Wednesday, September 12, 2012

Interesting recent science that's not ENCODE

While people are still frothing over ENCODE, I thought I would draw some attention to some other significant works that you might fancy.

Remember that Denisovan genome?  The Siberian fossil finger bone that turned out to have a really different genome from any Homo species we'd seen before?  Well, now there's a new Denisovan genome that's even more accurate. Analysis of this new genome sequence basically reinforces the findings from the draft genome.  They estimate that modern humans from Papua New Guinea derive about 6% of their genetic alleles from ancestral interbreeding with Denisovans.  They also note significantly fewer Denisovan alleles on the X chromosome, which might suggest a one-way gene flow from Denisovan males into the ancestral Papuans.  It might also suggest some kind of hybrid incompatibility or selection or population substructure.  The authors also suggest that the Denisovans had a smaller population size than modern humans due to the frequency of non-synonymous substitutions.  They also note that the Denisovan had alleles for dark hair, skin, and eyes, and that they likely share the modern human karyotype of 46 chromosomes.

When the Neandertal genome first appeared with its evidence of interbreeding between Neandertals and the ancestors of modern humans, I was sharply critical of Reasons to Believe, which you may recall holds that Neandertals are not human descendants of Adam and Eve.  To maintain that position, RTB advocated bestiality to explain how Neandertal alleles could end up in the genomes of modern humans.  I found that to be shocking and fraught with theological problems, not to mention entirely unnecessary if they would just admit that Neandertals are humans too.  In light of the Denisovan findings, I find it very interesting that while RTB was quick to trumpet ENCODE, I can find precisely nothing about the Denisovans on their website.  Don't believe me?  Search for yourself.  Meanwhile, the interbreeding of Denisovans and the ancestors of modern humans continues to be quite consistent with my own position that Denisovans are human descendants of Adam and Eve.

Meyer et al. 2012. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science DOI: 10.1126/science.1224344

In the same issue of Science that announced the new Denisovan genome, there's a report on antibiotic resistance in soil bacteria.  Soil bacteria?  Why would there be antibiotic resistance in soil bacteria?  What's even more interesting is that the antibiotic resistance genes found in the soil bacteria are 100% identical to antibiotic resistance genes from human pathogens.  There were integrase and other transposon-type genes associated with these antibiotic resistance genes, implicating horizontal gene transfer as the source.  Here's the $64 question: Did the soil bacteria transfer them to the pathogens, or did the pathogens transfer them to the soil bacteria?  Or maybe a little bit of both?  Complicating matters is the widespread use of antibiotics in livestock, whereby antibiotics could enter the soil by manure, thus providing a selectional advantage for soil bacteria to be resistant to antibiotics. The authors don't draw any conclusions in that regard, and I'll be interested to follow this line of research.  Any way you slice it, bacteria are really good at sharing DNA.

Forsberg et al. 2012. The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens. Science 337:1107-1111.

In other news, Marcus Ross alerted me to a report of Rapid, Long-Distance Dispersal by Pumice Rafting in PLoS One.  It's definitely interesting.  I like rapid dispersal, and I like long-distance dispersal.  The species dispersed, however, were marine species, although not all were microscopic.  For a creationist, the interest here is in post-Flood dispersal, but I'm not sure that this would help all that much for terrestrial critters.  Immediately after the Flood, there would certainly be a lot more pumice around, which might help move things around the ocean.  I'd like to see some other creationists' take on this report.  Whatever its significance for creationists, it's a really interesting report.

Bryan et al. 2012. Rapid, Long-Distance Dispersal by Pumice Rafting. PLoS One 7(7): e40583.

Finally, PNAS has a report on Triassic(!) amber with two modern-looking gall mite species inside.  I'm not one to get too excited over "living fossils" or evolutionary "stasis," but I thought it was a really interesting report.  I do think there's something interesting about the stability of "types" (baramins?) in the fossil record.  Don't get me wrong, I don't think it's a home run for creationism or a "huge problem" for evolution.  It's just interesting.  That's all I'm saying.

Schmidt et al. 2012. Arthropods in amber from the Triassic Period. PNAS 109:14796-14801.

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