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July 30, 2012

Correcting Science and PNAS, evolution of more-deadly suicide bombers, blind composers, transcending tradeoffs, light-responsive rhizobia

Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells
GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism
Surprise! They don't use arsenic instead of phosphorus after all.

Unobserved time effects confound the identification of climate change impacts "PNAS reported statistical evidence of a weather-driven causal effect of crop yields on human migration from Mexico to the United States. We show that this conclusion is based on a different statistical model than the one stated in the paper."

Evolution of music by public choice ...as in natural selection, variation is random but selection isn't.

Explosive Backpacks in Old Termite Workers ...they weren't going to reproduce anyway, but I wonder how long these "suicide vests" took to evolve.

Compensatory mechanisms for ameliorating the fundamental trade-off between predator avoidance and foraging "enhanced nutritional physiology allows caterpillars to compensate when threatened. However, we report physiological costs of predation risk, including altered body composition (decreased glycogen) and reductions in assimilation efficiency later in development." Similarly, reducing investments in research may not affect economic development much between now and the next election.

Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine
"illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids."

Page 99 test

Thumbnail image for Thumbnail image for BookCover.gifYou can't judge a book by its cover, but Ford Madox Ford supposedly claimed that:

"Open the book to page ninety-nine and read, and the quality of the whole will be revealed to you."

The website Page 99 test has an excerpt from page 99 of my book, along with some context.

Someone must have bought a copy from Amazon.com, since it moved up from the two-millionth most-popular to 200,000th. No reviews yet, though.

July 26, 2012

This View of Life

A press release about my Darwinian Agriculture book is circulating and ended up at This View of Life, "a new online general interest magazine in which all of the content is from an evolutionary perspective." They have a wide range of content (much of it from other sources) including evolutionary perspectives on economics and religion as well as biology.

July 24, 2012

Using "Darwinian Agriculture" for a seminar class?

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Although my just-published book is...

* More profusely illustrated than The Origin of Species
* Better-referenced than Collapse
* Somewhat cheaper than the Encyclopedia Galactica

...it's probably too opinionated and not comprehensive enough to work well as a textbook. But a few people have suggested that they might want to use it for a seminar. I think that could work well and am wondering what sort of help from me might be useful.

Within reason, I would be happy to :
* Supply images (pictures and graphs) that could be useful in discussions.
* Answer questions from instructors via email.
* Host Google Hangout discussions (if 3-4 seminars could agree on a time).

Any interest in these or other ideas? I'm assuming that even people who might be interested mostly haven't read the book yet, so this may be premature...

July 20, 2012

The Macroecology of Sustainability

That's the title of a recent open-access paper in PLoS Biology by Joseph Burger and colleagues. They argue that "sustainability science" has focused too much on local issues, ignoring the importance of large fluxes of materials and issues of global supplies. For example, Portland, Oregon is considered "sustainable" because more residents ride bicycles than in other US cities, yet the city imports and consumes fossil fuels and other resources at rates similar to other cities of similar size. So we need to ask whether those imports can be sustained.

Their Figure 3 is particularly interesting. Global use of land for agriculture, withdrawal of fresh water from surface and underground sources, harvest of wild fish and wood, and mining of phosphorus are all similar today to what they were 20 years ago. Is this because we all decided to conserve scarce resources or because we are reaching the limits of what can be obtained at reasonable cost? Increasing production of coal and copper seem inconsistent with the "conservation hypothesis."

I learned of this paper by reading a post by Jeremy Cherfas in the always-interesting Agricultural Biodiversity Weblog. Some of these issues are discussed in my just-published book on Darwinian Agriculture, particularly in Chapter 2.

July 19, 2012

Grok Science interview -- limitations of transgenic drought-tolerant crops and, uh, learning from wild potatoes, etc.

Grok Science has posted a lengthy podcast interview with me about my just-published book, "Darwinian Agriculture." Some of their other interviews look interesting, too.

If you want to hear more, Carl Zimmer interviewed me for Microbe World in 2010. That interview is also still available. I was still writing the book, but I mention a 2003 paper in Quarterly Review of Biology, also titled "Darwinian agriculture," written with E. Toby Kiers and Stuart West. Much of Zimmer's interview focuses on the evolution of cooperation and conflict between legume plants and the rhizobia bacteria that live inside their root nodules and, to varying extents, provide them with nitrogen.

July 18, 2012

At least they spelled my name right

Science is listing my just-published book as "Darwinian Architecture." I suppose that could expand my potential audience, at the risk of disappointing readers who expected something about the survival of the fittest buildings or northern Australian landmarks.
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A PDF of the first chapter is available on the Princeton University Press page, here.

July 17, 2012

University of Minnesota UROP Undergraduate Research Opportunity Program

You could have gone to a 4-year college with smaller classes and professors focused mainly on teaching, rather than research. Why did you choose to go to a major research university, like the University of Minnesota? If you answered "football and beer", read no further.
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Alfalfa root nodules containing nitrogen-fixing rhizobia (photo by Alex May).

Maybe you hoped that professors actively involved in research would give more up-to-date lectures. I hope that's true. But to really take advantage of the opportunities at a research university, go to some current-research seminars -- every department has them. Even better, look for an opportunity to do some research yourself, as part of a team of grad students and undergrads working with a professor on a topic that interests you.
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Lab-evolved multicellular yeast showing simple division of labor (photo by Will Ratcliff).

At the University of Minnesota, one of the best ways to do this is to design your own research project in collaboration with a professor, and get it funded by the UROP Undergraduate Research Opportunity Program. You can request up to $300 for supplies -- many professors will supplement that, if needed -- and $1400 (140 hours at $10 per hour, say) as a stipend, so maybe you can afford to quit that pizza delivery job and get paid for doing research instead.

If this sounds like something you might want to do, you need to PLAN AHEAD. To work on a UROP during Spring 2013, you need to submit your proposal by 8 October 2012. That's only a month after classes start. A month isn't a lot of time to:
* find a Faculty Mentor
* discuss general ideas for a project
* find and read some relevant papers
* write a first draft of your proposal
* revise the proposal at least once based on suggestions from your mentor and then...
* submit it October 8.

So smart undergrads will start contacting possible Faculty Mentors during the summer -- what, you thought we were on vacation all summer?

Examples of possible research topics in the Microbial Population Biology group:
* Experimental evolution of multicellularity
* Evolution of cooperation between legume plants and nitrogen-fixing rhizobia bacteria
* Evolution of aging explored using Daphnia
A lab class that included careful note-taking, calculations with units (e.g., molar concentrations) and some microbiology (sterile technique) would be good preparation for any of these.
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July 12, 2012

Crossing the border

Homeland Security Guy: "What were you doing in Canada?"
Me: "Attending a scientific meeting."
HSG: "What do you do for a living?"
Me: "I'm an evolutionary biologist." (Usually, I just say "professor", but I had evolution on the brain.)
HSG: "Did humans evolve from primates?"
Me: "We're still primates... but [realizing I could miss my plane if he decided to hassle me] I work on bacteria."

He let me through.

Thousands protest suppression of science in Canada -- the "Death of Evidence" rally

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Photo by Larry Moran.

While in Ottawa, I went to hear speakers protesting the "Death of Evidence", in front of Parliament. They argued that:

The only scientific evidence the Mr. Harper wants the public to know about is that which supports his political objectives and ideology. That's not science, that's propaganda.
One example was defunding the Experimental Lakes research site. A speaker gave a long list of important discoveries made there (effects of phosphate detergents, acid rain, etc.) and argued that the loss of funds was motivated by politics (fear of how factual results from the research would reflect on government policies) rather than cost-effectiveness.

I happened to be carrying the poster Princeton University Press used to promote my Darwinian Agriculture book at the Evolution 2012 meetings. I was tempted to title this post "Thousands Demand Darwinian Agriculture", but refrained.

July 9, 2012

Sold out!

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The Princeton University Press table has sold all the copies of my Darwinian Agriculture book they brought to the Evolution meetings. They didn't have that many, but apparently it's out-selling their other books here. You can still order from them or your local independent bookstore.

July 8, 2012

Evolution 2012, people

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I am having fun at Evolution 2012 in Ottawa. Lots of great talks and poster presentations - see recent posts -- and discussions with interesting people. Last night I had dinner with several well-known bloggers: Larry Moran of Sandwalk, Carl Zimmer of The Loom, and Ryan Gregory of Genomicron. Unfortunately, I got in too late on Friday to join a group that also included Rosie Redfield of RRResearch (making a big splash debunking "the arsenic paper") and Jerry Coyne of Why Evolution is True. Imagine discussing evolution with the authors of two of the first three books cited in my just-published book on Darwinian Agriculture.

Tonight, dinner was with two of my former colleagues (and neighbors) from UC Davis, Rick Grosberg and Sharon Strauss, their new colleague Johanna Schmidt -- we figured out that we had met 40 years ago -- and various associates. Running for the elevator, back at my hotel, I discovered that the helpful couple holding the door for me were Rosemary and Peter Grant. Discussions with younger colleagues, like Maren Friesen (working on legumes and rhizobia) and Jon Sanders (studying bacterial symbionts of ants and deep-sea clams), have also been great. They all seem to be making impressive progress on interesting and important research. Let's keep funding the National Science Foundation, which is supporting much of this work.

Evolution of cooperation in Ottawa

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Mike Travisano discusses experimental evolution of multicellularity.

My talk here at the Evolution meetings inn Ottawa was taking 12 minutes in practice but I finished in 10. Nervous? Maybe, because I was arguing that most past measurements of fitness benefits to legumes from rhizobia are suspect, which would throw lots of results into question.

Typically, people who want to compare benefits from two different rhizobial strains inoculate host plants with each strain separately, then compare plant growth. But plants in the field are almost always nodulated by multiple strains. I showed that a plant inoculated with a slow-nodulating but highly efficient strain (which eventually provides lots of nitrogen, relative to its carbon cost) may provide no more growth than a less-efficient but faster nodulating strain, when each is inoculated alone. The problem is that plants with only the slow, efficient strain will be short of nitrogen at first, with compound-interest effects on growth. In the field, though, there will always be some fast-nodulating rhizobia. So it's not a matter of nodules vs. no nodules, but of how efficient those nodules are. So we inoculate plants with the two strains being compared, in different ratios, then measure plant growth as a function of the percent of nodules containing the focal strain. With this method, a computer model and actual data agree that an increase in growth with nodule occupancy by the focal strain indicates a more-efficient strain.

Maren Friesen suggested a similar method in a recent paper in New Phytologist. Unfortunately, her main conclusions were based on the old, one-strain-per-plant method.

Megan Frederickson gave a stimulating talk on cheating in symbionts. We have shown that soybean, alfalfa, and peas all impose fitness-reducing sanctions on rhizobia that fail to fix nitrogen, once established inside root nodules. Frederickson asked what maintains such sanctions? If they work, "cheaters" will be rare, so there will be only weak selection on legumes to maintain sanctions. She suggested that something else (such as a generalized response of sending more resources to parts of a root that supply more nitrogen) must select for the responses we call sanctions.

I agree that cheaters would be rare under consistent sanctions, which could relax selection to maintain sanctions. But sanctions may not be that consistent. See Toby Kiers' "measured sanctions" paper. And maybe only a fraction of less-beneficial rhizobia are cheaters, that is, strains that benefit from diverting resources from nitrogen fixation to their own reproduction. Many may be defective mutants, that fix less nitrogen but don't benefit thereby. Sanctions would keep any individual strain of defective mutant rare, but there could be many different strains.

Frederickson's talk stimulated a lot of useful discussion afterwards and I am looking forward to seeing her paper.

July 7, 2012

Evolution of aging talks at Evolution 2012 in Ottawa

Hwei-yen Chen described her experiments to explain why aging (an increase with age in the chance of death per year) sometimes levels off at an "aging plateau." For example, humans are more likely to die in their 101st year than their 70th, but not more likely to die in their 101st than their 100th. Do we "get our second wind" and stop aging? Or is it just that older cohorts have already lost the frailer individuals (the heterogeneity hypothesis).

Chen exposed nematode populations to high vs. low death rates caused either by temperature stress (preferentially killing the weak) or random assassination. The aging plateau was only seen in the temperature-stress populations, consistent with effects from elimination of weaker individuals earlier in life.

I think I missed something, though. As I've described it, seems like this experiment could have been done with a single cohort of individuals, which would be increasingly enriched with stronger individuals as the weaker were killed off. But this was described as experimental evolution. If the evolution treatments preferentially killed weaker genotypes, wouldn't that eliminate the variation the heterogeneity hypothesis needs to work? Maybe someone else who saw this talk can clarify or maybe I can find her poster. Or maybe we'll have to wait for her paper.

Alan Cohen gave an interesting talk in the same session. He showed chance of death per year data as a function of age for a bunch of species. In humans and many other species, death rate increases with age. This has been explained by, for example, tradeoffs between longevity and early reproduction. But apparently many species don't have an increasing risk of death with age. So maybe such tradeoffs aren't universal?

In a theoretical talk, Olivier Cotto discussed the evolution of aging in metapopulations. Local extinction and recolonization processes were shown to favor evolution of different life-history strategies (reproductive effort as a function of age) for dispersing and nondispersing individuals.

Later, Will Ratcliff presented our latest data on the evolution of aging after experimental evolution of multicellularity, research led by Mike Travisano. Excellent experimental work by Jennifer Pentz has been key to our success. As discussed in our recent PNAS paper, we started with unicellular yeast and imposed selection for rapid settling in liquid media. Within about two weeks, most of our replicate populations evolved a "snowflake" phenotype: clusters of connected cells that settle much faster than their unicellular ancestor. Under continued settling selection, clusters competed with each other based on differences in growth, reproduction (via multicellular propagules), and survival (settling fast enough to make it into the 5% of the population that made it into the next generation).

The first snowflake clusters to evolve didn't age significantly faster than their unicellular ancestor. In other words, only a few of the cells within a cluster would die over the course of a few days, and the ability to compete with a reference genotype wasn't much less for older than younger clusters. But, under continued settling selection, faster aging evolved. Older clusters accumulated more dead cells and were less competitive than younger clusters.

Why did aging evolve? The dead cells form break-points that facilitate reproduction (release of multicellular offspring). And aging doesn't really set in until after 24 hours, when settling selection is imposed. Only 5% of cluster survive that selection, so there's only very weak selection against traits that only reduce fitness after 24 hours. Imagine if humans only lived 30 years. There wouldn't be much selection against genes that cause cancer in 80-year-olds.

Live from Ottawa

I'm at Evolution 2012, a joint meeting of several evolutionary biology societies in Ottawa.

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First two talks I've heard were both great. Based on my notes, which could have errors:

Caroline Turner discussed feedbacks between ecology and evolution after one of Rich Lenski's long-term E. coli populations acquired a citrate-using mutant. The transporter that takes up the citrate actually swaps out a succinate, which is another potential food source. During the time when citrate(+) and citrate(-) genotypes coexisted, the citrate(-) part of the population evolved an improved ability to use succinate, with some decrease in its ability to grow on glucose.

Have I mentioned that evolutionary tradeoffs are a major theme of my book, Darwinian Agriculture? Princeton University Press is selling it here, along with Angela Douglas's book on symbiosis, among others.

Adam Waite discussed experiments with Wenying Shou on evolution of cooperation. Two yeast genotypes "cooperate" by each making something the other needs but can't make itself. But what keeps "cheaters", which consume those "common goods" without contributing, from taking over? Sure, the population would then go extinct, but evolution doesn't plan ahead.

When they divided a 1:1:1 mixture of the two cooperators and the cheater into 3 mL tubes, some populations grew fast and eliminated the cheaters, while others became all cheaters and then crashed. This apparently depended on whether a key beneficial adaptation (a mutated nutrient transporter) appeared first, within a given tube, in a cooperator or a cheater. I wonder whether, with much larger populations the cheater would usually get the adaptation soon enough to avoid being eliminated. But this does seem like a plausible explanation for the evolution of cooperation in the face of cheating. I was also liked their methods: 3 different fluorescent labels, so they could analyze composition of mixtures by flow cytometry.

Next I'm going to a series of talks on the evolution of aging.