Monthly Archives: June 2008

Wired drinks the Science 2.0 kool-aid

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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.

Unicorns existed, say Creationists

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How do we know that Answers in Genesis, the creation “science” clearinghouse, deserves the credibility previously reserved for actual scientists? Because it serves to publish important discoveries like this one: unicorns are real. This is made possible by the sort of insightful, unbiased thinking that only Creationists are capable of:

Some people claim the Bible is a book of fairy tales because it mentions unicorns. However, the biblical unicorn was a real animal, not an imaginary creature. The Bible refers to the unicorn in the context of familiar animals, such as peacocks, lambs, lions, bullocks, goats, donkeys, horses, dogs, eagles, and calves (Job 39:9–12 KJV).

Actually, the article is trying to claim that a word which has sometimes been translated into English as “unicorn” may refer to an extinct (and very fearsome) ungulate of some sort. Or the word may actually mean “wild ox.” But what kind of fun would that be?

Via dechronization.

Evangelism experienced

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At the tail end of the Evolution 2008 conference, I bumped into a character from my childhood in conservative Christian country: I got evangelized. I was hanging out with two colleagues from another lab at UI, whom I’ll call V and B – we’d had dinner, and were sitting on a bench in the park around the University of Minnesota alumni center, thinking about going for a beer once the sun set. When up come two fresh-faced undergraduate-looking types, and one of them says he wants to ask us some questions “for his blog.”

I smelled an overly-friendly rat immediately, and I think B did, too, as he’s another Mennonite-turned-biologist. V is a good secular Frenchwoman, and was, I think, less prepared to guess where this was going. The first fellow (he never actually introduced himself – I’ll call him the Talker) started in with a painfully obvious line of Socratic questioning about what we thought would happen to us after we died. He pretended great interest in our responses, then started on a we’re-all-sinners-but-good-news-Jesus-came pitch. Except we didn’t play by the script.

The Talker wanted to define sin (in a pretty traditional move) as basically nothing more than violating the Ten Commandments (“You’ve told lies, right?” he said. “So have I.” This is the whole of his argument for original sin.) I happen to object to that kind of moral reasoning. I said as much, pointing out that Jesus gave his disciples a new commandment that fulfills and transcends the Old Testament law; that it’s extremely dangerous to define morality purely in terms of divine fiat; and it’s clear that Jesus expected his disciples to make actual moral judgments, not follow some list of rules.

B pitched in to ask about the ultimate fates of the victims in the recent Chinese earthquake; V. expressed puzzlement. I pointed out the Talker and his friend, who (upon direct inquiry) admitted to being named Noah, seemed to have recently shaved their sideburns, and asked when they’d last had a ham sandwich. (“That’s Catholics,” said Noah. “No,” I said, “That’s Jews.” But it comes from the Old Testament laws they were setting up as the foundation of their theology.) We scientists quoted Scripture and church history and basic, humane moral logic. The Talker responded by trying to drag the conversation back to his script, until, I guess, it became clear we weren’t going to let him. At which point he claimed a pressing appointment, made sure I knew the address of his blog, and left with his wingman.

On the whole, I’d actually thought it was a pretty friendly not-quite-conversation, and I’d fancied we might have made the two of them think a bit. The Talker’s blog, however, indicates otherwise. It’s astonishing how little you can hear when you don’t want to. And it’s maddening that this fellow thinks that he’s practicing Christianity by accosting strangers in public like this. He couldn’t even get to the Good News because he was so busy trying to ram his theology of sin down our throats.

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

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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

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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

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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

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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

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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!

Mennonites and Jesus

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Jesus
Photo by birdfarm.

In a comment a couple posts back, Krista Smith asks, “how much does a Mennonite believe in Jesus?” Which is a great question, and one I’m going to try and tackle here.

(You should also check out Krista’s blog Salt City Food – even if you’re not in Salt Lake City, there are some delicious-looking recipes.)

So what do Mennonites think about Jesus? The short, flip answer is that Mennonites like him a lot. The longer, messier answer is that when this Mennonite says he likes Jesus (and, though he is a product of both Mennonite high school and undergrad, he is not necessarily a representative sample) he means something a bit different from what most Christians mean by that. Mennonites are good trinitarians, mind you, but we understand the crucifixion of Jesus as more than just a sacrifice for our personal sins – we understand it as the example by which we must live, and the lens through which we view the rest of the Bible.

Christus victor

This view was best articulated by the Mennonite theologian John Howard Yoder (no relation) in his book The Politics of Jesus. Yoder argued that, in freely submitting to death on the cross, God (in the person of Jesus) subverts and triumphs over the worldly power of the Roman Empire that crucified him – Yoder’s perspective here is related to the “Christus victor”, or Christ victorious, view of the Crucifixion. Furthermore, Yoder interprets the Gospel to mean that Christians are to imitate Jesus by freely submitting themselves to nonviolent service, even total sacrifice, for others around them:

It is often mistakenly held that the key concept of Jesus’ ethic is the “Golden Rule”: “do to others as you would have them do to you.” This is stated by Jesus, however, not as the sum of his own teachings, but as the center of the law (Mark 12:28f; Matthew 22:40, citing Leviticus 19:15). But Jesus’ own “fulfillment” of this thrust of the law, which thereby becomes through his own work a “new commandment”… is different, “Do as I have done to you” or “do as the Father did in sending his son.”

This is the underpinning of Mennonite pacifism, and our understanding that Christians are called to service and peacemaking as much as to proselytizing.

The Gospel first

This perspective on Jesus is closely associated with – or even gives rise to – the way Mennonites view the Bible. Though we believe that it is sacred, and “God-breathed,” we also believe that the Bible is not a “flat” book, with every verse given equal theological weight. For Mennonites, the “weightiest” part of the biblical text is the Gospel message, centering on the teachings of Jesus, his death on the cross, and his resurrection. All other passages are interpreted in light of the Gospels’ text. So, rather than understanding Old Testament passages that seem to sanction war or slavery as evidence that God likes either of those things, we look through the Gospel lens and conclude that these are records of life before the example set by Jesus, not models for Christian behavior.

This perspective is actually very important to me, as a scientist. If the Bible is not one monolithic whole, but a collection of stories, I can understand, say, the Genesis creation narrative as a symbolic account of God’s relationship to the universe without necessarily having to treat the Gospel in exactly the same way.

Further reading

But don’t take my off-the-cuff theologizing as the last word; the website of Mennonite Church USA has user-friendly explanations of Mennonite thought and doctrine and links to denominational documents that go into way more detail than this.

Evolution 2008: things I’ve learned

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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.