February 15, 2009

Sunday science sum-up: More Darwiniana, the neanderthal genome sequence

In response to the fact that I have less time than I would like to sit down and write longer in-depth entries, I thought I'd try posting shorter commentaries on a semi-regular basis.

This week has of course been dominated by Darwin Day, and I would like to amend the list of recommendations in my previous post with a few more entries:

- Leave it to Carl Zimmer to write the most informative and enjoyable summary of Darwin's significance. Most importantly, it addresses what giant leap forward we have taken since - The Ever Evolving Theories of Darwin.

It's only fitting to recognize the accomplishments of a great biologist. But there's a risk to all this Darwinmania: some people may come away with a fundamental misunderstanding about the science of evolution. Once Darwin mailed his manuscript of On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life to his publisher, the science of evolution did not grind to a halt. That would be a bit like saying medicine peaked when Louis Pasteur demonstrated that germs cause diseases.

Today biologists are exploring evolution at a level of detail far beyond what Darwin could, and they're discovering that evolution sometimes works in ways the celebrated naturalist never imagined.

- Little known fact is that many biologists, while well-versed in evolutionary theory, actually haven't read the whole volume that set it all in motion. Out of those that have, few have read the whole thing more than once. This feature in the latest issue of Current Biology departs from that - a group of scientists sit down to re-read 'On the Origin of Species' and write down their impressions from their own unique experiences and perspectives - (Re)Reading The Origin.

Another interesting thing that happened this week, on Darwin Day actually, was the announcement of the first rough draft of the neanderthal genome by researchers from the Max Plank Institute for Evolutionary Anthropology. The work was announced by Svante Pääbo in a press conference this past Thursday. You can watch a video here. Several news stories in the latest issue of Science highlight the details and the potential of this work.

I had the opportunity to hear Svante Pääbo talk at the "Building Complex Brains" symposium last June and this is what I wrote regarding the neanderthal genome in a previous post.

Finally, we heard from Svante Pääbo of the Max Planck Institute for Evolutionary Anthrolopogy in Leipzig on the subject of the genomic perspectives on human origins. I've written about his research on the FOXP2 gene before, but this was a more general talk, only using FOXP2 as an example. A lot of it was on the progress of the sequencing of a neanderthal genome, but also of course about how comparative analyses of the human genome and the neanderthal genome will shine a light on a very crucial point of our evolution. Will we be able to identify genes that were important in our evolution? Will we be be able to define what it is that makes us specifically human? It's difficult to pinpoint what makes us "so special" when more and more of those traits we jealously guarded as "ours" appear in traces in other animals - perhaps looking at the genome, rather than looking at our behaviors and abilities, will be the key. But to do so we need to know more about that last step in the road to where we are today.

It's unquestionably a hugely interesting development and the technology advanced in order to make it possible is impressive. The challenges of virtually "reviving" an extinct genome are humbling - first of all you need to identify a fossil in which ancient DNA has been preserved then the small fragment of bone from which the DNA was extracted needed to be positively identified as neanderthal, and even then only approx. 4% of the total DNA in the sample is of interest as extensive contamination from modern human DNA as well the the decay of DNA into small fragments will do their part.

Reactions to this report have been enthusiast but careful, with reason. They don't have the whole genome sequence so far, "only" approx. 60%, and they have only covered these regions 1,2 times on average. Due to degradation and low coverage it's reasonable to expect a lot of corrupted sequences and sequencing errors. Many genome sequences with higher coverage from existing species are quite problematic in this respect, which makes me question the extent of the analysis we will be able to make before a genome sequence with higher coverage is published. Pääbo seems to think that a 15-20-fold coverage will be possible in the future but even now he hints at many very interesting findings, including signs of selective sweeps in humans compared to the neanderthal genome. This means that they have found parts of the genome and maybe analyzed specific genes that have mutated in the modern human lineage and given such advantage that they are now fixed in the entire human population.

So far no actual publication is clearly in sight, although I can detect several hints that the publication is pretty close. I think most of us will wait and see what answers they deliver with a deeper analysis before cheering loudly.

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