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April 28, 2011

Are antibiotics weapons, signals, cues, or manipulation?

"Do you expect me to talk?"
"No, Mr. Bond, I expect you to die!"
Sometimes, there are more than two possibilities.

Many bacteria make antibiotics which, in high doses, kill other bacteria. But microbiologists have noticed that, at lower doses, antibiotics may change gene expression or alter behavior, without killing. So, they suggest, maybe antibiotics are mainly "tools of communication," rather than weapons.

Maybe, but those are not the only possibilities. Will Ratliff and I have just published a short Perspective in Science suggesting that two other possibilities are more likely. A PDF is freely available here, courtesy of the journal.

If communication (or "signaling") implies mutual benefit, what about nonlethal effects of antibiotics that benefit receiver or sender, but not both? For example, a bacterium that detects an antibiotic may hide in a biofilm to escape from the antibiotic, just as a zebra that smells lions hides in a herd to escape predators. If hiding in the biofilm benefits the bacterium that detected the antibiotic, but not the bacterium that made it, we would call the antibiotic a "cue."

Or, suppose a bacterium making antibiotics benefits by scaring competitors into dispersing (or hiding in biofilms)? This could benefit the producer, by reducing competition, but harm the receiver. We would call that "manipulation."

To distinguish among these possibilities, we need to measure actual fitness consequences, to producer and receiver, of bacterial responses to antibiotics.

April 22, 2011

More on PhD glut

Some religion professor has noticed a population that is growing faster than the resources needed to support its preferred lifestyle.

Yes, more PhD's are produced each year than academic jobs. Few science PhD's are unemployed for long, but going to grad school might sometimes decrease, rather than increase, your lifetime income. I've commented on that before and advised people not to go to grad school unless they think they will find grad school itself worthwhile. But I thought one of the comments (from Igor Litvinyuk) was quite insightful:

Fierce competition for academic positions is the only way to maintain excellence in academia. That's why academia needs more qualified Ph.D.-holding candidates than there are vacancies.... society gains from having an excellent merit-based academic research system. Some measure of frustration and disappointment among the less successful contestants who chose to participate in this competitive system is unavoidable and is not unreasonable price to pay. Is it really all that different from other walks of life where competition is the norm, i.e. sports, literature or show business?

I agree that the optimum ratio of PhD's to jobs (or the optimum funding percentage for grant proposals) should be determined by long-term benefits to societies, not just the short-term interests of PhD's or grant applicants. But I wonder whether, beyond some point, increasing competition may be counter-productive, and not just for the competitors.

This week's picks

Some of these papers look really interesting, but I'm trying to finish revisions to my book by the end of the month. We'll have a short Perspective in Science next Friday.

Modes of response to environmental change and the elusive empirical evidence for bet hedging [Cites our paper on bet-hedging in rhizobia.]

New behavioural trait adopted or rejected by observing heterospecific tutor fitness "the proportion of pied flycatcher females matching the choice of the tit tutor consistently increased with increasing number of offspring in the tit nest"

A latitudinal gradient in rates of evolution of avian syllable diversity and song length "evolutionary rates in traits important to reproductive isolation and speciation are influenced by latitude and have been fastest, not in the tropics where species diversity is highest, but towards the poles."

Late Carboniferous paleoichnology reveals the oldest full-body impression of a flying insect

Intracellular invasion of green algae in a salamander host "Fewer algal cells were detected in later-stage larvae through FISH [fluorescent in-situ hybridization labeling]"

Learning to live together: mutualism between self-splicing introns and their hosts

From the first intention movement to the last joiner: macaques combine mimetic rules to optimize their collective decisions "macaques vote and choose the majority. Individuals then join the movement according to a mimetism based on affiliative relationships"

April 15, 2011

Almost finished revising Darwinian Agriculture

I'm busy finishing revisions to my book on Darwinian Agriculture. Meanwhile, here are some recent papers that look interesting:

Digit ratios predict polygyny in early apes, Ardipithecus
"Ardipithecus ramidus have [index to ring finger length] ratios consistent with polygynous extant species, whereas the ratio of Australopithecus afarensis is consistent with monogamous extant species"

Rapid, global demographic expansions after the origins of agriculture
"the invention of agriculture facilitated a fivefold increase in population growth relative to more ancient expansions of hunter-gatherers."

Maternal investment, life histories, and the costs of brain growth in mammals "evolutionary changes in pre- and postnatal brain growth correlate specifically with duration of the relevant phases of maternal investment (gestation and lactation)"

Adaptive human behavior in epidemiological models
"explicitly model the trade-offs that drive person-to-person contact decisions"

April 8, 2011

This week's picks

Workers influence royal reproduction
"worker aggressive and non-aggressive behaviour towards queens predicted which queen monopolized reproduction. In contrast, among-queen interactions were rare and did not predict queen reproduction. Furthermore, parentage analysis showed workers favoured their mother when present"
[Maybe "inclusive fitness" is useful after all!]

Updated chronology for the Miocene hominoid radiation in Western Eurasia
"Eurasian pongines [orangutans and extinct relatives] and African hominines [humans, chimps, bonobos, and extinct relatives] might have independently evolved in their respective continents from similar kenyapithecin ancestors [apes living 14 million years ago], resulting from an early Middle Miocene [5-23 MYA] intercontinental range extension followed by vicariance [geographic separation, reducing or eliminating interbreeding so allowing evolutionary divergence]. "

Ribozyme-Catalyzed Transcription of an Active Ribozyme "we recombined traits evolved separately in different ribozyme [catalytic enzyme made of RNA rather than protein] lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. "

An evolutionary process that assembles phenotypes through space rather than through time "assortative mating between fast-dispersing individuals at the invasion front results in an evolutionary increase in dispersal rates in successive generations"

Fork-tailed drongos use deceptive mimicked alarm calls to steal food
"false alarm calls when watching target species handling food, in response to which targets flee to cover abandoning their food"

Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups
"a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three"

Differences in the temporal dynamics of phenotypic selection among fitness components in the wild "The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival."

Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias "Rickettsia sp. nr. bellii swept into a population of an invasive agricultural pest, the sweet potato whitefly, Bemisia tabaci, in just 6 years. Compared with uninfected whiteflies, Rickettsia-infected whiteflies produced more offspring, had higher survival to adulthood, developed faster, and produced a higher proportion of daughters. The symbiont thus functions as both mutualist and reproductive manipulator. "

The evolutionary biology of child health "cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes"

Tradeoffs associated with constitutive and induced plant resistance against herbivory "Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species."

Towards a quantitative understanding of the late Neoproterozoic carbon cycle
"all of the main features of the carbonate and organic carbon isotope record can be explained by the release of methane hydrates from an anoxic dissolved organic carbon-rich ocean into an atmosphere containing oxygen levels considerably less than today"

April 1, 2011

Transferable skills

Mike the Mad Biologist makes some good points, commenting on the claim that employment options are worse in biology than other scientific fields.

...most of the skills you learn are only useful in...the biomedical sciences. Most don't learn enough 'generalist' skills, such as high level math or serious programming skills, to have other career alternatives if academia doesn't work out.

Jessica Palmer says the key is to develop "transferable skills." I agree. And not just skills that can be applied outside biology, but skills that can be applied to new problems within biology. As Mike the Mad Biologist continues:

Worse, many of the skills they learn become obsolete. A decade ago, sequencing was a Ph.D. activity, or at least, an activity supervised very closely by a Ph.D. Now, it's largely automated...

So, grad students and postdocs should learn skills that will continue to be needed and can't be automated, especially critical reading, writing, and thinking skills. Can you spot flaws in scientific papers, especially flaws that are only evident in light of information from other papers or even other fields? Can you combine information from different fields and come up with new questions and hypotheses? Can you import useful ideas from economics into biology, or vice versa? Can you express complicated ideas clearly, orally and in writing? If so, you have little to fear from automation.

But, Mike continues

one reason that won't happen is the shortage of funding.... It isn't in the career interest of those doing the training to have students do many things that aren't related to the [short-term?] success of their lab's--their PI's--research program.

I agree that 6% funding rates for grants put Principal Investigators under a lot of pressure. But does that really translate into pressure on students and postocs to crank out data with the skills they already know, rather than learning new ones? Maybe in big, multipostdoc labs, only the most creative postdocs are encouraged to develop new ideas, while the rest become glorified technicians. I wouldn't know.

In my own small lab, interactions with grad students and postdocs are motivated by the hypothesis that fierce competition for grants puts a premium on creativity and new ideas, often combining theory and methods from different fields, even if that means having a little less preliminary data. I therefore encourage them to learn a variety of highly transferable critical-thinking skills, in addition to whatever technical skills may be needed for a particular project.

It might help if the career success (in academia or elsewhere) of former grad students and postdocs in a lab (pro-rated by the number of years spent in that lab) was weighed more heavily by grant programs.