On competition, ecological opportunity, and Sahney et al.

There's already been a lot of blogospheric discussion of the BBC's recent declaration that "Darwin may have been wrong" based on a recently-published paleontology paper. I hadn't paid it much attention, because while sloppy science journalism irritates me, it's not quite in my wheelhouse, expertise-wise. Then I actually got around to reading the paper, and it turns out that it's directly related to some of my own work—and the conclusion that led to the sensationalistic sub-headline doesn't make any sense.

Coauthors Sahney, Benton, and Ferry analyze the fossil record of four-limbed vertebrates—tetrapods—to show that in general, as more species evolve, they also evolve to fill a wider variety of ecological roles [$a]. Ecological roles are here defined by combinations of body size, diet, and habitat. (Sahney et al estimate there are 207 such combinations possible, though only 75 are "occupied.") That's a straightforward and mostly unsurprising result—the number of tetrapod species increases as tetrapods evolve new ways to make a living. But then we get to the conclusions of the paper, and things get weird.

Thomas Jefferson Adams: Reason

Major, embarrassing update, 2010.09.20: So it turns out that the Slate article from which I learned that Jefferson was the FAITH portrait was pretty much dead wrong. In fact the image is of Samuel Adams, and the source is the same painting in the Adams Wikipedia article. (Although, Shepard Fairey-ized, he still looks like Jefferson to me.) Jefferson makes so little sense for a portrait of FAITH that not even Glenn Beck is stupid enough to try and make him one. I've pulled the image from Flickr to prevent propagation of a false meme. Oy.

So there's this guy who's really popular with folks who hold political opinions mostly in opposition to mine. It's come to my attention (probably late, I know) that he's been waving around images of Thomas Jefferson, George Washington, and Benjamin Franklin, à la Shepard Fairey's Obama posters, with the words "Faith," "Hope," and "Charity" appended to each, respectively.

Science online, counting chlorophylls edition

Photo by Jonathan Cohen.

• It's the hot new pigment this season. A just-discovered form of chlorophyll allows the algae that produce it to photosynthesize using infrared light. (Wired Science)
• One, two, three ... many? Studies of monkeys, babies, and chickens suggest that the ability to count small numbers is innate, and separate from the ability to count larger numbers. (The Thoughtful Animal)
• Can you hear me now? On the Galapagos islands, marine iguanas listen for the alarm calls of mockingbirds to know if a predator is approaching. (The Thoughtful Animal)
• Crocodile tears from the Adaptationist Programme. Crying confers fitness advantages by eliciting empathetic responses. Or something like that. (NPR)
• Long-term forecast: 60% chance of dueling results. Remember all that oil in the Gulf of Mexico that hadn't magically disappeared? Analysis of DNA microbial DNA sampled in that oil plume just found lots of oil-eating bacteria. (Deep Sea News, Wired Science, NPR; original peer-reviewed article in Science [$a])
• Climate's changing, with or without you. As temperatures warm throughout the Mojave Desert, Joshua tree, my favorite woody monocot, may disappear from 90% of its present range. (Voltage Gate)
• 10-mm frogs. Discovered living inside pitcher plants. (io9, Wired Science; species description in Zootaxa [PDF])

I start another semester as Teaching Assistant for Mammalogy next week, so here's David Attenborough discussing mammalian dentition, with reference to an ancient omnivore I'd never heard about up to now.

Hmm. Do I dig it?

Trying out Digg.com, which is apparently rolling out a new UI. It has serious competition from incumbent systems Facebook and Twitter, but I'll give it a week, at least.

Haven't written this much html in a while

I just built my first course webpage, for the Mammalogy lab I'll be leading for this semester's teaching assistantship. It pulls together a bunch of resources I developed for the same lab last year—photos of lab specimens taken by students (thanks to a little extra credit for inducement) and Anki decks. Now I need to get started on the slides for my first week's lecture ...

Are mutualists monogamists, while antagonists play the field?

Two of the most diverse groups of living things on Earth are flowering plants and the insects that make their living from flowering plants. Biologists have long thought that the almost incessant, intimate interactions between plants and plant-eating insects might be the evolutionary cause of each group's spectacular diversity. On a smaller scale, this means that we're interested in the reasons that specific insects and plants interact in the first place—what evolutionary trails leads one insect species to specialize on a single host while others eat pretty much any plant they land on.

A new study of one group of plant-eating insects suggests that the kind of interaction between insects and their host plants also determines how specific those interactions are. Examining a group of moths that, like the yucca moths I study, pollinate their host plant and then eat some of its seeds, the authors of the new study find that related, non-pollinating moths use more host plant species than the pollinators [$a]. I think it makes a particularly nice companion piece to my post about the evolutionary origins of yucca moths, because it provides an example of one or two other things biologists can deduce from phylogenies—and, as we'll see, some things they can't.

Epicephala: like a yucca moth without the snappy name

The moths in question are in the genus Epicephala, and they have an obligate pollination relationship with trees in the genus Glochidion, a diverse group of plant species found in southern Asia. That is, female moths carry pollen between Glochidion flowers in special mouthparts, deliberately apply pollen to the flower, and then lay eggs in the flower so that, when it develops into a fruit, her larvae can eat some of the seeds inside. Epicephala species are highly specialized, with most species only using one species of Glochidion [$a]. That's a higher degree of specialization than what's seen in yucca moths, in fact.

Pollinating moths (genus Ephicephala, left) use fewer host plant species than related non-pollinating moths (genus Caloptilia, right). Photos by CharlesLam and Bettaman.

The family of which Epicephala is a member happens to include other moths that interact with Glochidion, but only as herbivores: species in the genera Caloptilia and Diphtheroptila, whose larvae all eat Glochidion leaves. Do these antagonistic moths use more, or fewer, species of the host plant than the mutualistic Epicephala? Kawakita and his coauthors set out to answer that question by reconstructing the phylogenies of Caloptilia and Diphtheroptila.

Scienceblogging.org will be one-stop shop for, um, exactly what it says on the tin

And right on the heels of the Carnal Carnival launch, Bora has another big announcement: a new site aggregating online science writing from pretty much everywhere, appropriately located at scienceblogging.org. The site draws from every science blogging collective I follow—ResearchBlogging, Discover Blogs, Wired Science, Field of Science, the still-shiny new Scientopia, and good ol' ScienceBlogs—along with a lot I don't run across as often.

Right now there's a single page listing recent feed results from all these group blogs, and another devoted to science-y blog carnivals, but no independent blogs (ahem), and no particular way of sorting through the contents. It looks more like a starting point than a finished product, and that's just fine—Bora and his co-founders Anton Zuiker and Dave Munger are still looking for input. Says Dave:

The site is really just an aggregator of aggregators. Everything you see on the front page is a feed from some other bundle of blogs. In a couple cases, we made our own bundles using Friendfeed. The site is flexible enough to add additional bundles as bloggers and publishers form new blogging communities. It’s not ideal — I think the ultimate science blog aggregator will allow users to view blog posts by topic, and perhaps have some way of identifying the best posts. But it’s flexible enough that with some input from the community, we might be able to shape it into something really special. Check it out, and let us know what you think.

As a blogger without a network, I'm naturally interested in seeing independent blogs added to the ScienceBlogging.org stream (although, as Bora points out, we're already partially accounted for by including the Research Blogging feed). The large number of indy science bloggers would make this challenging, to say the least, but I think many of the issues are the same ones that show up, in smaller scale, on the new ScienceBlogging.org homepage—how to make it easy for a visitor to sift through a large number of posts to find writing by particular people, on particular topics, written in a particular time-frame.

Maybe what's needed is an analogue to ResearchBlogging that aggregates all posts from member blogs and sifts them into topic-labeled feeds—but that's a whole different class of infrastructure, and effort from member blogs, than what's provided at the new site right now. Still, the value of a true one-stop shop for online science writing should be great enough to justify the effort. In the meantime, I've added a new bookmark, and I'll be keeping an eye on ScienceBlogging.org.

Introducing the Carnal Carnival

A brand-new blog carnival promises to unleash the naughtier impulses of the science blogosphere which, let's be frank, were never particularly tightly leashed to begin with. Except for the ones that are into that sort of thing.

Ahem.

Anyway, the inaugural edition of the Carnal Carnival is now online at A Blog Around the Clock, where host Bora Zivkovic called for any and all posts relating to poop, feces, dung, and/or excreta. The only shit-related question left unanswered in this fecund roundup is, shouldn't they have saved this topic for Carnal Carnival #2?

Science online, older than we thought edition

A little brown bat covered with the white nose fungus. Photo by U.S. Fish and Wildlife Service, Northeast Region.

• First Ginsu salesman still millions of years away, though. Newly discovered bones bear scratch marks that could have been made by flaked stone cutting tools 3.4 million years ago—more than 800 thousand years earlier than previous evidence of such toolmaking by human ancestors. (Greg Laden's Blog, Not Exactly Rocket Science)
• I thought they said it had all magically disappeared? As much as 70% of the oil spilled by the now-plugged Deepwater Horizon well is still out there, somewhere. In fact, it's probably suspended in the deep ocean, where microbes expected to break down oil may take months to finish it off. (Deep Sea News, Wired Science)
• Thesis, antithesis. Synthesis! Razib Khan describes how R.A. Fisher united Mendelian genetics and quantitative trait theory into a single mathematical model. (Gene Expression)
• Really? Life doesn't look a day over 640 million. New 650-million-year-old fossils may be the oldest examples of animal life. (Science Daily, Highly Allochthonous)
• Being pecked to death never looked so unpleasant. Stress analysis of terror bird skulls suggest they killed prey by repeatedly stabbing it with the dagger-like tip of their beaks. (Not Exactly Rocket Science)
• Is there an HVAC engineer in the house? We might be able to save bats from white-nose syndrome by heating their hibernation caves. (Wild Muse)

And now, via Ed Yong and BoingBoing, Humbolt penguins chasing a butterfly:

Pakistan

I would hope you don't have to be as much of a news junkie as I am to know that, right now, tens of millions of people have just watched their lives—fields, homes, entire villages—wash away in Pakistan. (NASA has some astonishing
before-and-after images.) For reasons political and logistical, aid is not arriving very fast where it's most needed. So let me take this opportunity to suggest that my readers direct a contribution to Doctors Without Borders/Médicins Sans Frontières, which was on the scene pretty much from the start. I make a (very small) monthly contribution to MSF, which they like because it's income they can count on—if you can, I'd suggest going that route.

Satellite image of flooding in Nowshera, taken 5 August. Photo by DigitalGlobe-Imagery.

Re: Cite more papers, get more citations?

Courtesy Zen Faulkes's Twitter feed: Philip Davis of the Scholarly Kitchen shows that the study I discussed earlier, purporting to show that journal articles that cite more sources are themselves more likely to be cited is, um, quite probably bunk. Davis was skeptical of the cite-more-be-cited-more (henceforth, CMBCM) correlation, so he did what any good scientist would, on reading a result he didn't believe: he tried to replicate it, collecting his own data set from articles published in the journal Science in 2007.

Davis replicated the CMBCM result with his own dataset, but then he started looking for other correlations in the data. It turns out that longer papers are also more likely to be cited—and, when Davis statistically controlled for that effect, the CMBCM result not only disappeared, it reversed. That is, long Science papers with more citations are slightly less likely to be cited than long Science papers with fewer citations. Building a still more complicated statistical model that incorporates the paper's length, subject area, and number of authors, Davis totally eradicated the effect of variation in the length of the Works Cited list.

Controlling now for pages, authors, and section, reference list length is no longer statistically significant. In fact, it looks pretty much like a random variable (p=0.77) and adds no information to the rest of the regression model.

Davis's analysis looks convincing to me. It's hard to say, however, whether it conclusively refutes the result reported in Nature News. That's partly because the CMBCM analysis is derived from a much larger data set than Davis's; but more importantly, it was presented at a conference, not in a published article.

Conference papers often present preliminary results, and in the absence of a published Methods section, the News article doesn't tell us whether the coauthors controlled for the effects of the confounding factors Davis identifies or not. (Although it seems logical to conclude from the News piece that they didn't.) If the CMBCM data set is going to make it through peer review at a journal, however, its authors will have to account for confounding factors.

If your idea of a fun time might include snarky dissection of illuminated manuscripts,

Then you should definitely be following Got Medieval. You might also consider checking out Carl Pyrdum's blog if your idea of a good time might include being told another way in which Newt Gingrich is an ass. If your idea of a good time does not involve such things, consider following those links anyway; you many rapidly change your mind.

Turning up the alarms makes aphids careless

The oven in my apartment needs a serious deep-cleaning. A really serious deep-cleaning. To the point that, when I want to do some baking, smoke is more or less inevitable. As a result, I've developed the habit of responding to the apartment's smoke alarm by reaching up and un-mounting it from the ceiling, which completely disables it. If a fire were to start somewhere else in the apartment while I'm baking, I'd probably be in trouble.

That's more or less the idea behind an approach to agricultural pest control proposed in a paper just released online at PNAS: if you saturate insect pests with a predator warning signal, they become used to the signal, and more vulnerable to predators [$a]. Aphids are the target pest—they form huge, clonal swarms to literally suck the life out of plants, as described very nicely in this BBC Nature video.

Giants Shoulders #26 online at Neurotic Physiology

Host Scicurious has just posted the 26th edition of the Giant's Shoulders history of science blog carnival, and wow, it's a doozy. The "Fools, Frauds, and Failures" theme drew a huge list of contributions in all three categories (including my own piece on Sewall Wright and Linanthus parryae). And Sci introduces it all with a lovely olde-worlde flourish.

Greetinges, all ye who enter here.
Beholde, before you doth appear
A moste unusual carnivale!
And this one hath a grand moral.
This speakes of fools, failures and fraudes.
Those findings no longer we applaude.

I may very well spend the rest of the month until the next edition reading it all.

Cite more papers, get more citations?

Update, 18 August 2010: An attempt to replicate the result discussed here finds serious issues with the statistics.

Nature News is reporting some interesting results presented as a paper at a meeting of the International Society for the Psychology of Science & Technology last week: articles published in the journal Science with longer "Works Cited" sections are themselves more frequently cited.

A plot of the number of references listed in each article against the number of citations it eventually received reveal that almost half of the variation in citation rates among the Science papers can be attributed to the number of references that they include. And — contrary to what people might predict — the relationship is not driven by review articles, which could be expected, on average, to be heavier on references and to garner more citations than standard papers.

The same authors did a similar analysis of papers published in the journal Evolution and Human Behavior over 30 years, and found similar results [PDF]. Here's the relevant figure from that paper:

Cite more, be cited more. Figure 2 from Webster et al. (2009) [PDF].

The lack of a "review effect" is surprising, but I don't think this overall result is. Academia, as much as we might describe it as cutthroat, also runs on reciprocal altruism. Authors notice when their papers are cited, and are more likely to cite papers that build on or relate to their own work. I'd be interested to see the network of citation underlying the pattern Webster et al. have found—I suspect that there's a lot of clustering around disciplines and sub-disciplines and sub-sub-sub-disciplines that contributes to all this mutual back-scratching citing.

Updated, 15 August 2010, 2126h: Fixed the link to the original Nature News article, which turns out not to be access-restricted.

Reference

Webster, G.D., Jonason, P.K., & Schember, T.O. (2009). Hot topics and popular papers in evolutionary psychology: Analyses of title words and citation counts in Evolution and Human Behavior, 1979-2008. Evolutionary Psychology, 7 (3), 348-348 Other: http://www.epjournal.net/filestore/ep07348362.pdf

How Wright was wrong: When is it genetic drift?

Science is often said to work in three easy steps: (1) observe something interesting, (2) formulate a hypothesis for why that something is interesting in the way it is, and (3) collect more observations to see if they also support that hypothesis. Wash, rinse, repeat, and you eventually get from Newton to Einstein, from Aristotle to Darwin.

Sewall Wright, pioneer of population genetics. Photo from Wikimedia Commons.

Except, of course, it's never that straightforward. Sometimes scientists come up with a hypothesis without a clear-cut example to support it, and then go looking that example. Sometimes observations that support a hypothesis turn out not to, if you look closer. And—here's the funny thing—this can even happen with hypotheses that are, in the end, pretty much correct.

In the spirit of this month's Giants Shoulders blog carnival, which focuses on "fools, failures, and frauds" in the history of science, I'm going to recount a case in which one of the greatest biologists of the Twentieth Century was fooled by a small desert flower. Sewall Wright was no fool or failure, and he certainly didn't commit fraud, but he does seem to have been totally wrong about his favorite example of a particular population genetic process, one he discovered. That process, isolation by distance, is widely documented in natural populations today—but it also doesn't seem to have worked the way Wright thought it did for Linanthus parryae.

Science online, developmental pointilism edition

Mosaicism. Photo by docman.

• Probably delicious with a nice Chianti. A new species of monkey has been discovered in the Amazon, and is already critically endangered. (Short Sharp Science)
• Also link to fewer knitting patterns than crafts bloggers. A systematic comparison finds that science bloggers link to more original scholarly articles, and fewer news media sources, than political bloggers. (CMBR)
• Don't panic. Yet. The evolution of drug-resistant bacteria may mean the end of usefulness for current antibiotics within a decade. (The Guardian; Original article in Lancet Infectious Diseases)
• We should probably set up more. On balance, marine protected areas seem to have improved biodiversity and productivity. (Conservation Bytes)
• We're all mosaics. Patterns of cell proliferation and specialization during development are pretty, as well as informative. (Pharyngula)
• Brought to you by the government agency responsible for Tang. Scicurious walks through a ground-breaking NASA study of urination in zero gravity. (Neurotic Physiology)
• Adds up to trouble. American students don't fully understand what the "equals" sign means. (Cocktail Party Physics)

Video this week: the first part of a USGS-made film about desert tortoises, which are awesome, and very, very endangered. Via Chris Clarke, who posted the whole thing.

43 seconds

Mike D'Angelo of the AV Club, on 2001: A Space Odyssey, pretty much my favorite movie ever:

What makes the human beings in 2001 seem a bit less than fully human isn’t just the nature of the performances—it’s that every interaction among them is completely functional. We’re seeing people say and do whatever is required to achieve their objective at that particular moment, and nothing more. HAL, by contrast, demonstrates what we all recognize as neurosis. And while it’s mostly implied by his behavior, it does have one explicit manifestation: that refusal to answer Dullea’s summons for 43 seconds, followed by capitulation when it becomes clear that Dullea isn’t gonna shut up. That’s so human, it almost hurts.

Science online, speak up in the speakeasy edition

Nope. Not going for a single-entendre in the caption, either. Photo by law_keven.

• Oh, that's why he didn't respond when I asked for a phone number. Drinking alcohol induces measurable hearing loss. (Neurotic Physiology)
• No naughty intro necessary. Male ducks adjust when to grow a penis, and how long to grow it, based on the presence of competitors. (Wired Science, Discoblog)
• They're just hopping on the alternative energy bandwagon. Spotted salamanders may be effectively photosynthetic, thanks to algae living inside their cells. (Nature News)
• Thousands of species in the sea, most of them not fish. A new comprehensive census of marine biodiversity estimates that for every known species in the sea, four are waiting to be discovered. (EveryONE)
• Wild. Radioactive. Boars. More than 24 years after the Chernobyl disaster, Germany's booming population of wild boars are still radioactive. (The Two-Way; original article in Der Spiegel)
• Sip, don't swig. Dave Munger sifts through evidence about the effectiveness of caffeine, and concludes that if you must drink coffee, it's best in small, regular doses. (SEED Magazine)
• Smells like adaptation. Selective breeding has reshaped dogs' brains, particularly the location of the olfactory bulb. (80beats)
• Batpocalypse now. The most common bat species in eastern North America could be extinct in the region within decades, thanks to a mysterious disease striking overwintering colonies. (Wired Science, original article in Science [$a])

Here's a good video description of the syndrome that might wipe out those bats. (The Kentucky state biologist interviewed is exceptionally careful in her use of the word "hypothesis," too.)

Carnival of Evolution #26 at The Thoughtful Animal

I'm late to the party on this one: the 26th Carnival of Evolution is on over at this month's host, Jason Goldman's The Thoughtful Animal. This round of submissions is more concentrated on the "endless forms most beautiful" than directly challenging creationism, which is a welcome change if I do say so myself. Don't get me wrong; creationists need (apparently endless) debunking. But I think the argument is made just as effectively by showing that there's "grandeur" in the scientific view of life—which these posts do in spades.

Double the mutualists, double the fun?

For all living things, information is critical to survival. Where's the best food source? Is there a predator nearby? Will this be a good place to build a nest? It probably shouldn't be surprising, then, that lots of animals do what humans do when faced with a host of hard-to-answer questions—they take their cues from their neighbors.

Red-backed shrikes place their nesting sites near where other shrike species have set up territories. Many bird species recognize each other's predator alarm calls, and respond appropriately. And a new natural history discovery published in the latest issue of The American Naturalist shows that treehoppers let one species of butterfly know where to find ants that will tend its larvae [$a].

The ant-tended butterfly (Parrhasius polibetes, above) looks for ant-tended treehoppers (Guayaquila xiphias, below) to know where to lay her eggs. Photos from Kaminski et al. (2010), figure 2.

The treehoppers help out the butterfly inadvertently, because both of them are dependent on a common resource: ants. Like many true bugs, treehoppers make their living sucking the sap of a host plant. This gives them a surplus of simple sugars and water, which they excrete as "honeydew" to attract ants for protection. As it happens, the larvae of the butterfly Parrhasius polibetes do the same thing—so the new study's authors hypothesized that P. polibetes females might prefer to lay their eggs on plants where treehoppers were already present, since those would likely already have ants ready to protect butterfly larvae.

To test this, the authors set up experimental pairs of host-plant branches, one occupied by ant-tended treehoppers, and one not. They excluded ants from accessing the unoccupied branch with Tanglefoot, a water-resistant glue used in insect traps. After 48 hours, they checked the experimental plants for newly-laid butterfly eggs, and found that P. polibetes was both more likely to lay eggs, and laid more eggs at a time, on branches occupied by treehoppers.