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August 28, 2012

The importance of titles

Years ago, someone reinvented a method I'd published in a journal he regularly read (and published in), without citing my paper. I complained. He pointed out that the title of my article didn't hint at that aspect of the contents.

Since then, I've tried to get the main point of each paper into the title. For example:

When Stress Predicts a Shrinking Gene Pool, Trading Early Reproduction for Longevity Can Increase Fitness, Even with Lower Fecundity

But journal editors don't always cooperate. For example, we wanted to call our recent Perspective in Science (discussed here) "Are Antibiotics Weapons, Signals, Cues, or Manipulation?" The editor insisted on "Alternative Actions for Antibiotics."

We worried that people would glance at the title and think, "Oh, another one of those antibiotics-as-signals articles." A "signal" is information whose transmission benefits sender and receiver. A "cue" is information used in ways that don't necessarily benefit the source. For example, bacteria may respond to low doses of antibiotics by turning on protective mechanisms, by fleeing, or by hiding in a biofilm. I would only call antibiotic production a "signal" if scaring away competitors, rather than killing them, is the main way it increases the producer's fitness.

Just as we feared, a recent paper miscites our work:

"Antibiotics, especially at subinhibitory concentrations, can act as signal molecules aside from their antibacterial effect (Davies et al. 2006; Yim et al. 2007; Ratcliff and Denison 2011)."

Choose your title carefully.

August 27, 2012

Another route to drought-tolerant crops?

My book, Darwinian Agriculture, argues that the quickest route to crop genetic improvement is to identify tradeoffs that were rejected by past natural selection, but which we are willing to accept. Tradeoffs between individual-plant competitiveness and the collective performance of the whole crop are particularly promising. "MAT kinase", the Scientist Gardener suggests that this is the key to Monsanto's DroughtGard corn:

"From what I've heard, the yield gain of this variety under drought occurs because it slows its growth specifically under drought stress such that existing soil moisture is saved for the critical period surrounding flowering, resulting in less kernel abortion, higher harvest index and greater yield. This is certainly ironic given the expectations of many field physiologists and breeders. It also occurs to me that this is consistent with the thesis of Denison's Darwinian Agriculture - that evolution has already maxed out our crops' ability to deal with most stresses and environments, and that the greatest potential for improvement exist in traits that only work in an ecosystem (such as a farm field), where plants aren't in competition with their neighbors. "

This drought-tolerance-via-slower-growth would be quite interesting, if true, and similar to an idea I discuss in the book in the context of drought-tolerant Drysdale wheat.

In a recent post, I had suggested an alternative idea, that the bacterial gene they transferred to corn might result in a phenotype so radically different that natural selection had never had a chance to test it, in corn or its wild ancestors. I like The Scientific Gardener's hypothesis better. The problem with radically new phenotypes, of course, is that it's very hard to predict all of their effects and side effects.

August 17, 2012

Small farmers benefit from transgenic insect resistant crops... but what about cheaters?

Economic impacts and impact dynamics of Bt (Bacillus thuringiensis) cotton in India
The authors write that:

"Bt has caused a 24% increase in cotton yield per acre through reduced pest damage and a 50% gain in cotton profit among smallholders. These benefits are stable; there are even indications that they have increased over time."
So far, so good, but what will happen when the pests evolve resistance? The high-dose / refuge strategy seems to be working to slow the evolution of resistance, prolonging the useful lifetime of Bt crops. But...

Success of the high-dose/refuge resistance management strategy after 15 years of Bt crop use in North America can be undermined by "failure to use high-dose Bt cultivars and lack of sufficient refuge."

Getting the dose high enough is the responsibility of the seed companies, but how do we keep individual farmers from "cheating" -- growing Bt crops on their whole farm, rather than allocating some land to the Bt-free refuge this strategy requires? Should we rely on pressure from individual neighbors, or something more organized?

An economic experiment reveals that humans prefer pool punishment to maintain the commons "...where the punishment act is carried out by a paid third party, (e.g. a police system or a sheriff)"

Bacillus thuringiensis, the original source of the Bt gene, also has problems with cheaters. Making the toxin is expensive, so "free riders" (which don't pay the cost of making the toxin) can potentially multiply faster than "cooperators" that make the toxin. But they can only achieve that potential inside host caterpillars that are simultaneously infected by a toxin-making strain. Co-infection is more common at high bacterial population densities, but as cheaters become more common overall reproduction decreases bringing down the population density. So cheaters and cooperators co-exist in the field, as reported in "The Dynamics of Cooperative Bacterial Virulence in the Field."

We have suggested a somewhat similar mechanism for the co-existence of cooperative (N2-fixing) and cheating rhizobia: host sanctions against nodules that fix less nitrogen reduce the fitness of cheaters when mixed nodules are rare, but high rhizobial population densities lead to more mixed nodules, where cheaters may escape sanctions by sharing nodules with strains that fix more nitrogen.

August 10, 2012

Fossils, convergent evolution, cooperation, and "groundwater footprints"

New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo "The new fossils confirm the presence of two contemporary species of early Homo, in addition to Homo erectus, in the early Pleistocene of eastern Africa."

A transitional snake from the Late Cretaceous period of North America "...snakes evolved from burrowing lizards. The skull is intermediate..."

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase The same molecular change to a sodium pump, previously seen in Monarch butterflies, was found in four insect species (separated by 300 million years of evolution) feeding on plants making the same natural insecticides.

Heterogeneous networks do not promote cooperation when humans play a Prisoner's Dilemma "1,229 volunteers chosen among last year's high school students"

Water balance of global aquifers revealed by groundwater footprint" "80 per cent of aquifers have a groundwater footprint that is less than their area" but "the global groundwater footprint is currently about 3.5 times the actual area of aquifers", putting water supplies for 3.5 million people at risk. My book briefly compares the ecological footprints of conventional and organic farms.

August 9, 2012

Darwinian agriculture and Darwinian medicine: beyond resistance management

DarwinianMedicine.jpg Thumbnail image for BookCover.gif

Evolution happens. Careless use of antibiotics selects for antibiotic-resistant pathogens, careless use of insecticides (including crops that make their own insecticides) selects for pesticide-resistant insect pests, and careless use of herbicides selects for herbicide-resistant weeds.

Many people seem to assume that this well-known problem, evolution of resistance, is all there is to "Darwinian medicine" or "Darwinian agriculture." But check the tables of contents of the books above. You'll only find one chapter on the "arms race" between pathogens and their hosts and one chapter (titled "Stop Evolution Now!") that focuses on slowing the evolution of resistance to pesticides and other pest-control measures.

Both books (Nesse and Williams, 1994, Denison, 2012) and the earlier review articles on which they were based (Williams and Nesse, 1991, Denison, et al., 2003) devote much more space to the implications of past evolution.

"If evolution by natural selection can shape sophisticated mechanisms such as the eye, heart, and brain, why hasn't it shaped ways to prevent nearsightedness, heart attacks, and Alzheimer's disease?"

Similarly, biotechnology allows us to increase the expression of crop genes that enhance drought tolerance, but

"mutations that increase gene expression happen all the time, and natural selection maintains those that are beneficial to the plant. So why does corn normally have lower expression of this gene than was obtained by genetic engineering?"

We don't have definite answers to these questions. Both books present hypotheses with various amounts of supporting data, but additional research is needed. With aging populations and rising food prices, maybe there will even be some money available to fund that research.

Should evolutionary biologists working on fundamental problems and/or wild species consider adding applied work to their research portfolios? If so, you or your students might get some useful ideas from Nesse and Williams or from my book, just published by Princeton University Press.

Literature Cited

Denison RF. 2012. Darwinian agriculture: How understanding evolution can improve agriculture. Princeton: Princeton University Press.

Denison RF, Kiers ET, West SA. 2003. Darwinian agriculture: when can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78: 145-168.

Nesse RM, and Williams GW. 1994. Why we get sick: The new science of Darwinian medicine. New York: Vintage Books.

Williams GW, Nesse RM. 1991. The dawn of Darwinian medicine. Quarterly Review of Biology 66: 1-22.

August 3, 2012

Defense against malaria, cuckoos, mobile elements, and creationists

Fighting malaria with engineered symbiotic bacteria from vector mosquitoes
"symbiotic bacteria to deliver antimalaria effector molecules to the midgut lumen"

PLoS Biology: The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi
"recombinant blood stage malaria vaccines can drive the evolution of more virulent malaria parasites"

Cuckoos Combat Socially Transmitted Defenses of Reed Warbler Hosts with a Plumage Polymorphism
"social learning is specific to the cuckoo morph that neighbors mob"

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs
evolving defenses against active mobile elements

A complete insect from the Late Devonian period
400 million years ago? Like 400 million years (to three significant digits) before the Earth was created?

ResearchGate, Google Circles, Linked In -- useful or annoying?

Watergate, ClimateGate, ResearchGate?

I keep getting emails saying someone I know has "invited" me to join these "professional networks." In some cases, the person who supposedly sent the "invitation" denies it. So either the networks are outright lying (sending an invitation without any authorization by the "inviter") or they're asking permission to send an invitation, but in a way that it's not clear that's what they're doing. Like they translate "yes, I'm interested in what this person is publishing" into "this person is inviting you to join our network."

In my experience, most scientists are pretty willing to answer email questions (in their area of expertise, beyond what one could learn in 5 minutes on Wikipedia) and to collaborate when it makes sense, whether or not you're a friend of a colleague of a relative. So I don't see the point to these artificial networks. But I haven't used them, so maybe I'm missing out.