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Bay Area Population Genomics

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I am old enough to remember card catalogs. They did not make me happy. As a small child I noticed omissions and incorrect classifications so often that for long periods of time I would simply avoid the catalog, and methodically consume books from whole sections of the public library in line with my preferences through tedious manual browsing. I am also old enough to remember when the internet was still primitive in its data organization and storage capacity (i.e., pre-Google, pre-Wikipedia), and the library was the first, last, and best, recourse toward retrieving data. When Braveheart was released in 1995 I ran down to the local university library to see if I could find more about the protagonist’s biography than was present in Britannica. By chance there was a book available on the life and times of William Wallace, but it was checked out, and there were more than 10 holds ahead of me! This was not an uncommon occurrence in the age before the data rich internet. The reality is what I wanted to know about Wallace is probably found in the Wikipedia entry, but then there was no Wikipedia! These are just a few of the reasons that I have little patience for neo-Luddites such as Nicholas Carr. When I read Carr’s “old man” jeremiads I always wonder, “son, were you even around back in my day?”*

This line of thought crossed my mind as I was sitting in the audience at BAPG IX**; the ninth Bay Area Population Genomics meeting. Started by Dmitri Petrov at Stanford, it brings together research groups at from Petrov’s institution, Berkeley, UCSF, and UC Davis which work at the intersection of population genetics and genomics (I noticed a non-trivial UC Santa Cruz contingent this time around, so I suspect it’s getting more popular). BAPG illustrates the fact that the internet changes the way we communicate and consume information, but in a synergistic, not antagonistic, fashion in relation to traditional person-to-person interactions. The core elements of the meetings would be recognizable to someone from 1990 (perhaps replace PowerPoint with transparencies?), presentations and posters. But these two informational centerpieces are embedded in a scaffold of richer transmission and dissemination modalities. I first heard about BAPG through an email notice. Many people no doubt became aware via Twitter and blogs (which may have triggered word of mouth or emails). Prominent researchers in population genomics such as Dmitri Petrov, Graham Coop, and Carlos Bustamante, have robust and accessible internet presences, so you can hear about what their labs are doing from the horse’s mouth, so to speak. Not only can events like BAPG be organized rapidly with minimal overhead because of the ease of the spread of information, but the proceedings are often relayed on Twitter in real time.

And yet the fact that the BAPG meetings are “in the flesh” reflects two realities. The prosaic one is that this sort of meeting is probably only feasible in the San Francisco Bay region, due to the existence of the Berkeley-Stanford axis, as well as concentration of private sector genomics related firms.*** The deeper truth though is that even academics as comfortable with computation and information technology as population genomicists still thrive on interpersonal contact face to face. They are human. Despite all the worries about the ubiquity of smart phones, tablets, and notebooks (all on display at the meeting!), and their impact on social interaction, there was a copious amount of old fashioned free spirited conversation. WALL-E is not real. Yet.

The human element can not be abolished, only modified. And unforutnately the scarcity of human interest is often the shortcoming, not the technology. I thought of this while taking in Kelley Harris’ fascinating presentation on the distribution of mutations across the genome. Using 1000 Genomes data Harris found that point mutations are not randomly distributed; they cluster. And, they exhibit unexpected patterns in their proportions of transversions to transitions. As I said, these were very interesting results. But I wondered why it was that Harris was the one who had to discover this. As a Harvard and Berkeley educated mathematical biologist she obviously has some skills and aptitudes, but it isn’t as if there aren’t many competent thinkers across the Bay area working at places such as Google who couldn’t have done the same in their spare time. The data is there. It reminds me of a conversation I had with a very prominent statistical geneticist who I visited with in Cambridge. He wondered why bright minds around the world weren’t excavating the same mathematical and computational gold freely available to his research group.

I hold that the problem here has to do with the humans, and not what technology is doing to the humans. As outlined in works such as The Lunar Men it seems that the diversion of the energies of those with leisure and inclination toward intellectual pursuits is subject to the whims of fashion and cultural Zeitgeist. The problem is not the technology. Technology is used by people, to serve their interests and preferences. If you have a problem with the preferences of the human race, take that up with the human race, don’t crucify technology for the sins of humanity.

* I am joking, as I know Carr is older than I am.

** For your amusement. The keynote speaker was rattling off a series of population genetic parameters. So the individual directly in front of me was furiously Googling, and for about 30 seconds he was browsing one of my blog entries! I was tempted to tap him on his shoulder and inform him that the author was sitting directly behind him, but I did not do so.

*** I am aware there is now a southern California equivalent.

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Since the last post on genomic tools was a bit parochial, I figure it’s acceptable to put up this notice for the Bay Area Population Genomics meeting on June 8th. Registration closes on June 3rd (that is, Monday). Here’s the announcement:

Hello Everyone,

We are excited to be hosting the 8th meeting of the Bay Area Population Genomics group at UCSF Mission Bay on June 8th! Thanks to support from and the Institute for Quantitative Biosciences (QB3 @ UCSF), this conference will include breakfast and lunch. In addition, we will also have a reception during the poster session, so we highly encourage you to preview your work at BAPG before heading out to summer conferences.

Please register at, and sign up to give a talk or poster. Registration is again free, but required by June 3rd.

There is paid parking in the lot/garage at the corner of 4th and 16th streets, and we have a limited number of parking passes for people that sign up to present and/or make a strong effort to carpool (please email me for details).

We are very much looking forward to seeing you at UCSF in a few weeks!



Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"