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September 30, 2009

Off topic: Frank view of blasphemy

A couple of months ago, I read this New York Times article by economist Robert Frank, suggesting that Darwin's ideas may be a better guide to economics than (popularized versions of) Adam Smith's ideas. I was impressed and have been reading his books with considerable interest.

Many of his economic ideas parallel ideas I'm exploring in my book on Darwinian Agriculture. A singer, runner, or lawyer who's only 1% better may make ten times as much money, just as a leaf that's only 1 mm above the leaf of a competing plant may have ten times the photosynthesis. "Arms races" among humans -- working overtime will let you afford a house that is more expensive than average, so that your kids can go to a better-than-average school, but if everyone works overtime half the population still sends their kids to below-average schools -- parallel arms races among plants -- being taller than your neighbor means more photosynthesis and so more seed production, but if every plant grows taller that doesn't increase total photosynthesis and wastes resources on tall stems. And so on.

But today, in honor of Blasphemy Day, I want to summarize an interesting idea from his book, Choosing the Right Pond.

Freedom of speech is often presented as an "inalienable right", perhaps granted by (though never actively protected by) some hypothetical Creator. Frank suggests an alternative origin, based on freedom of association and economies of scale....


Although migration in and out of most countries is somewhat restricted, a sufficiently motivated person can often evade those restrictions. Mobility within countries is typically even less restricted. So freedom of association is, to some extent, a truly inalienable right.

Often, people would prefer to associate with those who share their views on particular issues. But no two people agree on everything. The larger the group, the more areas of disagreement. You may be able to find a small country where most people share most of your views, but any large country is likely to include many people with different, perhaps deeply offensive, views.

Now, add economies of scale. There are many advantages to living in a larger country. Trade within countries isn't hampered by borders or tariffs. Bigger countries have more influence on international agreements. And so on. If you want the advantages of living in a larger country, you have to accept (in some sense) sharing it with those with different views.

Back to blasphemy. Hearing or seeing their religion (Islam, Christianity, Gaea/group-selection, whatever) or national/tribal symbols insulted often upsets people. Frank argues that blasphemy may sometimes actually harm people, in the same sense that noise or smog does, even if the only physical effect is an increase in stress hormones. This was a new idea for me, but I think he may have a point. But, he continues, preventing people from speaking their mind also causes stress.

You can imagine a market-based approach to this problem, where religious zealots and aspiring blasphemers discuss how much money to exchange, and in which direction, to compensate zealots for not having to hear blasphemy or to compensate nonbelievers for restricting their freedom. But the transaction costs would be huge, particularly in a large (and hence inevitably diverse) country, where one person's blasphemy is another's dogma.

A better solution is to classify hearing offensive speech as one of the costs of living in a large country. You may object to noise ordinances that limit your right to hold late-night parties or you may think you pay more than your share of taxes. Of course you can work to change those laws, but no large group is going to agree with you on everything. Get used to it.

Or move to some tiny country whose laws are more consistent with your views. But be prepared for disappointment. Northern Ireland, Bosnia, Iraq, and the Palestinian Territories apparently aren't small enough to ensure unanimity. I bet Quebec wouldn't be either.

Happy Blasphemy Day!

September 25, 2009

Off topic: Sears spied on customers

Sears tricked customers into installing software that recorded:

"the contents of shopping carts, online bank statements, drug prescription records, video rental records, library borrowing histories, and the sender, recipient, subject, and size for web-based e-mails. The software would also track some computer activities that were not related to the Internet."
The Federal Trade Commission asked them to destroy the data and to be more honest about their plans next time they do something like this. I wonder whether that is a strong enough punishment to deter similar activities by other companies?

I hadn't seen anything about this in the news before reading about it on Bruce Schneier's blog. Why isn't he in charge of Homeland Security?

September 21, 2009

Guest Blog: Sneaky slime mold

Slime molds allocate less to costly public goods when sharing then when alone.

(Special Guest Blogger: Will Ratcliff )

The slime mold Dictyostelium discoideum ('dicty' for short) spends most of its life alone, hunting soil bacteria and yeast. But when food runs out, tens of thousands of individuals aggregate into a mobile slug (cool youtube video) which crawls to an advantageous place and differentiates into a ball of spores on top of a long stalk. Individual dicty either become a dead stalk cell or a reproductively viable spore.
dictyEM.jpg
© Copyright, Mark Grimson and Larry Blanton

What possible incentive could there be for a dicty to sacrifice its life (become a stalk cell) for the benefit of those that become spores? If you answered 'there is no direct advantage to dying for others', you're right! Nonetheless, kin selection can lead to this type of self-sacrifice if a) the dicty in the stalk are highly related to the dicty that form spores (so are highly likely to have the same "unselfish genes"), and b) spores benefit from being higher off the ground (better chance of dispersal?).

But what happens when slugs are composed of more than one genotype? Here stalk formation becomes a 'tragedy of the commons' in which it is in each clone's interest to cheat, letting the other clone form a greater fraction of the stalk. So do dicty cheat? If so, how do they do it?

The short answer, as reported by Buttery et al. in the paper Quantification of Social Behavior in D. discoideum Reveals Complex Fixed and Facultative Strategies recently published in Current Biology is that:

Yes, dicty cheat; they cheat like crazy.

There are two ways in which a dicty clone in a mixed slug could cheat, producing less stalk and leaving more spores than its competitor....

First, the dicty clone could have a higher intrinsic frequency of spore formation. In some clones, most cells become part of the stalk, putting their spores high up in the air, while others favor shorter stalks and thus produce more spores. When mixed together, a clone that forms many spores might automatically cheat a clone that forms a lot of stalk, benefiting from the tall stalk while contributing relatively little to its construction. Second, a dicty clone may sneakily increase its frequency of spore formation when in a mixed slug, relative to what it would do alone, letting the other strain make most of the stalk.

The authors tested 6 natural isolates that varied substantially in their intrinsic frequency of spore formation, and made all possible combinations of two-genotype mixed slugs. What they found is that 5 out of 6 genotypes cheated facultatively, forming more spores when in a mixed slug then when alone. Surprisingly, strains that formed more spores in mixed slugs were also able to keep the competitor strain from doing the same to them . This is a really cool result, demonstrating that evolutionary conflict over stalk production has led to this humble slime mold's ability to measure social context and preferentially cheat nonrelatives.

But here's the catch: while facultative cheating was rampant, it seemed to have little overall impact on fitness (here measured as spore number alone, ignoring the potentially important but unknown effects of stalk size) under test conditions. The fitness rank order of the 6 strains in mixed sporangia was almost completely determined by each strain's intrinsic spore:stalk allocation.

The evolutionary persistence of genes for facultative cheating suggests that it was sometimes important to these strains ancestors in the wild, but that remains to be shown. This is great work, but is hampered by the current black-box status of this microbe's ecology. Stalks are presumed to be beneficial, otherwise natural selection would have long ago eliminated them, but the quantitative benefit of greater stalk height is currently unknown. As a result, the authors had to define fitness only in terms of the number of spores formed. Their 6 strains that varied in spore:stalk ratio therefore differed greatly in 'fitness', but each might have the stalk:spore ratio that maximizes fitness in its source environment, if the benefits of greater stalk size are considered. If this were the case, mixed slugs in the wild would usually form between strains with similar stalk:spore ratios. Once differences in that ratio are taken out of consideration, the fitness consequences of facultative cheating may in fact be quite large.

September 18, 2009

How to maybe possibly get a grant

I'm not doing a paper-of-the week (although I'm expecting a guest post) because I'm too busy reading a bunch of proposals for a grant panel. I can't give any details, of course, but here are some general observations that may be of interest to people who apply for or fund grants.

So far, every proposal I've read has seemed worth funding. This was not true the last time I served on a similar panel. Maybe the word has gotten out that grant funding is highly competitive, so few people bother sending weak proposals? This makes it easier to understand why some of my own recent proposals were rejected, often for what seemed like minor problems.

Unfortunately, we can only fund a small fraction of the proposals submitted. Of course, we could fund more proposals if we gave each group less money. There might be some merit in that approach, but I'll leave that topic for another time.

For those who are writing or thinking about proposals, here are some generic tips:

You need a good idea (typically, an important question and a plausible way to answer it) or a few related good ideas and (at least in biology) some preliminary data showing your idea might work. If you don't already have a grant, it may be hard to get those preliminary data. Someone should do something about this problem, but you need to realize that you're competing with proposals that do have preliminary data.

Given the strength of the competition, research that "may be relevant to" something important (a question that lots of people want the answer to, or a solution to some important practical problem) is probably going to rate lower than research that will actually answer the important question or solve the important problem. If you can't reasonably promise that from your current proposal, can you at least show how it's an essential (rather than optional) step towards that goal?

To be competitive, you need to have published something related to the proposed work. If you've published one or two relevant papers each of the last 2-3 years, I'll be pretty confident that you'll publish your results from a new grant promptly. Unpublished results are much less likely to get used, even if you tell a few people about them at a meeting or something, so don't expect public funding if you don't publish. Maybe we shouldn't expect as many publications from people without past grant support; I'll have to get the grant program's guidance on that.

Make life easy for reviewers! Author-year citation (Adams, 1979) is better than numbers (42); if I already know the paper, it saves time; if I don't, and I look it up (maybe just the abstract), it's easier to remember. Avoid acronyms nonspecialists don't know. If there are one or two you need to use repeatedly, define and use. Otherwise, it's better to spell it out or use a plain-English substitute: "the sensor" [described when first referred to], rather than WTFIANAEE. Both of these suggestions cut into the space you could otherwise to repeat vague claims for how important your work is or provide details on how many microliters of master mix you plant to use. Do explain once why your work is important (preferably to people beyond your subspecialty) but data showing that a method works in your lab is more convincing than minuscule detail of what you plan to do. That's my opinion, anyway.

If your proposal isn't funded the first attempt -- this is now common, even for pretty good proposals -- assume that you may get some of the same reviewers again, but most will be new. So address pat reviewer concerns in a constructive way, without belaboring the point.

September 11, 2009

Applied Evolution Summit

I've just agreed to give a talk in January at the Applied Evolution Summit: a small group of experts meeting at an island research station near the Great Barrier Reef to apply evolutionary biology to critical problems in human health, agriculture, fisheries, etc. It might surprise some evolution denialists to learn that pornography, abortion, atheism and "death panels" are not on the agenda, just science. Of course, when we talk about how global warming is affecting the coral reefs critical to some fish, we may need to go look!
Heron Island aerial.jpg
I'm going to try really hard to finish my book before the meeting, which will keep me quite busy until then. I don't teach regular classes -- as an adjunct professor, I'm paid only from our grants -- but reading proposals for a grant panel, writing a paper on "spiteful solar tracking" in alfalfa for Evolutionary Applications, and helping my hard-working and brilliant grad students with methods and manuscripts can't wait until my book is done. So I may be posting only sporadically for a while.

September 4, 2009

Where do new genes come from?

When a few members of a family have a gene not found in most other members, one explanation is that the gene is newly evolved, rather than inherited from the common ancestor of that family. (The other possibility is that their ancestor had it, but most descendants lost it.)

New genes often turn out to be copies of old genes, sometimes with modifications that give them very different functions. But a paper just published in Current Biology reports "Emergence of a new gene from an intergenic region", rather than duplication of an existing gene....


One definition of a gene is "a section of DNA which, if altered, has some effect on phenotype (observable traits)." Many genes are transcribed into messenger RNA and then translated into protein (perhaps an enzyme). But there is an increasing list of examples of genes whose phenotypic effects depend on activity by the RNA transcript, which may never be translated into protein. Such genes often have a regulatory function, controlling the expression of other genes.

The gene reported in this paper was detected as an RNA transcript in house mice and some of their close relatives, but not in more distant relatives like rats. Their analysis of the family tree for the gene suggests that it evolved about 3 million years ago, after the last common ancestor of mice and rats lived.

The new gene is apparently not translated into protein. Antibodies designed to detect the protein, if it is made, didn't find any. Also, evolutionary changes in the DNA sequence appear to be indifferent as to protein structure: DNA-base changes that would have no effect on protein amino acid sequence were about as common as those that would effect the protein.

There was a phenotypic effect, however, meeting our criterion for a gene. When the researchers knocked out the DNA corresponding to the transcript, sperm motility decreased. Apparently the RNA transcript had some beneficial effect on expression of other genes.

Although the DNA was in every cell, the RNA transcript was produced almost exclusively in the testis. Apparently conditions for gene expression are looser there than elsewhere, so that a variety of mutations can get a stretch of DNA transcribed. Most such mutations are presumably harmful, but the mice with beneficial mutations (like the one described in this paper) have increasing representation in successive generations.

September 2, 2009

Effective communication on preserving crop diversity

This talk by Cary Fowler, on the Global Seed Vault at Svalbard, is worth watching both for the content and as a model for effective public speaking. For that reason, I've categorized it under "careers in science" as well as "agriculture." Note the lack of bullet-point slides!

[Note added 9/11: text slides can make presentations boring, but handouts of text slides help students focus on understanding rather than scribbling notes. So I'm going to cut down on text slides in talks at meetings, but not necessarily in guest lectures to undergraduate classes.]

It's worth noting that even dry, frozen seeds may lose viability in storage. (You could probably still recover DNA, but that's only of practical value for the few traits, if any, whose value can be identified from DNA sequence alone.) So it's good to take seeds out of storage and grow fresh seed periodically. Usually, you want to do this in a way that minimizes natural selection in the seed-increase environment, to avoid losing traits that were useful where the crop was grown originally. For example, you want plants far apart enough that tall plants don't shade shorter neighbors enough to keep them from producing seed. And you don't want plants that were particularly prolific in the seed-increase environment to be over-represented in your next stored sample. Preserving crop diversity is a vastly under-funded activity, although that is true of most areas of agricultural research without immediate links to short-term profit.

Although even a few stored seeds can be multiplied enough in a few years to deal with slowly developing problems, such as climate change, if there's a global wheat epidemic you need at least enough disease-resistant seed on hand that one cycle of seed multiplication will meet farmer needs for the next growing season.

September 1, 2009

This is scary

Amazon.uk and a couple of other sites are advertising my book before I've even sent a completed version to Princeton University Press. I'm fairly happy with what I've written so far, but I'm not sure I'll finish this month.

Amazon.com doesn't have my book listed yet, but they are selling a crop physiology book with a chapter I wrote on Darwinian Agriculture.