Carnival of Evolution—two weeks left to submit!

Photo by mrjojo.

The 32nd edition of the Carnival of Evolution will be hosted right here at Denim and Tweed on the first of February! So you have until midnight, 31 January to submit your posts about evolutionary biology and all its myriad cultural, political, and historical ramifications on the CoE blog carnival form, or e-mail links to denimandtweed AT gmail DOT com.


The remains of #scio11: Openness to #drunksci

In session at ScienceOnline 2011. More photos are in the ScienceOnline 2011 Flickr group. Photo by cephalopodcast.

Saturday at ScienceOnline 2011 was the meat of the conference, a full day of moderated discussion sessions at the Sigma Xi building. Video of many sessions was webcast live, and will later be archived online, courtesy of the National Association of Science Writers. Highlights from the ones I attended:

In data discoverability, Kiyomi Deards, Molly Keener, and Steve Koch covered the logistics of open notebook science from making published papers freely available online to opening up datasets as they’re collected. There wasn’t discussion about the point at which scientific results ought to be freely available outside the lab—I’m all for making my papers and the final data underlying them open access, but I don’t necessarily want to post my working notebooks.

In the first line of response, the crew of Deep Sea News and John Amos of the organization SkyTruth discussed how online coverage of the Gulf of Mexico oil spill this spring helped to counter frequently inaccurate official stories, and how they could maintain public awareness in the aftermath. It was the only session I attended that performed a formal post mortem on one of the biggest events for online science writing in the last year, and it had some useful insight for covering and responding to future disasters.

How to explain science in blog posts was the closest I’ve come to a writing workshop since undergrad. A long list of top-notch bloggers and writers (Scicurious, Joanne Manaster, Maryn McKenna, Vivienne Raper, Eric Michael Johnson, Brian Mossop, Carin Bondar, Melody Dye, Christie Wilcox, and Ed Yong) split the attendees into groups to discuss content choices, the writing process, blog design, and how best to promote work online.

After the sessions, Saturday’s activities concluded with a banquet that shaded smoothly into drinks at the hotel bar, and then more drinks in the suite rented by a couple members of The Gam. I called it a night at about 2 a.m. Now I’m leaning heavily on the free coffee in this morning’s final sessions about blogging in academia and the purpose of public science outreach.

It’s been a great weekend. Unlike most academic conferences, ScienceOnline is an opportunity to talk with scientists outside my immediate field and, maybe more importantly, a lot of non-scientists. It’s been good to see a bunch of folks I met last yearagain, and to meet more folks I’ve previously known only as Twitter avatars and/or fantastic online writers, especially Dr. Skyskull/Greg Gbur, Dr. Freeride/Janet Stemwedel, Eric Michael Johnson, Holly Bik, and Steve Silberman.

Apologies if I’ve missed anyone, but there was quite a bit of booze involved.


#scio11 day one: Krulwich to climate change

In the Duke University research forest, towers like these dosed experimental plots with carbon dioxide to simulate the effects of climate change. Photo by jby.

I arrived last evening at ScienceOnline 2011 barely coherent after thirteen hours of travel from Moscow, Idaho (2 a.m. Pacific time) to Durham, North Carolina (about 6 p.m. Eastern time). Robert Krulwich’s keynote address woke me back up. Krulwich explained his approach to science journalism and illustrated it with clips from his work, including the transcendently good Radiolab. How do you get your audience excited about science, according to Krulwich? Talk about what excites you, and lead them to discover it with you.

I spent this morning touring the Duke University research forest outside Durham, where scientists from Duke and many other institutions are conduction some amazingly ambitious ecological experiments. Biogeochemist Ben Coleman presented studies of nanoparticle movement through terrestrial and aquatic ecosystems using mesocosms—semi-contained natural communities.

View inside an experimental warming plot. Photo by jby.

Carl Salk, a Ph.D. candidate in biology, walked us through plots that are being heated to simulate a changed climate. The plots are enclosed on four sides by plastic, with warm air pumped in via ductwork and electric lines warming the soil to bring them up to 3 or 5 degrees Celsius warmer than the outside. It doesn’t sound like much, but it makes a difference. Salk says plants in the warmed plots are developing leaves days and, in some cases, weeks earlier in the spring than plants in control plots.

The final stop was the biggest experimental setup, Duke’s Free Atmospheric Carbon Enrichment site, which has been testing how forests will grow in an atmosphere containing more carbon dioxide by pumping more carbon dioxide into forest plots. This is achieved with rings of towers like the ones pictured at the top of this post spraying carbon dioxide into experimental plots. The gas is reclaimed from fertilizer production, and into the air anyway; the experiment simply boosts it locally. The sheer volume of research done within these plots is amazing, but the site is now shutting down after 15 years.

The tour was over by noon, and the afternoon devoted to workshops. I attended a talk on how to develop course websites—with forums and online quizzes and integrated chat!—using Drupal, and another on the logistics of moving between blogging platforms. Once I’m done with this post, it’s off to a book-themed happy hour and dinner in Durham. Until tomorrow, here’s a slideshow of the other photos I’ve taken so far:


Science online, packing for #scio11 edition

Photo by foshydog.

As this post goes live, I’ll be waking up for the first full day of Science Online 2011, for which I expect to do a lot of blog coverage. So I’m just listing a handful of links this week:

  • And the twist is? It’s a much bigger pill. Thalidomide may be making a comeback to treat cancer.
  • Hey! Eyes up here. Ringtailed lemurs follow each other’s gaze, a key behavior in social cognition.
  • Geshundheit. Is it possible to sneeze while you’re asleep? Scicurious wonders.
  • Coming soon: Checkers-wrestling, Risk-fencing. In chess-boxing, the cognitive challenge is all about emotional control.

And here’s a ScienceOnline-appropriate video, produced on behalf of NASA because “NASA is the most fascinating, adventurous, epic institution ever devised by human beings, and their media sucks.”


Gardening ants grow their own treetop nests

This post was chosen as an Editor's Selection for ResearchBlogging.orgIf you were to combine ants’ dispersal of seeds and plant protection interactions, and maybe squint a little, you might see something like epiphitic ant gardens. Ant gardens form when tree-nesting ants collect the seeds of some epiphytes—plants evolved to grow in the branches of trees—and the collected seeds sprout. The nests provide congenial conditions for the plants, since gardening ants frequently use dung as a building material. The roots running through the nest help stabilize its structure and suck out moisture to control interior conditions.

Ants cultivate “gardens” of epiphytes like Anthurium gracile to provide nesting space. Photo by gjofili.

This adds up to a mutually beneficial relationship between ant and epiphyte [$a]. A number of tropical epiphytes grow almost exclusively in ant gardens, and the inclusion of plants in the structure of their nests apparently helps gardening ant species to establish nests wherever food is most abundant.

Association with ant gardens has evolved independently in a number of epiphytic species, from arums like Anthurium gracile (pictured to the right) to orchids and philodendrons. When distantly-related species begin to perform the same ecological role, they often evolve convergent traits that facilitate the common role. Almost all ant-dispersed plants attach fatty bodies called elaisomes to their seeds to reward the ants that pick them up. Almost all ant-protected plants grow domatia in which the ants can nest, and nectaries to reward them with sugary sap. But plants that grow in ant gardens don’t seem to have a common trait that prompts ants to collect their seeds. Can it be that every ant-garden plant species has a unique way to be an ant-garden plant?

That’s what studies of ant-garden plants, including a new one just published in PLoS ONE, suggest. Plants associated with ant-gardens don’t have elaisomes on their seeds. Many produce fleshy fruit, but ants will collect their seeds even if no shred of fruit flesh clings to them. In some cases, ants will even collect seeds from the dung of fruit-eating birds and mammals.

This leaves the possibility that ant-garden plants produce some ant-attracting chemical in their seeds. In the new paper, Elsa Youngsteadt and her coauthors set out to identify chemical compounds that might be the common attractant used by nine different ant-garden plants from seven different plant families. Youngsteadt et al. isolated seven different compounds found in the seeds of ant-garden plants but not in closely related species that do not grow in ant gardens. (The absence of the seven compounds from the non-ant-garden relatives is established, rather amusingly, with a blank data table.)

The authors then painted crude extractions of all soluble organic compounds from two ant-garden plants onto seeds from species that gardening ants do not cultivate, and found that the ants were indeed more likely to collect them. (As a control, the ants were also offered seeds coated in the pure solvents used to extract attractive compounds. They didn’t like those.) However, analysis of the extracts failed to find a compound or set of compounds present in all three species.

It’s possible that Youngstead et al. simply failed to isolate the compound or compounds that all three ant-garden plants use to prompt ants to collect their seeds. But it’s not that far-fetched to think that these distantly-related plants might each use different attractive compounds to interact with ants in the same way. Natural selection may often arrive at different solutions when shaping different species for the same ecological role. It might also be that ant-garden relationships were established not by plants evolving a way to prompt ants to pick up their seeds, but by ants evolving to recognize seeds of plants that work well in gardens.


Davidson, D. (1988). Ecological studies of neotropical ant gardens. Ecology, 69 (4), 1138-52 DOI: 10.2307/1941268

Youngsteadt, E., Guerra Bustios, P., & Schal, C. (2010). Divergent chemical cues elicit seed collecting by ants in an obligate multi-species mutualism in lowland Amazonia. PLoS ONE, 5 (12) DOI: 10.1371/journal.pone.0015822


Writing without a spotter

Photo by athena.

Writing is hard, but writing alone is even harder.

Most writing projects are team efforts. Even if only one person is responsible for the final product, there’s someone else to read drafts and help shape the text into something clear and pleasing. Books or newspaper and magazine articles have editors. Scientific papers usually have coauthors, or at the very least colleagues who’ll provide feedback on a draft—and then peer reviewers and journal editors who will point out inaccuracies and missed commas with equal delight.

You can even ask your roommate to look over the essay you’re writing for English 102, if he’s still awake at 2 a.m.

By comparison, blog posts are often composed in a vacuum. I’ll read a scientific paper or a news article, or view a video on YouTube, compose my thoughts about it, drop in a Creative Commons-licensed photo or two from Flickr, and then give the whole thing a read-through in Blogger’s “preview” mode to make sure I like it. Sometimes I’ll repeat that final read-through a couple of times for a long post, but that’s all the editorial process I have. I’m the only one to see the work until I click “publish post.”

This never really seemed like a problem to me until I was working through my reviewing for the Open Lab 2010 anthology, and began to suspect that I’m not the only one writing this way. Time after time I read Open Lab submissions and caught myself thinking about the comments I’d scribble in the margins if I were editing them, instead of rendering yes/no judgements.

Not that these OL submissions weren’t good writing—several were among the best in my list to review. But as a reader who wasn’t also the author, I could see how small changes—moving a few paragraphs to create a clearer train of thought, or returning to an idea from the first few sentences to provide a neater ending—could improve the work. I’m left to wonder what improvements someone else would suggest if he or she could look over my posts before I publish them.

I’m not about to hire an editor for this one-man blog, and I don’t know how often I’ll get up the nerve to ask colleagues or my roommate to look over blog posts and give feedback. Short of that, I think I’m going to spend more effort thinking about what I like in the kind of writing I want to do here—science, for non-scientists—and how I can emulate it. If I can’t have an editor or a coauthor, I can at least pay deliberate attention to what works and what doesn’t, and see if I can’t get better at writing without a spotter.

I may end up with some bruises to the ego, but I’ll survive. After all, I’ve only just realized that I’m in danger of falling.


Open Lab 2010 finalists: I’m in a book!

More specifically, my post about J.B.S. Hadane’s involvement in a Soviet propaganda film featuring the revival of a severed head will be included in the Open Lab 2010 anthology of online science writing. It’s a huge honor to be chosen alongside such an incredible list of writers from such a long list of awesome submissions.

As one of forty volunteer reviewers, I know how stiff the competition was, and how hard the final decisions must have been. I only have an inkling, though, of the amazing effort editor Jason Goldman put in to sort through all the submissions, coordinate reviews, and develop a final list.

The cover design for the final print volume will apparently be unveiled at Science Online 2011 (which is next weekend!), and the book itself will be available for purchase once all the submissions are revised for dead-tree formatting.


Science online, decline of the “decline effect” edition

Bumblebee. Photo by je-sa.

Mutualist matchmaking made simple

This post was chosen as an Editor's Selection for ResearchBlogging.orgBack in September, I wrote about a new economic model of mutualism that proposed mutualists could keep their partner species from cheating—exploiting the benefits of a mutualistic relationship without returning the favor—without explicitly punishing them, so long as failure to play nice led to a reduction in mutualistic benefit [$a]. Now the same research group has published an elaboration of the economic approach to mutualism in the January issue of The American Naturalist, which suggests that mutualists can recruit better partners by manipulating the cost of entering into partnership [$a].

The bobtail squid, whose mutualism with luminescent bacteria is an example for the new model. Photo by megpi.

As a concrete example for their model, the authors refer to the mutualism between bobtail squid and a species of bioluminescent bacteria, which colonize the squid’s light organ and makes it glow. Short of some kind of complicated squid-bacterium signaling system, how does a squid ensure that its light organ is only colonized by bacterial strains that will pay it back and generate light?

They charge a cover.

More specifically, while the squid’s light organ supplies food for colonizing bacteria, it is also full of toxic reactive oxygen compounds. In order to take advantage of the food supply, a bacterium has to clear out these toxins—and conveniently, the bacterial enzyme that generates light consumes oxygen and removes the toxins in the course of the light reaction. So the only bacterial strains that colonize the squid’s light organ are those that can pay the cost of eating up the oxygen-based toxins and still make a “profit” on the food supply provided by the squid, generating light in the process.

The trick in setting up this screening is to find the right balance of cover charge and reward for prospective mutualists. The cover charge paid by high-quality partners has to be high enough that low-quality partners won’t accept it, and the reward offered for paying that high cost must be sufficiently good to make it worthwhile.

The authors suggest that this model should also apply not just to other mutualisms in which a host takes on microbial partners, such as plants’ partnerships with nitrogen-fixing bacteria, or animals’ interactions with the bacteria living in their guts—but also to interactions like obligate pollination mutualism or ants’ protection interactions with some plants.

Yuccas and ant-protected plants have to screen mutualists, too—and may impose their own cover charges. Photos by jby and Alistair Rae.

In the case of obligate pollination mutualism, like the one between yuccas and yucca moths, the cover charge is the effort involved in pollination—to guarantee a supply of yucca seeds for their larvae to eat, yucca moths must deliver plenty of pollen and do relatively little damage to the flower as they lay their eggs in it. There do exist yucca moth species who don’t pollinate, but lay their eggs on yucca flowers after they’ve been pollinated and are starting to develop into fruit. The new model would predict that the lower effort of this strategy is reflected in a lower payoff, maybe a lower rate of survival for the eggs of these “bogus” yucca moths.

In the case of ant-protected plants, the cover charge is the effort involved in defending a host plant from other ant colonies that would like to occupy it. As it happens, parts of an ant-plant that are better protected grow to provide better food and shelter for the ants occupying them, which gives a competitive advantage to a colony of effective defenders trying to fight off a colony of less-effective defenders.

Both of these scenarios, and similar ones in other interactions, suggest ways to test for self-screening mechanisms like the one described in this new model. The model suggests that active screening using signaling between interacting species should be rare in nature, and that a simple cost/benefit structure usually underlies the process of establishing associations between partners. I’ll be very interested to see whether new experimental or observational data further supports the self-screening hypothesis.


Archetti, M., Úbeda, F., Fudenberg, D., Green, J., Pierce, N., & Yu, D. (2011). Let the right one In: A microeconomic approach to partner choice in mutualisms. The American Naturalist, 177 (1), 75-85 DOI: 10.1086/657622

Weyl, E., Frederickson, M., Yu, D., & Pierce, N. (2010). Economic contract theory tests models of mutualism. Proc. Nat. Acad. Sci. USA, 107 (36), 15712-6 DOI: 10.1073/pnas.1005294107