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That's kinda what I thought you meant, which is why I asked for clarification. Because that's not really true is it? Isn't that what IDers and creationists do with irreducible complexity? Since there is no plausible explanation as to how this could have evolved then it must be intelligently designed. And the answer is usually "just because we don't have an explanation right now doesn't mean there isn't one." So lack of a plausible explanation may cause us to question the hypothesis, but is not a means of falsification.
You need to be careful there. That is the position some ID supporters retreat to, since the actual IC argument has failed but even there they demand a huge amount of detail, which I do not.
The key issue is the level of knowledge we have. Obviously we do not have the knowledge to reconstruct the complete history of a complex adaption including all the relevant mutations, in order and the selective pressures that caused them to become fixed in the population. By my understanding we do have a fairly good idea of the sorts of mutations that are possible, and if we could not explain the chromosomal difference in those terms we would have a problem. If we did NOT have that knowledge, it would be a different matter.
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Why would we not if we had limited other clues to go on. Differing chromosome numbers usually indicates infertility. In the case of the 44 chromosome man, we have many other clues that he is still of the human race. With the limited amount of ancestral human remains we have, any significant differences would give reason to separate them into different species. And we would also not expect to find the first or only person who had such a rearrangement, but a representative of the population.
Of course you are assuming infertility, but it would seem a huge leap to conclude a new species without morphological differences. While cryptic species do exist I think that we would want a little more. And don't forget that the article on the 44 chromosome man says he would have fewer infertility problems than his parents, even if his partner had 46 chromosomes.
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No, of course it wouldn't happen immediately. Is there a more plausible explanation for the break between humans and chimps? Chromosome 2 is presented as evidence of human - chimp evolution (and I agree it's quite a strong piece of evidence) but if it is not a plausible explanation for the evolution of chimp - human, doesn't that still leave us without a plausible explanation?
Well it isn't a plausible explanation for the whole evolution of humans and chimps, at most it is a component of how the populations that evolved into humans and chimps diverged. The very fact that the new chromosomal arrangement was able to spread into the population and persist argues that the infertility problems were not too severe, at least at first.
However, there's a problem here. The chromosomal difference can only significantly contribute to one population split, one speciation event. But there must have been several between us and our common ancestor with the chimpanzees. How do you narrow it down to the split between our ancestors and those of chimpanzees rather than one of the later speciation events ?