One nice thing about E. coli is that they can freeze samples of their evolving populations every few thousand generations, for later analysis. So they were able to compare the fitness of different generations by competing each against a thawed ancestor. They also found the complete DNA sequence for many of these strains....

I should be working on my book, but a paper that just came out in Nature got me thinking about sex. A population with half males and half females will grow only half as fast as one consisting only of females that self-fertilize or clone themselves. So, many people have asked why sex evolved.

That's an interesting question, but I'm not sure about the rationale. As noted by Michod, a population of self-fertilizing hermaphrodites doesn't have any intrinsic growth advantage over a population of hermaphrodites that mostly cross-fertilizes. So is the problem sex, or males?

Evolutionary changes in gene frequency over generations depend on whether individuals with a given gene survive and reproduce more than other members of their population, not on the consequences for overall population growth. (Individuals can move between populations.) So we really have two related questions:
1) why do genes for producing male offspring persist? and
2) why do genes for cross-fertilization persist in species that can self-fertilize?

From an individual perspective, it's not apparent that producing male offspring is always a bad idea. Do couples with two sons have fewer descendants than those with two daughters? It can depend on the sex ratio in the population. If a human couple produces one offspring of whichever sex is in the minority, their offspring may have an easier time finding a mate.

But what about cross-fertilization? If a female cloned herself, her offspring would have all of her genes, rather than just half of them. So the frequency of genes for self-fertilization would tend to increase, unless individuals resulting from cross-fertilization were more likely to survive and reproduce. An offspring with half as many of one's genes, but a 2.1-fold better chance of survival (maybe because a sexual partner contributes different disease-resistance genes) gives a greater increase in fitness. So, one key to understanding the evolution of sex (cross-fertilization) is to measure the survival of individuals with one parent versus two, under conditions that plausibly occurred at critical points in a species ancestry.

This week's paper, "Mutation load and rapid adaptation favour outcrossing over self-fertilization", set out to "recapitulate the evolutionary process under the specific conditions predicted to favour either selfing or outcrossing." Levi Morran, Michelle Parmenter, and Patrick Phillips used the nematode, C. elegans, which consists of males and hermaphrodites. (This mix, and the lack of pure females, suggests there can be individual benefits to maleness, whatever the consequences for the population as a whole.) They used genetic manipulation to make populations that only self-fertilized or never self-fertilized, exposed them to high mutation rates or to a bacterial pathogen, and let them evolve.

When two Dictyostelium strains are mixed in a reproductive structure, cheaters contribute fewer cells to the stalk that holds up the reproductive spores. Could the presence of such cheaters select for cheater-resistance genes, just as the presence of owls or hawks selects for mouse genes that make their coats match the soil color?

The Darwin exhibit is off the entrance hall with the elephant and has a mix of biographical and scientific exhibits. My main criticism was their definition of "co-evolution" as being limited to evolution for mutual benefit. Evolutionary arms races (e.g., between hosts and parasites) are also coevolution. The entrance hall on the other side, where I came in, has two display cases of Darwiniana.

The butterfly exhibit was dominated by a live butterfly room inside a larger room with displays on the coevolution of plants and butterflies, with fossils labeled "examine the evidence." I was happy to pay $6 admission to the butterfly room since I wanted to make a donation anyway and enjoyed having a frittilary land on my nose.

Near the Oceans exhibit was a display of Burgess Shale fossils I hadn't seen before, including Pikaia, a tiny 500-million-year-old chordate. We chordates have evolved a lot since then. Nearby were some fossil stomatolites.

The mammal room was great, focusing on adaptations in everything from bats to giraffes (splaying front legs to drink, with an explanation of adaptations to limit blood flow to head) to pangolins with termite mounds. Right in the middle of the floor was a window down to fossil hominid footprints.

I wish I could have stayed longer. One problem with a quick visit to the Smithsonian is that post9/11 hysteria has closed most of the bag-check rooms. You can't bring your luggage into the museum and if you leave it somewhere, they'll try to detonate it. (Luggage made of sapient pearwood can defend itself, but I wouldn't recommend bringing it to Washington!) But here's a secret tip for my regular readers only: the 4th St. entrance to the National Gallery still has a check room, complete with x-ray machine. Don't tell too many people, or they'll probably close it.

Coming up in March: the Hall of Human Ancestors!

That's a paraphrase of how our local TV news covered Ardipithecus ramidus, the fossil hominid discussed in a series of papers in this week's issue of Science. Read all about it on Carl Zimmer's blog. The TV anchor didn't say which scientists claimed we are descended from chimps, perhaps because no scientist has made that claim. Chimps have evolved over the six million years or so since our last common ancestor, including their split with bonobos. Can we expect the story below on the TV soon?

Startling breakthrough in human genetics! You aren't descended from brother after all, or even from your cousin. You and your brother still have the same parents, and you and your cousin have the same grandparents, though. I hope that doesn't upset you too much.

We don't know for sure that present-day humans are descended from Ardipithecus . It's a reasonable hypothesis, but any hypothesis is, by definition, subject to possible disproof. For example, if we found another fossil that was clearly much more similar to modern humans, dating from the same time or earlier, then we'd conclude that Ardipithecus probably has no surviving descendants.

But this species probably isn't too far from the direct line of descent between our common ancestor with chimps and modern humans. Suppose you wanted to know what your great grandmother looked like, but there was no surviving picture of her. If you had pictures of her sister or her daughter, that would give you some idea, even if all her living descendants are descended from a son.

Of course, much of what we know about our ancestors now comes from analyzing DNA in humans and closely related species. We can figure out when vitamin C synthesis was lost or adult lactose tolerance gained, for example. But we don't yet understand development enough to predict height, foot shape, etc., from inferred DNA sequences of ancestral species. So keep those fossils coming!

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....

"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."

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?

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:

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....

[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.