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March 05, 2009

What I should have said to Richard Dawkins

Richard Dawkins gave a pretty good talk here last night. I have often thought that much political and religious speech (Jindal trying to talk folksy, for example) sends the underlying message "We X are kin, distant cousins or something maybe; They are not; give me your vote, your money, or your sons' lives and I will defeat Them." But I hadn't heard the term "fictive kin" used to describe this illusory relationship.

I also got to join a large group of students and faculty for lunch with Dawkins. What I should have said was "I'm writing a book called Darwinian Agriculture, heavily influenced by The Selfish Gene." Instead, I thanked him for calling my attention (when we met several years ago) to a paper about human-imposed group selection in chickens leading to increased egg production. A theme of my book is that humans can sometimes impose strong enough selection for group-level performance to overcome individual selection that undermines group performance (e.g., selecting for wheat that puts more resources into grain and less into tall stems to shade out competitors), whereas nature rarely if ever does that. But I think he just heard "group selection" and tuned me out. It must be tiring touring like that.

December 21, 2008

Spatial structure and the evolution of cooperation between microbes and plants

Evolutionary theory suggests that cooperation should often be unstable, even when it benefits all concerned. Toby Kiers and I discussed this problem and some possible solutions in a recent review article in Annual Review of Ecology and Evolution. Meanwhile, Jim Bever and colleagues have published some important experimental data in Ecology Letters, helping to explain cooperation between plants and fungi, a little too late to include in our review. Their paper is titled: "Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism."

Many bacteria and fungi associated with plant roots benefit more from healthy plants than from dead or dying ones. If each individual plant were colonized by only one strain of bacteria or fungus, then strains that helped their host plants (by providing them with nitrogen or phosphorus, for example) would indirectly help themselves, gaining an evolutionary edge over their competitors of the same species. These beneficial strains would become more common in each generation. In other words, cooperation would evolve.

The problem is that each plant is typically associated with several strains of each species of bacteria or fungus. Strains that invest less in helping the plant have more resources to spend on their own reproduction. If less-generous strains benefit equally from the contributions of more-generous strains on the same plant, then less-generous strains will become more common over generations. In other words, “cheating� will evolve.

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August 28, 2008

Bias in science vs. honest errors

Some comments attached to the previous post discuss cases where scientists made statements or drew conclusions that turned out to be wrong. When should we suspect bias, as opposed to honest errors? Some scientists, of course, may have financial conflicts of interest, such as stock in tobacco or biotech companies. But strong opinions can be a source of bias even without a direct conflict of interest.

Here's an example from my own past research. For ten years, I directed the Long-Term Research on Agricultural Systems project at UC Davis. This huge field experiment included comparisons of organic and conventional farming methods. (LTRAS also compared irrigated and nonirrigated systems, which you might think would generate more interest, given how much of California's limited water supply is used by agriculture. But these comparisons never generated as much controversy, for some reason.)

The simplest way to compare conventional and organic systems would be to have the organic system exactly like the conventional one, only without the synthetic fertilizers and pesticides. But no serious organic farmer would farm that way.

So, for example, we substituted compost and nitrogen-fixing cover crops for fertilizers in the organic system (and in several alternative systems that were not strictly organic). OK, but which cover crops? A scientist biased against organic methods could tilt the balance in favor of the conventional system just be choosing a bad cover crop. A lazy scientist, or one pressed for time or money, could choose a cover crop based on published data (trying to match local conditions) or by asking a nearby organic farmer for a recommendation. Ideally, one would start with such sources but then test various alternatives before making a final decision. At LTRAS, Martha Jimenez tested four cover crop species, each at two seeding rates, and two combinations. Woollypod vetch or a mixture of vetch and peas did best in her one-year experiment, so Dennis Bryant and his crew tested these options over three years before deciding. (Vetch+peas proved to be the least risky, even though vetch-only did slightly better under ideal conditions.) Similarly, we tested Farm Advisor Tom Kearney's suggestion that we should use a different corn cultivar in systems without nitrogen fertilizer. (These tests and other results for the first nine years of this 100-year experiment have been published: see Field Crops Research 86:267; email me if you want a PDF). Without this "tuning", the organic system would have done worse than it did. Similarly, we tried to optimize each of the nine other systems at LTRAS within its particular system-specific constraints. For example, irrigating the nonirrigated system was not an option, but we did choose a wheat cultivar suited to nonirrigated conditions.

Here's where concerns about bias come in. For each system, someone who suspected us of bias could claim that we should have done more to optimize their favorite system. For example, if timing of cultivation is important in all systems, but especially in organic ones, should we always have given the organic systems priority when scheduling, even if that meant neglecting conventional ones in ways no conventional farmer would do? I know that we were committed to finding out which methods are best, rather than trying to prove preconceived ideas. But that doesn't mean we always made perfect decisions. And why should you believe me? After all, my brother Tom Denison is an organic farmer; I could be biased by that or by a graduate education and postdoctoral work in Crop Science that those not familiar with my advisers Tom Sinclair and Bob Loomis might assume was "brainwashing." (It would be more accurate to call their efforts "brain-building.")

If individual scientists or groups of scientists have conscious or unconscious biases, that may influence their conclusions and even their results. Fortunately, two solutions to this problem are built right into the fabric of science today. The first is peer review. Before a paper is published in any reputable scientific journal, it is reviewed by at least two experts with no direct connection to the authors of the paper. (We may know each other, however.) These reviewers look for problems such as unreliable methods, inconsistency between results and conclusions, and inconsistency with previously published results. The latter should not lead to rejection, but reviewers should insist the discrepancy be discussed. Note that most books, web sites, pamphlets, popular magazines, television program, and even certain "junk journals" (low citation impact is a clue) have little or no peer review. As I result, I have usually found reading such sources to be a waste of time. For example, critical details needed to assess the reliability of results are often left out.

Second, and more important, any really important conclusions need to be based on results confirmed by at least two independent groups. This is the best way to detect fraudulent or biased results: do other research groups, who may have different biases, nonetheless get the same results? This is one reason society would benefit from investing more in research. When research money is scarce, studies needed to confirm or refute important results may not get done.

With peer review and independent testing of important results, the biases and errors of individual scientists do not prevent the scientific community from reaching reliable conclusions, sooner or later.

August 21, 2008

Ask the right experts

A book review titled "Redefining 'natural' in agriculture" makes some interesting points. I haven't read the book, which is about organic farming and transgenic crops, although I know both authors slightly from my years as a professor at UC Davis. The review notes that many people have strong opinions about agricultural issues even though they lack relevant expertise. Anthony Trewavas, the author of the review, suggests that even "being a scientist doesn't qualify you to advise on any subject except your specialty."

So what is his own specialty?

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May 25, 2008

Pest control for ants

Ant.jpeg

(Top) A small leafcutter worker atop a leaf guards her sister against attacks by parasitic flies. Ants carrying leaves cannot use their mandibles for defense, so they carry hitchhikers to ward off the parasites. (Bottom) The fungus garden in a nest of Atta leaf-cutter ants. Notice the diversity of ant sizes within a colony, from the large red soldier ants to the minute orange ants tending to the garden. Atta ants have some of the most sophisticated caste systems among the social insects. -- photos and captions from Alex Wild (mymercos.net)

"Ant2.jpeg
This week’s paper, “Black yeast symbionts compromise the efficiency of antibiotic defenses in fungus-growing ants" by Ainslie Little and Cameron Currie, was just published in Ecology. Elsa Youngsteadt interviewed me, among others, for a story in Science about this research.

I’ve never done research on the fungal “farms" of ants and termites, but I’ve been interested in them every since a camera company bought a close-up photo (not Photoshopped like this one) of an ant carrying a leaf along a barbed wire “bridge" on its way back to its nest, from my mycologist father, William Denison. Dad was best known for pioneering research in the tops of tall trees, but never had to fight a shaman, as far as I know.

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April 09, 2008

Welcome, fellow Dr. Tatiana fans!

Olivia Judson's latest column includes a good summary of work in my lab on cooperation between soybean plants and the rhizobium bacteria that (typically) provide them with nitrogen. As she points out, "cheating" is less likely to evolve in symbiont populations if they are transmitted in eggs or seeds, relative to symbionts that are acquired from the environment. In the former, if the host dies before reproducing, the symbiont dies, too. Symbionts without brains (bacteria, say) can't anticipate the effects of their actions; it's just that those whose genetically programmed behavior increases host survival become more common over generations.

Similarly, low symbiont diversity within an individual host may favor symbiont investment in costly activities that benefit the host. If each host has many different symbionts, on the other hand, then helping the host indirectly benefits competing symbionts sharing that host.

Rhizobium bacteria reach new host plants through soil, not via seeds, and they can do so even if the host dies without reproducing. Furthermore, each individual plant has multiple strains of rhizobia, which should undermine cooperation. Why then, do most rhizobia use their limited energy supply to fix nitrogen, giving most of it to the host plant? Why not use that energy for their own reproduction, instead?
NoduleChambers.jpg
Although there are several rhizobium strains per plant, they are typically segregated into individual root nodules. So, Toby Kiers and I reasoned, if plants monitor individual nodules and do something nasty to those that provide less nitrogen, that would act as a form of natural selection against cheating rhizobia. A computer model by Stuart West came to similar conclusions. To test this hypothesis, we forced some nodules to cheat, by surrounding them with an argon-oxygen atmosphere lacking nitrogen gas. Control nodules on the same plant got normal air, which is 80% nitrogen. Would rhizobia freed from the burden of fixing nitrogen redirect resources into their own reproduction? Would the plant impose sanctions on nonfixing nodules? If the answers to these questions are yes and yes, what would be the overall effect of cheating on rhizobium reproductive success?

Continue reading "Welcome, fellow Dr. Tatiana fans!" »

February 18, 2008

Natural enemies complicate reproductive tradeoffs

Semelparous plants and animals are those that reproduce only once, whether after a few months of growth (annual plants, like wheat) or after years (“century plant� or most salmon). Iteroparous species iterate. That is, they reproduce repeatedly. For example, perennial grasses may produce seeds every year for a decade or more.

One reason this difference matters is that perennial crops may have some environmental benefits, relative to annual crops. Plowing, traditionally more common with annual than perennial crops, can greatly increase soil erosion, especially on steep slopes. So there is increasing interest in developing perennial grain crops as an alternative to wheat.

However, perennial plants have lower seed yield than their annual relatives, so we would need to devote more land to agriculture to get the same amount of grain. One reason for the yield difference is that an annual plant can transfer most of the carbon (energy) and nitrogen (needed for protein) from its leaves, stem, and roots into its seeds. It’s going to die anyway, so the next generation gets its accumulated wealth. A perennial plant needs to hold back some carbon and nitrogen for winter survival and spring regrowth. The more resources it puts into this year’s seed production, the less it can carry forward to support reproduction next year.

This week’s paper shows that iteroparous plants face additional costs when they reproduce, namely, ecological costs. “Herbivore-mediated ecological costs of reproduction shape the life history of an iteroparous plant� was written by Tom Miller and colleagues at the University of Nebraska (where I’ll be speaking on Darwinian Agriculture in April) and published in American Naturalist.

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January 21, 2008

Sustainable Darwinian Agriculture and Organic Tomatoes

I will be reviewing another recent journal article today or tomorrow, but meanwhile we seem to have convinced someone that an evolutionary perspective is useful in agriculture. A recent book review mentions a chapter we wrote:

There is also food for thought in some of the chapters, particularly the one by R.F. Denison and E.T. Kiers on sustainable crop nutrition. This perceptive analysis raises questions about the simplistic assumptions that often underlie attempts to improve crop mineral-use efficiency and highlights areas where such attempts are likely to be useful and others where they are not. This reviewer certainly changed his thinking as a result of the ideas put forward.
I doubt that the reviewer, Roger Leigh, remembers a mostly positive review I wrote of a book on long-term field experiments (mostly agricultural) that he edited over ten years ago, when I was directing UC Davis's Long-Term Research on Agricultural Systems (LTRAS) "100-year experiment." Our chapter discussed the implications of "our crops' legacy of preagricultural evolution", a topic we previously addressed in Darwinian Agriculture. For example, past natural selection for individual competitiveness may have favored more investment in roots than is optimal for maximum grain yield. On the other hand, human goals like reducing nitrate loss to groundwater (an environmental problem ignored by natural selection) might call for deeper rooting than would be needed for yield alone. We also discussed evolutionary conflicts in nutritional symbioses (e.g., with nitrogen-fixing rhizobium bacteria or the mycorrhizal fungi that provide many plants with phosphorus), the topic of our current research -- watch for our review in Annual Review of Ecology and Evolution.

Our recent paper comparing organic vs. conventional tomatoes also has an evolutionary twist...

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October 16, 2007

Soybean symbiosis isn't what it used to be

Older soybean varieties benefit more from mixtures of good and bad symbiotic nitrogen-fixing bacteria than modern soybean varieties do. This work has also been
discussed on the Nature website by Heidi Ledford and on the Agricultural Biodiversity Weblog by Jeremy Cherfas.
MaineSoybeans.JPG

"variations… profitable to the individuals of a species… will tend to the preservation of such individuals, and will generally be inherited by the offspring. I have called this principle… natural selection, in order to mark its relation to man's power of selection."
-- (Darwin, 1859)
Darwin was rightly impressed by what plant breeders have accomplished. I'm glad that potato breeders have reduced poisonous tomatine concentrations enough that we no longer need to eat absorbent clay with our potatoes, as was necessary with wild potatoes (Johns, 1990 p. 92). But sometimes selecting for a beneficial trait can have negative side effects. This problem applies both to natural selection and to selection by humans. Trade-offs among desirable traits can result from physical linkage between genes, intrinsic constraints (a given amount of sugar can be diluted in a larger strawberry), or random drift in traits not under selection.

This week, Toby Kiers, Mark Hutton, and I are reporting an apparent decrease, over the course of 60 years of soybean breeding, in the ability of plants to benefit from rhizobium bacteria. Our paper “Human selection and the relaxation of legume defences against ineffective rhizobia� is published on-line in Proceedings of the Royal Society.

Continue reading "Soybean symbiosis isn't what it used to be" »

July 28, 2007

Darwinian Agriculture III

Next week I will be meeting with a publisher to talk about the possibility of writing a book on Darwinian Agriculture to be published in 2009, the 150th anniversary of The Origin of Species. (I apologize to one reader who apparently thought it was a done deal.) Here's a short draft of the first chapter, mostly about sustainable agriculture by ants and termites.

Farmers of 50,000 millennia

“We’ve been farming sustainably for three years�, read the email. I was glad to learn that my friend was farming in ways that he hoped could continue indefinitely, but how could he be sure, after only three years?

It might have been a reasonable assumption, if the farming methods he used were similar to those that other farmers have used successfully for a long time. But how similar is similar enough? And what qualifies as “a long time?� As director of “the world’s youngest 100-year experiment�, I often thought about these questions....

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July 12, 2007

Rhizobia, pesticides, and peer review

I have some comments on a recent paper that's only tangentially related to evolution. Actually, it's more relevant to science fair projects, the topic of my last post.

One type of science fair project my fellow judges and I are really sick of is "The effect of X on plants", where X is mouthwash, vinegar, cola, etc. The obvious question, which we always ask, is "how often are plants in the field exposed to high concentrations of mouthwash?" Unfortunately, whoever reviewed this paper in Proceedings of the National Academy of Science, claiming that "Pesticides reduce symbiotic efficiency of nitrogen-fixing rhizobia and host plants" apparently failed to ask this question.

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June 30, 2007

Tracing the spread of agriculture with stone-age human DNA

This week's paper is "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe" by M.L. Sampietro and others, published online in Proceedings of the Royal Society. The paper is interesting both for its findings and for its methods.

We know that agriculture spread from the Near East -- do people in Asia call this the Near West? -- to western Europe, starting around 10,000 years ago. But did this mostly involve farmers moving, or the spread of agriculture without major movement of people?

People have tried to figure out past population movements using genetic differences among modern populations, but it would help to have genetic information from people who lived thousands of years ago, as well. This is technically challenging, however...

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June 27, 2007

Individual and kin selection in legume-rhizobium mutualism

OK, I've been critiquing other people's work for a while. Your mission, should you choose to accept it, is to critique something I've written. It's the summary for a grant proposal I'm about to submit. It will be reviewed by ecologists and/or evolutionary biologists, but they're not likely to be specialists in legume-rhizobium symbiosis. So if something isn't clear to an intelligent but nonspecialist audience, you'll let me know, right? If you're not all too busy reading the many interesting evolution articles in today's New York Times, that is. By the way, the great Myxococcus xanthus photo in Carl Zimmer's article is from Supriya Kadam, who did her PhD with Greg Velicer and just finished a year as a postdoc in my lab.

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April 17, 2007

Darwinian agriculture II

Last week, I was at a meeting in the Netherlands on “Darwinian agriculture: the evolutionary ecology of agricultural symbiosis.� Topics included: the effects of cows on human evolution, the independent invention of “agriculture� by ants and termites, and some disadvantages of diversity. As promised, here are a few highlights.

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April 06, 2007

Darwinian agriculture I

Next week, I'm speaking at a one-day symposium on "Darwinian Agriculture: the evolutionary ecology of agricultural symbiosis", in Wageningen, The Netherlands. So, instead of reviewing a recent paper, this week I'm going to discuss some of the not-quite-so-recent papers on which my talk will be based. The following week, I plan to summarize some of the talks I hear at the meeting.

I may do the same thing in August, when my grad students and I speak at the much larger Ecological Society of America meetings in San Jose, California. Feel free to comment if you feel cheated of your weekly paper review, and I might reconsider. The Evolution meetings are in Christchurch, New Zealand, this year, but my grant won't stretch that far.

"Darwinian Agriculture: when can humans find solutions beyond the reach of natural selection?" was the title of a paper that Toby Kiers, Stuart West, and I published in 2003. Our answers to the title question suggested how increased understanding of past and ongoing evolution could improve: 1) breeding of crops and livestock, and 2) design of agricultural ecosystems.

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February 20, 2007

Evolutionary trade-offs: how are soybeans like salmon?

Answer: they're both semelparous (reproduce once, then die), so evolutionary trade-offs between number and size of offspring are expected to be similar.

This week's paper is "Evolutionary aspects of the trade-off between seed size and number in crops" (Field Crops Research 100:125-138) by Victor Sadras. You can read the abstract on the web for free. For the full version, you can pay $30 to download, visit your nearest agricultural research library (in the U.S., often at a state university), or email the author at: sadras.victor@saugov.sa.gov.au. My discussion is mostly based on a shorter version presented at the Australian Agronomy Conference.

Demand for grain is increasing, to feed growing human and livestock populations and more recently for ethanol production. Unless those trends are reversed, we will either need to expand the land area used for agriculture or increase grain yields per unit area. Grain yield is the product of plants per area, seeds per plant, and weight per seed. Unfortunately, increasing any one of these (by increasing seeding rate, or through plant breeding) tends to decrease the others.

This paper looks at how natural selection (in the wild ancestors of crop plants and in fish) and plant breeding (especially in maize and sunflower) shape trade-offs between seed number per plant and seed size. The similar patterns in plants and fish show that, as predicted by the relevant aspects of evolutionary theory, we are dealing with fundamental constraints that we are unlikely to change.

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