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December 29, 2011

Shrimp on treadmills

Politicians who didn't hesitate to spend a trillion dollars invading and occupying Iraq apparently think they can win a few votes from ignoramuses by ridiculing spending on scientific research. Their latest target is "shrimp on treadmills." Here's a NSFW (National Science Foundation Website) link to the project in question.

Looks worthwhile to me. They're studying how bacterial infection affects respiration and swimming ability in shrimps and crabs. One could argue that the main beneficiaries are the shrimp and crab industries, so they should have paid part of the cost. But work with one species often helps us understand other species. Much of what we know about genetics of humans and crops goes back to research done with fruit flies. I'm glad Thomas Hunt Morgan didn't have to depend on the banana industry to fund his research.

I agree that we should be scrutinizing public spending to make sure we're getting value for money, but NSF is a model of efficiency and transparency. How about starting with the most-expensive programs and working down? And it seems only fair to give those criticized a chance to respond.

Evolution tourism

You've heard of ecotourism? This month's Smithsonian magazine has an article on "evotourism", highlighting ten sites around the world that tourists interested in evolution might want to visit. The Smithsonian's own Museum of Natural History isn't one of the ten sites, although they have a lot of great material on evolution, as I discussed in an earlier post. The two sites nearest to my home are Ashfall Fossil Beds Historical Park, in Nebraska -- the Nebraska State Capitol has a great evolution-themed mosaic on the rotunda floor -- and Isle Royale, Michigan, where coevolution of wolves and moose has apparently led to larger moose. There are two sites in Europe and one each in Asia, Australia, Africa, and South America (if the Ecuadorian territory of the Galapos Islands is considered part of South America). Smithsonian's evotourism website has more.

December 24, 2011

BRCA linked to reproduction-versus-longevity tradeoff

This is amazing. BRCA mutations have been linked to increased risk of breast cancer and ovarian cancer. Yet these mutations are not that rare. Hasn't natural selection been doing its job? Or is there some benefit that balances the risk?

The authors of "Effects of BRCA1 and BRCA2 mutations on female fertility," recently published in Proceedings of the Royal Society, hypothesized that women with a BRCA mutation might have more children, even if they don't live as long, on average.

Today, enough couples use birth control that the number of children born depends on preferences for family size, not just innate fertility. So the authors compared women (with and without the mutation) born before 1930. They used the Utah Population Database, which has data on births, deaths, and family relations for large numbers of Utah residents. Most of those women are no longer alive, however, so how can we know whether they had the BRCA mutation or not?

The authors used a variation on ancestral state reconstruction. When two women had the same BRCA mutation -- apparently there are various versions -- the authors assumed that their most-recent common ancestor had that mutation also. They also identified a number of controls -- women who presumably did not have a BRCA mutation, because none of their descendants did -- from the same time period.

So, was there any difference in fertility between women with versus without a BRCA mutation?

Yes. For women born before 1930, those with a BRCA mutation had an average of 6.2 children, while controls had 4.2. There wasn't much difference in survival up to about age 50. By age 75, however, about half of the women with a BRCA mutation had died, while 80% of those without the mutation were still alive.

How does birth control change this picture? More recently, women with a BRCA mutation had an average of 4.1 children, versus 3.4 for controls. Is that difference small enough that we can expect the BRCA mutation to become less common over generations?

Natural selection increases the frequency of whatever genes lead to the most descendants, whatever the cost in human misery. Natural selection will tend to preserve the health of postreproductive women if they contribute to the survival and reproduction of their relatives, particularly their own children and grandchildren. But it must take a lot of grandmothering to make up for having two fewer -- or even 0.7 fewer -- children.

I've written about trade-offs between reproduction and longevity before, including our theoretical work showing that natural selection can favor mechanisms to switch between reproduction and longevity, depending on whether overall population size is increasing or decreasing.

December 16, 2011

This week's picks

High Relatedness Is Necessary and Sufficient to Maintain Multicellularity in Dictyostelium

Evolution of a mimicry supergene from a multilocus architecture
Cause and Effect in Biology Revisited: Is Mayr's Proximate-Ultimate Dichotomy Still Useful?

Trophic network structure emerges through antagonistic coevolution in temporally varying environments

December 15, 2011

Fighting back against fake-conference spam

An anonymous scientist apparently figured that if BIT is inviting speakers randomly, he could invite himself, submitting an obviously-fake CV and satirical "abstract." BIT not only failed to spot the obvious joke, they invited him to chair a session. (For an additional fee, maybe?)

December 14, 2011

Thanks, Google Scholar !

Keeping publication lists on web pages up to date is a task that often gets neglected. Now Google has made it easy. Search Google Scholar for "Ford Denison" and you should get this page, which took me about three minutes to set up. The list of publications is updated automatically, supposedly, and it also plots citations over years and provides links to abstracts and sometimes to PDFs.

If you're a published scientist, information on how to set up your own page is here.

December 8, 2011

This week's picks

Just when I was starting to get back into the lab, the proofs for my book on Darwinian Agriculture arrived. It's due out in June or July, but I have to check everything and do the index by January. So I only have time to read the abstracts of these interesting-looking papers.

Equitable decision making is associated with neural markers of intrinsic value
"making equitable interpersonal decisions [behaving fairly] engaged neural structures involved in computing subjective value, even when doing so required foregoing material resources... not simply a response to external pressure"
[In other news, people enjoy sex. In both cases, natural selection has shaped our brains based on what maximized contributions to gene pools, in past environments. I wonder how many generations it would take for this to change, in environments where fairness doesn't help you win mates or allies, or where sex is decoupled from reproduction?] "Four participants [of 19] produced no generous/equitable choices; their data could not be modeled and were excluded." [Any difference in the ancestral environments of these four? Or were they finance majors?]

Conflict, sticks and carrots: war increases prosocial punishments and rewards
[On the other hand...] "during wartime, people are more willing to pay costs to punish non-cooperative group members and reward cooperative group members."

Trade-off between warning signal efficacy and mating success in the wood tiger moth
"yellow males had lower mating success than white males" but birds don't eat them.

Global human mandibular variation reflects differences in agricultural and hunter-gatherer subsistence strategies

Fitness consequences of plants growing with siblings: reconciling kin selection, niche partitioning and competitive ability
Impact of epistasis and pleiotropy on evolutionary adaptation

December 2, 2011

Exporting Livescribe Smartpen notes as a PDF

I've been using a Livescribe pen for lab and seminar notes. The pen has a little camera that tracks dots on their special paper to record pen-strokes. Various notebooks using this paper are available, at a reasonable price. Their Livescribe Desktop software is amazingly good at searching my handwritten text, so I don't have to spend time paging through notebooks looking for the data or notes I need. Automatic backup of my lab notebooks, plus search capability... who could ask for more?

Well... a nonproprietary file format would be nice.

NSF is asking for data management plans in grant proposals now, to make sure data are stored in a format that will still be readable years in the future. These pens would be a simple way to meet that requirement, if only:

1) there were a simple way to link lab notes to computer files (photos, sequence data, instrument outputs, etc.), and

2) the handwritten notes were stored in a nonproprietary format.

Proprietary formats like DOC or XLS, which can be changed at the whim of their corporate overlords, are not suitable for data archiving. Livescribe's file format is proprietary, so that seems to rule them out for serious use.

But wait... you can output notes as PDF files. But wait... no you can't, not in the latest version. But wait... by uninstalling the latest version, and reinstalling version 2.3.4, you can. The resulting PDF is just a bitmap, so not easily searchable, but at least it makes it simple to generate a copy of the notebook. I just filled my first notebook and backed it up as a PDF using Dropbox. You can also back up your notebooks on their website, but only in their proprietary format. What happens if they go out of business, or decide to start charging for access to your data?

As long as you don't upgrade the desktop software beyond version 2.3.4, Livescribe's pen and notebook combination is worth considering.