It has not been a quiet week in Lake Wobegon

The Onion goes for the low-hanging fruit with above-average results:

According to officials, the bodies were discovered when hundreds gathered to watch Mr. Berge’s 1949 maroon Pontiac sink into the thawing lake as part of the annual Sons of Knute Ice Melt contest. As the car submerged, onlookers witnessed a number of purplish- looking corpses float to the surface, most of them decapitated.

URL shortners = actually evil

Via Kottke.org: Joshua Schachter points out a few hazards of handing your links over to TinyURL and their ilk, and suggests some solutions.

The worst problem is that shortening services add another layer of indirection to an already creaky system. A regular hyperlink implicates a browser, its DNS resolver, the publisher’s DNS server, and the publisher’s website. With a shortening service, you’re adding something that acts like a third DNS resolver, except one that is assembled out of unvetted PHP and MySQL, without the benevolent oversight of luminaries like Dan Kaminsky and St. Postel.

Since starting up on Twitter, it’d occurred to me that clicking a shortened URL is a pig in a poke at best. Yet somehow it doesn’t feel as dangerous to accept a shortened URL from @apelad or @nprscottsimon as it would if I just found one in my email. Perhaps because, if they did post a hazardous link, I’d just un-follow?

Speciation changes ecosystem

ResearchBlogging.orgWe know that ecosystem processes can act on organisms to help create reproductive isolation and speciation – now, a new paper released online in advance of publication in Nature shows that speciation can change the ecosystem [$-a].

The study’s authors are a group of University of British Columbia scientists, including Luke Harmon (who occasionally blogs at Dechronization) and Simone Des Roches, who have since come to my department at UI as a faculty member and doctoral student, respectively. They focus on the case of ecological speciation in sticklebacks (Gasterosteus aculeatus), which have repeatedly into evolved two reproductively isolated, ecologically different forms [$-a] after colonizing North American freshwater lakes from the ocean about 10,000 years ago. One of the two forms is “limnetic,” living in open water near the surface and feeding on plankton; the other is “benthic,” living on lake bottoms and feeding on invertebrates.


A stickleback
Photo by frequency.

Harmon et al. reasoned that the presence of these two different fish must have a substantial effect on lake food webs. To test this hypothesis, they set up mesocosms – big cattle tanks seeded with a standard mix of sediment, plankton, and invertebrates – and introduced either (1) sticklebacks of the “generalized” type ancestral to the benthic and limnetic types, (2) either the benthic or limnetic type alone, or (3) both the benthic and limnetic types together. They found that the fish species present in the mesocosm strongly affected the plankton species diversity – limnetic-type nearly eliminated one of their preferred prey species – and on measures of total ecosystem productivity and metabolic activity.

Perhaps the most important effect was on dissolved organic content (DOC) and light transmission in the water column. Mesocosms containing both fish types had about the same amount of (non-living) organic material as those containing the generalist ancestor, but the two-species treatment changed the DOC composition to make the water column more transparent to light. In a real lake, this effect could significantly change the productivity and composition of the aquatic plant community, which would in turn reshape the rest of the food web.

The buzzword for this phenomenon is “ecosystem engineering,” which the ESA blog puts front-and-center in its discussion of this paper. I think Harmon et al.‘s result is most interesting as the closing of a feedback loop between the ecosystem and a population undergoing speciation. It’s evidence that a speciation event can actually alter the conditions that created it in the first place – which might prevent future speciation events, or create opportunities for new ones.

Reference

Harmon, L., B. Matthews, S. Des Roches, J. Chase, J. Shurin, & D. Schluter (2009). Evolutionary diversification in stickleback affects ecosystem functioning Nature DOI: 10.1038/nature07974

Vines, T., & D. Schluter (2006). Strong assortative mating between allopatric sticklebacks as a by-product of adaptation to different environments Proc. R. Soc. B, 273 (1589), 911-6 DOI: 10.1098/rspb.2005.3387

“There were a few flipper babies.”

The AV Club gives the under-appreciated Brain Candy its dues.

The Kids In The Hall’s ill-fated debut feature is closer in conception, ambition, and scope to Monty Python movies like Life Of Brian and Monty Python And The Holy Grail than the Saturday Night Live movies being churned out at the time by SNL Studios. Like Idiocracy,it’s less about a character or a set of characters than society as a whole.

Comedy doesn’t come much blacker than when one of your movie’s most quotable laugh lines is a crack about birth defects.

Scientific methods in the genomic age

Nature Methods has a good editorial considering the issues around defining what science is in the age of exploratory genomics [$-a].

As schoolchildren we are taught that the scientific method involves a question and suggested explanation (hypothesis) based on observation, followed by the careful design and execution of controlled experiments, and finally validation, refinement or rejection of this hypothesis. … Scientists’ defense of this methodology has often been vigorous, likely owing to the historic success of predictive hypothesis-driven mechanistic theories in physics, the dangers inherent in ‘fishing expeditions’ and the likelihood of false correlations based on data from improperly designed experiments.

Their conclusion is that hypothesis-driven science will absorb the the current flood of genomic data as the basis for new hypotheses to direct future large-scale data collection:

But ‘omics’ data can provide information on the size and composition of biological entities and thus determine the boundaries of the problem at hand. Biologists can then proceed to investigate function using classical hypothesis-driven experiments. It is still unclear whether even this marriage of the two methods will deliver a complete understanding of biology, but it arguably has a better chance than either method on its own.

As I’ve said before, massive genomic datasets change science mainly through their quantity, not their quality. On the one hand, science has always involved undirected observation – Darwin didn’t have any strong hypotheses in mind when he hopped aboard the Beagle. Classical natural history is a discipline devoted to almost nothing but undirected data collection, and it’s been the grist for evolution and ecology research since the beginning of time. On the other, it seems to me that genomic “fishing expeditions” are more hypothesis-driven than we realize, even if the only hypothesis is “Neanderthal genomes will be different from modern humans.”

Carnival of Evolution #10 at The Oyster’s Garter


The tenth issue of the The Carnival of Evolution is now live at The Oyster’s Garter, complete with a whimsical framing narrative. Topics range from the relationship between stress and testosterone levels to an essay on the species problem that complements my own contribution, to the suprising usefulness of half a wing.