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June 14, 2013

Recent and upcoming talks

Last week I was at Mexico's National Laboratory of Genomics for Biodiversiity (Langebio), giving a keynote talk on Darwinian Agriculture and learning about the diverse research program there, from microbial communities to manipulation of ant "bodyguards" by Acacia plants to using yeast to answer fundamental evolutionary questions.

On Sunday, June 23, I'll be giving a talk on Darwinian Agriculture, as part of the "Evolution Out of Bounds" symposium at the Evolution 2013 meeting, in Snowbird, Utah. These annual evolution meetings are usually really interesting, as I've discussed previously, and other talks in the symposium range from evolution of disease to evolving robots. Those interested in our evolution-of-multicellularity research should look for the talk by Kristin Jacobsen on Sunday afternoon and the poster presentation by Jenn Pentz Monday evening.

April 15, 2013

YouTube videos go fungal...

...or whatever we call over 100 but fewer than 1000 views.

This page has links to an interview Michael Joyce did with me at the end of my week-long visit to the International Rice Research Institute, as well as the five lectures I gave there (plus audience questions and discussion).

Also still available are:
* a 60-second AAAS story on my most-cited paper.
* a video of my keynote talk at the Applied Evolution Summit
* a lower-quality video of a talk on Evolutionary Tradeoffs as Agricultural Opportunities
* an audio interview with science writer Carl Zimmer

Or, you can find an updated list of my publications, with links to many of them, here.

February 19, 2013

No comment

I've disabled the comment feature for This Week in Evolution, because I'm getting almost exclusively spam comments these days. That may be partly because of the decrease in content here. I'm mostly just posting weekly lists of links to papers that look interesting, often with brief excerpts from their abstracts.

These days, most of my blogging effort is going to my Darwinian Agriculture Blog, where comments are still enabled. Or you could send me an email.

January 29, 2013

A citation a day keeps ideas in play

GoogleScholar2012.jpg
I'm always amazed how badly out-of-date many of my colleagues' publication lists are. Spend a few minutes setting up a Google Scholar page, and you'll always be up-to-date with publications and citations. Here's mine.

My first evolution-themed paper, proposing host sanctions as an explanation for the evolutionary persistence of legume-rhizobia cooperation, was published in 2000.

November 11, 2009

About "This Week in Evolution" and R. Ford Denison

See my Google Scholar page for an up-to-date list of publications.
Or, see "recent publications and publicity" for news and commentary.

"Can you tell me, in lay language, what makes this achievement significant?"
"I can try", said Denison, cautiously.
-- The Gods Themselves (Asimov)
ford.jpg
Ford Denison explains why eating more kale and less meat may trigger physiological changes that sacrifice some potential reproduction but increase longevity (Ratcliff et al., 2009).

Podcast interview with Carl Zimmer on "Darwinian Agriculture."
Short audio story
on our host-sanctions research, produced by AAAS.

About this blog:
Time permitting, I discuss one scientific journal article per week, presenting new data on past evolution or ongoing evolution. My interests in the evolution of cooperation and in agriculture make me include more papers on microbes and plants than some other blogs with an evolutionary focus. I occasionally discuss other topics.

About me:
You know how evolution-denialists sometimes claim that they "used to believe in evolution", as if one person's changed opinion trumped the thousands of scientific articles on evolution published each year? For what it's worth, I didn't start as an evolutionary biologist. I earned a PhD in crop science from Cornell in 1983 and was a US Department of Agriculture researcher for several years, before becoming a professor of agronomy at UC Davis in 1993. There, I taught crop ecology, directed a major field experiment on agricultural sustainability (LTRAS), and did research on cover crops that get nitrogen from symbiotic rhizobium bacteria in their root nodules.

My interest in evolutionary biology developed gradually. I wanted my teaching to explain as many facts as possible, using a framework of universal principles, rather than jumping randomly from one fact to another. The universal principles that explained the most crop-ecology-related facts turned out to be conservation of energy, conservation of matter for each chemical element, and evolution by natural selection. The Selfish Gene, by Richard Dawkins, helped clarify my thinking and introduced me to the work of George Williams, John Maynard Smith and especially Bill Hamilton on the evolution of cooperation and, more recently, aging.

Their evolutionary ideas spread to my research, as I tried to answer a question few people had even asked: why do rhizobia invest their resources in taking up nitrogen from the atmosphere and giving it to their host plants, rather than using those resources for their own reproduction? Our 2003 paper in Nature, showing that soybean plants impose fitness-reducing sanctions on rhizobia that fail to fix nitrogen answered that question (although we are still working out some details), and is probably my best-known contribution to science, so far. But our less-cited paper on Darwinian Agriculture, also published in 2003, has generated more speaking invitations and a book contract with Princeton University Press.

In 2005, I took early retirement from UC Davis and a grant-supported adjunct position at the University of Minnesota, in order to live with my horticultural-scientist wife, after many years working in different cities. Here, I have been collaborating with Mike Sadowsky on legume-rhizobia symbiosis and with Mike Travisano on experimental evolution of multicellularity, a project he initiated with Will Ratcliff, who did his PhD with me. I am also trying to develop an experimental system to test our explanation for why certain stresses increase longevity. I provide occasional advice to groups concerned with food security and agricultural sustainability. As long as the National Science Foundation keeps giving me grants, life is good.

R. Ford Denison

Favorite publications through 2011 :
(Google Scholar maintains an up-to-date list, with citations and links, here.

Ratcliff,W.C., R.F. Denison. 2011. Alternative actions for antibiotics. Science 332:547-548.

Denison, R.F., E.T. Kiers. 2011. Life histories of symbiotic rhizobia and mycorrhizal fungi. Current Biology 21:R775-R785.

Oono, R., C.G. Anderson, R.F. Denison. 2011. Failure to fix nitrogen (N2) by nonreproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proceedings of the Royal Society B 278:2698-2703.

Denison, R.F. 2011. Past evolutionary tradeoffs represent opportunities for crop genetic improvement and increased human lifespan. Evolutionary Applications 4:216-214.

Ratcliff, W.C., R.F. Denison. 2010. Individual-level bet hedging in the bacterium Sinorhizobium meliloti. Current Biology 20:1740-1744.

Oono,R., R.F. Denison. 2010. Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids. Plant Physiology 154:1541-1548.

Denison, R.F., J.M. Fedders, B.L. Harter. 2010. Individual fitness versus whole-crop photosynthesis: solar tracking tradeoffs in alfalfa. Evolutionary Applic. 3:466-472.

Oono,R., I. Schmitt, J.I. Sprent, R.F. Denison. 2010. Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation. New Phytol. 187:508-520.

Oono R., R. F. Denison, and E. T. Kiers. 2009. Tansley review: Controlling the reproductive fate of rhizobia: how universal are legume sanctions? New Phytologist 183:967-979.


Ratcliff W. C., P. Hawthorne, M. Travisano, and R. F. Denison. 2009. When stress predicts a shrinking gene pool, trading early reproduction for longevity can increase fitness, even with lower fecundity. PLoS One 4:e6055.

Sadras, V.O., R.F. Denison. 2009. Do plant parts compete for resources? An evolutionary viewpoint. New Phytologist 183:565-574.

Ratcliff, W.C., R.F. Denison. 2009. Rhizobitoxine producers gain more poly-3-hydroxybutyrate in symbiosis than do competing rhizobia, but reduce plant growth. ISME Journal 3:870-872.

Kiers E. T., R. F. Denison. 2008. Sanctions, cooperation, and the stability of plant-rhizosphere mutualisms. Annual Review of Ecology, Evolution, and Systematics 39:215-236.

Ratcliff, W. C., S. V. Kadam, and R. F. Denison. 2008. Polyhydroxybutyrate supports survival and reproduction in starving rhizobia. FEMS Microbiology Ecology 65:391-399.

Mitchell, A.E, Y.J. Hong, E. Koh, D.M. Barrett, D.C. Bryant, R.F. Denison, and S Kaffka. 2007. Ten-year comparison of the influence of organic and conventional crop management practices on the content of flavonoids in tomatoes. J. Agric. Food Chemistry 55:6154-6159

Kiers, E.T., M. Hutton, R.F. Denison. 2007. Human selection and the relaxation of legume defences against ineffective rhizobia. Proceedings of the Royal Society B 274: 3119-3126.

Denison, R.F., D.C. Bryant, and T.E. Kearney. 2004. Crop yields over the first nine years of LTRAS, a long-term comparison of field crop systems in a Mediterranean climate. Field Crops Research 86:267-277.

Martini E. A., J. S. Buyer, D. C. Bryant, T. K. Hartz, D. Barrett, and R. F. Denison. 2004. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research 86:255-266.

Okano, Y., K.R. Hristova, C. Leutenegger, L. Jackson, R.F. Denison, B. Gebreyesus, D. LeBauer, and K.M. Scow. 2004. Effects of ammonium on the population size of ammonia-oxidizing bacteria in soil -- Application of real-time PCR. Applied and Environmental Microbiology 70:1008-1016.

Kiers E. T., R. A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

Denison R. F., E. T. Kiers, and S. A. West. 2003. Darwinian agriculture: when can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78:145-168.

Denison R. F., C. Bledsoe, M. L. Kahn, F. O'Gara, E. L. Simms, and L. S. Thomashow. 2003. Cooperation in the rhizosphere and the "free rider" problem. Ecology 84:838-845.

Kinraide T. B., R. F. Denison. 2003. Strong inference, the way of science. American Biology Teacher 65:419-424.

West, S.A., E.T. Kiers, E.L. Simms & R.F. Denison. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proceedings of the Royal Society 269:685-694.

Denison R. F. 2000. Legume sanctions and the evolution of symbiotic cooperation by rhizobia. American Naturalist 156:567-576.

Hasegawa, H., D.C. Bryant, and R.F. Denison. 2000. Testing CERES model predictions of crop growth and N dynamics, in cropping systems with leguminous green manures in a Mediterranean climate. Field Crops Research 67:239-255.

Jacobsen K. R., R. A. Rousseau, and R. F. Denison. 1998. Tracing the path of oxygen into birdsfoot trefoil and alfalfa nodules using iodine vapor. Botanica Acta 111:193-203.

McGuire, A.M., D.C. Bryant, and R.F. Denison. 1998. Wheat yields, nitrogen uptake, and soil moisture following winter legume cover crop vs. fallow. Agron. J. 90:404-410.

Denison R. F., R. Russotti. 1997. Field estimates of green leaf area index using laser-induced chlorophyll fluorescence. Field Crops Research 52:143-150.

Denison R. F., T. B. Kinraide. 1995. Oxygen-induced depolarizations in legume root nodules. Possible evidence for an osmoelectrical mechanism controlling nodule gas permeability. Plant Physiology 108:235-240.

Denison R. F., J. F. Witty, and F. R. Minchin. 1992. Reversible O2 inhibition of nitrogenase activity in attached soybean nodules. Plant Physiology 100:1863-1868.

Denison R. F., D. B. Layzell. 1991. Measurement of legume nodule respiration and O2 permeability by noninvasive spectrophotometry of leghemoglobin. Plant Physiology 96:137-143.

Denison R. F., B. Caldwell, B. Bormann, L. Eldred, C. Swanberg, and S. Anderson. 1976. The effects of acid rain on nitrogen fixation in western Washington coniferous forests. Water Air and Soil Pollution 8:21-34. My first publication, funded by my first grant, funded by the National Science Foundation's since-abandoned Student Originated Studies program, when I was an undergrad at The Evergreen State College.

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 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.

July 31, 2009

Grants!

Just as I was starting to dip into retirement savings to keep my lab going, we got word that both of the grant proposals we sent to the NSF in the latest round were funded, one of them with money from Obama's stimulus funding. We won't be paying ourselves any billion-dollar bonuses, but I may be able to get two months salary this year after all. Both proposals are resubmissions, significantly improved based on suggestions and criticisms from past reviewers. Both projects will use rhizobia, bacteria best known for providing legume plants with nitrogen, but the second project may have eventual applications in medicine (e.g., curing persistent infections) rather than agriculture. The summaries below are intended for a nonscientific audience, such as members of Congress.

"Suppression of rhizobial reproduction by legumes:
implications for mutualism"

(with Prof. Michael Sadowsky, largely based on ideas and preliminary results from grad student Ryoko Oono -- see this recent review article we wrote with Toby Kiers)

Rhizobia are bacteria that can live in soil, but also symbiotically, inside root nodules on plants like soybean or alfalfa. Although many rhizobia provide their host plants with nitrogen, saving farmers billions in fertilizer costs, less beneficial strains cause problems in some areas. Some hosts, including alfalfa and pea, make rhizobia swell up as they start to provide nitrogen. Unlike the nonswollen rhizobia from soybean or cowpea nodules, swollen rhizobia apparently lose the ability to reproduce, but does rhizobial swelling somehow benefit the plant?

To find out, the investigators will map this trait on the family tree for crops and wild plants that host rhizobia, to see if causing swelling evolved more than once, suggesting a positive benefit to the plants. Three dual-host rhizobia (plus mutants that differ in their ability to hoard resources) will be used to measure effects of rhizobial swelling on costs and benefits to the plants. Plant defenses against rhizobia that provide little or no nitrogen, already demonstrated in soybean, will be tested in species that impose bacterial swelling.

This research will increase understanding of a symbiosis that supplies nitrogen to agricultural and natural ecosystems, with implications for other important symbioses. Results could guide the development of crops that selectively enrich soils with the best rhizobia, decreasing future fertilizer requirements. Educational opportunities will be provided for undergraduates, at least one graduate student, and a postdoctoral researcher. Two female high school students have already won trips to the International Science Fair for research done in the principal investigator's laboratory, where such mentoring will continue to be a priority.

Evolution of persistence in the model bacterium, Sinorhizobium
(with Prof. Michael Travisano, largely based on ideas, preliminary data, and writing by grad student Will Ratcliff, with some ideas from Andy Gardner and colleagues -- see the second paper discussed in this post -- and possible relevance to our work on evolution of aging.)

Some bacteria can enter a nongrowing "persister" state that allows them to survive antibiotics and other treatments that normally kill them. By suspending growth, they may also free resources for their genetically identical clonemates.

Most species form only a few persisters. This makes persisters hard to study, despite their importance in long-term infections. However, certain harmless bacteria from plant roots can form up to 40% persisters. These will be used to determine whether persisters benefit mainly from enhanced stress resistance or by increasing the growth of their clonemates.

Successful completion of this research will provide two main benefits: First, this research will determine the conditions that favor the spread of persister-forming bacterial strains over nonpersister strains, and the genetic basis of persistence. This can provide direct medical benefits by aiding the development of novel management strategies, drug targets, and eventually treatments for patients infected with persister-forming bacteria. Second, some conclusions may apply to other species that are difficult to eradicate because they, too, form dormant, stress-resistant stages. These include many agricultural weeds and some species of mosquito. One key advantage of the proposed approach is speed: experiments that would take decades with weeds or mosquitoes can be conducted in months with bacteria. This research will provide training opportunities and jobs for undergraduates, high school students, and a post doctoral researcher.

I am planning to accept another grad student for autumn 2010.

July 20, 2009

Join my lab?

I hope to welcome one or possibly two new graduate students in autumn 2010.

As I noted on the Ecology, Evolution and Behavior web page, much of my research can be seen as following up on ideas first discussed by W.D. Hamilton. This includes our work on the evolution of cooperation (Nature 425:78-81) and on longevity-versus-reproduction tradeoffs as a possible explanation for the health benefits of eating low doses of plant toxins (PLoS One 4:e6055). Often, my grad students use crop plants and/or noncharismatic microfauna (bacteria, yeast, etc.), so if aesthetics is more important to you than science, choose a different major professor. I am also interested in agricultural implications of past and ongoing natural selection (Q. Rev. Biol. 2003 and forthcoming book), although I don't currently have any grant funding for this work.

I also accept students in the Plant Biology grad program, which has been unusually generous in financial support for grad students, providing first-year and summer stipends, paying for meeting travel, etc. (Budget cuts could change this.) Also, unlike most Plant Biology programs, their vision extends beyond molecular biology of Arabidopsis, with significant strength in evolution and in legume (especially Medicago) symbiosis. So students interested in plants should consider both programs.

January 2, 2009

Ford Denison, amateur scientist

My NSF grant will run out soon, so I get to spend the year in which we celebrate the 200th anniversary of Darwin's birth and the 150th anniversary of The Origin of Species as an amateur scientist, like Darwin himself. I'm not as smart or as rich as he was, but I do have imaginative and hard-working students and much better equipment.

I'm working on two grant proposals and several papers while dreaming of getting back to writing my book, so no detailed paper analysis this week. But Nature is highlighting 15 major papers on evolution they have published in the last few years.

March 15, 2008

100th post: reversing evolution II: mimicry in snakes

This is a kilometerstone of sorts: my 100th post! Also, cumulative visits passed 10,000 this week. I know some blogs get more hits than that in only one day, but I used to spend hours preparing a lecture for 25 students, so I guess it's worthwhile to write a blog post for 10,000/100=100 readers. My readership trend over months seems to be slightly downward, however; I hope that's due to other blogs are getting better and readers having limited time, rather than my posts getting worse. Maybe I should be spending the time on my research or my Darwinian Agriculture book instead.

I recently wrote about mimicry in butterflies, then saw an interesting paper on how natural selection and migration affect mimicry in snakes. Selection and migration ("gene flow") are two of the four main processes responsible for evolutionary changes in the frequency of alternative genes in populations; the other two are the random ("drift") processes that can have a big effect in small populations but get smoothed out in large populations and, of course, mutation.

Selection and gene flow often act in opposite directions, because animals migrating into an area (or seeds or pollen blowing in) tend to be less well adapted to their new home, relative to animals or plants that have been evolving there. This general rule held up in this week's paper, as evident from the title: "Selection overrides gene flow to break down maladaptive mimicry", written by George Harper and David Pfenning and published in Nature.

Continue reading "100th post: reversing evolution II: mimicry in snakes" »

September 21, 2007

Thanks, Google Scholar!

I'm sure I could make more money doing something else, but this made my day. That and getting another rhizobium paper accepted by Proceedings of the Royal Society. Would it be greedy to go for the top three?

July 6, 2007

Tagged

John Dennehy, the Evilutionary Biologist, has tried to live up to his name by "tagging" me and seven others. He doesn't seem that evil to me, but I like his blog. I'm supposed to post eight "random" facts about myself...

Continue reading "Tagged" »

May 14, 2007

Who are you?

Visitors per day: 42 (one of my favorite numbers)
Longest visit: 52 minutes
Only 26% use Internet Explorer (obviously a sophisticated bunch!)
Leading source of incoming links: Terry Tao’s “What’s new? math site (wow!) and Carl Zimmer's "The Loom"
Second-most-common language: Usually Portuguese (equal numbers from Portugal and Brazil) or Finnish
Islands: Islas Canarias (Spain), Iceland, Ireland, UK, New Zealand (both islands), Honshu (Japan), Dominican Republic, Australia? Kama`ainas too busy with real surfing?
Under-represented continents: Africa (cradle of human evolution) and Antarctica
Favorite compliment: "er zu einer wirklich raren Spezies gehört: ein Science Blog (fast) ausschließlich über Science (*gasp*)"

March 10, 2007

Troll refuge may prevent local extinction

I reserve my blog-given right to delete off-topic comments -- except in this Troll Refuge. "Comments" whose only purpose is to link to a commercial or crackpot site will generally be deleted everywhere. This is a free service to people who may not realize they are crackpots.

Comments immune from deletion outside the Troll Refuge are either:
1) comments on the particular paper-of-the-week, or
2) suggestions for papers to discuss that meet the criteria in my first post.

"But", you may say, "I've got this great proof that evolution is all wrong! This scientist said something that could be interpreted as inconsistent with some aspect of evolutionary theory! That proves that both versions of the creation story in Genesis (cattle and trees created before and after humans) are literally true, doesn't it?"

If the scientist said it in a peer-reviewed paper published in the last month and containing new data, you can suggest it as a paper of the week. Otherwise, post your proof here in the Troll Refuge.

The comments section for this entry is also the place to whine about censorship, or to complain about my failure to delete someone else's comment that you think is off-topic. Off-topic comments attached to other entries are subject to deletion, or, if particularly amusing, transfer to this troll refuge, possibly with appropriate editing. Trolls repeatedly posting outside the refuge will be banished.

Troll hunters are welcome in the refuge, too. This may seem cruel, but we need to keep the population below carrying capacity. However, no firearms will be allowed, only sticks and stones. And words, of course.

February 14, 2007

Evolution triumphs over photosynthesis

In general, I don't want to waste time responding to tired old creationist criticisms of evolutionary theory that have already been refuted elsewhere (such as here or here) -- criticisms backed by new data would be another story -- but I do need to address one issue that could undermine my ability to find a paper to discuss each week. Some creationists have suggested that scientists are increasingly rejecting evolution. Actually they've been saying this for a long time. Is my paper pipeline drying up?

Continue reading "Evolution triumphs over photosynthesis" »

What's new in evolution? Lots!

A member of the audience at a recent Cafe Scientifique on "Understanding Evolution" complained that the speakers spent more time talking about the political battle with fundamentalists who don't want evolution taught in schools -- this is especially a problem in the US and Turkey -- rather than discussing new discoveries in evolutionary biology. The theory of evolution is the cornerstone of biology, in the same sense that the germ theory of disease is a cornerstone of medicine, so I agree that increasing the amount and quality of coverage of evolution is a critical educational goal.

But I also sympathized with the audience member who wanted to hear more about science and less about politics and religion. It's not that hard to find out about new discoveries in evolutionary biology if you have access to a university library or even just a good internet connection. But I liked the name, "This Week in Evolution", and nobody seemed to be using it!

Each week, I plan to discuss a scientific paper that meets the following criteria:
1) published during the previous month;
2) about some aspect of evolution;
3) published after peer review in a journal with a citation impact of at least 1.0 (i.e., no third-tier journals);
4) containing significant amounts of data, not just mathematical modeling or discussion.

Continue reading "What's new in evolution? Lots!" »