Kinds and diversification through microevolution and hybridization

Hi TB: I agree with my colleagues here that starting a new "kinds" thread was a great idea.

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Originally posted by TB:

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There are creationists who have been thinking about this - see their barimin stuff. But I prefer the genomics angle and when we've got more genomes we'll have a better idea.

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I have read some of the baramin stuff. It appears very loooong on sheer out-of-thin-air speculation and really really short (microscopic ) on actual data. Perhaps you might point me to a reference you feel provides compelling evidence that any of the so-called baraminologists have the first clue what they're talking about?

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What gene families distinguish? To a large extent I'm saying any gene families will. But if you have two identical genomes apart from one gene family it is certainly possible that the 'new' gene is one that became a pseudo-gene in the other so that should be considered. So I would suggest studying large numbers of genomes and see if there is an abrupt jump where suddenly a whole swag of genes comes in. If this occurs across life we would identify that with kinds. The data does approximately fit this scenario already but we need more genomes to really see.

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So you're saying (if I understand you) that each kind will have a completely unique genome? That no genes from the same family will be shared across kinds? I think you just shot yourself in the foot. No one doubts there are genetic differences between organisms - the more distantly related, the more differences appear. However, this doesn't translate to novel protein families. Unless you can show which ones actually delimit organisms (good luck), you have no argument.There's a lot of mainstream interest in this subject. The Promise of Comparative Genomics in Mammals. And another, Phylogenetic Origin of Human Chromosomes 7, 16, and 19 and their Homologs in Placental Mammals, which although dealing with chromosome homologs, talks quite a bit about the evolutionary development and divergeance of various proteins.

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I do plan (in my own mainstream research) to get into the sorts of questions you have asked (eg cat vs dog families). But, as you know, we only have two mammalian genomes and the other genomes we have are very differnet. But I am interested in catching up on the comaprative genomics of fly vs. mosquito for example.

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We may not have the complete genomes of many animals yet, but there is nothing indicated to date in those parts of the genomes that HAVE been sequenced that show the existence of whole unique families rather than individual genes.

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I agree this needs to go beyond hand waving. But at this point it is without doubt that there are core genomes, there are sub-genomes for each novelty (like the immune system) and these sub-genomes are characterizable by unique protein families. That is undeniable. I have started a new project in this area and I will report here even before I publish, OK!

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Sure - if all you're saying is that data at some unspecified point "in the future" may lend some evidence to your contention about protein families, that's fine. However, the problem has been here that you continually assert the existence of these families as one of your key arguments against so-called macroevolution. The truth is that nothing in any comparative genomics study to date shows even the inkling that there might be protein families that are unique to even taxonomic classes, let alone family or genus.Could there be? Of course. Is there ANYTHING ANYWHERE in the literature that even hints at it to date? Nope. IOW, you're using a pure "god-of-the-gaps" argument. Here's the catch: until and unless such data is produced, you cannot use the hypothetical existence as proof that your putative kinds exist. It's pure 18th Century taxic discontinuity - which is no more scientifically valid today than it was 200+ years ago.