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

_{Salvador Cordova

May 18, 2009

Darwinism, Intelligent Design}

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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.

Comments

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.scordova_{May 18, 2009
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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%.scordova_{May 18, 2009
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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.Mapou_{May 18, 2009
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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?Upright BiPed_{May 18, 2009
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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.scordova_{May 18, 2009
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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.beelzebub_{May 18, 2009
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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.Mapou_{May 18, 2009
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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.beelzebub_{May 18, 2009
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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.Mapou_{May 18, 2009
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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.beelzebub_{May 18, 2009
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No. The converse of my statement would have to be true in order to draw the conclusion that evolution is not falsifiable.beelzebub_{May 18, 2009
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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.Mapou_{May 18, 2009
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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/2/1/24Khan_{May 18, 2009
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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).beelzebub_{May 18, 2009
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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?
Upright BiPed_{May 18, 2009
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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?Mapou_{May 18, 2009
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And, thank you for addressing the idea that materialism conforms to all observations (including the ones it cannot hope to explain).Upright BiPed_{May 18, 2009
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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.Upright BiPed_{May 18, 2009
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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.Khan_{May 18, 2009
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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?Upright BiPed_{May 18, 2009
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"God" is supposed to be in strikethrough above. It worked in the preview window.beelzebub_{May 18, 2009
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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.beelzebub_{May 18, 2009
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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.derwood_{May 18, 2009
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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.PaulN_{May 18, 2009
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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.derwood_{May 18, 2009
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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.PaulN_{May 18, 2009
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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.PaulN_{May 18, 2009
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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?derwood_{May 18, 2009
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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.derwood_{May 18, 2009
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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?Nakashima_{May 18, 2009
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