Better e-flashcards: Anki

Following up on my previous post about Genius, an electronic flashcard program I was thinking about using as a resource for my students in this semester’s mammalogy lab. (There’s a double benefit here — I’m no mammalogist, so I’m really creating study materials for myself, but it’s nice if I can pass them on to the students.) Anyway, I think I’ve found something better than Genius: Anki.

Anki is basically the same thing as Genius, but with cross-platform compatibility where Genius is Mac-only, and with a utility to find and upload decks of virtual flashcards from a server full of shared user-created material. So I can put the cards online, and any student who installs Anki just has to type “Mammalian” into the search function to use them.

Anki also makes use of “spaced repetition” to schedule individual cards during study sessions; it’s less clear to me how useful that will be. To plan spaced repetitions, Anki doesn’t ask you to type in answers as Genius does, but to recall an answer, reveal the correct one, and rate how easy the recall was. That seems less helpful, but we’ll see how it goes.

Ten Thousand Villages making millions

Via Roxy Allen: Ten Thousand Villages, the not-for-profit seller of fairly traded handicrafts founded by Mennonite Central Committee, earns a write-up in Forbes. TTV’s roots apparently go back to 1946, when a Mennonite mission worker started bringing embroidery back from Puerto Rico — last year the U.S. branch of the charity brought in $24 million. And, as Forbes has it, they’re doing well by harnessing upscale consumerism for good.

New stores are in tony suburbs, in gentrifying neighborhoods and near college campuses. The typical consumer: an educated, socially conscious woman, aged 25 to 54, with a household income of $70,000 to $100,000. She might be looking for an inexpensive wedding present, replenishing her supply of Equal Exchange coffee or browsing racks of cheap jewelry for a gift to herself she’ll feel virtuous for buying.

Microsoft patenting phylogenetic methods?

Over at Dechronization, Liam Revell points to a recent report in Science that Microsoft has filed one or more patents [$-a] on the methods biologists use to reconstruct evolutionary relationships among living things.

The patent filing, by Stuart Ozer, claims invention of a variety of techniques already in wide use by systematists and evolutionary biologists – and (so far as I could tell) none of these inventions are original in quality. The whole patent filing can be read (at one’s own risk) in its entirety here, however I have also chosen a few select passages for reproduction, below.

Among the claims of invention in this patent filing, the author purports to originate:

“a method of generating biomolecular clustering patterns”

“counting evolutionary events in each of the identified plurality of positions at each identified node in the evolutionary tree”

“counting evolutionary events further includes: generating an event rate . . . wherein identifying related positions includes identifying related positions based on the event rate”

This is worrying to systematic biologists because they don’t typically worry about patenting new methods — in academia, the payoff from devising a new method is to have the paper in which you publish it cited by everyone who uses it. And, although it’s polite to ask the original author first, those methods are understood to be freely available for improvement and extension. The last thing anyone wants is to have to consult a patent attorney before publishing. The comments on Revell’s post reflect this perplexity and worry, and are well worth following.

That possum you just ran over? It might have saved you from Lyme disease

ResearchBlogging.orgGrowing up in suburban Pennsylvania, where the most hazardous wildlife not extirpated from our woods is the occasional crazed whitetail deer, there was really only one danger I associated with the outdoors — ticks. Specifically, ticks carrying Lyme disease, a not-very-pleasant bacterial infection that attacks the joints, heart, and nervous system if left untreated. According to a paper released online early in Proceedings of the Royal Society B, my risk of picking up Lyme disease on an excursion into the woods behind my parents’ house may have depended on the diversity of bird and mammal species in those woods [$-a].

Sure, it looks like a giant rat, but that opossum is a walking death trap for disease-carrying ticks. Photos by ricmcarthur and jkirkhart35.

In a way, the ticks that carry Lyme disease are a threat to humans precisely because they don’t rely on us as a regular source for blood. Instead, they feed on a variety of mammals and birds, which allows them to maintain population densities high enough that a human wondering into a woodlot stands a good chance of picking up one or two of the little buggers.

But it turns out that not all of these non-human hosts are equally hospitable for ticks. The new paper’s authors, Keesey et al., caught a range of tick hosts — white-footed mice, eastern chipmunks, gray squirrels, opossums, veeries, and catbirds — and experimentally infested them with ticks. They found a huge range of tick success across the six host species: almost half of all ticks introduced onto mice were able to feed, while only 3.5% of ticks introduced onto opossums were. Most ticks that failed to feed disappeared — they were probably eaten when the host groomed itself.

The authors’ field surveys of ticks carried by these animals in the wild make the difference even more pronounced. Wild-caught opossums carried an average of almost 200 ticks — if that’s 3.5% of the ticks that try to feed on a opossum, then that means each opossum had attracted, and eaten, up to 5,500 ticks!

But the real impact of this result comes into focus in a mathematical model the authors develop to determine the effects of removing each of the six hosts from a woodland ecosystem. Removing intermediately-useful hosts like veeries or catbirds doesn’t have much effect on tick density. On the other hand, if you remove very tick-friendly hosts like the white-footed mice, tick populations plummet. And if you remove opossums, they increase dramatically. This is important because, the authors say, larger mammal species are the first to leave as patches of woodland are reduced to make way for human development — so an early effect of woodland fragmentation may be to reduce or eliminate opossums in that woodland, and boost the density of disease-bearing ticks.

This result goes a long way to fulfilling a proposal the authors made in a 2006 review article, that the diversity of alternative hosts for disease vectors like mosquitoes and ticks may shape the risk they pose to human populations [$-a]. It shows that, even in the relatively tame landscapes of suburbia, the way we humans manage what wildlife remains may have real consequences for our own well-being.


Keesing, F., Holt, R., & Ostfeld, R. (2006). Effects of species diversity on disease risk Ecology Letters, 9 (4), 485-98 DOI: 10.1111/j.1461-0248.2006.00885.x

Keesing, F., Brunner, J., Duerr, S., Killilea, M., LoGiudice, K., Schmidt, K., Vuong, H., & Ostfeld, R. (2009). Hosts as ecological traps for the vector of Lyme disease Proc. R. Soc. B, (online early) DOI: 10.1098/rspb.2009.1159

A helpful invasive species?

This post was chosen as an Editor's Selection for ResearchBlogging.orgIntroduced species can wreak havoc on the ecosystems they invade. But what happens after they’ve been established for centuries? A new study in the latest Proceedings of the Royal Society suggests that, in one case, an introduced species has actually become an important part of the native ecosystem — and helps protect native species from another invader [$-a].

Dingoes (above) control red
foxes, which is good for native
Photos by ogwen and

The introduced species in question is the Australian dingo, the wild descendant of domestic dogs [$-a] that moved Down Under with the first humans to settle the continent. Today, 5,000 years after their introduction, dingoes are the largest predator in much of Australia, and they were a prominent part of the ecosystem encountered by European settlers. Europeans, like previous waves of human arrivals, brought their own domestic and semi-domestic animals — including red foxes, which prey on small native mammals.

The new study’s authors hypothesized that because dingoes reduce red fox activity both through direct predation and through competition for larger prey species, dingoes should reduce fox predation on the smallest native mammals. At the same time, dingoes prey on kangaroos, the largest herbivore in the Australian bush — and reducing kangaroo populations should increase grass cover, providing more habitat for small native mammals. When the authors compared study sites with dingoes present to sites where dingoes had been excluded to protect livestock, this is what they found: increased grass cover, and greater diversity of small native mammals where dingoes were present.

Recently a news article in Nature discussed ragamuffin earth [$-a] — the idea that human interference in nature has so dramatically changed natural systems that it may often be impossible to restore “pristine” ecological communities. In these cases, some ecologists say, conservation efforts might be better focused on how to maintain and improve the diversity and productivity of the novel ecosystems we’ve inadvertently created. It looks as though the dingo could be a poster child for exactly this approach.


Letnic, M., Koch, F., Gordon, C., Crowther, M., & Dickman, C. (2009). Keystone effects of an alien top-predator stem extinctions of native mammals Proc. R. Soc. B, 276 (1671), 3249-3256 DOI: 10.1098/rspb.2009.0574

Marris, E. (2009). Ecology: Ragamuffin Earth Nature, 460 (7254), 450-3 DOI: 10.1038/460450a

Savolainen, P. (2004). A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA Proc. Nat. Acad. Sci. USA, 101 (33), 12387-90 DOI: 10.1073/pnas.0401814101

Munger on Milk editor Dave Munger inaugurates his new column on the Seed Magazine website by drawing together RB-aggregated posts about milk — and giving very kind attention to my own recent post about a new study of lactation lactase persistence in European and African populations. (Thanks, Dave!) It looks like the new column will shape up to be another good way to keep abreast of the ever-expanding science blogosphere.

Nature blogging from the ivory tower

Over at the Nature Blogging Network, N8 discusses the network’s “academic” category, with examples including a very nice nod to D&T.

I thought the addition of the category made a lot of sense — when I joined NBN in March, the best match I could find was “ecosystems,” which is fine, but maybe not as fitting as it might be. I think of D&T not so much as a blog about nature as a blog by someone who studies nature, which lets me post about pretty much whatever catches my attention, not just peer-reviewed research or photos from my latest hike. Also, to be honest, some of the appeal in switching to the “academic” category is that it’s a smaller pond — albeit a pond I share with Greg Laden.