See Spot. See Spot run. See Spot’s meds.

I expected the New York Times Magazine piece on veterinary pharmacology, “Pill-Popping Pets” to be an exercise in hand-wringing over feline neuroses and dogs on Prozac. And it is, to some extent. But it also takes an interesting detour into the implications of pets on antidepressants:

The debate about animal minds is at least as old as Aristotle, who posited that men alone possess reason. The 17th-century French philosopher Nicolas Malebranche wrote that animals “desire nothing, fear nothing, know nothing,” while Voltaire asked, “Answer me, mechanist, has Nature arranged all the springs of feeling in this animal to the end that he might not feel?” Darwin’s view was, Of course not. In “The Descent of Man” he wrote, “We have seen that the senses and intuitions, the various emotions and faculties … of which man boasts, may be found in an incipient, or even sometimes in a well-developed condition, in the lower animals.”

In other words, if Prozac has the same kind of effect on Spot that it does on Dick or Jane, then maybe Spot’s brain is more like theirs than we might want to admit.

Sir John Templeton, RIP

Sir John Templeton, billionaire investor turned philanthropist, died today. I mainly knew him for his creation of the Templeton Foundation, which aimed to find scientific approaches to spiritual topics. (Think studies of the effect of prayer on life expectancy, or the neurobiology of meditation.) As both a scientist and a Christian, I disagree with Templeton’s blithe assurance that faith could be quantified; but I wouldn’t join Slate deputy editor David Plotz in calling him a full-bore crank. At the very least, Templeton started from the assumption that faithfulness is not incompatible with a scientific worldview, and that’s a perspective the world needs these days.

150 years of Descent with Modification

Today’s also the 150th anniversary of Charles Darwin and Alfred Russell Wallace’s joint presentation of the concept of evolution by natural selection to the Linnean Society of London. Darwin had been carefully assembling on a massive book on natural selection for years, until Wallace came up with the same idea and gave Darwin sudden impetus to publish. On the Origin of Species, which was really only an “abstract” of the intended longer work, was published the next year, in 1859. Wired.com has a very nice retrospective on the event.

Wired drinks the Science 2.0 kool-aid

Just a few months after computer scientist Ben Shneiderman heralded a new kind of science based on, well, nothing particularly new, Wired magazine hops on the bandwagon with a cover article announcing the end of science. This is an historic event, indeed – but only in the Henry Ford sense. Which is to say, mostly bunk.

Basically, Wired‘s argument, as laid out in the introductory article by Chris Anderson, is similar to Shneiderman’s – that a deluge of newly-available data (the “petabyte age”) will somehow make the longstanding scientific method of observation-hypothesis-experiment obsolete:

This is a world where massive amounts of data and applied mathematics replace every other tool that might be brought to bear. … With enough data, the numbers speak for themselves.

Doesn’t anyone read Popper any more? Just walking through some of the case studies listed by Wired makes it clear that, although the petabyte age will allow us to ask and answer new questions about life, the universe, and everything, we’ll still have to use good old-fashioned hypothesis testing to do it.

Predicting agricultural yields. Agricultural consultants Lansworth predict crop yields better than the USDA by using new data on weather and soil conditions. They crunch a lot of numbers – but they’re still testing hypotheses, by fitting predictive models to all that data and determining which ones explain more of the variation. Or so I surmise, since we’re never actually told anything about their methods.

Micro-targeting political markets. Since 2004, the amount of data collected on who votes for whom has ballooned. And, from what I understand of the description here, political consultants are having a field day looking for trends in the data – which is to say, mining the data to develop and test hypotheses about voter behavior.

Guessing when air fares will rise. The website Farecast looks for trends in flight data and ticket prices to predict whether fares will change in the near future. This is – you guessed it – just another way to say that they’re testing hypotheses.

It’s true that most of the examples Wired cites don’t require active formulation of hypotheses by the people overseeing analysis of big data sets; instead, they let computers find the best-supported hypothesis based on the available data. And that is new – kinda.

Biologists use a similar approach for reconstructing evolutionary trees and solving other computationally challenging problems, called Markov chain Monte Carlo, or MCMC. In MCMC, you feed the computer a dataset, and tell it how to judge if one possible explanatory model (or hypothesis) is better than another. Then you sit back and let the computer explore a whole bunch of slightly different models, and see which ones score better. Far from making hypothesis testing obsolete, this is hypothesis testing on steroids. And it is, at least for the moment, the future of science.

Evolution 2008: Graduate student attention span does not decrease due to conference attendance

Scientific conferences are widely regarded as good opportunities for social networking, the exchange of ideas, and the development of collaborative relationships. However, these events often contain contradictory elements: programmed talks in which scientists present their latest work to their peers, and planned social events in which the same scientists consume alcohol with their peers until the wee hours. The latter is not, traditionally, conducive to the effectiveness of the former, and it is a point of great importance whether the two are compatible at all.

To test the effect of the social aspects of conference attendance on the scientific aspects of the same, I measured a surrogate for the attentiveness of a doctoral student attending the Evolution 2008 conference, held at the University of Minnesota, Minneapolis campus between 21 and 24 June, 2008. Statistical analysis shows that, although the subject’s attentiveness varied significantly between days, it did not change systematically as the conference progressed.

The subject, a third-year doctoral student in the biology department of a state land-grant school, attended a mixture of concurrent sessions, which consisted of 15-minute presentations of submitted papers, and symposia, which consisted of 30-minute invited presentations, and took notes on each attended talk (total n = 62). The student was allowed cheap coffee during the day, and pre-paid beer of middling quality (“meso-brew” sensu Godsoe) during scheduled social activities and extracurricular networking, both ad libidum.

The length of notes taken on each talk was measured, in lines of handwritten text, as a proxy for the student’s attention span. To compensate for the greater length of the symposium talks, the length of notes taken on these was divided by a factor of 1.5; although the total time of symposium talks was twice that of concurrent session talks, it is understood that the student’s attention waned as a roughly linear effect of the length of individual talks, so that he took fewer notes on a single symposium talk than he might have on two consecutive concurrent session talks. A one-way ANOVA was used to test for an effect of conference day on attention span, and a regression analysis was used to see whether there was a trend of increasing or decreasing attention span over time.

Results are displayed in Figure 1; the length of notes for each talk attended are provided as box-and-whisker plots for each day, with the number of talks attended each day (sample size) listed over each box plot. One-way ANOVA found a significant effect of conference day on attention span (p = 0.041); however, no gross trend is visible in the data, and linear regression of attention span on conference day explained very little variance (R-squared = 0.0217). I therefore conclude that, despite forces to the contrary, the subject successfully retained his faculties for the duration of the conference. I am unable to speculate, however, whether conference attendance has been ultimately productive, though the subject has been heard to say it was “a good time.”

Thanks to the conference organizing committee! It was all sorts of science-y fun.

Evolution 2008: day four

Today, at the last day of Evolution 2008, I learned:

  • Interactions between wasp species living in and around fig trees vary in strength and significance from year to year.
  • The coalescent is the future of phyologenetics.
  • The coalescent is complicated.
  • Evolutionary theory will help defeat cancer.
  • Elevated atmospheric carbon dioxide doesn’t seem to have direct effects on plant growth, but might have indirect effects by changing plant communities.
  • I can stay awake through a whole week (well, four days) of scientific talks!

Evolution 2008: day three

Today, at Evolution 2008, I learned:

  • Almost 150 years after The Origin of Species, evolutionary biologists still don’t really know why sexual (as opposed to asexual) reproduction is so popular.
  • Reconstructing evolutionary trees is tricky.
  • Sexual reproduction might help evening primroses to adapt more quickly in response to insect attacks.
  • Fungus-cultivating ants are way more diverse than I realized.
  • A nap before the poster session really, really helps.

Evolution 2008: day two

Today, at Evolution 2008, I learned:

  • The nectar-feeding bat Anoura fistulata has a tongue 150% as long as the rest of its body, which retracts all the way into the ribcage. This seems to be because it’s in an evolutionary “arms race” with the corollas of the flowers that it pollinates.
  • Luciferase, the enzyme that makes fireflies light up, probably arose by gene duplication from a metabolic protein – and it still retains the original metabolic function.
  • The horns of male hissing cockroaches are “honest indicators” of immune system health.
  • It is totally possible to start a talk by saying that you’re going to answer a question which, by the end of the talk, you still haven’t answered.

Evolution 2008: day one

In the first full day of talk sessions at Evolution 2008, I’ve learned:

  • Getting up early for a run pays off.
  • Different species of toads might have different kinds of sex determination systems.
  • Mimulus is a very popular genus for studying speciation – whether via ecological divergence, pollen incompatibility, or allopolyploidy.
  • Some legumes might be able to force their nitrogen-fixing bacterial symbiotes to play nice.
  • Coevolution is important and ubiquitous.
  • Coevolution is really, really hard to test for.
  • Name tags are better worn around the neck than on the belt.
  • The Minneapolis skyline looks awesome at sunset (see photo).
  • I need a bigger notebook.

My presentation is first thing tomorrow – gotta try and rehearse!

Evolution 2008: things I’ve learned

Yesterday, at Evolution 2008, I learned

  • The University of Minnesota has the most bike-friendly campus ever. Think dedicated bike lanes through pedestrian plazas
  • U of M also has a lot of covered walkways between buildings, and the Washington Avenue pedestrian bridge has a full-length enclosed passageway. I bet it gets fricken’ cold here, winters.
  • Dinkytown is a lot cooler than the name suggests.

The conference per se (presentation sessions) didn’t start till this morning. Actual science (and hopefully photos) next time, I promise.