Darwinism Intelligent Design

“The Unbearable Lightness of Chimp-Human Genome Similarity” by Rick Sternberg

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Walter ReMine once said to me, the supposed 99.5% identity between chimps and humans is like taking two books, creating an alphabetical listing of all the unique words in each book, and then comparing the lists of unique words derived from each book. It would be really easy then to use these lists to argue: “see the books are 99.5% identical!”

Another ID proponent, David Pogge, argued that the sequence comparison are like comparing driving directions: two sets of directions can have 99% similarity, but a few differences can lead to radically different destinations.

With this in mind, here is Rick Sternberg’s Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity.

109 Replies to ““The Unbearable Lightness of Chimp-Human Genome Similarity” by Rick Sternberg

  1. 1
    scordova says:

    Ok, how many noticed Rick Sternberg’s reference to the music by Piero Umiliani (1969)? Nice bar music eh? 🙂

  2. 2
    twvolck says:

    You don’t mean “unique.” If a word is unique to book A, by definition it can’t appear in book B, so the similarity would always be zero. “Individual,” maybe? Or “distinct?”

  3. 3
    eintown says:

    ReMines is not quite correct. The analogy does not fit. He compares the smallest units of meaning (words) between the books. However nucleotides are not being compared between organisms – rather genes. So for his analogy to be correct, one would compare strings of words – or concepts – between the books.

    Pogge is however correct. Tiny differences – between genes – or directions – can make huge differences.

  4. 4
    scordova says:

    However nucleotides are not being compared between organisms – rather genes.

    Thank you for your comment.

    I believe Walter was referring to genes as words and nucleotides (or even nucleotide triplets) as letters. So I beleive Walter’s analogy is correct.

    Does that seem reasonable?

  5. 5
    tribune7 says:

    Good post, Sal.

  6. 6
    eintown says:

    Hmm, that is better, but the analogy is not very effective.

    If I take 2 books about how to play sports – one on soccer and another on rubgy, they will have, 99% alignment. However the outcome – i.e. once the books are read practiced- 2 very different games are played. It’s misleading to say that the two books are 99% the same. The structure, maybe, but not the content.

    Its the same thing with genetic similarity. 99% is very similar, but there are differences.

  7. 7
    scordova says:

    Eintown,

    I understand your specialty is in molecular biology. Can you describe a little bit about sequence alignments.

    Do we have to do considerable amount of sequence alignment between chimps genomes and human genomes versus comparing two human genomes to each other?

    Isn’t comparing two human genomes more like comparing two versions of the same book?

    Whereas comparing chimp and human genomes involves quite a bit of realignments, like Walter suggested.

    Thanks.

    Sal

  8. 8
    eintown says:

    I don’t have extensive experience with complicated alignments. I usually work on simple intra-specie genomes.

    When doing alignments, you can’t really take an entire genome and align it with another. That would require way too much computer power. Instead, the genomes are spliced up and those bits are aligned, which is far less computationally intensive.

    Generally when comparing genomes, one looks at highly conserved regions. As the regions are highly conserved, there will be little change over time. If there is a lot of change, the 2 organisms are evolutionary distant (i.e. diverged a while ago); a little change, would show a more recent time of divergence.

  9. 9
    scordova says:

    When doing alignments, you can’t really take an entire genome and align it with another. That would require way too much computer power. Instead, the genomes are spliced up and those bits are aligned, which is far less computationally intensive.

    Which is like comparing words between books, and a lot less like comparing paragraphs and chapters.

    However, with intra-species comparison, do we have these same problems with alignment.

    I would presume we could compare entire chromosomes of linkgage blocks between humans, say hundreds of millions of base pairs at a time versus individual genes (with about 1200 base pairs). Thus comparing between members of the same species (like human to human) is more like being able to compare entire chapters.

    Is this correct?

    Thank you again for your comments. We don’t have enough biologists at UD, most are engineers like me….

  10. 10
    scordova says:

    For starters,

    I posted here:
    Humans only 94% similar to chimps, not 98.5%

    Homo Sapein Genome size = 3,4000,00,000
    Pan Troglodytes= 3,577,500,000

    That is technically a difference of 177,500,000.

    3,577,500,000 / 3,400,000,000 -1 = 5.2%

    That figure is 10 times larger than the supposed 0.5% difference suggested in some literature.

    And Rick noted:

    Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes.

  11. 11
    Green says:

    A good point that Casey Luskin makes about human chromosome 2 and how it is a fusion of two chimp chrosmomes (2a and 2b) is this:

    Humans may have begun with 48 chromosomes, and undergone a chromosomal fusion *within* the human lineage.

    This has happened in mice, and horses. Mice generally have 40 chromosomes, but some populations have undergone a chromosomal fusion and now have 38 chromosomes. Other races of mice have as low as 22. The same goes for different breeds of horses.

    So our fused chromosome 2 is equally compatible with comon ancestry as it is uncommon ancestry.

  12. 12
    Green says:

    N.b. that our fused chromosome 2 has similar contents to two of the chimp chromosomes doesn’t say a lot when you consider that we are 90 odd percent identical.

  13. 13
    eintown says:

    Which is like comparing words between books, and a lot less like comparing paragraphs and chapters.

    No, its not. Comparing words is analogous to comparing nucleotides. Comparing ideas in a book is analogous to comparing genes.

    Also what you were saying about linkage blocks and genome lengths. The position of genes does not have as much affect that the sequence of the genes.

    Also, the coding parts of the genome are very important for alignment and similarity. Parts of the genome that do not have a function will accumulate random mutations over time, so conserved regions (i.e. coding regions) are more useful, as there is a constraint to changes.

  14. 14
    Nakashima says:

    I don’t understand why Dr Sternberg bothers having this conversation in the first place, unless his correspondent is extremely good looking. He could have simply stated that from an ID perspective, no one doubts the common descent of humans and simians, and the details are being worked out. Is he actually trying to argue that the ITSs observed in different species are designed artifacts? That would seem to be a testable prediction.

  15. 15
    eintown says:

    sorry about the italics!

    Also, Nakashima is correct… I thought ID is OK with common descent?

  16. 16
    PaulN says:

    Sure ID is compatible with common descent, but not exclusively.

    Obviously another pursuit of high interest would be common design among species that share similarities at the phenotype and genotype level. Of course this pursuit requires a fundamentally different perspective from all of the presuppositions that build the explanatory framework for common descent. The first step in doing so would be to realize that there’s more than one way to explain similarities between species, including but not limited to genetic engineering and artificial selection where intelligence is guiding the process. Also quantifying the testable and observable physical/chemical limits to RM+NS and other naturalistic processes would serve to bolster this proposition.

  17. 17
    eintown says:

    genetic engineering and artificial selection where intelligence is guiding the process

    How precisely would test for this?

  18. 18
    PaulN says:

    I assume that if we were to gain higher understanding of the syntax and logic used in the highly specified multi-dimensional genetic code that we see in organisms, including how the code itself could possibly be standardized(Such as the assembly language used in HMIs for example), then we’d be that much closer to a solid conclusion for a design inference. But again we’re just now discovering layers of the code that were never even conceivable before, and were initially written off as vestigial junk. Once we truly understand from every angle how the code is integrated within biological systems, then I’m sure we could positively quantify the plausibility of common descent vs. common design.

    From my own perspective, every single further discovery we make is moving the goalposts closer for common design. I do however feel that the philosophical bias within purely naturalistic thinking is retarding this process, kind of like trying to look for a field of daisies within the heart of a volcano, and shutting out anyone who advises that you won’t find them in there.

  19. 19
    eintown says:

    So… the answer is, normal scientists will continue working and as more information about biology comes to light, the more it reinforces ID.

  20. 20
    Nakashima says:

    Mr PaulN,

    Sure ID is compatible with common descent, but not exclusively.

    Are you saying that ID does not (cannot) make a prediction that would falsify either special creation or common descent?

    Judging from his editorial position on Meyer’s survey in the Proceedings of the Biological Society of Washington (repudiated), it seems clear that Dr Sternberg accepts the reality of deep time and common descent. If he was just advocating baraminology, not ID, why would the DI publish this blog entry?

  21. 21
    derwood says:

    Hello Sal,

    While the human and chimp genomes are not the exact same size, it is also true that any two human genomes are not the exact same size. In addition to indels producing genome size differences, gene copy numbers and similar such issues also affect the relative lengths. A 2007 paper, for example, found that the human genomes they were examining differed from each other by some 12 million nucleotides – and that is referring to the ‘lengths’ of the genomes and does not count things like SNPs and such.

    So, your statement:

    3,577,500,000 / 3,400,000,000 -1 = 5.2%

    That figure is 10 times larger than the supposed 0.5% difference suggested in some literature.

    does not take such things into account, and it not really relevant. For starters, indels are one-time events, regardless of their size. That is, it is possible for there to be, say, a deletion of 1,000 nucleotides in one genome which was the result of a single replication error. The absolute number of nucleotides between two genomes is therefore not a very meaningful number, especially when one considers the differences within a species as indicated above.


    Whereas comparing chimp and human genomes involves quite a bit of realignments, like Walter suggested.

    How much is “quite a bit”? And what is getting ‘realigned’?

    If you reproduced ReMine’s statement accurately, I’d say it is highly misleading. There is no “creating an alphabetical listing of all the unique words in each book, and then comparing the lists of unique words derived from each book. It would be really easy then to use these lists to argue: “see the books are 99.5% identical!”

    As written, the statement appears to imply that when doing such analyses, it is necessary to ‘rearrange’ the loci in order to maximize homology. This is not the case.
    A more accurate analogy/metaphor might be that it is like taking two books, comparing them, and realizing that while one of them seems to be missing a few pages, and some of the paragraphs within the chapters are not quite the same, and some of the words have weird spellings that the other book does not have, the books are, when we can directly compare them word for word, are 99.5% identical.
    While if we do a ‘word count’ we can see that the discrepency seems more substantial than that, when we look at the words in context, we can see that much of the “misalignment” is due to printer errors – see here half of one chapter is missing in one book.

    Well, I’m not much for analogies, but maybe you can get the picture.

    However, with intra-species comparison, do we have these same problems with alignment.

    The short answer is Yes. There is a species (of guinea pig, if I remember correctly), for example, which maintains different karyotypes within their populations. Trying to ‘align’ them would produce entire missing chromosomes with many many millions of nucleotide differences, were we to merely do an alignment as ReMine seems to suggest.

    PaulN writes:
    But again we’re just now discovering layers of the code that were never even conceivable before, and were initially written off as vestigial junk.

    Written off by whom? When one bothers to look beyond the sound bites and assertions of the supposed abandonment of “junk DNA” by “materialists”, one sees that, in fact, it was those very folk who did the research hypothesizing and discovering the functionin some of this ‘junk’, dating back to early 1970s.
    Besides postdictions presented as predictions, I am unaware of any actual research done by any non- or anti-evolutionists on any such material. Perhaps I am wrong.

  22. 22
    derwood says:

    PaulN:

    Sure ID is compatible with common descent, but not exclusively.

    Since, in your eyes, ID is “compatible” with common descent, at what point does ID no longer allow for naturalistic evolution?

    I assume that common descent as such would not require ID action?

  23. 23
    PaulN says:

    Eintown,

    So… the answer is, normal scientists will continue working and as more information about biology comes to light, the more it reinforces ID.

    Yes and no. Yes in the sense that new breakthroughs and discoveries in highly specified information will reinforce ID. No in the sense that any of said “normal” scientists will explicitly give any credence to this idea, and will further reshape their own explanations of the data to fit a philosophically naturalistic world view, regardless of how uncomfortably it fits.

    Nakashima,

    Are you saying that ID does not (cannot) make a prediction that would falsify either special creation or common descent?

    Well considering the lengths some go to in order to cater towards a neutral position on this, it’s hard to say, as I don’t speak for people like Dr. Dembski or Dr. Sternberg. However, I personally feel that the methodology embedded within ID will play a critical role as new information is discovered in falsifying common descent, especially considering the empirical observations on the limitations of mutation in creating novel complex specified information and consequent function. This in addition to Dr. John C. Sanford’s observations in “Genetic entropy” make it much harder to believe that such similarities between species were evolved via Darwinian processes. However if such similarities were expressed due to front-loaded information within the genome of the ancestral species, then that would be a different, yet ID compatible story altogether.

    Judging from his editorial position on Meyer’s survey in the Proceedings of the Biological Society of Washington (repudiated), it seems clear that Dr Sternberg accepts the reality of deep time and common descent. If he was just advocating baraminology, not ID, why would the DI publish this blog entry?

    My views on common descent vs. common design are my own, and I don’t speak for Dr. Sternberg or any other IDer for that matter. My reasons for believing the case for common design are due to the studies and research that I’ve personally followed up to this point in my own life. While I respect Dr. Sternberg’s views on common descent, I believe that the concepts of ID itself conditionally support common design and common descent alike until more definitive evidence is discovered. However my adherence to common design is mostly sourced from complimentary(to ID that is) studies carried out by creationists such as John C. Sanford among others.

  24. 24
    PaulN says:

    Derwood,

    Since, in your eyes, ID is “compatible” with common descent, at what point does ID no longer allow for naturalistic evolution?

    There are explanations within ID framework that involve the entire evolutionary course of any given species having been front loaded with all of the necessary information for such changes from the start, allowing for the unraveling and expression of such pre-existing information over the given timespan.

    I assume that common descent as such would not require ID action?

    Only initially, following what I explained above.

  25. 25
    derwood says:

    Green writes:

    So our fused chromosome 2 is equally compatible with comon ancestry as it is uncommon ancestry.

    Luskin’s point was a red herring. The chromosonmal fusion has NEVER been presented as evidence for a speciation event, it has always been presented, as far as I know, to explain why we have differing karyotypes.

    PaulN:

    There are explanations within ID framework that involve the entire evolutionary course of any given species having been front loaded with all of the necessary information for such changes from the start, allowing for the unraveling and expression of such pre-existing information over the given timespan.

    I’ve read such ‘front-loading’ claims, but have yet to see any evidence that convinces me that they have merit.

    me:
    “I assume that common descent as such would not require ID action?”

    Paul:

    Only initially, following what I explained above.

    Indeed, and when evidence for such a scenario is established, I’ll give it some thought.

  26. 26
    PaulN says:

    Either way, I answered your questions. Whether or not you feel these explanations are currently worthy of your attention is a different story altogether. As I said, I don’t hold front-loaded or common descent positions myself, but it is of no detriment to me if these pursuits are followed by genuine scientific inquirers. I see nothing wrong with theorizing and speculating about such concepts and any consequent evidentiary research that would therefore ensue, but I do have the capability to properly(at least to the best of my knowledge) convey, represent, and endorse scientific ideas that I don’t necessarily agree with. I do see something wrong with research on these pursuits being limited(whether explicitly or implicitly) by those who’s world views are in disagreement however.

  27. 27
    derwood says:

    It seems to me that the Biologic Institute fellows and researchers should have no impediments in churning out valid scientific research premised on their supernaturalistic mindframe. If they produce valid results that explicitly support their ID position, so be it. I reserve the right to be skeptical, however, if the best that can be done is for such research to indicate that the results are ‘compatible’ with design/creation.

  28. 28
    beelzebub says:

    Particularly when every possible empirical finding is compatible with design.

    Q. Why does it appear that [insert observation here]?

    A. Because God the Designer made it that way.

  29. 29
    beelzebub says:

    “God” is supposed to be in strikethrough above. It worked in the preview window.

  30. 30
    Upright BiPed says:

    Belzip – “Particularly when every possible empirical finding is compatible with design.”

    Now that you have established the criteria you look for, can you please give us a list of what findings have been uncovered that are not comapatible with materialism?

  31. 31
    Khan says:

    Upright,

    Now that you have established the criteria you look for, can you please give us a list of what findings have been uncovered that are not comapatible with materialism?

    none. I could think of a few that would be incompatible with materialism (miracles), but no concrete evidence for them has surfaced thus far. so while there are findings that would contradict materialism, there are none that would contradict design.

  32. 32
    Upright BiPed says:

    Khan, any (at least conceptual) pathway that would give chance a chance in organizing dicreet chemical objects within the structure of a living system…or perhaps coordinating a symbol system…would falsify design.

    And, you already know this.

  33. 33
    Upright BiPed says:

    And, thank you for addressing the idea that materialism conforms to all observations (including the ones it cannot hope to explain).

  34. 34
    Mapou says:

    Khan @31:

    I could think of a few that would be incompatible with materialism (miracles), but no concrete evidence for them has surfaced thus far. so while there are findings that would contradict materialism, there are none that would contradict design.

    Well, I can think of a future discovery that could potentially falsify both design and materialism. Suppose we found that the entire history of the physical universe was recorded in 4-dimensional space and that we could go back and read this recording. We could then see things exactly as they happened and correct our theories and hypotheses.

    Now you may say that this is highly unlikely (your opinion, of course). But I would respond, as opposed to what? miracles?

  35. 35
    Upright BiPed says:

    Khan. these are the questions asked of Belzip that he has seen fitr to ignore. You are certainly wlecome to adress them:

    To attack the physical evidence against materialism you have to address the actual issue:

    1) Is Life functionalized by a physically-inert symbol system of information embedded into living tissue that builds, organizes, and coordinates discreet chemical objects and activities?

    2) Chance has been observed to only operate at maximum uncertainty (this is the very definition of chance). Does any individual chance result ever lead to the next chance result not operating at maximum uncertainty?

    3) What aspect of a mechanism that only repeats maximum uncertainty is expected to not only build complex discreet objects, but to organize and coordinate those discreet objects into a complex functioning whole?

  36. 36
    beelzebub says:

    Upright Biped wrote:

    Khan, any (at least conceptual) pathway that would give chance a chance in organizing dicreet chemical objects within the structure of a living system…or perhaps coordinating a symbol system…would falsify design.

    No, because any structure that could arise via chance and necessity could also be produced de novo by a sufficiently powerful and intelligent agent.

    Even Dembski recognized that false negatives are inevitable for this reason.

    Design in the abstract is not falsifiable. It only becomes falsifiable if certain restrictions and constraints are placed on it (as in the case of the YEC God, which has been resoundingly falsified).

  37. 37
    Khan says:

    Upright,

    here’s a link to a conceptual pathway. now, by the standards you just set up, is design falsiifed?

    http://www.biology-direct.com/content/2/1/24

  38. 38
    Mapou says:

    beelzebub @36:

    No, because any structure that could arise via chance and necessity could also be produced de novo by a sufficiently powerful and intelligent agent.

    So, you’re admitting that evolution is not falsifiable.

  39. 39
    beelzebub says:

    No. The converse of my statement would have to be true in order to draw the conclusion that evolution is not falsifiable.

  40. 40
    beelzebub says:

    Uptight Biped asks:

    Is Life functionalized by a physically-inert symbol system of information embedded into living tissue that builds, organizes, and coordinates discreet chemical objects and activities?

    If you are trying to ask whether life contains information processing systems, the answer is yes. If you are asking whether such systems are incompatible with materialism, the answer is no.

    2) Chance has been observed to only operate at maximum uncertainty (this is the very definition of chance). Does any individual chance result ever lead to the next chance result not operating at maximum uncertainty?

    You’re not new to the evo wars, are you, Upright? How many hundreds of times has it been explained to you that evolution does not operate purely by chance?

    3) What aspect of a mechanism that only repeats maximum uncertainty is expected to not only build complex discreet objects, but to organize and coordinate those discreet objects into a complex functioning whole?

    Ditto. Modern biologists do not think that evolution “only repeats maximum uncertainty”, and neither did Darwin.

    It’s time to give up that strawman, Upright.

  41. 41
    Mapou says:

    beelzebub @38:

    No. The converse of my statement would have to be true in order to draw the conclusion that evolution is not falsifiable.

    I don’t think so. If you cannot perform an experiment to distinguish between chance/necessity on the one hand and design by a sufficiently powerful designer on the other, how is evolution falsifiable? And the same goes for ID.

    If your statement @36 is true, then neither ID nor evolution is falsifiable, at least not in the forseeable future.

  42. 42
    beelzebub says:

    Mapou,

    Here’s my original statement:

    Any structure that could arise via chance and necessity could also be produced de novo by a sufficiently powerful and intelligent agent.

    Here’s the converse:

    Any structure that could be produced de novo by a sufficiently powerful and intelligent agent could also arise via chance and necessity.

    These are distinct statements with independent truth values.

    The original statement is true, which is why the hypothesis of an unconstrained designer is unfalsifiable.

    The converse is false, which is why evolutionary theory is falisifiable.

    All things are possible with an unconstrained designer. Many things are out of evolution’s reach. The latter is falsifiable, but the former is not.

  43. 43
    Mapou says:

    beelzebub @41:

    Here’s my original statement:

    Any structure that could arise via chance and necessity could also be produced de novo by a sufficiently powerful and intelligent agent.

    Why is this so hard to understand? If you cannot demonstrate via a specified experiment or a logical argument that any structure could not have been produced by a sufficiently powerful designer, your hypothesis that it did arrive by chance and necessity is not falsifiable. That’s simple logic, no?

    All things are possible with an unconstrained designer.

    Precisely. If your original statement is true (I disagree with it, BTW, even though I am a Christian), neither ID nor evolution is falsifiable unless you had access to the past history of the universe.

  44. 44
    beelzebub says:

    Mapou asks:

    Why is this so hard to understand?

    My question exactly.

    If you cannot demonstrate via a specified experiment or a logical argument that any structure could not have been produced by a sufficiently powerful designer, your hypothesis that it did arrive by chance and necessity is not falsifiable. That’s simple logic, no?

    That’s completely wrong.

    A hypothesis H is falsifiable if there is (at least in principle) an observation that would show H to be false. If no such observation is possible, then H is not falsifiable.

    The hypothesis of an unconstrained designer is not falsifiable, because there is no conceivable observation that would show it to be false. Any possible observation could be accommodated by simply stating “the designer did it that way.”

    Evolutionary theory is falsifiable, because there are millions of conceivable observations that would show it to be false. If you show me a normal E. coli cell spontaneously mutating and dividing into two giraffe zygotes, you have falsified evolutionary theory.

  45. 45
    scordova says:

    derwood wrote:

    That figure is 10 times larger than the supposed 0.5% difference suggested in some literature.

    does not take such things into account, and it not really relevant

    Thank you for your comment, however, I would argue that the figure of size is relevant in that it emphasizes the 99% identity isn’t what it may appear to most.

    The 5% difference (of extra base pairs) is just tossed out. If we toss out differences, of course the supposed identity numbers will be misleadingly inflated.

    We really don’t know that those extra base pairs are junk after all, do we.

    And even if they are junk, we still have the nasty problem of how 177,500,000 base pairs got fixed into a population. How does 177,500,000 base pairs of junk get fixed in a population?

    I wouldn’t be too quick to presume random drift could be a good explanation for such a large amount of base pairs.

  46. 46
    Upright BiPed says:

    If you are trying to ask whether life contains information processing systems, the answer is yes. If you are asking whether such systems are incompatible with materialism, the answer is no.

    Apparently so, and by nothing more than edict alone…since neither you, nor any other person on the surface of this planet, can address the observable evidence at the level of the details in such a system.

    You’re not new to the evo wars, are you, Upright? How many hundreds of times has it been explained to you that evolution does not operate purely by chance?

    The funny man. 1) Evolution has absolutely nothing to do with it. Evolution, in all its grand glory and enumerable possibilities, only operates on what is already there. Well (psssst)…at one time there was nothing already there…leaving nothing but chance to deliver the goods. 2) Does any single chance event lead to the next chance event not operating at maximum uncertainty? If not, then how does the complex organization and coordination of discreet physical objects come about? How do discreet physical objects agree to the meaning of symbols as the information is passed between them? Is it by chance? Try it and let me know how well it works.

    Hey, let’s try it right now, what does hgb fy dtajd n, fjfy sbn 009 nf hft sb mei uwsg dvfy5yhd fij mean to you?

    Ditto. Modern biologists do not think that evolution “only repeats maximum uncertainty”, and neither did Darwin.

    This is a cheap deflection away from the observable facts. 1) Modern biologists never address the question…and 2) Darwin himself was stupid to the evidence. This is the guy that thought life was made up of amorphous clumps of protoplasm. Gimme a break. Imagine in 2009 you suggesting that Darwin as an authority on biology. (Can you say poof?)

    It’s time to give up that strawman, Upright.

    Sure, why not?

  47. 47
    Mapou says:

    beelzebu @43:

    That’s completely wrong.

    I beg to differ for reasons that I have already explained. At any rate, this horse is dead from my perspective. I don’t have any particular need to beat it into a pulp. See ya.

  48. 48
    scordova says:

    eintown wrote:

    Also what you were saying about linkage blocks and genome lengths. The position of genes does not have as much affect that the sequence of the genes.

    I appreciate your comment, however that wasn’t the point I was trying to make.

    The point was that if we consider the architecture of the non-coding regions, then isn’t it much harder to argue for 99.5% identity between chimps and humans. For starters we have those extra 177,500,00 base pairs that are usually unaccounted for in pouplarized comparisons.

    I don’t know that we have any standard methodology for comparing the identity of the non-coding regions between chimps and humans. What figure would we come up with?

    Yes it is true we have large “conserved” non-coding regions between mice and men, but how do we characterize the total divergence in non-coding regions? I’ve shown the amount is at least 5%.

  49. 49
    scordova says:

    Derwood wrote:

    However, with intra-species comparison, do we have these same problems with alignment.

    The short answer is Yes. There is a species (of guinea pig, if I remember correctly), for example, which maintains different karyotypes within their populations. Trying to ‘align’ them would produce entire missing chromosomes with many many millions of nucleotide differences, were we to merely do an alignment as ReMine seems to suggest.

    Thank you for that comment. That was very informative. I was not aware of issues with guinea pigs.

  50. 50
    Mapou says:

    scordova @10:

    Homo Sapein Genome size = 3,4000,00,000
    Pan Troglodytes= 3,577,500,000

    That is technically a difference of 177,500,000.

    Should we be counting genes or bases? I note that homo sapiens has 11,953,879,540 bases whereas Pan Troglodytes has only 533,669,351. That is a huge difference by ant measure.

    By comparison, wheat has 16,978,500,000 genes but only 349,010,415 bases. This complicates any comparison formula, does it not?

  51. 51
    scordova says:

    Rick wrote:

    How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique “suborganelle” — for the lack of better term — at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations.

    I try to outline all the functions of telomeric repeats, but my friend tells me that I am getting off the subject.

    He wants to me to focus on the ITSs, the tracks of the hexamer TTAGGG that reside within chromosome arms or around the centromere, not at the ends. I tell him that I was just coming to that topic. The story, you see, is that in the lineage leading up (or down, I forget which) to chimps and humans, a fusion of chromosome ends occurred — two telomeres became stuck together, the DNA was stitched together, and now we find the remnants of this event on the inside of chromosomes. And to be fair, I concede at this point that the 2q13 ITS site shared by chimps and humans can be considered a synapomorphy, a five-dollar cladistic term meaning a genetic marker that the two species share. As this is said, it is apparent that the countenance of my acquaintance lightens a bit only to darken a second later. For I follow up by saying that of all the known ITSs, and there are many in the genomes of chimps and humans, as well as mice and rats and cows…, the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates (Farré M, Ponsà M, Bosch M. 2009. “Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates,” Cytogenetic and Genome Research 124(2): 128-131.). In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed.

    Does anyone disagree with this?

  52. 52
    beelzebub says:

    Mapou wrote:

    I beg to differ for reasons that I have already explained.

    And as I have explained, the reasons you gave were incorrect.

    Don’t take my word for it. Read about it so that you can use the concept correctly the next time around.

  53. 53
    Mapou says:

    PS. My source is the link that you provided in a parallel thread. Am I reading the numbers wrong?

  54. 54
    Mapou says:

    beelzebub @51:

    And as I have explained, the reasons you gave were incorrect.

    In your opinion, of course.

  55. 55
    scordova says:

    PS. My source is the link that you provided in a parallel thread. Am I reading the numbers wrong?

    I believe the “bases” are the number that are actually studied and recorded. Notice the number of “bases” per year is increasing, so this must be the number that is in the database, not necessarily in the genome.

    Does any have a different interpretation than mine?

    Thanks in adavance.

  56. 56
    beelzebub says:

    Upright Biped wrote:

    Evolution, in all its grand glory and enumerable possibilities, only operates on what is already there. Well (psssst)…at one time there was nothing already there…leaving nothing but chance to deliver the goods.

    You’ll need to express yourself more clearly, Upright. Are you talking about the origin of life? If so, then surely you recognize that the earth’s primordial environment and the laws of physics amount to more than “nothing but chance.”

    How do discreet physical objects agree to the meaning of symbols as the information is passed between them?

    They don’t have to come to an agreement on anything. They just follow the laws of physics. Surely you don’t think there’s anything magical going on in your liver right now as cells divide, grow and die, do you? Nobody’s in there assigning meaning to symbols.

  57. 57
    vjtorley says:

    scordova

    Does anyone disagree with this?

    Sal, I’m not a biologist, so I hope you’ll be patient with me if I’m a little slow to comprehend certain points in Dr. Sternberg’s argument.

    First of all, I can’t see why the fact that ITSs usually don’t square up with evolutionary breakpoints weakens their significance as arguments for common descent (which, of course, is quite a different thing from arguing for natural selection as the driving force of evolution). For the mere fact that ITSs exist at all is what needs explaining here. What are they, if not relics of a past in which the ancestral form had a different number of chromosomes? And if there happens to be a genetically similar species, still living today, with the same number of chromosomes as the ancestral form of the species exhibiting the ITS, then isn’t that strong prima facie evidence that the two species share a common ancestry? Or am I missing something here?

    Second, I wasn’t able to access the article by Farre, Ponsa and Bosch, but it might interest readers to know that even for humans and chimps, the chromosome 2 fusion event did not occur at an evolutionary breakpoint, according to this paper at http://genome.cshlp.org/content/17/10/1420.full . An extract:

    Based on a speciation event 6 million yr ago (Mya), we estimate the fusion date at 0.74 Mya with a 95% confidence interval 0–2.81 Mya. This finding argues against the hypothesis that this fusion was the speciation event that separated the human and chimp lines (Navarro and Barton 2003).

    In other words, the fusion event almost certainly took place less than 2.81 million years ago, whereas the chimp-human split occurred around 6 million years ago.

    Third, it occurred to me that the fusion event might coincide with the emergence of Homo ergaster (roughly, the African form of Homo erectus) approximately 1.9 million years ago. The emergence of this species remains a mystery, as two paleoanthropologists writing in Nature have noted:

    [Early forms of erectus] mar[k] such a radical departure from previous forms of Homo (such as H. habilis) in its height, reduced sexual dimorphism, long limbs and modern body proportions that it is hard at present to identify its immediate ancestry in east Africa. Not for nothing has it been described as a hominin “without an ancestor, without a clear past”

    (Robin Dennell & Wil Roebroeks, “An Asian perspective on early human dispersal from Africa,” Nature, Vol 438:1099-1104 (Dec. 22/29, 2005)

    On the basis of the current state of the evidence, we should remain skeptical of the view that natural selection alone can account for the emergence of Homo erectus (or more precisely, Homo ergaster) from its unknown hominin ancestor.

    Finally, would someone be kind enough to explain the following sentence in the last paragraph of Dr. Sternberg’s scintillating and excellently written essay?

    My rejoinders are, simply, that ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered — literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots.

    I’m sorry, but I don’t understand what this means. Is Dr. Sternberg saying that the ITSs in chromosome 2 (a) have a biological function; (b) are non-vestigial; or (c) both?

  58. 58
    Nakashima says:

    Mr Vjtorley,

    When I read that last sentence of Dr Sternberg, it seems to me that he is arguing that ITSs are designed artifacts with specific actual functions, they just look like old fusion points.

    Mr Cordova,

    I just came across this article today, linked from the Not Exactly Rocket Science blog, on retroviruses in the chimp genome. perhaps this helps explain how such a large number of bases gets added – entire viral genomes added over and over again.

  59. 59
    scordova says:

    First of all, I can’t see why the fact that ITSs usually don’t square up with evolutionary breakpoints weakens their significance as arguments for common descent

    I don’t think Rick was specifically criticizing common descent, but rather the supposed 99% identity.

    He references an argument used in favor of common descent, namely, the ITSs, but then points out that most of the ITSs (or where they are located) are not that similar.

    Hence, he reinforces the point that the 99% identity is an artifact of what one is deciding to compare. If instead of comparing genes, we compared the locations of ITSs, we wouldn’t expect 99% identity.

    That said, it would seem that Rick would argue, even if common descent were true, that ITSs would not be a legitimate argument in favor of common descent of the humans and chimps.

    The argument specifically for chimp human ancestry ( as opposed to say, gorilla human ancestry) would have to come from other lines of reasoning than ITSs.

  60. 60
    Upright BiPed says:

    Belzip,

    You’ll need to express yourself more clearly, Upright. Are you talking about the origin of life? If so, then surely you recognize that the earth’s primordial environment and the laws of physics amount to more than “nothing but chance.”

    Okay.

    1) Is Life functionalized by a physically-inert symbol system of information embedded into living tissue that builds, organizes, and coordinates discreet chemical objects and activities?

    2) Chance has been observed to only operate at maximum uncertainty (this is the very definition of chance). Does any individual chance result ever lead to the next chance result not operating at maximum uncertainty?

    3) What aspect of a mechanism that only repeats maximum uncertainty is expected to not only build complex discreet objects, but to organize and coordinate those discreet objects into a complex functioning whole?

    And this time, try to make your answer more pertinent to the questions asked. No more poof, okay?

    They don’t have to come to an agreement on anything. They just follow the laws of physics. Surely you don’t think there’s anything magical going on in your liver right now as cells divide, grow and die, do you? Nobody’s in there assigning meaning to symbols.

    This may come as a shock to you, but the convention by which information is passed from nucleotide to effect is not contingent upon physical law.

    This fact is supported by direct experimentation.

    Physical law has nothing to do with the existence of the code, nor the information transferred from it.

  61. 61
    vjtorley says:

    Sal and Mr. Nakashima:

    Thanks to both of you for clarifying Dr. Sternberg’s argument.

  62. 62
    Frost122585 says:

    Sal,

    The argument that human beings are even 90% similar to chimps is absurd. You can look at chimps and see there is a huge physical and aesthetic gap. Then if you look at cognitive ability- as exemplified by impact on environment- you have one class eating bananas in a cage or perhaps tree and other is flaying spaceships to the moon.

    How about this analogy.

    These two numbers are 90% identical…

    1999999999
    and
    9999999999

    Right?

    Whenever I hear “apes are 99% human” I put that in the metal folder right next to the story about “bat boy lives”.

  63. 63
    scordova says:

    I’m sorry, but I don’t understand what this means. Is Dr. Sternberg saying that the ITSs in chromosome 2 (a) have a biological function; (b) are non-vestigial; or (c) both?

    I vote for (a).

    Can something be vestigial and functional at the same time?

    from wiki:

    Vestigiality describes homologous characters of organisms which have seemingly lost all or most of their original function in a species through evolution.

    The definition of vestigiality is suspect. How can we empirically declare what the original function was?

    But consider this, if the ITSs that are different between chimps and humans are functional, how can we possibly argue that ITSs are evidence for similarity.

    I may use words that are identical to the words other writers use, but how the words are used distinguishes me from others. That is the issue iwth ITSs. They are literally spelled the same way “TTAGGG”, but their usage is diffent in Chimps and Humans. How can we say we’re really that identical except to say that “TTAGGG” is spelled the same way. But this is like saying I spell the word “the” the same way as William Shakespeare. It would be a mistake to say William Shakespeare’s writings are 100% identical to mine based on the fact we spell one word the same way. The same would thus be true of ITSs.

    Two ropes made of identical material may be knotted in diffent ways that are functionally significant. This is the issue with things like quadraplex DNA and ITSs. To ignore the knotting is to ignore a significant informational, heritable, functional feature. The way the knot is tied is significant, and from a biophysics standpoint, the “TTAGGG” spelling makes the knots feasible.

    How do such functions evolve?

    There are limits to how many things natural selection can be fixing into a population simulatneously.
    If we are confronted with enough differences, they will be well beyond the population resources available to fix these traits into a population. This is Haldane’s dilemma.

    The more functional difference we find, the more difficult it will be to explain it through natural selection because of Haldane’s dilemma.

  64. 64
    scordova says:

    Sal,

    The argument that human beings are even 90% similar to chimps is absurd. You can look at chimps and see there is a huge physical and aesthetic gap. Then if you look at cognitive ability- as exemplified by impact on environment- you have one class eating bananas in a cage or perhaps tree and other is flaying spaceships to the moon.

    How about this analogy.

    These two numbers are 90% identical…

    1999999999
    and
    9999999999

    Right?

    Whenever I hear “apes are 99% human” I put that in the metal folder right next to the story about “bat boy lives”.

    A very eminent scientist agrees with you:

    man cannot be understood by laws applicable to other mammals whose brains hae a very similar physiology….

    The emergent feature of man have, in one form or another, been discussed by numerous anthropologists, psychologists, and biologists. >It is part of the empirical data tha cannot be shelved just to preserve reductionist purity….Primates are different from other animals, and human beings are very different from other primates.

    We now understand the troublesome features in a forceful commitment to uncritical reductinism as solution to the problem of mind.

    ….

    What emerges from all this is the return of “mind” to all areas of scientific thought. This is good news from the point of view of all varieties of natural theology. For a universe where mind is a fundamental part of reality more easily makes contact with the mind of god than does a mindless world.

    Harold Morowitz
    page 280
    Cosmic Joy

    Ironically for all these amazing statements, Morowitz is staunchly opposed to ID, despite the fact his own writings state:

    the return of “mind” to all areas of scientific thought. This is good news from the point of view of all varieties of natural theology. For a universe where mind is a fundamental part of reality more easily makes contact with the mind of god than does a mindless world.

  65. 65
    eligoodwin says:

    There are plenty of examples of vestigial organs whose former function is known–two famous examples: whales having hip bones and hind limbs during development and snakes having pelvic bones.

  66. 66
    scordova says:

    There are plenty of examples of vestigial organs whose former function is known–two famous examples: whales having hip bones and hind limbs during development and snakes having pelvic bones.

    eligoodwin,

    But how can one actually know that these structures were actually functioning as hip bones and hind limbs? This is like pointing to male nipples and saying they were used to feed the young. One does not formally know that for sure.

    Male Nipples

    Darwin proposed that male mammals once shared the job of providing milk to their young. It’s delightful conjecture, and not unreasonable, but it remains in the realm of just-so stories because (so far) there is no way to test its validity. If the story were true, you might expect the most anatomically primitive mammals – monotremes such as the duck-billed platypus and echidna – to have males with more highly developed nipples. In fact, we see the opposite: monotremes – male and female – have no nipples at all (but the females still lactate, expressing milk via little pores in the skin). I’m only aware of a couple mammal groups in which the female has nipples and the male doesn’t (a feature we might call “mammillary sexual dimorphism”): horses and rodents. If male nipples are on their way out, they sure are tenacious.

    Whether or not male nipples are a relic of evolution, they are almost certainly a relic of development. In the earliest weeks following conception, the male and female embryo follow a virtually identical developmental trajectory.

    I’m not saying the whale bone is not vestigial, but you can’t formally argue it without admitting some speculation, just like Darwin speculating on male nipples.

    The reason I call the idea of vestigial organs suspect, is that we’ve had a bad history of misinterpreting function.

  67. 67
    beelzebub says:

    Upright,

    Having a dialogue requires more of you than simply repeating your questions verbatim after I’ve already answered them.

    Regarding the genetic code, you seem to believe that if more than one code is physically possible, then the code in use could not have arisen naturally. Why do you think that? What principle would be violated in such a case?

  68. 68
    Green says:

    Sorry this is a bit out of sinc with the discussion – I couldn’t get to my pc last night.

    But jumping back to the fusion event of human chromosome 2, I pointed out that this doesn’t compel belief in common ancestry, since humans may have begun with 48 chromosomes and undergone a fusion *within* the human line.

    derwood writes:

    Green writes:

    So our fused chromosome 2 is equally compatible with comon ancestry as it is uncommon ancestry.

    Luskin’s point was a red herring. The chromosonmal fusion has NEVER been presented as evidence for a speciation event, it has always been presented, as far as I know, to explain why we have differing karyotypes.

    But derwood, nowhere did Luskin claim that it caused the speciation event. In fact, I think in recent podcast, he affirmed that it *didn’t*. Likewise, nor did I say that it caused the speciation event.

    We have evidence today that fusion events DON’T cause speciation events (e.g. different BREEDS of horse, and different RACES of mice).

    This is good evidence for the idea that chromosomal fusion events happen fairly commonly (without adverse effects) *within* species. Thus it is perfectly plausible that 2 human chromosomes fused to give human chromosome 2, rather than 2 chimp chromosomes fusing to give human chromosome 2.

  69. 69
    Green says:

    Re-Dr Sternberg’s paper, his main point is diffult to discern. But I think he’s saying several things:

    1. Question the “99%” figure

    2. Most ITS’s are not relics of our evolutionary past; they serve specific functions and are not junk.

    3. BUT, the ITS in human chromosome 2 *IS* evidence of a fusion event, and it IS evidence of our evolutionary past.

    He goes on to say that the ITS of human chromosome 2 is a synapomorphy, so it seems he agrees that 2 chimp chromosomes fused to form it.

    But as I mentioned above, however, it is equally plausible that 2 human chromosomes fused to form it.

  70. 70
    Green says:

    This might also add to the discussion of percent similarity between humans and chimps:

    “81% of human introns are found in the same position and phase in the sea anemone Nematostella and 82% of the anemone introns are found in orthologous positions in human genes”

    From: Putnam, N. et al. (2007) Sea Anemone genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organisation. Science. 317:86-94.

  71. 71
    Nakashima says:

    Mr BiPed,

    I answered your three questions on another thread. Are you just collecting answers from different people, or are you interested in discussing the answers?

    DNA is obviously not physically inert. One of the issues of this thread, quadraplex DNA, is based on the physical chemistry of guanine. This is the kind of interface between guanine the chemical and guanine the store of information that is expected to exist.

    As we clarified earlier, your questions 2 and 3 related to independent trials. Independent trials is the exact opposite of evolution.

  72. 72
    Nakashima says:

    Mr Cordova,

    But consider this, if the ITSs that are different between chimps and humans are functional, how can we possibly argue that ITSs are evidence for similarity.

    Even if they were functional, if they occured at the same place, they would be evidence of common descent. A fusion, transposition, or viral insertion creates an ITS in the common ancestor, and both species inherit it.

    One of the ways in which ‘book’ analogies fail for DNA is that, yes, you can rearrange the DNA and it still does the same thing, code proteins. There are many examples of genes jumping from one chromosome to another, and retaining function.

    This is also where analogies to computer programs go wrong. Humans write programs with loops, function calls, conditional logic, etc. DNA is not such a program. A DNA program looks like this:


    BEGIN
    print("VAL");
    print("ARG");
    print("MET");
    /*
    print("LEU");
    */
    print("ARG");
    END

    Sorry the above mix of syntax is cringeworthy. Zoom out a little, and the program looks like


    print("protein1");
    print("protein4");
    print("protein2");
    print("protein22");
    print("protein35");
    print("protein26734");

    To the extent that the cell just needs the proteins printed, and doesn’t care about the order they are printed, then YES, you can rearrange the words in the book. Why doesn’t the order matter? Because the ‘book’ is being read and reread simultaneously, over and over, by readers in different positions.

  73. 73
    scordova says:

    Nakashima-san,

    Sorry for my delay in responding to your comments. Even granting that common descent is true, the point of Rick’s article is that the differences between Chimps and Humans are more than 0.5%!

    One of Rick’s point is that DNA is far more than genes! We can’t merely look at the spelling of a word like the telomeric sequence “TTAGGG”, the way understand these chains of long repeated sequences is not to look at the spelling:

    TTAGGG-TTAGGG-TTAGGG-TTAGGG-…….

    the way to understand their significance is to look at how they are tied in knots and where they are located.

    To ignore these differences is very misleading.

    Also, from John Sanford’s Genetic Entropy:

    There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).

    The non-coding regions are significant! And its not just how they are spell but how they are tied in knots!

  74. 74
    scordova says:

    The reasons large sections of DNA had been formerly written off as junk were:

    1. it would be easier to explain life if it were NOT that complex

    2. if all the areas of DNA were functional or even POLY-functional this would pose a problem for evolution because of Haldane’s dilemma and Nachman’s U-Paradox.

    I may have to post on these issues to illustrate.

    But perhaps before posting, does any one here have background in population biology or population genetics?

    Sal

  75. 75
    Dave Wisker says:

    Hi Green,

    We have evidence today that fusion events DON’T cause speciation events (e.g. different BREEDS of horse, and different RACES of mice).
    This is good evidence for the idea that chromosomal fusion events happen fairly commonly (without adverse effects) *within* species. Thus it is perfectly plausible that 2 human chromosomes fused to give human chromosome 2, rather than 2 chimp chromosomes fusing to give human chromosome 2.

    I agree that chromosomal fusions are not primary drivers of speciation. Interestingly, the evidence you cite to support this undermines a different point Luskin has made elsewhere:

    In other words, Miller has to explain why a random chromosomal fusion event which, in our experience ultimately results in offspring with genetic diseases, didn’t result in a genetic disease and was thus advantageous enough to get fixed into the entire population of our ancestors. Given the lack of empirical evidence that random chromosomal fusion events are not disadvantageous, perhaps the presence of a chromosomal fusion event is not good evidence for a Neo-Darwinian history for humans

    From:
    http://www.ideacenter.org/cont.....hp/id/1392

  76. 76
    Joseph says:

    Is there any scientific data that would demonstrate that the changes required are even possible?

    As far as I know there isn’t any genetic data which says the transformation is genetically possible.

    So that is the first step.

    We have data showing why the jaw muscles in humans are not as robust as chimps.

    But what does that mean? Was a chimp born with diminished jaw muscles? And then that chimp was the father/ mother of humans?

    Also the whale’s diminished pelvis has a function.

    Many alleged vestigials do. And the only way around that is to say well that isn’t the original function, as if that person knows what the original function was. (it is assumed to be the functionality of the less evolved forms)

  77. 77
    Dave Wisker says:

    Hi Sal,

    But perhaps before posting, does any one here have background in population biology or population genetics?

    I do, to a certain extent (btw, I’m “KC” from ARN). However, I’m on moderation, so there may be delays in my replies.

  78. 78
    Nakashima says:

    Mr Cordova,

    How to measure species similarity is an intersting question. You’ve laid out a few different choices. Now the questions in my mind are – why prefer one choice over another,and what are the values for all species-species comparisons with this method, not just human-chimp? I don’t know if 0.5% is big or small without comparing it to other ratios. The same would be true for 13.7% or any other number.

    I think that your point in your OP is that a number like 0.5% has a certain PR value with the public uneducated in the issues. If the basis of comparison has been chosen for PR value rather than scientific utility, that is a valid concern.

  79. 79
    Nakashima says:

    Mr Cordova,

    The reasons large sections of DNA had been formerly written off as junk were:

    1. it would be easier to explain life if it were NOT that complex.

    I disagree with this. I think if you go back and read the literature, you will see that scientists expected all of DNA to be significant, and for there to be many more genes than there actually are. It was more important that large stretches of DNA were found to not code for proteins, than that the scientists working on them had an a priori commitment to a belief in the simplicity of genome.

  80. 80
    scordova says:

    why prefer one choice over another,and what are the values for all species-species comparisons with this method, not just human-chimp?

    Part of the problem is we don’t yet have the ability to measure some of these differences.

    For example, to actually analyze the knots we need Nuclear Magnetic Resonance imaging. This is not cheap and it is not easy compared to dna sequencing.

    It’s relatively easy to do gene comparisons, but how do we correctly analyze the non-coding regions?

    The reason gene detection is easy is we can often look for a DNA sequence and then test the organism to see if a particular protein is expressed. That is relatively “easy”. We can test if an organism expresses insulin, but determining if it expresses it properly and how it relates to the non-coding regions is not so easy.

    Some forms diabetes are suspected to originate in the non-coding regions. These are not easy inferences to make.

    I don’t think we have even scratched the surface in terms of all the real complexities at play in order to even begin to think we can make valid comparisons beyond superficial similarities like genes and the proteins they code.

  81. 81
    scordova says:

    think if you go back and read the literature, you will see that scientists expected all of DNA to be significant

    I was referencing considerations by Ohno-sensei:

    http://www.junkdna.com/ohno.html

    Ohno coined the term “junk DNA”. The considerations were from the U-Paradox. He doesn’t mention the U-Paradox explicitly, but you can see elements of it in his calculations in the link.

  82. 82
    Nakashima says:

    Mr Joseph,

    We have data showing why the jaw muscles in humans are not as robust as chimps.

    But what does that mean? Was a chimp born with diminished jaw muscles? And then that chimp was the father/ mother of humans?

    I would say ape instead of chimp, but otherwise correct. Let’s say this ape has taken to feeding on softer fruits, and so does not need such strong jaws (which help grind tougher plant matter). Its muscles are now over-developed relative to its diet. Energy spent during development on strong muscles is available (in a less well muscled lineage) for other survival activities.

    It is really no different than cave fishes not developing eyes. What we see as a loss is a survival advantage. Nature doesn’t editorialize.

  83. 83
    scordova says:

    For the reader’s benefit, I describe the U-Paradox here:

    Other problems for Human Evolution, Nachman’s U-Paradox

    One solution to the U-Paradox was to invoke “junkDNA”, but that “solution” is no longer feasible since we now know, junkDNA isn’t junk.

  84. 84
    Nakashima says:

    Mr Cordova,

    Clearly, Ohno-sensei’s paper came to teach something to people that they did not expect. Prior to this paper is when you might have seen estimates such as what he shoots down at the beginning – millions of genes based on an assumption that all of DNA coded for a gene.

    It is interesting to see that the actual number of genes is within an order of magnitude of his estimate. Also, at the same time as he coins the term “junk DNA” in the title, he finds many uses for non-coding DNA in the text! It’s a pity people only remember the catchy phrase.

  85. 85
    scordova says:

    Nakashima-san,

    Thank you for you insight. Yes, I was very impressed with Ohno’s insight into the number of genes.

    As a side note, while discussing the dis-similarities between chimps and humans, I don’t want to give the impression that I think chimps are so dis-similar from humans as but butterflies are dis-similar from humans.

    The creationist Linnaeus was correct to group humans along with primates because of their similarities. Primates are certainly more similar to each other than they are to plants!

    However, if we wish to make an accounting for how much evolution had to take place, we ought to examine the number of diffences and the number of separte events that are needed to be accounted for.

    I think the diffences are far more than 177,000,000 base pairs. If we have to account for the non-coding regions as well as the 3-D architectures, and the epignetic features, I think the number would be truly enormous.

    This is not to say that it is improper to group chimps and humans together, but rather to emphasize the difficulty in evolving creatures even in the same order, namely primates.

  86. 86
    Nakashima says:

    Mr Cordova,

    Thanks for the links on the Nachman paper. I googled it and read it.

    Looking over his methods and assumptions, it lookslike some things in the paper could use updating, now that we have complete sequences for humans and chimps. He assumes 70,000 genes for humans, which we know is wrong.

    Two points which I found interesting – he shows that much more mutation is going on in males than females. As I have read elsewhere, we males are the disposable guinea pigs, testing solutions which will be stored (if useful) in the female genome. Also, his 40 children really means 40 zygotes, 40 pregnancies begun. We don’t know the prevalence of spontaneous abortion in our primitive ancestors. Even now the rate can be as high as 33%.

    So it would be interesting if this kind of study could be re-done today to see if there is still a “paradox” at all.

  87. 87
    scordova says:

    So it would be interesting if this kind of study could be re-done today to see if there is still a “paradox” at all.

    Even though the number of genes is smaller, the number of nucleotides we have to consider is no longer 1.5 % of the genome but may now 100% of the genome since we are now realizing the non-coding sequences are significant. Even mis-spellings in the telomeric repeats “TTAGGG” will degrade the knotting properties.

    You are correct to cite the issue of spontaneous abortion, but we know that most mutational changes, are only slightly deleterious, not fatal enough to cause spontaneous abortion.

    I do agree it would be a good idea to revisit the U-Paradox, but I think the paradox has gotten worse not better. But I think we can both agree more research is in order.

  88. 88
    Nakashima says:

    Mr Cordova,

    I think you are too willing to ascribe significance to the entire non-coding genome. Its obvious that some of it is important. For example, HAR1 and HAR2 are in non-coding regions. But there are also the remnants of ERVs scattered around, I find it hard to believe these are “functional” now even if they were functional (from the point of view of the virus) in the past.

    This is similar to being excited about “polyfunctional” DNA. Sure, a stretch of DNA could be read in any of 12 different ways, but that doesn’t mean that DNA is actually read more than one way over most of its length. If it were, the proteome would be 12 times larger than predicted by a simple reading of the genome, which would be very obvious and very big news. It isn’t.

  89. 89
    Borne says:

    Nakashima:

    This is similar to being excited about ‘polyfunctional’ DNA. Sure, a stretch of DNA could be read in any of 12 different ways, but that doesn’t mean that DNA is actually read more than one way over most of its length. If it were, the proteome would be 12 times larger than predicted by a simple reading of the genome, which would be very obvious and very big news. It isn’t.

    Your conclusion on that is a non sequitur. It does not follow logically any more than saying an iPhone should be 12 times bigger because it is polyfunctional. Polyfunctionality is, I think, been demonstrated more than once. Polyfunctional implies poly-constrained as well. Think the implications of that over.

  90. 90
    Nakashima says:

    Mr Borne,

    What does polyfunctional mean to you? From the quote of Dr Sanford’s book, I assumed it meant that one sequence of DNA could (and did) produce more than one protein transcript. If you object to specifying proteins, lets just say transcriptome. The argument remains that if large sections of DNA actually were read in multiple ways all the time, then the transcriptome would be 2x, 3x, up to 12x larger than a reading of a single strand in a single direction in a single reading frame. That would be evidence that large parts of our DNA genome are polyfunctional. I don’t know of such evidence.

    If the genome was polyfunctional to a great degree, we wouldn’t see gene duplications and frame shift mutations revealing new proteins. Those proteins would be already being produced by the original gene under multiple reading frames.

  91. 91
    Upright BiPed says:

    Khan, you and Nakashima should do a stage act.

    One is demanding that the code is a physical issue, while the other pushes a paper that demonstrates how non-physical the system is.

    – – – – –

    Nakashima, a red plastic ball does not violate any physical laws. But the existence of a red plastic ball is physically inert. Certainly, the elements that make up the ball are all acting in accordance with the physical laws that govern the matter in this Universe, but there is nothing in those laws that says “dye yourself red and form a sphere”. (That required something else 🙂 )

    Khan, give it a rest. I have a research paper due in 72 hours, so I am going to leave it to you to figure out what elements of the issue that Novo-Koonin-Wolf left out of their paper.

    (Hint: it is the reason for the questions I asked)

    (Second Hint: re-read their own conclusions)

  92. 92
    Nakashima says:

    Mr Biped,

    Good luck on your paper, gambatte!

    I originally thought that your phrase “physically inert” meant something like “chemically inert”, and that is how I have been answering your first question. But now I see that just as your questions 2 and 3 use very idiosyncratic language to describe the idea of independent trials, your question 1 is also using terms in a very special way. I have never heard anyone say ‘existence is inert’ before.

    Newell and Simon treat with physical symbol systems, and address the idea that data should be “inert” – A computer should be able to store any arbitrary pattern of 1s and 0s without setting itself on fire, for example. (A counterexample would be a computer that represented 1 with a heavy disk, and 0 with a light one. The computer might actually tip over in some configurations of memory! This representation would not be inert.)

    In this Newell & Simon sense, the code table of DNA is mostly inert, but not completely, as we saw with guanine quadraplexes.

    I’ve read that paper cited by Khan previously. It seems to argue that our code is somewhat mediocre, and therefore quite possibly a frozen accident. The paper also brings up in passing another example of how the genetic code is not perhaps completely inert if there is a chemical relationship between arginine and its codon.

    So I would give you a qualified “yes” as an answer to Q1. The symbols are physical, and (for the most part) inert.

  93. 93
    scordova says:

    I assumed it meant that one sequence of DNA could (and did) produce more than one protein transcript.

    Providing sequences that describe proteins is not the only function of DNA.

    There is more to DNA than providing a sequence that describes coding. Visit JunkDNA.com for the other functions of DNA.

  94. 94
    Nakashima says:

    Mr Cordova,

    Yes, I addressed that possibility in the next sentence after the one you quoted. The Sanford quote you provided begins and ends with the protein coding polyfunctional possibilities, and discusses other possibilities in between.

    On the subject of polyconstraint, there seems to be an assumption that no other part of the genome is a backup to any other, in any of its functions.

    We were talking recently here on UD about a gene (an opsin gene? I forget) where there were over one hundred variants in the human population thus far sampled. This gene is not ‘polyconstrained’. There are a large number of acceptable variations and substitutions – variations possible because they do not significantly affect the electrosurface of the protein.

  95. 95
    Joseph says:

    Nakashima,

    What is the evidence that demonstrates an ape-like organism with diminished masseter muscles can even eat?

    IOW do all the other muscles in that area also have to “shrink” such that the diminished masseter can then work?

    Where is the data?

    And does anyone know how many mutations it would take to go from an ape-like organism to a fully developed human?

  96. 96
    Joseph says:

    Do we even know what makes a chimp a chimp and a human a human? No.

  97. 97
    scordova says:

    On the subject of polyconstraint, there seems to be an assumption that no other part of the genome is a backup to any other, in any of its functions.

    I don’t think that is the case. Something can be polyconstrained and also serve as a back up.

    In the software engineering world (of which you are familiar), functional modules are poly constrained. Changing the module (like say a print routine) may or may not have a radical outcome on all the system parts that depend on this routine. We might make changes (say for maintenance purposes) to the module but the functional results are the same. The fact that we can make these changes does not mean the module is not polyconstrained. There are acceptable variations, but it is still poly constrained. Being polyconstrained constrains the limits of variation, it does not imply no variation can exist.

    The problem is determining which variations actually compromise function, and this is not so easy for the reasons I outlined here:

    Airplane Magnetos Contigency Designs and Reasons ID Will Prevail

    In deeply redundant systems (such as space ships) it is customary for copies of software to be located in numerous places. This provides backup and robustness. So we can have copies of poly constrained entities.

    Polyconstraint does not imply there cannot be redundancy. Further, because something is a copy or a backup that is rarely if ever used cannot be an argument that it is not really functioning. A spare tire or spare magneto in an aiplane that is never used still serves an important function. Trying to use immeditate selective advantage as a criterion for determining if something is functioning is a questionable philosophical approach to characterizing integrated systems.

    I put forward some of my objections to using immeditate selective advantage as a metric for measuring functionality here:

    Airplane Magnetos Contigency Designs and Reasons ID Will Prevail

    and

    Survival of the Sickest

    I believe there are desirable variations and undesirable variations. We do not yet know what are and aren’t. That was the philosophical issue with “Survival of the Sickest”. We might argue sickle-cell anemia is an acceptable variation since in some contexts it lends survival advantage, but I find this viewpoint problematic.

    This leads to a discussion of a good point which you made:

    We were talking recently here on UD about a gene (an opsin gene? I forget) where there were over one hundred variants in the human population thus far sampled. This gene is not ‘polyconstrained’. There are a large number of acceptable variations and substitutions – variations possible because they do not significantly affect the electrosurface of the protein.

    Polyconstraint does not imply everything is prevented from having some variation. The way Sanford argues for detecting poly constraint is the manner in which the same stretch of DNA can be used for different functions (such as in alternative splicing). That is the main idea in the way Sanford describes polyconstraints.

    What variations are and are not consistent with the original design intent is an open question. But if system biologists are attempting to characterize systems in terms of what are the intended functions, these philosophical question will come up again.

    I can say sickle-cell anemia is not an intended function, but on what grounds can this be argued? The question remains open, but it is an important one.

  98. 98
    Adel DiBagno says:

    What is the evidence that demonstrates an ape-like organism with diminished masseter muscles can even eat?

    I’ll have to chew on that.

  99. 99
    scordova says:

    One thing I should add, the chimp-human similarity issue has some independence from the question of the discussions about function a polyconstrained regions.

    If a nucleotide posistion is different between a chimp and a human, this change still has to be accounted for. For example, if there is an indel in humans which are not in chimps, we still have to account for how the indel was fixed into the human population, independent of whether the indel is functional or not.

    If the indel is not subject to selection, this is probably as much a problem for it overtaking the populaiton without any seleciton pressure, especially in populations that are not well-stirred due to geographic distribution.

    So even granting (only for the sake of argument) that the non-coding regions are non-funcitonal, the differences in the regions still need to be accounted for when trying to model the evolution after the supposed chimp-human divergence.

  100. 100
    Joseph says:

    Adel (98),

    Are you trying to say that you are a knuckle-walker? 🙂

  101. 101
    derwood says:

    Sal:
    Thank you for your comment, however, I would argue that the figure of size is relevant in that it emphasizes the 99% identity isn’t what it may appear to most.

    So, you are arguing semantics, essentially?
    I am unconcerned with how ‘most’ would interpret something. If most see no problem with drawing conclusions on what they do not fully grasp, so be it, but I don’t think that we should dimiss the reality of sequence analyses because ‘most’ misinterpret them.

    The 5% difference (of extra base pairs) is just tossed out. If we toss out differences, of course the supposed identity numbers will be misleadingly inflated.

    You seem to have ‘tossed out’ the explanation. The ‘extra bases’ are largley the product of a much smaller number of mutational events. It is the mutational event that is relevant, not the exact number of bases. If that were so, again, it should be made clear that any two humans differ by millions of nucleotides.

    We really don’t know that those extra base pairs are junk after all, do we.

    I don’t recall implying that they are. Although, since intraspecies differences can rank in the millions, it would seem that if they were NOT ‘junk’, or at least not ‘required’, that there would be major phenotypic consequences.

    And even if they are junk, we still have the nasty problem of how 177,500,000 base pairs got fixed into a population.

    How do you know they are fixed? If our population has a variationin genome size of some tens of millions of BPs, chances are pretty good that similar populations will, too.

    How does 177,500,000 base pairs of junk get fixed in a population?

    How did the human population get nearly 50% of its’ genome fixed via duplication events?
    First, since we are comparing the genomes of different species, with similar generation times (more or less), it is safe to assume that roughly half the difference is found in each species, not all change in one. Second, there is no quarantee that ALL of the differences are fixed, as should be pretty obvious.

    I wouldn’t be too quick to presume random drift could be a good explanation for such a large amount of base pairs.

    I wouldn’t be too quick to presume that because we do not have all answetrs to all questions this very day that the better answer is to lay it all at the doorstep of one’s preferred Intelligent Designer.

  102. 102
    derwood says:

    Green writes:
    derwood writes:
    “Luskin’s point was a red herring. The chromosonmal fusion has NEVER been presented as evidence for a speciation event, it has always been presented, as far as I know, to explain why we have differing karyotypes.”

    But derwood, nowhere did Luskin claim that it caused the speciation event. In fact, I think in recent podcast, he affirmed that it *didn’t*.

    Right – which is why it is a red herring. Since evolutionists have never, as far as I know, posited the fusion as an explanation for speciation, going to lengths to claim that it did NOT cause speciation is at the very best irrelevant, since we’ve never said anything else. At worst, which is what I conclude, Luskin’s goal is to argue against human/chimp ancestry by claiming that the fusion event cannot account for human evolution, therefore, talking about the fusion event is a distraction.

    Likewise, nor did I say that it caused the speciation event.

    We have evidence today that fusion events DON’T cause speciation events (e.g. different BREEDS of horse, and different RACES of mice).

    Right. Like I said, we’ve never claimed, as far as I know, that it did. The discussion of the fusion is to explain WHY we have fewer chromosomes than chimps do, for this has in the past been used as an argument against evolution.

    This is good evidence for the idea that chromosomal fusion events happen fairly commonly (without adverse effects) *within* species. Thus it is perfectly plausible that 2 human chromosomes fused to give human chromosome 2, rather than 2 chimp chromosomes fusing to give human chromosome 2.

    I’m not so sure about all that, but again, the karyotype issue has been used as an argument against evolution. It is good to see that Luskin is now arguing the evolution position, according to you.

  103. 103
    derwood says:

    Sal writes:

    Thank you for that comment. That was very informative. I was not aware of issues with guinea pigs.

    No problem – but remember, I am not certain that it is in guinea pigs. Dave W. will probably know.

  104. 104
    Nakashima says:

    Mr Joseph,

    IOW do all the other muscles in that area also have to “shrink” such that the diminished masseter can then work?

    That is the point of gene regulatory networks. Vary a gene near the beginning of the chain, and all the downstream development adapts. There is not one gene per muscle, bone, neuron, and blood vessel. You can find out more by looking up FGF and BMP, for example.

  105. 105
    Nakashima says:

    Mr Joseph,

    And does anyone know how many mutations it would take to go from an ape-like organism to a fully developed human?

    This article estimates only a few hundred mutated genes.

  106. 106
    Nakashima says:

    Mr Cordova,

    The point I was trying to make about polyconstraint goes back to Dr Sanford’s original quote “polyfunctional implies polyconstrained”. The clear implication I see in Sanford’s text is that a string of polyfunctional DNA is less able to vary because of these multiple constraints. My point about backup is to show how backup undercuts this concern. Any function that is provided for in two separate places can then begin to vary in one of those places.

    I think Dr Sanford’s argument on “poly” is that overlapping function would be hard for a human to design, therefore it is evidence of superhuman design. However, we do design this way when trying to optimize certain parameters, such as code size. The unexplored alternative hypothesis is whether evolutionary methods also result in overlapping functional descriptions, and under what set of optimization pressures does this happen.

  107. 107
    scordova says:

    derwood worte:

    If our population has a variationin genome size of some tens of millions of BPs, chances are pretty good that similar populations will, too.

    If so this is devastating evidence against natural seleciton’s ability to manage large numbers of nucleotides and hence it shows almost total non involvement by natural selection in the large numbers of base differences between chimps and humans. 🙂

    So your counter claim is a double edged sword against Darwinian evolution as being responsible for the chimp human divergence. Whether the regions are functional or not is beside the point. The differences are there, they are substantial, and natural selection can’t be argued as the driving force.

    Your cliam:

    If our population has a variationin genome size of some tens of millions of BPs, chances are pretty good that similar populations will, too.

    unwittingly underscores selection’s irrelevance to the supposed chimp human divergence.

  108. 108
    scordova says:

    If that were so, again, it should be made clear that any two humans differ by millions of nucleotides.

    But the proper way to do the comparison is to create a representative genome for humans where there are large scale monomorphic regions. Do the same for chimps, and then human-human difference will be zero, the chimp-chimp difference will be zero and the chimp-human differences will be at least 5%.

    This sort of comparison would be no less legitimate than the 99.5% identity claimed by making comparisons of only 1.5% of the regions between humans an chimps and humans that are similar.

    The 99.5% identity figure is misleading.

    I already said that I don’t mean to say that chimps are so far away from humans as to be placed in different orders. Even the creationist community of Linnaeus and friends would consider the chimp-human relationship to be close relative to chimps vs. plants or humans vs. plants.

  109. 109
    derwood says:

    Sal writes:
    derwood worte:
    “If our population has a variationin genome size of some tens of millions of BPs, chances are pretty good that similar populations will, too.”

    If so this is devastating evidence against natural seleciton’s ability to manage large numbers of nucleotides and hence it shows almost total non involvement by natural selection in the large numbers of base differences between chimps and humans.

    Complete non-sequitur. Why would natural selection have to ‘manage’ large numbers of nucleotides?
    It appears that you want to argue that all nucleotide sites must be under the control of natural selection, and if there are large numbers of nucleotide variation within/among species, then this is a problem.

    How do you propose that this was set up by your preferred Intelligent Agent? Are there computer programs designed to function with variable amounts of code, yet still be the same program?
    Must be.

    So your counter claim is a double edged sword against Darwinian evolution as being responsible for the chimp human divergence. Whether the regions are functional or not is beside the point.

    Not at all. You seem to be arguing a very strict selectionist position here, yet I know from reading your posts for some time that you should at the very least understand that this is not a realsitic position.
    The functionality part in fact is devastating to your position, since it is clear that any two humans caqn differ by tens of millions of bases yet they are still both humans and neither will exhibit any particulat phenotypic deficits. Thus, the argument that all DNA is ‘fully functional’ seems to have been devastated just by investigating human genome variation.

    The differences are there, they are substantial, and natural selection can’t be argued as the driving force.

    The driving force for what? Controlling how much variation occurs? I can’t see what you think your argument actually is here, other than tossing something out to counter what the facts show.
    Why on earth would natural selection HAVE to ‘manage’ genome size?
    You are not making sense.

    Your cliam:
    “If our population has a variationin genome size of some tens of millions of BPs, chances are pretty good that similar populations will, too.”

    unwittingly underscores selection’s irrelevance to the supposed chimp human divergence.

    Actually, my point was that YOUR claim regarding the number of “fixed” differences between species is in error for at least two reasons – you presented it as occurring only in one species, hoping to make the genetics more difficult to explain; because there is relatively large scale variation WITHIN species, the ‘fixed’ differences are likley to be somewhat smaller than you indicated.
    Beyond that, as I’ve already explained, since the raw nucleotide differences are due not only to small scale mutations, but also larger indels and duplication events, lumping ALL nucleotide differences together in one big pot and declaring THAT number to be what must be explained by population genetics is simply absurd.
    It is sort of like looking at the 4000 or so American deaths in Iraq and insisting that each one represents a unique battle.


    derwood:
    “If that were so, again, it should be made clear that any two humans differ by millions of nucleotides.”

    But the proper way to do the comparison is to create a representative genome for humans where there are large scale monomorphic regions. Do the same for chimps, and then human-human difference will be zero, the chimp-chimp difference will be zero and the chimp-human differences will be at least 5%.

    Yes, when you count indels and the like, as should have been obvious by now. You are still talking raw nucleotide difference.

    Let us look at it this way:

    Say we have a locus from two species. This locus starts out 1000 bp in loength for both. Over time, species A accumulates 5 unique substitutions. Species B accumulates 4 unique substitutions and experiences one insertion even of 100 bps in length.
    If we compare the sequences from a raw nucleotide difference POV, we would see that they differ by 109 bps, or about 9%. If we compare them from a mutational POV, we see that they differ by 10 such events, or less than 1%.
    Sure, the raw nucleotide difference has certain applications and relevance, but it is true that the raw nucleotide difference will be larger than the number of mutation events required to produce it.

    This sort of comparison would be no less legitimate than the 99.5% identity claimed by making comparisons of only 1.5% of the regions between humans an chimps and humans that are similar.

    The 99.5% identity figure is misleading.

    The legitimacy of the number depends on what is being measured and in what context.

    It is misleading to claim that all individual nucleotide differences – the raw nucleotide divergene – has a greater import when discussing descent than does the number of mutations required to explain the difference.

    I already said that I don’t mean to say that chimps are so far away from humans as to be placed in different orders. Even the creationist community of Linnaeus and friends would consider the chimp-human relationship to be close relative to chimps vs. plants or humans vs. plants.

    It is good that you recognize this. Do you also recognize that using the raw nucleotide difference for ALL interspecies comparisons, as you want to do with the human-chimp issue, would make ALL relarted species more divergent (by measurement only)?
    What ever would the Baraminologists do when they realize that all turtles may NOT be in the same holobaramin using these new criteria? Their ark, it seems, suddenly has to get larger.

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