Went to Francis Collins’ afternoon talk “fireside chat” with David Baltimore on the future of medicine, as illuminated by genomic work. Too much introduction and rambling biographical information, but some good discussion anyway. I thought his best comments had to do with the positive effects of the open data model that the Human Genome project initiated – it’s had a long lasting impact on the entire field of genomics, and thank goodness! Also, he mentioned that as of now, there aren’t any major studies seeking to correlate and analyze the relationships between genotypes, phenotypes, and environment in the human population, and that such a study is really what’s needed to truly understand what’s actually heritable, what our real low frequency (rare allele) genetic variation is like, and what kinds of effects environmental factors play. He pointed out, interestingly, that we don’t need to wait until thousand dollar genomes are available to start this study – what we need to do is get people signed up, and start tracking their health history and environmental factors, and we can sequence them when it becomes cheap enough. He suggested that we ought to do this for roughly 500,000 people, and that it would likely cost on the order of half a billion dollars a year, and need to run for a few decades. And then we’d know, and medicine would be forever changed. He also suggested that those $1000 genomes are likely on the order of 5 years away. Really, once we’ve got fast, cheap sequencing – this study will almost do itself, so long as we can at some point get access to the medical histories and genomes of people. The real value add is in starting it now, so we have the information as soon as possible, and in getting all the environmental/lifestyle data, in addition to the healthcare records.
A bill duplicitously entitled the “Fair Copyright in Research Works Act” (HR 6845) has been introduced in congress with the goal of prohibiting federal science funding agencies such as the NIH, NSF, NASA, etc. from making their grants contingent upon open access to the published results. Currently, a large proportion of federally funded biomedical research comes with a requirement that the results be listed in the Open Access PubMed database. Proponents of Open Access journals have seen this policy as an example of the way things should work – publicly funded research should have publicly accessible results – but now this system, and progress in that direction, is in jeopardy. HR 6845 would prohibit any federal funding agency from making their funds contingent on public access to the results.
The bill has been referred to the House judicial committee. Our representative, Adam Schiff, is on the committee. If you support open access to scientific publications – especially publicly funded scientific research, please contact him and tell him to oppose the bill. Senator Feinstein is on the Senate Judiciary Committee, and should also be contacted.
More information including background on the NIH open access policy can be found at the Alliance for Taxpayer Access. You can track the bill’s progress at OpenCongress.org. If you do call, write, fax, or e-mail your representative or senator, please e-mail Jennifer McLennan (jennifer [at] arl [dot] org) and let her know.
Michelle and I just finished reading The Botany of Desire by Michael Pollan. It was good. He can get a little rambling at times, but overall it was entertaining and enjoyable. The book follows the relationships between people and four plants, through history. The four plants are: apples, tulips, cannabis, and potatoes. It pairs with them four desires, respectively: sweetness, beauty, intoxication, and control. The connections are more than a little tenuous, but the histories are certainly worth examining. The apple chapter in particular has inspired me to learn more about hard cider (since it turns out that’s largely what Johnny “Appleseed” Chapman’s apples were used for, all across 19th century America). And who can resist an examination of cannabis’s relationship with humans, written at least partially while stoned?
One theme Pollan has touched on repeatedly, in this book and his others, is the competition between Apollonian and Dionysian impulses in nature and society. Apollo representing order and control, Dionysus wildness and chaos, both being utterly necessary for civilization to be dynamic and persistent, for knowledge to increase and broaden through time. E.g. our Apollonian monocultures of Russet Burbank potatoes are vulnerable because of their uniformity, but are also productive and economically efficient. The Andean potato farmers of antiquity grew dozens of different varieties in different micro climates, all the while allowing the plants to hybridize with the local wild potatoes, maintaining a possibly less productive, but certainly more diverse and robust system of potato cultivation, in which new biological innovation was constantly taking place, and in which the farmers were well protected against catastrophic collapse in any one year… unlike the potato farmers of Ireland in the 1840s. The potato chapter in particular focuses largely on a very recent interaction with the potato: the introduction of a genetically engineered variety called the “New Leaf” by Monsanto, that produces Bt toxin to guard the plant against the Colorado potato beetle and other insect pests. Continue reading We need more Dionysian Science
Michelle and Jeremy and I went to a talk entitled Sacred Science at Caltech last night put on by the The Skeptics Society, it was part of Suart Kauffman’s book tour for Reinventing the Sacred. It was okay, but it could have been great. If you’re interested, he gave essentially the same talk at Beyond Belief in December (41 minutes long).
His purpose seemed to be to outline a semi-formal proof that atheistic humans are justified in reinventing the sacred for themselves as something which is wholly naturalistic, and that doing so has great value. I agree, but I’ve agreed for years. I guess some atheists haven’t yet come to this conclusion. This is the same conversation that we ended up in at Amy’s Salon a couple of months ago, and I’m always like “Yes, YES already, so let’s just get on with reinventing it, instead of continuing to try and convince ourselves that we should do it. It’s a meta conversation. We’re talking about talking about what we think should be revered. Are we afraid that we won’t be able to come to any kind of common ground, and that just having the conversation will somehow splinter us into even smaller non-theistic sects?
Continue reading Meta-reinventing the sacred, yet again
Chris Mooney and Matt Nisbet came to Caltech and gave SASS talk on Monday night, and ran a science media messaging workshop entitled Speaking Science Bootcamp all day Tuesday. It was great. Anybody who’s getting a PhD in science should go through at least that much communication training, and if they’re in an area that has policy implications, or they have any interest whatsoever in doing outreach or communication of science, they should have a week long course on the same material.
Continue reading Science Framed at Caltech
I just finished reading Richard Alley’s little book The Two Mile Time Machine. It’s by far the best climate change book I’ve read so far. More information, less polemic. Personally I would have loved more plots and fewer long complex sentences explaining the relationships between different climatic variables, but maybe that’s just because I’m a scientist. Continue reading The Two Mile Time Machine by Richard B. Alley
The futurist and physicist Freeman Dyson wrote a piece for the New York Review of Books on Climate Change. He’s a very (very) bright guy, but I think he is wrong. Actually, I think that the whole framing of the climate issue in the media, in the government, and possibly in many scientific circles, is wrong. Continue reading Freeman Dyson on Climate