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.

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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.

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Turning up the alarms makes aphids careless

ResearchBlogging.orgThe 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.

As the video notes, those clonal swarms are vulnerable to all sorts of predators, most famously ladybird beetles. So when attacked, the aphids emit an alarm pheromone to warn the rest of the clone. But it’s possible to habituate aphids to the alarm pheromone—if they’re surrounded by it long enough, they won’t respond to it by running away. The new study’s authors proposed genetically engineering crop plants to produce the alarm pheromone, to automatically produce that habituation.

To see if this would work, they raised aphids on a line of Arabidopsis thaliana (the white lab mouse of the plant world) that had been engineered to produce the alarm pheromone. And, indeed, habituated aphids were much less likely to be repelled by the alarm pheromone—and were even in some cases attracted to it. Perhaps the most telling test involved leaving habituated and non-habituated aphids on an experimental plant with ladybird beetles introduced—habituated aphids were less likely to survive 24 hours with the beetles.

This is a pretty clever approach to pest control, but there’s an obvious caveat. I don’t see any reason why aphids couldn’t evolve a way around this attempt to swamp out their own alarm signals—the paper notes that different aphid species have different responses to the particular alarm pheromone tested, so engineering one pheromone into crop plants doesn’t leave the aphids without evolutionary options. Unless it’s very cleverly designed, any pest-control strategy creates strong natural selection—and the better the strategy is, the stronger the selection is—to evolve resistance. Alarm-pheromone-producing crops might be another tool for pest control, but they won’t be the last one we need.


A ladybird beetle makes short work of some aphids. Photo by kenjonbro.

See also this press release from Cornell University, which discusses the paper’s results.

Corrected, 17 Aug 2010, 2305h: Fixed the photo of the ladybird with aphids, which was meant to be full-width, and added a jump. Why do I keep forgetting those?

Reference

de Vos, M., Cheng, W., Summers, H., Raguso, R., & Jander, G. (2010). Alarm pheromone habituation in Myzus persicae has fitness consequences and causes extensive gene expression changes. Proc. Nat. Acad. Sci. USA DOI: 10.1073/pnas.1001539107

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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.

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Cite more papers, get more citations?

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

ResearchBlogging.orgNature 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

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How Wright was wrong: When is it genetic drift?

This post was chosen as an Editor's Selection for ResearchBlogging.orgScience 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. (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.

Continue reading

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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.

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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.

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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.)

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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.

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