“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

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.Nakashima_{May 19, 2009
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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.Nakashima_{May 19, 2009
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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.
Dave Wisker_{May 19, 2009
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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)Joseph_{May 19, 2009
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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/contentmgr/showdetails.php/id/1392Dave Wisker_{May 19, 2009
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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? Salscordova_{May 19, 2009
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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!scordova_{May 19, 2009
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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.Nakashima_{May 19, 2009
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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.Nakashima_{May 19, 2009
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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.Green_{May 19, 2009
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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.Green_{May 19, 2009
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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.Green_{May 19, 2009
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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?beelzebub_{May 18, 2009
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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.scordova_{May 18, 2009
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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_{May 18, 2009
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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.
scordova_{May 18, 2009
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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.scordova_{May 18, 2009
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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".Frost122585_{May 18, 2009
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Sal and Mr. Nakashima: Thanks to both of you for clarifying Dr. Sternberg's argument.vjtorley_{May 18, 2009
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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.Upright BiPed_{May 18, 2009
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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.scordova_{May 18, 2009
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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.Nakashima_{May 18, 2009
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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?vjtorley_{May 18, 2009
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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.beelzebub_{May 18, 2009
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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.scordova_{May 18, 2009
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beelzebub @51:
And as I have explained, the reasons you gave were incorrect.
In your opinion, of course.Mapou_{May 18, 2009
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PS. My source is the link that you provided in a parallel thread. Am I reading the numbers wrong?Mapou_{May 18, 2009
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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.beelzebub_{May 18, 2009
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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?scordova_{May 18, 2009
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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?Mapou_{May 18, 2009
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