i’m a chordata! urochordata!

I love modeling! I love modeling! Modeling will solve everything!

Let’s model the spatial distribution of Bigfoot!

WAIT, WHAT?!

Figure 1 from the paper. Foots denote sighting of Sasquatch footprints. Circles for just visual/auditory sightings. I ask, how does one know what Bigfoot sounds like?

Yes, it sounds silly, but in the current issue of the Journal of Biogegraphy, Lozier et al give us their stunning contribution Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling. Finally, all will be revealed. And for those wondering:

Sasquatch belongs to a large primate lineage descended from the extinct Asian species Gigantopithicus blacki, but see Milinkovich et al. (2004) and Coltman & Davis (2005) for phylogenetic analyses indicating possible membership in the ungulate clade.

They do this to prove a point - that Ecological Niche Models for determining species ranges are amazing - invaluable conservation tools, really. But if the taxonomy on the data that goes into them are shoddy (like, say, calling a Black Bear a Sasquatch), the results will be, well, interesting.

They use data on sightings (see Fig. 1 above) from… the Bigfoot Field Research Organization
and then used the latest and greatest in Ecological Niche Modeling to determine, given environmental parameters, just where does Bigfoot live? And, under current climate change scenarios, where might we find Sasquatch in the future?

So cryptozoologists take note! Here is a veritable treasure trove of information as to where to place your next tripwire camera!

In fairness, the authors use this dubious analysis to point out that, when we have a record of species occurrences that seem tidy and orderly, we often don’t question their taxonomic validity. The output of these models, vital to some conservation efforts, will only be as good as their input. Indeed, in this case, the authors find striking overlap with the (far less frequently observed) Black Bear (yes, people report sightings of Sasquatch more than that of Black Bears). It’s a real problem, and the assessment of data uncertainty is a real pressing issue for any method that attempts to draw inference from sparse data.

But, really, in the end, this is an Ig-Nobel award winner in the making. Bravo.

Lozier, J., Aniello, P., & Hickerson, M. (2009). Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02152.x

Yes, it’s time for squirts to take the limelight in America’s most fashionable magazine! I know this is a little old, but in the 2007 article, If You Knew Sushi by Nick Tosches, the author encounters a delicacy, Halocynthia roretzi aka the Sea Pineapple. (That’s right, they’re even on wikipedia now!)

Among a biochromatic wealth of mysterious mollusks and other sea invertebrates of unknown nature, I see the weirdest creature I’ve ever seen. Now, that’s a fucking organism. Tom Asakawa looks at it awhile, too.

“Sea pineapple,” he says. “Attaches to rocks in the ocean. Tastes something like iodine. Sendai people like it.”

It looks nothing like a pineapple. It looks like something that could exist only in a purely hallucinatory eco-system. It looks like, I don’t know, maybe an otherworldly marital aid of inscrutable purpose for the brides of Satan.

“I need to eat that,” I say.

Googling around, you can find a lot more info on Sea Pineapples, including info on their Aquaculture and more.

It’s only a matter of time before they come to the states! Right?

Happy World Oceans Day to all! And to all a good…night?

In celebration of World Oceans Day, BlogFish is hosting the 25th Carnival of the Blue, that monthly feast of simply the best ocean blogging. So dive in and enjoy!

For the fashionable marine biologist: Some months back, I fell upon a website called Sir Critter selling t-shirts of organisms bedecked by a monocle, top-hats, and cane. I asked the designer if he would create a Sir Sea Squirt. He was delighted, and just posted the resulting shirt, Sir Sea Squirt.

For those of you out there who don’t think Sea Squirts are, indeed, the coolest thing on earth. *ahem* They also have Sir Urchin (I’m getting one with a purple S. purpuratus), Sir Squid, Sir Jellyfish, Sir Sea Slug, and more. The designer has also mentioned that he’ll be updating with a few new critters every month.

There’s nothing so satisfying as pulling back and seeing your brand new experiment out there in the water.

It’s been a crazy week or three getting this up and running, but now my first big postdoctoral experiment is soaking in the water, with urchins grazing away.

I’m testing some ideas regarding how diversity mediates the impact of disturbance by urchin grazing, and vice-versa - how disturbance by grazing can alter diversity. In essence, I’m testing a model of a community feedback process based on a framework whipped together by Randall Hughes, myself, and a few other fabulous co-authors.

But even though your ideas may be high-up and lofty, they always meet some interesting realities on the ground. Reality point 1 - my god, we built a lot of large cages.

This is about 1/4 of the cages before deployment. The rest were in the water. Thank fod for cheerful undergrad labor (fueled by brownies made from scratch - the key is to underbake them, and use a combination of eggs and egg yolks for extra gooey-ness) They look like such simple cheap affairs - some garden fencing, some PVC, some netting around the bottom…and then there’s about 1 ton worth of chain and half a ton of rebar stuffed into them. Subtidal work: unless it’s heavy, the waves will sweep it away.

Reality 2 - sometimes, you’ve gotta do it topless. Yes, the cages have no tops. This would seem the height of insanity if you want to keep something INSIDE. However, urchins appear to not like bendy flexy things. Sure, they’ll crawl up to the tops, but then they get to that wave strip at the margin, and freak out and freeze up. I’ve watched it. It’s kinda odd. And those cages that did have a top on them? That top, even if it’s mesh, creates a LOT of lift. So, a small wave washes by, and suddenly the cage top becomes an airplane wing. Unless you’ve added a huge amount of weight to your cage (see above), you may well never be able to find your cage again.

Reality 3 - nature is variable. Well, duh. See the two cages with two very different species compositions, som providing more or less biomass. I mean, the whole premise of this experiment was to use a natural gradient in species diversity as a treatment. But sometimes adding or subtracting one species can make a huge difference. Sampling (Reality 4 - ID-ing to the species level in the field on SCUBA gets pretty tedious after one hour, let alone 4 or 5) was pretty interesting, showing that large differences were indeed generated by both position on the reef, local topography, etc, as well as whether, say, tiny sea cucumbers had colonized a plot, whether the plot was full of lush Pterygophora, or the presence of the squat thick gorgonian Muricea.

Reality 5 - hungry urchins are hungry. And devious. Upon addition of urching to plots, they zoomed over to any brown algae (particularly the aforementioned Pterygophora or any juvenile giant kelp) and began munching in earnest. Some ran for the sides of the cages (and a few managed to squeeze out - Reality 6, the best laid plans of underwater mice and men… I’ll be doing some replacements this week with larger urchins). But the instand voracious consumption was really quite impressive.

I’m pretty stoked, and deeply curious as to how this will turn out. I’m sure there will be cursing, frustration, and bizarre results in the future, but for now, SCIENCE! Love it!

I’ve gotta, say, Roughgarden’s The Genial Gene is so far pretty awesome. It is fulfilling its promise of being meaty, laying out the real some real testable predictions for her theory of Social Selection, and also pointing out some of the logical, historical, and cultural fallacies of sexual selection. I’m going to be very curious to read some of the reviews that will come out by sexual selection advocates, but so far, I think she is presenting a fairly compelling argument.

I just finished reading a section on penis fencing in hermaphroditic flatworms. The example was used to demonstrate how we write the narrative that we want to see - virile strong rapacious flatworms, dueling it out! The loser slinks away in shame to bear the burden of being a female. The winner is victorious, not having to incubate their own genetic progeny, but instead have farmed it out. It’s inspired papers such as Sex and Violence in Hermaphrodites (which shows that insemination is usually dominated by one individual, but doesn’t show anything about multiple copulation attempts, or the cost of being inseminated) or Evolutionary Conflict: Sprem Wars, Phantom Inseminations (about sea slugs, but, again, no fitness benefits v. costs). It’s also inspired at least one great comic strip.

There are a few questions this raises. First, if such a system of mating is SO harmful, then wouldn’t it be selected against? I mean, if “losing” a mating bout is such a huge cost to an individual…which implies a cost to their fitness, then selection should ultimately find a way around that? It doesn’t sound like the most evolutionarily stable of strategies - hurt the one who will bring your genetic contribution into the next generation! Make sure they’re in the worst possible condition while they go off and incubate your genetic future! This is not to mention the fact that all of the energy you’ve been putting into the eggs you yourself have produced (remember, these little suckers are hermaphrodites) have now been wasted! Yippee!

This does not sound like a good thing, when one stops to think.

More likely, she points out, a lot of this is just cultural bias creeping into our observations. I mean, I’ll be honest, fast moving flatworms whipping their penises around? It sounds like some frat parties I’ve been to! Well, ok, not really - I was in a co-ed literary society, but that is neither here nor there!

The point is, you can see how easy it is to write a narrative to these behaviors that can override more dispassionate reasoning. An example may help, however.

Below are two movies of flatworm penis fencing. One, the original, is dark, gritty, with the full on sexual selection narrative as its underpinning. If you’d like, ignore the narration, and just pay attention to the underscoring of the actual mating.

Now, compare this to the same mating event, but this time underscored with “No Quiero Otro” by the Bajofondo Tango Club.

Interesting stuff. Makes you think a little bit more about the true meaning (and evolutionary costs and benefits) of Apophallation.

UPDATE: Unbeknownst to me, it’s sex week over at Deep Sea News! All of which was inspired, in part, by their amazement at the very video shown here! How perfect! Whadda ya think of penis fencing, now, guys?

Amazing! Made by gooseflesh:

Recently on ecolog-l, there has been a thread going around about journal publishing - open access v. pay-for access, impact factor, elitism, reviewing, etc. The central question seems to be, is the publication system somehow broken? Do we need to fix it? Is the model of journals such as PLoS Biology or The Open Ecology Journal not enough?

I think the answer is that in the realm of experimental or solid theoretical work, yes, the open access model of science publishing is alive and well (although I often wished that more of the journals out there, such as Research Letters in Ecology, got more attention - but the question of why to submit in a new journal, and what makes a journal high on ones priority list is a whole different ball of wax).

What seems to not have as clear a home in the world of Open Access science is short novel opinion pieces. True, PLoS One and others may have some room for forum, review, and opinion articles. But it is not their mission. Indeed, even in the world of non-open access, the primary publishing point for these sorts of articles is the Trends series, such as Trends in Ecology and Evolution. Articles there are often high-impact and intriguing. But, not open access and can be long-in-the-publishing-cycle (which is not as ideal for ideas types of papers).

Now, one might say, if you want a short, rapidly published, open access opinion piece - well, that’s called a Blog. But this does not have the cachet of a formally published journal (even an online-only one).

So, I’ve been intrigued to see the emergence of Ideas in Ecology and Evolution. It’s mission is to be quick (5 days from acceptance to publication), idea focused, very open to peer-reviewed commentary, and open access. Their entire publishing model is laidout by Lonnie Aarssen, the journal’s editor, in this opening editorial. Some seems like relatively standard stuff. For example, the criteria for publication are:

(i) The paper must present a genuinely novel idea or commentary.
(ii) The new idea /commentary must be well-argued and plausible.
(iii) The paper must demonstrate the potential for the new idea /commentary to impact significantly on the subject area or broader discipline.
(iv) The paper must clearly differentiate the idea or commentary from any previously published similar ideas or commentaries.
(v) A new idea must be accompanied by a proposal for testing the idea, even if it is completely impractical with current technology. Testability may be addressed directly, e.g. through empiricism, or in terms of the consilience of inductions.

But then it gets interesting. What is perhaps most intriguing (and most controversial) is how the journal attempts to speed up the initial review process and ensure that all ideas are given a fair shot, rather than try to maintain ‘prestige’ of a journal. It begins with the premise that the current review system is somewhat broken, and that referees have little incentive to be speedy in their reviews or easily embrace new ideas that are counter to dogma. So, it proposes to whopping changes to the system. 1) Referees are paid for their job (current $150). 2) No blind reviewing. Reviewers are fully credited when a paper is published. Not only that, but 3) “If the paper is accepted for publication, each referee is entitled to publish his/her views on the paper as a response article - peer reviewed by both the editors and the author.” Although, reviewers are also allowed to merely click through a standard form and submit no written comments if they wish, in order to speed up the process.

In their own words “Ideas in Ecology and Evolution represents a completely transparent peer-review publication model that rejects elitism, guards against sources of publication bias, and serves to break down traditional barriers to the release of creativity…”

Lofty stuff. Assuming that this bias against new ideas is real. I have to admit, I’m skeptical. Reviewers are rigorous and sometimes slow. And yet, I am highly skeptical of the idea of buying objectivity. When I review, I always strive for editorial objectivity, money or no. I like the idea of publishing commentaries and reviews along with papers - I’ve long wished that more journals would allow access to general reviewer comments. But my skeptical side really has to wonder if paying reviewers might make them actually less objective and more likely to accept a paper. I’m just not sure if I would feel comfortable being paid good money, reading something, and then giving it a thumbs down.

Also intriguing, authors pay a $400 submission fee up front (which goes towards reviewers) and $300 afterwards if accepted. The up front fee is indeed novel, and I admit, I can see many an author blanche at the idea of paying $400 for a possible rejection. It also ups the ante on the question of whether introducing money into the reviewing system will actually change objectivity.

This far, not much has been published there - one paper on parasites in behavior research and a response by one of the reviewers. Will there be more? Is this The Way? Or, is there an even more streamlined semi-peer reviewed meta-blog more the way to go for this sort of thing (something to think about, folk)? And how ethically sound is the journals reviewing policy? I am indeed curious.

Aarssen, L. (2008). Ideas in Ecology and Evolution – A new open-access model dedicated to the rapid release of creativity in peer-review publication Ideas in Ecology and Evolution, 1, 1-9 DOI: 10.4033/iee.2008.1.1.e

Lately, I’ve been dreaming of webs.

I’ve been asking myself, how do we visualize the hidden complexity of the natural world? This is not an idle question, but draws on some of my current research. It is vital to how we think about ecosystems when we attempt to preserve and restore them. It is inherently beautiful, in and of itself.
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Carnival of the Blue #24 is up over at the Monterey Bay Aquarium Sea Notes There are some great articles about clams, corals, and more!  I’ve been a slacker on these, so it was great to participate and see how the carnival has grown into such a wide and varied range  of posts!