demonstrates that mammals were diverse in their locomotor strategies and life styles.” ... “The semi-aquatic mammal Castorocauda and the new gliding mammal,” Dr. Luo said, “literally stretch the boundary of paleontologists’ imagination about what would be possible for the earliest mammals.”
http://www.nytimes.com/2006/12/13/science/14mammalcnd.html?ex=1166677200&en=93adc60788ea005e&ei=5065&partner=MYWAY Pretty soon we might actually have rabbits in the cambrianJehu
December 14, 2006
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Jehu, this one looks like convergence to me. I don't think that NDE explains the level of convergence that is, but the same mechanism that caused the greater and lesser pandas to have matching thumbs, did this.bFast
December 14, 2006
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Here's another good one. "Humpback whales have brain cells also found in humans" Horizontal gene transfer? http://www.eurekalert.org/pub_releases/2006-11/jws-hwh112006.phpJehu
December 14, 2006
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bFast, bFast, I don't know if a majority of the other genes line up as a phylogenic tree. In fact I doubt any of them line up 100%. If you recall the article Patrick posted, different genes give you different trees.Jehu
December 14, 2006
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Jehu, if I am understanding your quote correctly, this scientist is saying that the 4 HDAC gene does not by any means express itself as a phylogenic tree like the majority of other genes do, is that correct? In fact, he seems to be suggesting that if one used the HDAC gene as the source gene to determine the phylogenic tree, the tree would cross the philum barrier all over the place. Is that basically the bottom line? If so, these guys have a lot of work to do figuring out how all of this HGT is happening. At the moment, my bet is with little green men with microscopes and very sharp needles. When is this theory going to shatter? How loud will the explosion be?bFast
December 13, 2006
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This researcher sounds rather exasperated
The phylogeny of the class 4 HDACs appears, in many respects, at odds with the phylogeny of the species in which these proteins are found. In the mixed group, we identified, for example, a monophyletic group of nine animal proteins showing closer resemblance to eubacterial proteins than to those of other animals (Figure 1; red circle). This group includes sequences belonging to representatives of several animal lineages: a cnidarian (Nematostella vectensis), two arthropods (Callinectes sapidus, a crustacean, and Locusta migratoria, an insect), an annelid (Platynereis dumerilii), an echinoderm (Strongylocentrotus purpuratus), and four vertebrates (the teleost fishes Takifugu rubripes, Oryzias latipes, Gasterosteus aculeatus, and Pimephales promelas). Strikingly, the class 4 HDAC found in these teleosts is only distantly related to that found in another teleost fish, the zebrafish Danio rerio, and is more closely related to eubacterial proteins (Figure 1). Similarly, one class 4 HDAC found in Locusta migratoria is closer to those found in eubacteria than to those of other insects (Drosophila melanogaster, Anopheles gambiae, Apis melifera, and Tribolium castaneum) and to the second class 4 HDAC of Locusta migratoria. In the mixed group, we also found class 4 HDACs in two green algae, Chlamydomonas reinhardtii and Ostreococcus tauri (Figure 1), appearing more similar to eubacterial class 4 HDACs than to those of other viridiplantae, such as Arabidopsis thaliana, Oryza sativa, or to the second class 4 HDAC of Chlamydomonas reinhardtii. We further noted the existence of a monophyletic group including proteins of very distant eukaryotic species (Figure 1, yellow circle): the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum (chromalveolata), the red alga Cyanidioschyon merolae, and the green alga Ostreococcus tauri (plantae). The green alga sequence is thus more closely related to those of the diatoms, which are evolutionarily quite distant, than to those of any other viridiplantae. Finally, we found a monophyletic group comprising the second HDAC sequence found in the genome of the cnidarian Nematostella vectensis and the sequences of two distantly related eubacteria, Cytophaga hutchinsonii (a Bacteroides species) and Psychrobacter cryhalolentis (a γ-proteobacterium) (Figure 1, orange circle)
Maybe it's just me.Jehu
December 13, 2006
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DaveScot,
I’m fishing in the 59,000 hits from this google search. http://www.google.com/search?hl=en&q=%22comparative+genomics%22+unexpected It looks to be what we military types call a “target rich environment”.
I added "horizontal" to your search to find the instances where the special pleading of "horizontal gene transfer" is invoked. Here is one:
Multiple phylogenetic analyses indicate that the phylogeny of these proteins is, in many respects, at odds with the phylogeny of the species in which they are found. In addition, the eukaryotic members of the class 4 histone deacetylase family clearly display an anomalous phyletic distribution.
http://www.biomedcentral.com/1741-7007/4/24Jehu
December 13, 2006
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The voles are hardly a huge conumdrum for the YEC side, as you seem to be saying. YEC's accept large amounts of variation within kinds of animals. A question for those that claim that common descent is well supported: Apart from the evolutionary 'tree of life' (which, according to this topic title, has exploded) what evidence is there of common descent?StephenA
December 13, 2006
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Jehu, Yes, under an evolutionary worldview I recognize that. But alas, Homer entered in my body, DOH! My question was not well stated. And then I realized it is answered anyway. FL or PEH do not rule out environmental factors as input to regulatory processes and switches. So, it is a planned interaction vs random. The next Homer question. When the mechanisms are fully understood, do they generate leaps of new information across boundaries or not according to Common Descent or YEC interpretations? Voles are a huge conundrum for all sides I'd think and contribute to the great, "We don't Know." The study said the different species recognized each other although scientist did not. If they can breed two different species of voles, what does that mean? They never really speciated in the first place? I'd think right about now, there is one big, DOH!Michaels7
December 13, 2006
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bFast,
Jehu, you mean that evolution is front-loaded, that Dr. Davison’s PEH is correct?
No, I mean that is where the NDE seems to be headed. They keep finding common genes between two diverse species and so they have to posit a common ancestor that was further back than previously assumed. I am not sure how PEH deals with a common gene between two diverse species.Jehu
December 13, 2006
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bFast, I wondered if my use of the word "fact" on this blog would fly without a counter, but I do get your point. For me, it is fact. But, as I think we both agree, the matter of mechanism is up for grabs. I am content to wait and let the scientists uncover what they can in the years ahead. Can you imagine what we will learn in the next 50 years regarding these mattters? These times might be considered the dark ages.bj
December 13, 2006
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Jehu, you mean that evolution is front-loaded, that Dr. Davison's PEH is correct? Bj, "Evolution as common descent is a fact." I have personally bought into common descent, yet I respect some in the ID community that suggest that we are seeing common design rather than common descent. Depending how common design was implemented, it may be very hard to tell the difference between it and common descent. Bottom line, I find common descent to be a well supported theory, and common design to be a poorly supported hypothesis. This may be splitting hairs, I just like to be cautious about declaring something as "fact". The role of the two primary evolutionary mechanisms, random mutation and natural selection have certainly not been established. I believe that both mechanisms are in play, but as the evidence comes in, I don't think that these mechanisms come anywhere close to addressing the challenges placed before them.bFast
December 13, 2006
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“The existence of the genes in a coral indicates that rather than having evolved in vertebrates, many genes previously thought to be vertebrate-specific in fact have much older origins and have simply been lost from organisms like the fly and nematode worm  kicked out as these invertebrate lineages evolved,” he said.
The common ancestor is always being pushcd further and further into the past. It should be an axiom of NDE that, "New discoveries will always push theoretical common ancestors further into the past." And a corollary to that axiom should be that the theoretical common ancestor will always be speculated to have existed where there is not fossil evidence. It seems to me that the NDE narrative is moving more and more towards the idea that all of the real creative evolution occured before the cambrian explosion, and the only thing that has happened since then is the reshuffling of pre-existing information and the fine-tuning of proteins.Jehu
December 13, 2006
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Question. How is EvoDevo any different from FrontLoading?
EvoDevo = random chance and crazy improbable fortuitous events. Front Loading = a plan according to an intelligent designJehu
December 13, 2006
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bFast, The EvoDevo line was a paraphrase from PZ's site of a review for Carrolls book, Endless Forms Most Beautiful. "Chapter 11 concludes the book with summaries of how Evo devo is so important in biology today. Evo devo is the cornerstone of more modern synthesis. Genes per se were not “drivers” of evolution. Instead the key to the making of “endless” forms is in the astronomical number of possible combinations of regulatory inputs and switches.." I see a problem with the key being "astronomical." Instead I think there is a limited potential of combinations based upon environemental surroundings. I like EvoDevo from the symbiotic aspect of surrounding environment input factors and switches turned on/off. Weather influences bird migration. There must be some configurational entropy of a binding site that changes in relation to temperature that sends a signal for the birds to begin their migrations. I'd think it would be similar regulatory factors for bears eating and going into hibernation. I'll wait to form an opinion on Common Descent, PEH, FrontLoading, as the mechanisms are better understood and I myself understand more. Question. How is EvoDevo any different from FrontLoading?Michaels7
December 13, 2006
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bFast, "Actually, as I see it NDE is the foundational theory upon which the others are built. And NDE is the problem. Genetic drift happens, common descent (or something much like it) happened, the entire science of genetic is primarily valid (which is why it is blowing apart the eronious NDE.) When NDE shatters because of all of this evidence, a whole lot of evolutionary theory will rightfully continue on. However, the primary mechanism will enter the zone of “we don’t know.” “We don’t know” is a good place for science to get to. That’s about where physics is right now with the cause of the big bang. The philosophers need to be the ones who bridge the gap to say “I don’t know” equals Intelligent Design." I pretty much agree with you. Evolution as common descent is a fact. Mechanism, however, is up in the air. Those, materialists, who say that it isn't, that is all decided, and we know best, need to experience a humbling moment. I think they will as the evidence comes in. Then, hopefully, we can move back to a more level playing field. At that moment, teleology, in the broad sense can get a better hearing. It's going to take some time.bj
December 13, 2006
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Actually, as I see it NDE is the foundational theory upon which the others are built. And NDE is the problem. Genetic drift happens, common descent (or something much like it) happened, the entire science of genetic is primarily valid (which is why it is blowing apart the eronious NDE.) When NDE shatters because of all of this evidence, a whole lot of evolutionary theory will rightfully continue on. However, the primary mechanism will enter the zone of "we don't know." "We don't know" is a good place for science to get to. That's about where physics is right now with the cause of the big bang. The philosophers need to be the ones who bridge the gap to say "I don't know" equals Intelligent Design.bFast
December 13, 2006
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bFast, I thought the latest response was EvoDevo is the "Cornerstone" of more MET. So, the C. elegans and C. briggsae are like the Voles which is foundation shattering to NDE's sub theories. I'd be curious to see the evolutionary tree of dead fruit hanging on evolution theory as each each subtheory exploded over the last 150 years. NDE becomes nothing more than a worldview as atheist keep moving the goalpost and stating the future is ours.Michaels7
December 13, 2006
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Michaels7,"This is why the Modern Synthesis is superceeded and Darwinism is dead." The modern synthesis is dead too, haven't you heard. The appropriate term now is MET. However, Met, the modern synthesis is all just neo-Darwinism with supporting subtheories. (The neo in neo-Darwinism is the concept of random mutation, a concept that Darwin rejected. (not-neo)Darwinism = natural seletion.) The name of the theory is just like the C. elegans and C. briggsae, ever changing in name, but the functional theory looks just the same.bFast
December 13, 2006
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Thanks Sladjo, me too. If I understand, what Dave is pointing out and the argument is over is the total inconsistency of conservation between phenotypes, correct Dave? In the latest postings. Besides Conserved or UltraConserved. It appears that scientist are discovering there is absolutely no rhyme or reason of Coding Genes in proportion to morphology. Therefore the great prediction of complexity based upon original Genome hypothesis is thrown out the door and they must start all over again. Correct? This is why the Modern Synthesis is superceeded and Darwinism is dead.Michaels7
December 13, 2006
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Hmmm... Don't no so much about genetics, so I don't understand why similarities in the genes/genomes are so important for the OOL issue... If I put my programmer glasses on, I might see same code in different programs, and would not be surprised at all, because same code may be used for completely different applications... If my comparison is valid, this similarities won't be important neither for ToE, neither for ID... They don't prove anything... What would be very important, IMHO, is decoding & understanding THE FUNCTIONS of the genomes that are similar... So, can someone give me an "for dummies" kind of explanation why this similarities in the "ultraconserved" elements are so important ?... Thank you...Sladjo
December 13, 2006
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Here's a beauty that has the old weird shitometer pegged... http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20031118-02
Analysis of the sequence revealed that major evolutionary changes in genomes do not necessarily lead to gross physical changes in the adapted organism. "C. elegans and C. briggsae diverged 80 to 120 million years ago, somewhat longer ago than human and mouse," Stein wrote in an E-mail to us. "By several measures, the two nematode genomes are very much scrambled relative to each other - far more than human and mouse are. Yet while human and mouse are extremely different in ecological niche, behavior, and anatomy, the two nematode species occupy identical niches, have similar behavior, and are indistinguishable except to experts.
Oooooooooooookay. If that's not enough keep in mind these simple worms have 19,500 coding genes while humans have only about 5000 more.
Avril Coghlan at Trinity College Dublin told us, "What was astounding about the C. briggsae-C. elegans comparison is that of all the conserved regions that could be found between the two species, only one third lie inside coding regions of genes. This raises the question of what are the other two thirds of conserved regions that lie in introns and intergenic sequences?" In addition, among 60,775 intron orthologues in the two nematode species, 6579 were species-specific introns, suggesting a rate of evolution of intron-exon structure that is greater between the two nematode species than between humans and mice.
DaveScot
December 12, 2006
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Jehu, "They are only not colored if they don’t match, unless it is a deletion. So either you are way off or I am looking at the wrong page." They are only not colored if they don't match the coelacanth. If chimp and human match each other, but not the coelacanth, then in that bp, the chimp and human are more alike than either is to the coelacanth. DaveScot, I hear that the going explanation for the human immune system includes a convenient case of HGT. In truth, the first time I ever looked at HGT, it looked to me like genetic engineering. In fact, I think it would be very difficult for scientists from mars to tell the difference between non-human-caused HGT and human-caused HGT. The neo-Dawinian paradyme has become badly fractured. Its failure will be monumentous.bFast
December 12, 2006
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Oh yes. Target rich. This is not unexpected for the ID front loading hypothesis. Coral and Man: Not so distant relatives http://media.jcu.edu.au/story.cfm?id=245 Issue date: 17-DEC-2003
The earliest animals wandered around on the ancient seabed with a swag of genes common to you and I, a new study reveals. The research by scientists at JCU and the Australian National University turns upside down many traditional assumptions about what makes vertebrates such as man unique, and what has happened at the level of the genome during animal evolution. Researchers who analysed the genes expressed in the coral Acropora millepora discovered many of the same genes as those found in humans but which are distinctly absent from animals such as the fruit fly and nematode worm. The findings are reported this week in the Current Biology journal. Reader in Biochemistry and Molecular Biology at JCU and co-author of the paper, Dr David Miller, said many coral genes were surprisingly like human genes, although the roles of these genes remained to be established. Dr Miller said it had generally been assumed that the complexity of the human body relative to simpler animals such as insects, worms or corals was the result of new types of genes that arose during the evolution of vertebrates. These conclusions were drawn after studies of the fruit fly and nematode worm revealed both these creatures lacked many types of genes found in humans, he said. "The major surprise from the project is that the coral genome contains many genes previously known only from vertebrates," Dr Miller said. "The existence of the genes in a coral indicates that rather than having evolved in vertebrates, many genes previously thought to be vertebrate-specific in fact have much older origins and have simply been lost from organisms like the fly and nematode worm  kicked out as these invertebrate lineages evolved," he said. "That such a simple animal should contain many genes associated with complex functions in mammals is counterintuitive. "A major challenge now is to explore the likely roles of these coral genes in order to better understand which aspects of gene function are common between corals, some of the simplest of living animals, and humans, one of the most complex."
DaveScot
December 12, 2006
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I see horizontal gene transfer being called upon with some frequency to explain genotype anomalies sort of like convergent evolution rescues phenotype anomalies. http://www.biomedcentral.com/1741-7007/4/24/abstract/ Evolution explains EVERYTHING. No matter what surprises are in store, evolution has an answer for it. Phenotypes are inherited except when they evolve separately. Genotypes are inherited except when they arrive horizontally. :lol: I'm fishing in the 59,000 hits from this google search. http://www.google.com/search?hl=en&q=%22comparative+genomics%22+unexpected It looks to be what we military types call a "target rich environment". DaveScot
December 12, 2006
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