The Human Genome and Evolution

In some respects certainly, but there are a lot of even more similar non-drosophilid flies out there still to be sequenced. That rather depend on where they turn up. If they turn up in other dipterans more closely related to drosophila than mosquitoes then I would say that you would stil have a relatively good case for divergence. If they turn up in some vertebrate then it would certainly require a pretty hefty bit of suspension of disbelief to think of it as anything other than convergence or maybe some bizzare instance of lateral gene transfer.TTFN,WK

This seems to be verging on the tautological. You can't argue that something came about by evolution unless you accept the possibility that evolution is possible.TTFN,WK

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Yes, using my definition of kinds one could try to put man and the chimpanzee into the one kind.

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As a *postulate* we would of course state that this was not the case.

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I'm not interested in what one could do, but in what you are proposing, which is that humans and chimps do not share a common ancestor. (Unless I've misunderstood you here.)

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Empirically, human-specific genes aside

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What human-specific genes do you mean?

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one then has to note that the millions of SNPs in coding and regulatory regions that distinguish man and chimpanzee are doing something very important (to human intelligence for example).

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Technical notes . . . "Millions" is an exaggeration: there are fewer than 100,000 amino-acid-changing substitutions between human and chimpanzee, and the bulk of these are probably of little effect. The number of regulatory changes is pretty much a matter of guesswork at this point, but a number on the same scale seems likely. Also, differences between species are not SNPs; SNPs are polymorphisms, that is, variant alleles within a population.

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One cannot argue that this combination of SNPs could evolved easily unless one assumes evolution a priori.

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Why not? The number of substitutions is smaller than what one would predict for neutrally evolving DNA, based on the observed mutation rate. That is, we know mutations are occurring at a certain rate, and there's nothing special we know of that prohibits functionally important mutations from occurring. So why couldn't this combination have evolved easily?Getting back to my original question, however: if humans and chimpanzees do not share a common ancestor, why do their genomes look so much like they're descended from a common ancestral genome? Why does human chromosome 2 look exactly like a fused pair of ancestral chromosomes, chromosomes that are still separate in chimpanzees? Why do the differences between the two genomes look so much like they're the result of accumulated mutation, with larger differences in regions of high mutation rate, and with more differences corresponding to mutations that happen more easily?

OK. But what is this invisible boundary that delimits the human 'kind'.
For example, to persue your argument from an evolutionary perspective, we might use chimps as an outgroup and test sequence homology between humans chimps and Neanderthals and find the latter closer to humans than the former. So we have:Humans __________________________(common ancestor)
Neanderthals_______/..................../
Chimps______________________/Presumably, you deny common ancestry between humans and ANY other animal, so the human lineage has to be essentially unbranched beyond the level of human 'kind'. And yet the existence of Neanderthals shows that it HAS branched *below* the level of kind.So I ask, yet again, what is it that somehow prevents branching *above* the level of 'kind' ?Further, what sort of criteria are used to determine the boundary of a kind?For example, the boundary of a species is defined according to isolation of a gene pool. If you can't come up with a single objective criterium for determining the boundary of a kind, then it is simply an arbitrary designation without any real biological significance.Now, most biologists would accept that all taxonomic designations above species level are also essentially arbitrary because they are not based on a clear biological criterium as is the species. However, in evolution we assume they represent important branch points in common ancestry because they are associated with major morphological differences, regardless of our inability sometimes to infer their exact location, since this inference is supported by many independent lines of evidence. There is no evidence to suggest that any arbitrary taxonomic designation (e.g. a 'kind') should remain immutable indefinitely, nor that it does not converge back to some common ancestor with another 'kind', regardless of how you see fit to define one, even though you haven't yet.

Hi EZ (If I can call you that for short )
My understanding is that evolution has us evolving from apes and that chimps are closest to humans in their DNA composition. By your diagram you seem to be suggesting that humans, chimps and neanderthals separately evolved from a common ancestor.Are you just using this for purpose of illustration or is this generally considered a possibility?With no background in this at all I try to stay away from any of the technical discussions except to try and learn what I can, but I'm very curious about the basis for your diagram. Thanks

I couldn't help but notice that all of the data sets you linked to start with the error message "The page cannot be displayed - The page you are looking for is currently unavailable"Did you screw the links up, or is this diagnostic of ID research in general? This message has been edited by mick, 07-08-2005 04:43 PM

Hi EZscience,I thought you might enjoy this article, recently published in Nature, which shows that the biological species concept isn't always very good identifying "kinds" either.To put it briefly, the researchers analysed the genetic structure of Wasmannia auropunctata (little fire ant) populations. By analysing genetic sequences of queens, workers, gynes (winged queens), drones, and sperm collected from mated females, they got some pretty surprising results.All gynes in this species are reproduced clonally, asexually, by the queen. This means that males are unable to pass their genes onto their daughters. All new queens have only maternally-inherited DNA. Males are necessary, however, for the production of workers by sexual reproduction; but workers, of course, don't mate, so none of the males' DNA gets passed on to future generations.On the other hand, all males are produced by sexual reproduction. But some time after fertilization, it is thought the male genome destroys the maternally-derived copies of each gene. Only the genome derived from the father is used to create new cells as the zygote develops. This means that all DNA inside a male is paternally inherited. Females are unable to pass any genes on to their sons.If you think about this situation for a second, you realise that there is no common gene pool to the species. There is a female gene pool and there is a male gene pool, but there is no way for male DNA to get into the female gene pool, or vice versa.According to the biological species concept, the different sexes of the little fire ant are completely genetically isolated from each other and are hence different species. The males are evolving independently of the females.Phylogenetic analysis was consistent with this result: all the males in their sample formed one monophyletic clade, and all the females formed a separate monophyletic clade.Weird eh?This message has been edited by mick, 07-08-2005 05:22 PM

This indicates to me that the conceptually infinite division of phenotype and genotype is faulty. I agree that geneic selection(ism) is to go by the side but if this resolves the Catholic Church's prior bifucative view of human phlyogeny (in the 60s)seems dubitable as Occam's Razor need not solve this if resolved as Croizat suggested since infinite divisibilty could always be resorted to if actual infinte THEN be accepted by Catholics who disregarded Cantor's suggestions directly to its body. I assume the dashed line dispute (which occurs whenever biologists attempt to restruct all phylogeny) will not have to divide the niche as well (in the same infinty not potential) even if the two former concepts (phenotype and genotype) are at fault.

The icr host is down; ICMP messages are telling your browser that the destination host is unreachable. If you want to view the datasets you can view them in HTML through Google's cache.

Well I just assumed that at some point the 3 must have shared as common ancestor. Starting with the lineage that ultimately led to humans, I am simply assuming that Neanderthals diverged from this lineage later than chimps did, given they are obviously closer to humans. I am not an expert on hominid phylogeny either, I was just trying to make the point that once you accept branching lineages, you may as well accept that more and more branches occur all the way back. There is no known mechanism that could ensure the eternal integrity of a 'kind', however defined, because this would imply no branching had ever occurred above this level.

Hi Mick,Yes, this is a truly curious situation. There are other known examples of zygotes that, once formed, discard the male genome and then develop normally. This is gynogenesis and it yields exclusively maternal inheritance. (I am not in my office or I would dig out some additional examples from my library). However, in this case what you have is essentially the phenomenon occurring in parallel in both sexes, something I had certainly never heard of before. I am not sure it undermines the general usefulness of the biological species concept (it is a very anomalous situation), but it does sort of create a gray area. Note that the two sexes are still 'linked' biologically, if not genetically, by virtue of ttwo factors: the requirement for 'fertilization' of the egg to trigger its development with the male genome, and the requirement of both genomes to produce viable workers, without which neither genetic lineage could survive.Another interesting example that comes to mind is certain species of gynogenetic fish. In these fish there is sort of 'genetic parasitism' of one species by another that is actually parthenogenetic. The parthenogenetic eggs still require the stimulation of sperm to begin development, but the enitre male genome is discarded. Females of the gynogenetic species must therefore court and seduce males of the truly sexual species and induce them to 'waste' their sperm in spawning with them. This would seem to comprise a very unstable ecological relationship given that one would expect strong selection for males to discriminate and avoid these females. Again, I am away from my university access point, but I did find one article on a genetic analysis of some of these fish. You can view the entire article here, but it seems to be an interesting example of duplication of an entire genome leading to speciation via triploidy.Mode of origin and sources of genotypic diversity in triploid gynogenetic fish clones (Poeciliopsis: Poeciliidae).Quattro JM, Avise JC, Vrijenhoek RC.Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, New Jersey 08903-0231.Most tributaries of the Rio Fuerte in northwestern Mexico contain one or more clones of allotriploid fish of the genus Poeciliopsis. We used multilocus allozyme genotypes and mitochondrial DNA (mtDNA) haplotypes to examine several potential modes of origin of these gynogenetic all-female fish. The allozyme studies corroborated earlier morphological work revealing the hybrid constitution of two triploid biotypes, Poeciliopsis 2 monacha-lucida and Poeciliopsis monacha-2 lucida. Each biotype carries one or two whole genomes from the each of the sexual species P. monacha and P. lucida. Restriction site analysis of mtDNA revealed that P. monacha was the maternal ancestor of five electrophoretically distinguishable triploid clones. Four of five clones were marked by closely related, composite, allozyme/mtDNA genotypes, suggesting they had common origins from an allodiploid clone of the P. monacha-lucida biotype. Genotypic analysis revealed that all five clones arose via the "genome addition" pathway. Fertilization of unreduced ova in P. monacha-lucida females by sperm from P. monacha and P. lucida males, respectively, gave rise to both biotypes.

The loss of tracking deals with how far quasi-equilibRATED processes distributed genes differently than the unidirectional Fisher way IF
http://www.endeav.org/evolut/age/evol.htm
has as much relative frequency as some admitted group selection in the past.Biology is really a quite diverse discipline. You need to agree to this analysis but it feel correct to me.

WK Agreed. Whjen I say 'fly' I'm including all flies, not just drosophila. Sure. But my point is if we don't find the 1000-odd mosquito-specific genes anywhere else then it means these appeared just for the mosquito very early (given amber fossils).It's very consistent with the idea that God created a series of genomes that have since diverged primarily though gene loss. Agreed.

Fully agreed, but taking up a postulate and taking the corollaries as proof of the postulate are two different things. In this case, assuming mankind evolved from a common ansceastor with chimps indicates that millions of SNPs (not to mention human-specific genes) were involved. No arguement there. Does the listing of millions of SNPs further support the postulate? Not in the least.

sfs For the purposes of this discussion, I am quite happy to conceded that I can't prove genetically that mankind didn't evolve from other primates. I'm more interested in looking at the clear-cut data than discussing gray areas. Genetica. 2003 Jul;118(2-3):193-208."As a major breakthrough in the field, the heretical concept of 'human-specific' genes has recently received some supporting data."Sure, there aren't thousands of them, but they exist. Yes, but we know that regulatory regions will invovle many non-coding sites. I'm no expert on that. I was trying to be nice and evolutionry for you! But you're quite right. What do we call them then? Species-specific substitutions? Quite right. I agree with you that that number of point mutaitons would be expected to occurr. But then our viewpoints radiacally differ becasue then you ASSUME evolution. The chances that the *right* mutations will occur to generate human intelligence are astronomically lower than for any old set of 100,000 mutaitons occurring. They are anatomically very similar. Their intelligence is incredibly diffent however. For that matter, why does the human geneome look like a reorganized mouse one? Becasue they're all mammals! Feel free to argue against creation, but you can't expect a creator to re-invent the wheel everytime He needs a macromolecule. The answer to that is that many of those difference ARE due to aquired mutations no doubt. We'll agree with you there.This message has been edited by Tranquility Base, 07-10-2005 08:33 PM