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July 31, 2009


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 24, 2009

Microbes evolve; flies evolve and learn

"Can plants predict the future?" asked one of my Crop Ecology lectures at UC Davis. Yes, they can. Plants use decreasing daylength to predict oncoming winter, and flower early enough to finish seed development before it gets too cold. Some plants detect early signs of drying soil and reduce their own water use, saving water in the soil for later.(Davies & Zhang. 1991, Bano, et al. 1993) Others detect "distress signals" from neighbors under insect attack, turning on chemical defenses in anticipation (Karban, et al. 2004).

But these anticipatory responses do not require learning: a beneficial change in individual behavior in response to individual experience. An alfalfa plant will never learn that the farmer always irrigates before it actually runs out of water. At least, I assume it won't. An evolving alfalfa population is a different story. Over a few generations under irrigation, genotypes that reduce their water use as the soil starts to dry (thereby reducing their growth) will be out-competed by genotypes that keep using water and growing.

Like plants, microbes can predict the future. As in plants, this trait can evolve. As they pass through the gut, bacteria typically see lactose before they see maltose. So they have evolved to "anticipate" maltose availability, turning genes for maltose use on as soon as they are exposed to lactose. After 500 generations of evolution on lactose without maltose, however, the bacteria have lost lose this anticipatory response, so that they turn maltose genes on only when they actually see maltose.(Mitchell, et al. 2009) The title of the news story in Nature about this work asked whether microbes can "learn from history", but this is clearly not an example of individual cells modifying their responses to lactose based on their individual experience.

Individual insects can learn. But is learning always a good thing? Aimee Dunlap, a grad student in my department working with David Stephens, just published a paper in Proceedings of the Royal Society exploring the conditions under which natural selection will favor learning (Dunlap & Stephens. 2009).
Fly Learning Graphics.jpg

She reasoned that, if the behavior that maximizes fitness doesn't change over generations, then natural selection should turn that behavior into an instinct, rather than something that has to be learned. If fitness-maximizing behavior changes over generations, learning may increase fitness -- unless there is so much random change over an individual's lifetime that experience is a poor guide.

Dunlap used a system devised by Mery and Kawecki(2002) to test these hypotheses with fruitflies. The flies had to choose between laying eggs in a dish with pineapple- or orange-flavored medium. In the first, "experience" phase, one dish also had quinine, which the flies dislike. They won't lay eggs in a dish with quinine, but would they learn, and avoid that dish in the future, even when presented without quinine?

Dunlap let her fruitfly populations evolve for 30 generations in two different ways. One population experiences an "experience is reliable" treatment: any eggs laid in the type of dish (orange or pineapple) that previously had the quinine were discarded. For example, if a fly experienced pineapple+quinine early in life, any eggs it laid in quinine-free pineapple later were discarded. Only those laid in quinine-free orange made it into the next generation. In alternate generations, however, quinine would be paired with orange. So an evolutionary increase in instinctual preference for orange or pineapple wouldn't help. Instead, this population increased its ability to learn: whichever type dish had quinine at first was avoided in the future. In the "random" treatment, eggs from one dish were discarded at random, regardless of whether than dish had previously had quinine. 30 generations of this treatment caused no evolutionary change in learning ability. If the relationship between quinine and dish type was random, but eggs were raised from the orange dish, the populations evolved an instinctual preference for orange, and vice versa for pineapple. The authors concluded that, in addition to past emphasis on constant versus changing environments, we need to distinguish between "the reliability of experience [which selects for ability to learn], and underlying uncertainty about the appropriate action [which selects against ability to learn]."
Fly Learning Evolution.jpg
I wonder whether these results could be used to explain differences in learning ability among species. There's a squirrel in our neighborhood that has trained my wife and me to give her peanuts. If all humans were a friendly source of food, that would presumably select against fear of humans, without selecting for learning. But if some humans consistently chased squirrels while others consistently supplied peanuts, would that select (over many squirrel generations) for ability to learn to tell us apart, and to remember which were friendly?


Bano A, Dorffling K, Bettin D, Hahn H. 1993. Abscisic acid and cytokinins as possible root-to-shoot signals in xylem sap of rice plants in drying soil. Aust. J. Plant Physiol. 20 : 109-15

Davies WJ, Zhang J. 1991. Root signals and the regulation of growth and development of plants in drying soil. Annu. Rev. Plant Physiol. Plant Mol. Biol. 42 : 55-76
Dunlap AS, Stephens DW. 2009. Components of change in the evolution of learning and unlearned preference. Proceedings of the Royal Society B: Biological Sciences. 276 : 3201-8

Karban R, Huntzinger M, McCall AC. 2004. The specificity of eavesdropping on sagebrush by other plants. Ecology. 85 : 1846-52

Mery F, Kawecki TJ. 2002. Experimental evolution of learning ability in fruit flies. Proceedings of the National Academy of Sciences of the United States of America. 99 : 14274-9

Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, et al. 2009. Adaptive prediction of environmental changes by microorganisms. Nature. 460 : 220-4

July 21, 2009

This is a joke, right?

I've seen a lot of discussion lately about the poor quality of science reporting and scientific literacy today, but was still amazed to see this in the New York Times:

As this image makes obvious a 14.5-inch reflecting telescope is not 14.5 inches long, but considerably larger.

Doesn't everyone know that the "size" of a telescope refers to the mirror diameter? And that the light-gathering ability of a telescope depends on the area of the mirror, proportional to the square of the diameter? Next, it will turn out that people have been graduating from high school without understanding evolution.

It's a great story anyway: an amateur astronomer is the first to spot the after-effects of an earth-size planet hitting Jupiter. If he hadn't taken a break from his hobby to watch golf on TV, he might have seen the actual impact.

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.

July 17, 2009

Biofilms as selfish herds

"Scientists once thought that wolves chase deer and may even try to eat them, that sharks attack other fish, and that cold weather can kill penguins. But recent research has shown that these so-called threats are actually beneficial, because they encourage togetherness."

OK, I made the above "quotation" up, but the logic is the same as in a recent story in Science about antibiotics:

"there's scant evidence that bacteria or fungi deploy antibiotics to kill or ward off other microbes... These molecules, they assert, may be less weapons for competition or combat than tools of communication... When certain bacteria are exposed to nystatin, the microbes form slimelike communities known as biofilms... this may be just one of the molecule's natural roles."
For a bacterial cell, there are both disadvantages and advantages to crowding together in a biofilm. There may be more competition for available nutrients in a biofilm, but there may be more nutrients to compete for. One reason is that an individual bacterium may not be able to excrete enough enzymes to release nutrients from a solid surface; a bunch of bacteria growing in a biofilm may do better.

But why use antibiotics as signals to form biofilms, when bacteria can produce and detect plenty of nontoxic signals? See previous posts on "quorum sensing", but also this discussion.

The most logical reason to form a biofilm in the presence of an antibiotic is to escape from the antibiotic! I am reminded of this quotation about cattle in lion country:

" Yet although the ox has so little affection for, or individual interest in, his fellows, he cannot endure even a momentary severance from his herd. If he be separated from it by strategem or force, he exhibits every sign of mental agony; he strives with all his might to get back again and when he succeeds, he plunges into its middle, to bathe his whole body with the comfort of closest companionship."

The quotation is from Francis Galton, but I got it from Bill Hamilton's 1971 paper, "Geometry for the selfish herd." Other examples in this classic paper -- "Evilutionary Biologist" John Dennehy has written a nice summary -- include reindeer at the edge of a herd suffering much more attack from parasitic insects and gulls nesting at the edge of a colony suffering much more predation.

I am reading a couple of interesting papers relevant to biofilms and may have time to write about them this weekend. As for the real-world role of antibiotics as antibiotics, see this recent post.

Short version of our aging paper

Our ancestors who delayed reproduction when environmental cues predicted famine were more likely to survive to reproduce after the big die-off. Delaying reproduction therefore increased relative representation in the smaller post-famine gene pool.

Biological responses inherited from those ancestors are still triggered by cues that predicted past famines, such as eating less or eating "famine foods." These responses can therefore extend lifespan, with a decrease in potential fertility as a side-effect. But most of us don't want to achieve our maximum possible family size anyway.

July 10, 2009

What really causes tradeoffs between longevity and reproduction?

Now the New York Times is reporting on the two aging studies I mentioned yesterday. It's a good article, except for this part:

Dietary restriction seems to set off an ancient strategy written into all animal genomes, that when food is scarce resources [calories?] should be switched to tissue maintenance from breeding.
This is the "disposable soma" hypothesis of Kirkwood, and I don't think it applies to the monkey experiment. The monkeys in the study aren't reproducing anyway, so those on a low calorie diet should have fewer resources available for maintenance, yet they have lower rates of death from aging-related causes.

More generally, if the only way reproduction shortened lifespan were by consuming resources, then eating more (enough to outweigh the metabolic cost of reproduction) should increase longevity. It doesn't.

There is plenty of evidence for a tradeoff between reproduction and longevity, but I don't think it's mainly due to competition between reproduction and maintenance for calories. It's more likely that blood pressure or levels of insulin and testosterone have different optima for reproduction and longevity. Even in males for whom reproduction has negligible energy costs -- I know this is not true of males of all species -- testosterone levels that maximize reproduction have a long-term cost, reducing lifespan.

I suspect that many aging researchers would agree that there's more to the reproduction-vs.-longevity tradeoff than calories, so this isn't the really novel part of the hypothesis we published last week.

What's new in our paper is the reason that delaying reproduction increases fitness. The key point is that Darwinian fitness is the relative contribution to the next generation, not the absolute number of offspring produced. So, if population is decreasing, delaying reproduction can increase fitness, simply because each offspring makes a bigger splash in the smaller gene pool.

I think we're the first to link the fitness benefits of delaying reproduction in a declining population to environmental cues that predict such decreases: calorie restriction, crowding, or consumption of "famine foods" with toxins like resveratrol, asprin, glucosinolates, or alcohol.

July 9, 2009

Has natural selection been asleep at the switch?

"This new forage has great insect resistance", effused a former colleague, "we just need to eliminate the toxins that keep sheep from eating it."

Genetically engineered drought-tolerant crops are introduced with great fanfare, only to disappear when they turn out to have low yield under nondrought conditions.

When natural selection falls short of perfection, it may be because "you can't get there (some desirable adaptation) from here (current genotypes)" without passing through a series of intermediate generations that would have lower fitness. Natural selection favors genotypes best-adapted to current conditions, which are not necessarily steps towards any long-term improvement.

But natural selection often seems to miss even "simple" improvements, that might be achieved by changing as little as one DNA base. Such small changes are often enough to increase or decrease expression of key genes, for example. This sort of evolutionary progress may be blocked by tradeoffs, e.g., between seed production under different conditions (e.g., wet vs. dry), or between the competitiveness of individual plants and their collective seed production.

So what are we to make of two recent papers (in Science and Nature, respectively, discussed in Science News) on extending lifespan, one using calorie restriction and the other using the antibiotic, rapamycin?

Calorie restriction has been shown to increase longevity in model species like nematode worms and mice, but this latest study shows clear benefits in monkeys. The obvious question -- at least, it was obvious to me -- is why has past natural selection given monkeys (and fruitflies, and nematodes, and mice...) appetites that make them eat more than is good for them?

At least, that seemed to be the question, until it was shown that food odors can reverse the beneficial effects of calorie restriction, at least in fruitflies and nematodes. In humans, soft drinks with artificial sweeteners turn out to be just as likely to cause "metabolic syndrome" (related to diabetes) as those with sugar. So apparently our lives can be shortened by a perception of abundance, not just by actually eating too much. What is going on here?

In this case, the evolutionary tradeoff seems to be between current and future reproduction. As discussed in last week's post, delaying reproduction usually decreases fitness (representation in the next generation, relative to others) when population is increasing, but delaying reproduction can increase fitness when population is decreasing. Calorie restriction predicts population decline, triggering physiological responses that delay reproduction and thereby increase longevity. So do bitter-tasting foods, traditionally eaten only during famines. Food odors or sweet tastes have the opposite effect, because they predict population increase.

But what about life extension by rapamycin? One known tradeoff is suppression of the immune system, so we might get longer lives only in a hypothetical germ-free environment. But could the protein target of rapamycin (TOR) also be important to reproduction? Is this yet another example of a longevity-vs.-reproduction tradeoff?

July 6, 2009

Throwing the longevity switch

If you could choose a longer, healthier life, but only by having fewer kids, would you? What if you could eventually have the same number of kids, but only by having sex more often, and with no possibility of becoming a parent as a teen-ager?

Is this really possible? Based on the paper we published last week, we are pretty sure it is, although we don't yet know how much of an increase in lifespan is achievable, nor how much it will "cost" in reduced fertility.

A key assumption is that there are tradeoffs between longevity and reproduction, especially early reproduction. There is plenty of evidence for this antagonistic pleiotropy hypothesis: some gene variants that increase longevity nonetheless stay rare, because individuals with those variants have fewer kids. There are many possible reasons for this tradeoff. Calories used for reproduction aren't available for maintaining our bodies. Blood pressure and insulin levels optimal for reproduction are unlikely to be exactly optimal for longevity. Other risks associated with reproduction include sexually transmitted diseases and direct risks of childbirth. When there is a conflict between reproduction and longevity, natural selection will often favor reproduction.

There are, however, two ways we may be able to choose differently, increasing longevity at the expense of (potential, but maybe not actual) reproduction. First, once germ-line gene therapy is perfected and available (initially, perhaps, only in one or two "outlaw states"), maybe we could reverse some of the effects of past natural selection. We might be able to produce genetically engineered kids who would reach puberty later and with low enough intrinsic fertility that occasional unprotected sex would rarely lead to pregnancy, but who would still be healthy at age 100.

Second, what about people already born? Is there some biological "switch" we can throw, that tilts the longevity-vs.-reproduction tradeoff more towards longevity? Or has past natural selection welded the switch in the "reproduce now" position?

We think the switch is free to move, depending on environmental cues that affected our ancestors' survival and reproduction. Our paper shows that the switch position that maximizes Darwinian fitness depends on whether the overall population is increasing or decreasing. If population is decreasing, then individuals that live longer and reproduce later can contribute a larger fraction to their species' (shrunken) gene pool than those that reproduce earlier, on average, even if a few of them die before they get a chance to reproduce, and even if their lifetime reproduction is less than they might have achieved earlier.

Therefore, even though gene variants that always sacrifice early reproduction to increase longevity may not have persisted in the gene pool, variants that delay reproduction (thereby increasing longevity) only when populations were decreasing are likely to be with us, in each of our DNA molecules, today.

If this is true, all we need to do to increase our longevity is to give our bodies (false) cues that, over our evolutionary history, usually predicted population declines. To the extent that population declines were caused by food shortage, eating less may work, as it does in most species tested. Eating "famine foods" (leaves rather than meat, maybe) may also trigger physiological responses that reduce fertility but extend lifespan. On the other hand, if population declines were usually caused by cold winters, is there some reasonably comfortable way to trigger similar responses?

Delaying reproduction can only increase fitness if it increases the chances of surviving the famine or cold winter and reproducing later. So stresses that often predicted the death of the stressed individual (those associated with violent conflict, perhaps) won't necessarily delay reproduction or increase longevity. But there are lots of examples of mild stress increasing longevity. These stresses presumably trigger health-and-longevity-promoting mechanisms, but we may be the first to explain why such beneficial mechanisms aren't turned on all the time: they tend to reduce fertility.

Now, here's a question for you: would increasing human longevity be a good thing? I've seen this issue discussed in various places, but rather superficially. Assume that this option was made available to everyone, given that the cost could be quite low: inexpensive drugs or lifestyle changes that might even save money. Death rates would go down, in the short run, but so would birth rates, especially in countries where birth control is now rare. Death from old age is a fairly small component of overall population trends in these countries (relative to birth rate and infant mortality), so their rate of population increase might actually slow. But, if people expected to live longer, would they have more children (despite lower intrinsic fertility) or fewer, and at what age? Assuming some increase in population, we might need to grow more food -- a significant challenge -- but how would the overall impact of two healthy 90-year-olds who are still working (perhaps as doctors or nurses) and driving compare to that of one 90-year old who doesn't drive but needs expensive medical care? If professors keep working into their 90's, will that slow the spread of good new ideas, or only of stupid ideas that younger faculty may not know were debunked long ago? Would a longer-lived population produce too many bloggers?