Mailund on the Internet

It’s been more than a week since I last posted here.  I’ve been busy.  A different kind of busy than usual, though.

Yes, there’s the usual work on my research, plus I’m planning a new class that’s taking some time to do, and there just isn’t much to write about either here right now about that.  In addition to that, though, I have been reviewing papers a lot this month.  I usually review less than five papers a month, but this month I’ve reviewed ten papers so far and still have five unread manuscripts on my desk.

That is plus the papers I’m handling as editor, but luckily I only have a few of those at the moment.

I usually spend about a day per manuscript, depending on the manuscript of course.  Some are short and can be handled in a few hours – at least if there are obvious arguments for judgment in one direction or another – but some takes me a lot longer to handle.  Math heavy ones mostly, where I need to check a lot, or where I need some time to think about the results in some detail.  Those takes me a few days, but I usually split that up over a week or so, to give my subconscious some time to work on it as well.

Anyway, with 15 papers in one month, and a day per paper, you can see how fast reviewing eats up my time.  And I cannot blog about any of them, of course, but will have to wait for the papers to get published.

I usually always accept to review a paper if I think it is something I think is within my field of expertise (not that I usually accept the paper, but I do accept to review it).  Usually, I find reviewing quite enjoyable as well.

Yesterday, for the first time as I can remember, I declined to review a paper because I was too busy.  I even feel bad about that.  I probably shouldn’t, but I do.  I realize that I have to prioritize my time between my own research and paper reviews – especially considering that the former gives me a lot more credit on the CV than the other – but I still feel bad about it…

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Genetics and genomics

• Evidence that two main bottleneck events shaped modern human genetic diversity (Anthropology.net)
• Double the bottlenecks (John Hawks)
• Sergey Gavrilets on the two fitness landscapes (John Hawks) — interestingly, we just read this chapter for our book club at BiRC last week…
• The medium-rare biosphere (Byte size biology)

Paleontology and ancient DNA

• The Ardipithecus pelvis (John Hawks)
• Darwin, “Ardi” and the African apes (Laelaps)
• What conclusions can we draw from Neanderthal DNA, pt. 1 (A replicated typo)
• What conclusions can we draw from Neanderthal DNA, pt. 2 (A replicated typo)

Programming / computing

• Why desktop multiprocessing has speed limits (Computerworld)
• Google: Computer memory flakier than expected (CNET)
• OpenCL Tutorial: Shared memory kernel optimization (MacResearch)
• Unit testing in Coders at Work (A billion monkeys can’t be wrong)

Research life

• Speaking styles and papers: Academia divided (Expression patterns)

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As I have said before, I don’t know enough paleontology, so I’m just speculating now and would love to be corrected by someone with more knowledge in the field…

One thing that bothers me with the whole Ardipithecus brouhaha is its age and its relationship with chimps.  Simply because I cannot completely reconcile it with the genetic estimates of speciation with chimps.

Estimating speciation times

First some observations on species divergence, genetic distance and fossils… If we consider even the simplest scenario for speciation — an allopatric speciation (and more complex scenarios will just exaggerate the problem — a population is split into two that eventually evolve into separate species.

Due to the population genomics in the population before the split, individuals in the two resulting populations will have different degrees of relatedness within and between the populations.  On an individuals level, eventually everyone within a population will be more related than between populations, but because of recombination the relatedness between the populations — and eventually species — will vary along the genome and the average sequence divergence will be greater than the divergence between the populations / species.

If we date the speciation by considering genomic differences, we are thus overestimating the time back to the ancestor.

If we consider morphological changes between the two populations — as we do if we consider fossils — those will necessarily have evolved after the split.  At least if we are looking at morphological traits that clearly separates the two populations and not just variation within a single species.

So for fossil evidence we will get an underestimate of the speciation time.

(Please ignore that the skull in the illustration is a gorilla, it was what I had lying around when I made the figure, but my focus is on chimps so that is the speciation I am illustrating)

Now, human-chimp sequence divergence looks like it is about 6 million years ago, but remember that this is sequence divergence and not species divergence.  The speciation event must be more recent.

Through statistical models of population genetics we can estimate the speciation time from the sequence divergence time and if we do, we get estimates of the human chimp species divergence closer to 4-5 million years ago (Dutheil et al. 2009; Hobolth et al. 2007; Patterson et al. 2006).

This puts Ardi, at 4.4 million years ago, smack on top of the speciation event!

Humans, chimps and Ardipithecus

Now I’m not saying that I trust the genetics more than the paleontology.  I understand it a whole lot better, but that is a different issue.

One thing that is clear, though, is that if the genetic estimates are true, then Ardipithecus cannot have evolved a whole lot away from the common ancestor of man and chimp.  It actually could be the last common ancestor, just judging from the time estimates.

If we believe that Ardi shows us that many of the traits we believed were derived traits on the human line are actually ancestral traits that changed on the chimp line instead, then we could put Ardi close to the human-chimp split and reconcile the genetic and paleontological estimates for the time of the split.

If it has evolved significantly towards humans it is back to the drawing board for the genetic models.

Which is it?

I really look forward to see what John Hawks has to say about it when he gets to it in his Ardipethicus FAQ…

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Sorry, my web server was down over the weekend, but it is up again now and it is time for my list of favorite blog posts from last week:

Ardi

• Ardipithecus FAQ (John Hawks)
• Climbing on the branches of the family tree: The hands of Ardipithecus ramidus (A primate of modern aspect)
• The feet of Ardipithecus ramidus (A primate of modern aspect)
• Ardipithecus ramidus (Pharyngula)
• At long last, meet Ardipithecus ramidus (Laelaps)

Evolution

• Does evolutionary biology make predictions? (Genomicron)
• Where did you get that preposterous hypothesis? (The atavism)
• The “Theorum” of evolution (Tom Paine’s Ghost)

Genetics and genomics

• Viruses and icebergs (Mystery rays from outer space)
• It ain’t necessarily so (Byte size biology)

High performance computing

• NVIDIA’s next generation GPU architecture has a lot for HPC to love (insideHPC.com)
• NVIDIA takes GPU computing to the next level (HPCwire)
• NVIDIA’s Fermi takes direct aim at supercomputing (Ars Technica)

Paleontology

• Hobbits might not be a Homo after all (Anthropology.net)

Physics

• Dark matter part III: Dark matter of modified gravity? (Starts with a bang)
• Dark matter part 3.5: When clusters collide! (Starts with a bang)

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