Monthly Archives: July 2008

On the Media on Science 2.0: Sounds good to us!

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[Rant alert – I’m starting to get real tired of this nonsense. Although it is proving to be good blog fodder, and it got me published in the letters column of Science. Maybe it’s not so bad. And but so …]

Wired editor Chris Anderson is on this week’s On the Media, talking up the Petabyte Age. And OTM pretty much swallows it whole.


Photo by Pixelsior.

The Petabyte Age, as Anderson describes it, is the present time in which massive volumes of data (petabytes, in fact) are supposedly marking the end of the scientific method. If you actually read the Wired story, you’ll discover that Anderson has a pretty shaky grasp on what the scientific method actually is, and apparently thinks that “statistical analysis” is not hypothesis testing. As it turns out, it is.

On OTM interview, Anderson recants the sensationalist headline, possibly in response to the long string of critical comments it drew on Wired.com. But he repeats all of the mistakes and nonsense that generated the criticism: Craig Venter sequenced some seawater without a prior hypothesis, and Google summarizes lots of data to look for patterns without prior hypotheses; ipso facto, no one needs hypotheses anymore. (Anderson insists on talking about “theories” rather than hypotheses, which only highlights his unfamiliarity with basic philosophy of science.) The interviewer, Brooke Gladstone, pretty much lets him have his say. Does she then consult an actual working scientist, or, better yet, a philosopher of science? Not so much.

This is not the sort of coverage I’ve come to expect from OTM, which is basically in the running with RadioLab for the title of My Favorite Public Radio Show. Normally, OTM specializes in pointing out exactly this sort of failing in other news shows – interviewing pundits without actually talking to people who work in the fields in question. But it would seem that they don’t feel the scientific freaking method is important enough to cover properly.

Specialization: Not always a dead end

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Ruellia sp. – probably hummingbird specialized.
Photo by Tim Waters.

ResearchBlogging.org One of the big questions in evolutionary biology is about reversibility. That is, once an organism evolves down a path of adaptation to a particular climate or biological community, how easy is it for natural selection to make a U-turn and go back to a less specialized state? Many evolutionary changes are probably irreversible – an idea that was classically expressed in “Dollo’s Law”: “An organism is unable to return, even partially, to a previous stage already realized in the ranks of its ancestors.” But many evolutionary changes may not be irreversible – and it’s not always easy to predict which ones those are.


Ruellia brittoniana – probably bee-pollinated.
Photo by petrichor.

A new study in this month’s issue of Evolution aims to answer this question [$-a] for a group of flowers in the genus Ruellia. The authors, Tripp and Manos, use a phylogeny to reconstruct the evolutionary history of pollination syndromes, groups of floral traits like color, nectar tube length, scent, &c, that are associated with pollination by different groups of animals.

For instance, bright red flowers with longish, narrow nectar tubes, not much scent, and large volumes of dilute nectar (like the Ruellia species in the upper figure), are almost always pollinated by hummingbirds; blue flowers with short nectar tubes, stronger scent, and small volumes of concentrated nectar (like Ruellia brittoniana in the lower figure) tend to be pollinated by bees or other insects. Other Ruellia species are pollinated by hawkmoths (white flowers, very long nectar tubes) or bats (yellow flowers, short nectar tubes, lots of dilute nectar, strong scent). Generally, syndromes associated with a single, small group of pollinators (hummingbirds, hawkmoths, or bats) are considered “specialized”, while syndromes associated with many more different pollinators (bees and insects) are not.

With a phylogeny of the genus Ruellia, Tripp and Manos use the pollination syndromes of currently existing Ruellia species to estimate what pollination syndromes their ancestors may have had. Then they determine how common transitions between pollination syndromes have been in the history of Ruellia, and whether any pollination syndromes are “dead ends” – that is, whether Ruellia species that evolve to specialize on, say, hummingbird pollination are “stuck” that way.

Surprisingly, Tripp and Manos found that some specialized pollination syndromes are dead ends, but one, the hummingbird syndrome, isn’t. Hawkmoth- and bat-pollinated species tended to have evolved from ancestors with the bee/insect syndrome, and they seem to be “stuck” once they get there. But in several cases, hummingbird-specialized ancestors have given rise to bee/insect-pollinated species. This has never been seen before in other, similar groups of plants. Hummingbirds are generally thought to be more efficient pollinators than bees, so while it makes sense for flowers to evolve from using bees to using birds, it’s not clear how natural selection would work in the opposite direction.

Reference
Tripp, E.A., Manos, P.S. (2008). Is Floral Specialization an Evolutionary Dead-End? Pollination System Transitions in Ruellia (Acanthaceae). Evolution, 62(7), 1712-1737. DOI: 10.1111/j.1558-5646.2008.00398.x

A new plan for links

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I post about science quite a bit, and when I do, I try to link to the “primary” literature – peer-reviewed research articles in professional journals. But even in this modern age, lots of professional journals charge for access. Sometimes a lot. I get through on my university’s institutional subscription – but that doesn’t cover everyone. So I’ve been trying to mark links to journal articles based on whether it’ll cost you to read the full text, but I haven’t been happy with the way it looks. Therefore, I’m instituting a set of simple abbreviations, which I’ll append to linked text to indicate access levels:

  • [$$] = total lockdown; nothing but the title is free online
  • [$-a] = the article’s abstract is free, but more will cost you
  • No mark = totally free access

Check out an example of how this looks in a post. Links to an article at PLoS, which is fully open-source, aren’t marked. But links to an article at Science get the [$-a] mark. Links to article titles in the “References” section at the end aren’t marked one way or the other – I sort of assume those don’t get the same kind of follow-through that the in-text links do.

Climate change: bad for native plants

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[Correction/clarification appended]

This is how I can justify blogging as a scientific activity: once in a while, I find something really useful. Case in point is this post on the ‘blog of Pamela Ronald, the chair of the University of California Davis plant genomics program, which points to a new in the last volume of PLoS ONE that predicts (perhaps not surprisingly) climate change is going to be bad for rare plants in California.

The effect of climate change on plant communities is a major concern for me, because the range of my favorite woody monocot, the Joshua tree, may have to change quite a bit to compensate for a warmer climate. (For reference, see the photo of me setting up a pollination experiment on a Joshua tree in front of the Yucca Valley United Methodist church.) Previous projections have suggested that Joshua trees are going to be in trouble under a warming climate. Back in 2006, Science ran a cover article suggesting that climate change may make wildfires more frequent [$-a]. That’s a very real problem for Joshua tree’s range in the Mojave Desert – my lab has already lost field sites to brush fires in only about half a dozen years of focusing on Joshua trees. Another, more recent study has suggested that climate change is going to make the southwest U.S. even more arid&nbsp[$-a], which is also, obviously, a bad thing for plants (and people) in the region.

Earlier work of this sort usually modeled how climate change might increase or decrease the distribution of individual plant species – big, showy things like Joshua tree, Saguaro cactus, giant Sequoias. Loarie et al. improve over this by projecting changes in whole plant communities across the California floristic province. And they predict that up to 66% of plants endemic to California will lose more than 80% of their ranges. That’s a lot of diversity – more than just my study organism – at stake.

Correction:
In the original version of this post, I conflated the state of California, which does include a lot of Joshua tree’s range, with the California floristic province, which doesn’t. So Loarie et al.‘s new paper doesn’t directly impact Joshua trees. But it’s still cool/alarming, and decidedly post-worthy. In making that correction, I’ve also inserted a more recent study of climate change in the U.S. southwest, by Seager et al.

References:
Loarie SR, BE Carter, K Hayhoe, S McMahon, R Moe, CA Knight, and DD Ackerly. 2008. Climate change and the future of California’s endemic flora. PLoS ONE 3:e2502.

Seager R, M Ting, I Held, Y Kushner, J Lu, G Vecchi, H-P Huang, N Harnik, A Leetmaa, N-C Lau, C Li, J Velez, and N Naik. 2007. Model projections of an imminent transition to a more arid climate in southwestern North America. Science 316:1181-4.

Westerling AL, HG Hidalgo, DR Cayan, and TW Swetnam. 2006. Warming and earlier spring increase western U.S. forest wildfire activity. Science 313:940-3.

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

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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.

Preaching religious tolerance as the Crusades begin

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Harper’s has a fascinating piece on Nicholas of Kues (= Cusa, I think), or Cusanus, a fifteenth-century Roman Catholic cardinal who sought common ground between Christianity, Judaism, Islam, and even Hinduism in the wake of the Ottoman Turks’ conquest of Constantinople, when most of European Christendom was girding for the Crusades. I’d never heard of Cusanus before, but apparently he’s considered a leading theologian of the Renaissance in Continental Europe. And his perspective sounds like it would be invaluable for people of faith in the twenty-first century:

What Cusanus therefore proposes is tolerance. However, it is not the insulting sort of tolerance, which proposes official indifference. Rather it is a tolerance that has its roots in a philosophical commitment to the search for truth and a recognition that human frailties and imperfections will always lead to mistakes. “For it is a condition of the earthly human estate to mistake for truth that which is merely long-adhered-to custom, indeed, even to mistake this for a part of nature,” Cusanus writes (habet autem hoc humana terrena condicio quod longa consuetudo, quæ in naturam transisse accipitur, pro veritate defenditur.)

The Origin: worth your time

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The New York Time’s science columnist Olivia Judson argues that, nearly 150 years after the publication of its first edition, The Origin of Species is well worth reading, even (or especially) for scientists. She rattles off the usual reasons that biologists avoid Darwin’s magnum opus — page after page of natural history observations, occasionally unreadable Victorian prose — but then gets down to the point:

[Darwin] has a sophisticated view of how natural selection works, and the circumstances that make it powerful; indeed, his descriptions of the forces of nature — starvation, predation, competition and disease, to name a few — are as good as, or better than, those in most textbooks today. He appreciates that the biggest problems that most living beings face come not from features of the physical environment, such as climate, but from other organisms, whether of the same species or a different one. And in our current age of specialization, where deep knowledge of an animal or a plant often comes at the cost of broad knowledge of other members of the tree of life, it is deeply refreshing to come across writing that is so much about all of nature.

I read the Origin my first year of grad school, and it was hard going in parts. But elsewhere, it was indeed a great read.

Sir John Templeton, RIP

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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.

Human populations grow faster near protected areas

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New in Science: Protected areas like national parks and forests seem to stimulate economic development [abstract only]. The study’s authors examine more than 300 protected areas in 45 African and Latin American countries, and find that human populations near the preserves are growing nearly twice as rapidly as those in rural areas farther away from preserves.

On the one hand, this is good news – it might be evidence that, rather than depressing economic development, natural reserves actually provide benefits to locals in the form of jobs as park staff or ecotourism guides, or development projects coupled with conservation efforts. On the other hand, though, it could be that development associated with tourism actually puts more pressure on the land just outside protected areas, making the preserves more isolated and less ecologically functional. The paper also shows that deforestation of the areas around preserves increases as the human population growth rate increases.

Reference

Wittemeyer G, P Elsen, WT Bean, A Coleman, O Burton, and JS Brashares. Accelerated human population growth at protected area edges. Science 321:123-6.