There’s something intrinsically hilarious about a stable isotope geochemistry paper that begins:

By purchasing and eating 1 serving of the substrates of this study (i.e., 1 hamburger, 1 chicken sandwich, and 1 small order of fries), the consumer has gained 50% of that day’s recommended calories, 80% of carbohydrates, 75% of protein (90% if the consumer is a woman), and the full day’s limit of dietary fat at a cost of $3.

and includes the sentence:

Fastfood was purchased from America’s top 3 chains: McDonald’s, Burger King, and Wendy’s; each rest aurant was sampled at 3 locations within 6 major U.S. cities: Los Angeles, San Francisco, Denver, Detroit, Boston, and Baltimore [supporting information (SI) Table S1]. At each location, 9 items were purchased: 3 hamburgers, 3 chicken sandwiches, and 3 orders of fries.

Nonetheless, the point the paper makes — that corn permeates the American diet through a multitude of intermediaries — is quite serious.  Simon Donner has more.


Nature endorses…

In what I believe is a first, Nature (the scientific journal, not the universe) has issued a presidential endorsement, for Barack Obama.

There is no open-and-shut case for preferring one man or the other on the basis of their views on these matters. This is as it should be: for science to be a narrow sectional interest bundled up in a single party would be a terrible thing. Both sides recognize science’s inspirational value and ability to help achieve national and global goals. That is common ground to be prized, and a scientific journal’s discussion of these matters might be expected to stop right there.

But science is bound by, and committed to, a set of normative values — values that have application to political questions. Placing a disinterested view of the world as it is ahead of our views of how it should be; recognizing that ideas should be tested in as systematic a way as possible; appreciating that there are experts whose views and criticisms need to be taken seriously: these are all attributes of good science that can be usefully applied when making decisions about the world of which science is but a part. Writ larger, the core values of science are those of open debate within a free society that have come down to us from the Enlightenment in many forms, not the least of which is the constitution of the United States…

The Oval Office is not a debating chamber, nor is it a faculty club. As anyone in academia will know, a thoughtful and professorial air is not in itself a recommendation for executive power. But a commitment to seeking good advice and taking seriously the findings of disinterested enquiry seems an attractive attribute for a chief executive. It certainly matters more than any specific pledge to fund some particular agency or initiative at a certain level — pledges of a sort now largely rendered moot by the unpredictable flux of the economy.

This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.

The Anti-Science Party

John McCain is against Adler Planetarium.

Sarah Palin is against research in fruit flies, one of the most basic model organisms in animal genetic research.

If the worst examples of earmarks the GOP ticket can come up with are a token amount of support for a major institution promoting science education and fundamental biological research, they’re really hard up.

GPlates on the Mac

This post will probably be of interest to very few people, but it should go somewhere, so it’s here. GPlates is a promising new program for managing four-dimensional geological GIS-type data. Right now, it mostly handles reconstructing plate positions based on data in text files, though it also has some simple features for digitizing new data. It also doesn’t compile on the Mac as the code is shipped, but it can with a few slight changes.

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Freezing Science

According to Science, Ike Brannon, a senior policy advisor to the McCain campaign, indicated that science funding would be frozen at FY 2009 levels in the first budget proposed by a McCain administration:

Next year’s federal budget may not contain a penny more for research and education if Republican Senator John McCain (AZ) is elected U.S. president and has his way with Congress. An aide to the McCain campaign delivered that sober fiscal message today to science lobbyists, who pressed him unsuccessfully for leeway in the candidate’s promise to curb federal spending by imposing a 1-year freeze on domestic discretionary spending.

Such a freeze would translate into many hundreds of fewer grants funded by NSF, as well as a couple hundred fewer graduate research fellowships. Leaving science out to dry: that’s putting country first.

These speak for themselves, I think. (More here.)

I’m not a microbial ecologist, though I’ve studied the field a bit. I was invited to speak at the International Symposium on Microbial Ecology in the climate change session, to talk about my work on the Paleocene/Eocene Thermal Maximum and what magnetofossils indicate about changing microbial ecology during that ancient global warming event.

The big new breakthrough since I last took a microbial ecology class four years ago seems to be a technique known as “tag  sequencing”, in which researchers target short, highly variable sub-sequences of small sub unit RNA. Rather than sequencing the whole SSU RNA (the gene sequencing traditionally used for identifying organisms), which is typically a couple thousand base pairs long, they focus on regions of a hundred base pairs or so that are subject to relatively rapid evolutionary change. The shorter sequence length allows sequences from many more organisms to be sampled, which means that environmental studies capture a more accurate profile of all the microbes in a community.

In a session on the human microbiome, Rob Knight presented a comparison of tag sequencing analyses from a variety of environments. It turns out that the first order division in microbial community composition is between freshwater and saltwater environments. Invertebrate gut microbiota resembles those of the environment they live in; vertebrate gut microbiota resemble neither freshwater or saltwater environments. Among the vertebrate gut microbiota, the second order division of diversity is based upon diet: carnivores, omnivores, hind-gut herbivores, and fore-gut herbivores all fall into different classes. Humans have fairly typical omnivore gut microbiota.

But… that’s the higher order pattern of diversity. When looked at in detail, there’s quite a bit of variability in microbes between different individuals. They are very few specific taxa that are common to all human gut microbiota, and it’s similar for the rest of the human microbiome. Fun fact: on average, less than 20% of the taxa present in the skin microbiome of your right hand are present in the skin microbiome of your left hand.

On another topic, a number of people talked about the interaction between methane oxidation and nitrogen cycling in soil. Apparently, fertilizing soil with ammonium causes some bacteria to shift from oxidizing methane to oxidizing ammonium, thereby increasing the flux of methane into the atmosphere. Nobody presented estimates as to how significant this effect is globally, but it’s something worth thinking about.

Something else I learned: the word “Eocene” in a title apparently frightens audiences away. It shouldn’t be this way. The Eocene needs to become as much a popular concept as the Jurassic, and a representing of the sort of world that can develop under global warming. Eocene Park, anybody?