Intelligent Design

Of Mice, Men, and Coelacanths

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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.

70 Replies to “Of Mice, Men, and Coelacanths

  1. 1
    DaveScot says:

    Related article

    http://www.pubmedcentral.nih.g.....id=1518811

    Finally, we note that there is a single strong match in one distant organism: the human blood fluke (Schistosoma japonicum). This instance shares 88% sequence identity with the core region SINE3 over 72 bp (see Fig. 15, which is published as supporting information on the PNAS web site). Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered. Resolving this question will require extensive genomic sequence from platyhelminthes. If the element in blood flukes does represent vertical descent from a common ancestor, then the core element must be very old indeed.

  2. 2
    bFast says:

    1 + 1 = 47

  3. 3
    tb says:

    bFast@ 1+1 = 42! Meaning of Life and all, you know! I think I am growing gills!

  4. 4
    Jehu says:

    Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered.

    Just out of curiosity how does DNA get horizontally transferred from a fluke worm to a human?

  5. 5
    GeoMor says:

    I am not really sure what problem is being pointed out here. The ultraconserved elements are by definition shared almost exactly among the mammals. If you start to look for them further out, you hit some fish — which is not itself surprising, since mammals evolved from fishlike ancestors.

    The surprising thing was that the matching sequence in fish is a known transposable element, whereas in mammals it seems to have taken exapted into some other role. But none of this relates to the tree of life exploding…?

  6. 6
    jpark320 says:

    No, if it was a “transposable element” as you say you would think that there would be some incredible modification since the time fluke and humans were related. Those things, whether exapted or not shouldn’t stay ultraconserved (not merely conserved) only in flukes to humans, but across the multiple species amphibians, reptiles, and other primates.

    Tree of life is exploding b/c it skipped all the other “ancient” and related “organisms” and suddenly is found conserved on a very recent branch. In other words an ultraconserved sequence we have should be in our “close relatives” primates ~ b/c they’ve been ultraconserved so you’d expect primates who we have supposedly recently branched off from to be the closest match. But guess what you have to go back no to just the primate/hominid split, reptile/mammal split, but some place way back w/the flukes.

    So start yelling “TIMBERRRR!!!!”

  7. 7
    jpark320 says:

    Sorry for the grammar, but gotta catch a flight soon!

    My first two sentences in #6 are two separate ideas!

    And I didn’t mean to say any sequence cannot be ultraconserved since back then (but I don’t believe in back then), but that if there were other species closer to should have a more similar sequence to us, than should the fluke.

  8. 8
    Patrick says:

    Shared information in divergent lines where none is expected? Color me not surprised. Still looking for someone to compare the sugar glider and the squirrel but this will do for now

    Oh, and for those who missed it:

    http://biology.plosjournals.or.....io.0040352

    The tree of life is not exactly “exploding” but it is getting bushy even considering the included bias in interpreting the evidence: “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes.”

    EDIT: Added a “not” between is and exactly and clarified my sentence…

  9. 9
    Jehu says:

    GeoMor

    I am not really sure what problem is being pointed out here. The ultraconserved elements are by definition shared almost exactly among the mammals. If you start to look for them further out, you hit some fish — which is not itself surprising, since mammals evolved from fishlike ancestors.

    Well, you don’t expect the coelacanth and the human to have the highest degree of identity on a gene or that kind of homology with a fluke. This is why the author said,

    Given the large evolutionary distance between fluke and vertebrates (>600 million years), this single instance should not be assumed to imply vertical descent from a common ancestor; the possibility of horizontal transfer must be considered.

    BTW, how does a sequence get horizontally transferred from fluke to human?

  10. 10
    bFast says:

    Tb – sorry, I miscalculated. Your number is surely correct — until tomorrow.

    Patrick, when I look at a bush, it forks just like a tree. It seems, however, that you and your article are not talking about a “very busy” tree, but a tree-like structure that doesn’t simply fork as you climb up from the roots to the leaves. Rather it seems to show a tangled mess that resists a fork-based mapping.

    Alas, this particular thread started by showing that we are more Coelacanthlike than mouselike. I understand that the cytochrome C, of Denton fame, also shows that the rattle-snake is more human-like than snake-like. I believe that it shows to be more human-like than mouse-like even.

    1+1 = 36. I’ll never finish my lunch.

  11. 11
    Jehu says:

    bFast

    Patrick, when I look at a bush, it forks just like a tree. It seems, however, that you and your article are not talking about a “very busy” tree, but a tree-like structure that doesn’t simply fork as you climb up from the roots to the leaves. Rather it seems to show a tangled mess that resists a fork-based mapping.

    I think of it as branches hanging in thin air, not connected to anything but with certain “stastical probabilities” that make theoretical connections to the other branches. Kind of like the fossil record.

  12. 12
    bFast says:

    Jehu, it looks to me like if you follow the phylogenic tree painted by one gene you get one branching, if you follow the tree painted by another three you get another branching. This is a much worse problem than mere “no mapping clarifies which connection is correct”, rather it is, “this evidence declares this connection, this other evidence declares a different connection.” This should be a problem.

    1 + 1 = 43

  13. 13
    russ says:

    jpark320 // Dec 11th 2006 at 4:56 pm

    “Sorry for the grammar, but gotta catch a flight soon!”

    Don’t forget:

    3.4 ounces or less containers of liquids/gels/paste, in
    quart-sized plastic bags, removed from luggage prior to screening.
    😉

  14. 14
    Inquisitive Brain says:

    I think we need to know more about epigenetics and other possible routes of inheritance before we go drawing any conclusions about a tree of life. I think the gene-centrism required by neo-Darwinism has lead the science astray on this.

  15. 15
    dacook says:

    “Comparing the sequence to other species also turned up a big surprise.”

    I’ve noted it before: Darwinists are regularly surprised by real life findings.

    (I THOUGHT that fish looked an awful lot like my aunt Jean…)

  16. 16
    johnnyb says:

    Is it just me, or has there been a _lot_ of these kind of papers published in the last year? Is this an indication of a new trend in biology?

  17. 17
    DonaldM says:

    I wonder how long it will be before the Darwinists will claim that this finding is exactly what evolutionary theory would have predicted!!

  18. 18
    Srdjan says:

    DonaldM, this finding is exactly what evolutionary theory predicted! There you got it.

  19. 19
    GeoMor says:

    This is the third time I’m trying to post this. I’m not sure if it’s being intentionally held back, or what, but perhaps someone will recognize that it is a rather important clarification to make.

    The ultraconserved element in question is found almost exactly in all the mammalian genomes we have, and also very close in an amphibian (frog), while the fish sequence is less similar — basically consistent with the “tree of life”. This can be verified by reading the actual paper that this news article is about (Bejerano et al. 2006); unfortunately I don’t think it’s open access, but at least the key misunderstanding here can be resolved from the abstract:

    One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE,…
    http://www.ncbi.nlm.nih.gov/en.....t=Citation

    We don’t yet have much genome sequence from other species in between (besides the frog) to see what went on, but we would strongly predict that the sequence will be found in some form in such genomes. Something very interesting indeed had to happen for the transposable element to come under selection in a particular location, and that’s why this is in Nature.

    Jehu, in regards to horizontal transfer. Please note that DaveScot has referred to two separate studies here; the term “fluke” in the second (Xie et al.) does not refer to the fish of the first (Bejerano et al.), but rather to the mammalian blood parasite Schistosoma japonicum, colloquially known as “blood fluke”. It should be clear why it is at least plausible that horizontal gene transfer between a blood parasite and its host’s genome could occur.

    In summary, this blog entry and most of the comments seem to be based on a misunderstanding of what the study was actually saying, although I can see how it happened from the way the HHMI news article was written. There is no inconsistency with NDE or tree-of-life in either the Bejerano or Xie studies.

  20. 20
    Reed Orak says:

    Thank to GeoMor for clarifying the significance of the article.

    I think that DaveScot understood what the article was about when he posted this, but I’m still not clear on what this means:

    “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.”

    It sounds to me like the article was saying that the sequence in question has deteriorated similarly in coelecanths and humans.

  21. 21
    Jehu says:

    Well in that case the following statement is a bit misleading.

    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.

    As for horizontal transfer of genetic information; no it is not clear to me how the DNA of a blood fluke gets into the line of its host. It doesn’t exactly inject its DNA into the cells of its host does it?

  22. 22
    DaveScot says:

    It’s not misleading.

    http://bejerano.stanford.edu/t.....eOct06.pdf

    Go to page 33 where the ISL1 regulator is graphically compared between human, chimp, dog, mouse, rat, oppossum, chicken, frog, and coelacanth. The human and chimp versions are identical and most closely match the coelacanth.

    For a laugh, go to page 7 to see Bejerano make the gratuitous, obligatory “secret handshake” to assure readers he’s not “one of them”. This secret handshake is prerequisite to publication in respected journals. 😛

  23. 23
    DaveScot says:

    geomor and reed

    I don’t know what is being referred to in the Nature article as being 100% identical among mammals but it isn’t the ISL1 regulatory region. That is identical between humans and chimps then the next closest match is to the coelacanth. Language might be imprecise but the sequence data isn’t. Refer to page 33:

    http://bejerano.stanford.edu/t.....eOct06.pdf

    and compare the sequences for yourself.

  24. 24

    Some pre-Socratic Greek philosophers suggested humans were evolved from fish. So they must be feeling pretty smart right now.

  25. 25
    bFast says:

    Sorry Dave, I don’t see what you are talking about. When I count the matches between the human and the coelacanth, I get 54 matches. Between the dog and the coelacanth, I get 52. Between human and dog, I get 68. (It’s kinda rough countin’ but if we use the same “deletion” logic they use, that’s what I get.) Therefore the ISL1 is more similar between the human and the dog then between the human and the coelacanth.

  26. 26
    GeoMor says:

    Thanks bFast for actually counting. It’s pretty clear just by glancing at that figure that the coelacanth sequence is the most distant. It is purposely drawn to highlight the differences between the very closely related mammalian sequences and the coelacanth sequence.

    Jehu, I don’t know exactly how the horizontal transfer would work. Now that I’m going back and reading comments again, I see that I may have misinterpreted what you were saying and thought that you were thinking “fluke” referred to a fish swimming around in the ocean, in which case horizontal gene transfer with a land mammal would be pretty spectacular. Sorry if I misunderstood that. At least relatively speaking, horizontal transfer between a blood parasite and its host is easy to see =)

    One thing that might make it a little easier to envision is that it could be transfer from the host to the parasite, rather than the other way around. One also has to wonder if, when they took a sample of the blood fluke for sequencing, they took it from some human blood sample and there could have been human genomic contamination. Anyway, I don’t know anything about this guy, so that was all pure speculation.

  27. 27
    DaveScot says:

    By my count of ISL1 comparisons:

    human/coelacanth 54 matches
    chimp/coelacanth 54 matches
    dog/coelacanth 51matches
    mouse/coelacanth 50 matches
    rat/coelacanth 50 matches matches
    opossum/coelacanth 51 matches
    chicken/coelacanth 54 matches
    frog/coelacanth 45 matches

    chimp/human 54 matches
    dog/human 49 matches
    mouse/human 46 matches
    rat/human/rat 47 matches
    opossum/human 48 matches
    chicken/human 50 matches
    frog/human 40 matches

    The human ISL1 is closer to a coelacanth than it is to any of the other species listed except for chimps and they’re identical there. This makes little sense in light of evolution. Human/coelacanth should have the fewest matching bits not the most. Humans and chimps are closer to a coelacanth with 54 matches than they are to dogs, mice, rats, possums, chickens, or frogs which is 50 matches at best and the best case is a chicken of all things instead of another mammal.

    Otherwise it looks reasonable except perhaps that frogs shouldn’t be such an outlier from coelacanths compared to mammals and birds since they’ve presumably been separated from a common ancestor the same length of time as any of the mammal/bird lineages but frogs probably just mutate a lot faster than the others which explains that.

  28. 28
    Lurker says:

    I know little about this subject but I find it very interesting. What do you all make of this article? – “Evolution of ‘irreducible complexity’ explained”

    This part stood out to me:

    The experiments showed that the receptor had the capacity to respond to aldosterone long before the hormone actually evolved.

    Thornton’s group then showed that the ancestral receptor also responded to a far more ancient hormone with a similar structure; this made it “preadapated” to be recruited into a new functional partnership when aldosterone later evolved.

    Sounds like a telic process to me.

  29. 29
    DaveScot says:

    Interesting coelacanth trivia from wiki

    Coelacanths give birth to live young called pups. Their reproductive behaviors are not well known, but it is believed that they are not sexually mature until after 20 years of age. Gestation time is 13 months, females give birth to between 5 and 25 babies, which are capable of surviving on their own immediately after birth.

    The list correlates better with generation (sexual maturation) time in all the species rather than divergence time. I wasn’t aware before just now that coelacanths took so long to mature and had so few young. They’re the slowest to reach sexual maturity in the whole list and live by some estimates at least up to 80 years (they were only known as fossils until 1938).

  30. 30
    DaveScot says:

    Geomor

    The coelacanth sequence is the only one in black because it’s the template against which all the others are compared. That’s because it is the oldest phenotypically unchanged lineage in the group by the testimony of the fossil record.

    It’s odd enough that the SINE protein product (PCBP2) in frogs, birds, and mammals are identical and equidistant from the coelacanth. Ultra-conserved protein is one problem to explain. The second problem is that the SINE regulatory region (ISL1) doesn’t follow the pattern of the protein and surprisingly the human/chimp ISL1 resembles the coalencanth predecessor moreso than it does to critters with a closer common ancestor.

  31. 31
    bFast says:

    DaveScot #27
    chimp/human 54 matches

    For chimp/human I count 80 matches. I count 54 that are colored, and an additional 26 which are not.

  32. 32
    bFast says:

    I have notice another intriguing thing in the article (the link in post #22, page #13)
    It says:

    all functions we understand in our genome are encoded using redundant codes.

    (emphasis in original)

    On ISCS’s brainstorms, Peter Borger extensively discusses that natural selection is not capable of maintaining redundant code. Further we have had a major debate on this forum — something about magnito systems in light aircraft — where we reach the same conclusion. I challenge the anti-ID community to even make a decent simulation that shows a redundant system that doesn’t loose its redundancy under influence of random mutation.

  33. 33
    DaveScot says:

    bFast

    Mibad. You’re right of course. In my haste to find what the Howard Hughs Medical Institute writeup was talking about in the exploding quote I failed to count the uncolored sequences. I’m not convinced the quote is a mistake yet. Bejerano links to HHMI article I quoted in his own UCSC webpage, by the way. http://www.soe.ucsc.edu/%7Ejill/ (see Living Fossil Transposon) which kind of bolsters the notion that HHMI made no mistake.

  34. 34
    Jehu says:

    GeoMor

    This can be verified by reading the actual paper that this news article is about (Bejerano et al. 2006); unfortunately I don’t think it’s open access, but at least the key misunderstanding here can be resolved from the abstract:

    One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE,…
    http://www.ncbi.nlm.nih.gov/en.....t=Citation

    That quote from the abstract clearly refers to PCB2, not ISL1.

  35. 35
    Jehu says:

    bFast

    For chimp/human I count 80 matches. I count 54 that are colored, and an additional 26 which are not.

    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.

    For the record, looking at the segment labeled ISL1 on page 33, I see that the human/chimp/chicken are tied for closest to coelacanth. With the other vertebrates in the following order, Dog/Rat, Mouse/Opposum, and Frog. Not exactly the predicted tree of life but we are going off of a partial sample. I see from looking at the diagram at the top of page 33 that ISL1 is not 100% the same in human and chimp and the two are significantly different than the chicken.

  36. 36
    DaveScot says:

    Here is where they (HHMI) got it from. uc.338 homologs. My emphasis.

    http://www.osti.gov/energycita.....882757.PDF

    An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 are Derived From a Retroposon

    Gill Bejerano, et al

    One of the most evolutionarily constrained regions in mammalian genomes is ultraconserved element uc.338, a mammal-specific 223bp region perfectly conserved between human, mouse and rat, overlapping a short protein coding exon of PCBP26. This small region was observed to have multiple paralogs within the human genome, overlapping protein coding exons of otherwise unrelated genes, as well as conserved intronic and intergenic regions (Fig. S1). Unexpectedly, this region also has multiple homologs in coelacanth that are closer in sequence to the human ultraconserved element than many of its human paralogs (Fig. 1c).

    It should be noted that the coelacanth genome has only a small fraction of it sequenced so far so there’s much more yet to discover in it which probably prompted Haussler’s “tip of the iceberg” comment.

  37. 37
    DaveScot says:

    It’s also interesting to note that coelacanths have a genome size and chromosome number comparable to humans.

    http://www.genomesize.com/resu.....hp?id=4420

    human c-value=3.50 chromosomes(2n)=46

    http://www.genomesize.com/resu.....hp?id=3598

    coelacanth c-value=3.61 chromosomes (2n)=48

    http://www.genomesize.com/resu.....php?id=906

    chicken c-value=1.25 chromosomes (2n)=78

    http://www.genomesize.com/resu.....php?id=294

    clawed frog C-value=3.65 Chromosome Number (2n)=36

    http://www.genomesize.com/resu.....hp?id=5438

    opossum C-value=5.22 Chromosome Number (2n)=18

    More interesting than the coelacanth are the lungfishes such as this one:

    http://www.genomesize.com/resu.....hp?id=3604

    lungfish C-value=112.78 chromosome Number (2n)=38

    Over 30 times the size of the human genome. I wonder what mysteries lurk therein.

  38. 38
    GeoMor says:

    DaveScot, the emphasized sentence says that PCB2 is more similar to the coelacanth sequence than to ISL1 (and other similar sequences in the human genome), which was obvious in the figure you previously pointed to. “Paralogs” refers to other copies of the sequence in the human genome. Please consider carefully the implications (or lack thereof) of similarity in multiple copies within the human genome versus copies found across several species, given that PCB2 is the only copy that is ultraconserved.

  39. 39
    DaveScot says:

    Geomor

    Then why was the finding characterized as “unexpected”?

  40. 40
    GeoMor says:

    It was unexpected because there were multiple very similar copies in coelacanth, not just one — if there were just one, you would just say it is the ortholog (corresponding instance in another genome) of the mammalian ultraconserved element. The message of the paper is that a (repetitive) transposable element in coelacanth gave rise to this ultraconserved element in mammals through exaptation.

    The following paper gives a much better example of the problem that I think you intended to seize upon in this blog entry. It’s a little less sexy because it involves flies and not mammals, but it’s recent work that shows the current state of the art (which is somewhat limited) in explaining why many gene trees disagree with the species tree.

    http://genetics.plosjournals.o.....en.0020173

  41. 41
    DaveScot says:

    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/1...../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. 😆

    I’m fishing in the 59,000 hits from this google search.

    http://www.google.com/search?h.....unexpected

    It looks to be what we military types call a “target rich environment”.

  42. 42
    DaveScot says:

    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.”

  43. 43
    bFast says:

    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.

  44. 44
    DaveScot says:

    Here’s a beauty that has the old weird shitometer pegged…

    http://genomebiology.com/resea.....0031118-02

    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.

  45. 45
    Sladjo says:

    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…

  46. 46
    Michaels7 says:

    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.

  47. 47
    bFast says:

    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.

  48. 48
    Michaels7 says:

    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.

  49. 49
    bFast says:

    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.

  50. 50
    bj says:

    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.

  51. 51
    Michaels7 says:

    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?

  52. 52
    Jehu says:

    Question. How is EvoDevo any different from FrontLoading?

    EvoDevo = random chance and crazy improbable fortuitous events.

    Front Loading = a plan according to an intelligent design

  53. 53
    Jehu says:

    “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.

  54. 54
    bFast says:

    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.

  55. 55
    bj says:

    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.

  56. 56
    Jehu says:

    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.

  57. 57
    Michaels7 says:

    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!

  58. 58
    StephenA says:

    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?

  59. 59
    Jehu says:

    DaveScot,

    I’m fishing in the 59,000 hits from this google search.

    http://www.google.com/search?h.....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/1741-7007/4/24

  60. 60
    Jehu says:

    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.

  61. 61
    bFast says:

    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?

  62. 62
    Jehu says:

    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.

  63. 63
    Jehu says:

    Here’s another good one.

    “Humpback whales have brain cells also found in humans”

    Horizontal gene transfer?

    http://www.eurekalert.org/pub_.....112006.php

  64. 64
    bFast says:

    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.

  65. 65
    Jehu says:

    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.....tner=MYWAY

    Pretty soon we might actually have rabbits in the cambrian

  66. 66
    StephenA says:

    Don’t be silly. If a rock has a rabbit fossil in it then it is obviously not cambrian rock.

    [/sarcasm]

  67. 67
    Jehu says:

    And it wouldn’t be a rabbit anyway, it would be an interesting example of convergent evolution.

  68. 68
    bFast says:

    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.

  69. 69
    TheFallibleFiend says:

    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.

  70. 70
    DaveScot says:

    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.

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