Comments for first half of June 2010

In the course of asking, “What is graduate education for?”, DrugMonkey made a note of how long it takes to get a doctorate. I asked where the data came from.

Unbalanced Reaction asks whether students should get PowerPoint slides for their classes.

Sabina at the Postdoc Career Development Initiative asks whether people should chase the one big paper. That people seriously consider this blows my mind.

Doctor Becca talks about how senior researchers promote their students and post-docs (or don’t). But I’m not sure what a supervisor can do that the student or post-doc cannot.

Boing Boing features four fantastic scientists commenting on a New York Times piece by John Tierney. Dr. Isis accuses Tierney of pulling numbers “out of his ass.” Except that he didn’t. He pulled them from a peer-reviewed journal article. The numbers may be irrelevant or misleading, but they’re not arbitrary. Isis, to her credit, does a much better job of discussing this in the comment section of her blog than in her main post.

Mike the Mad Biologist is betting against Nature Publishing Group in its conflict with the University of California system. I rephrase the question.

Thoughtomics rants against the slapdash use of “living fossil.” But one possible meaning – maybe the best one – got missed.

Tuesday Crustie: Mandibles

I saw this and could think of nothing but the alien from the movie Predator.

This is a frontal view of the head of a male Branchinecta brushi. This species of fairy shrimp is interesting in several ways. First, it is a species new to science, having just been described in a paper last week.

Second, this is one of the two highest crustacean species on the planet. There is one other crustacean found in the same pools that B. brushi is found in.

I also have to give this paper credit for the best opening line for a Materials and Methods section I may have ever read:

Dr. Charles F. Brush collected our specimens on 13 December 1988 during a successful bid to break the world record for high altitude SCUBA diving.

And yes, the species was named after the record holder who discovered and collected them.

The location of this successful world record bid was Cerro Paniri, a mountain in Chile. This image of the crater pond where this species was found gives a sense of what you have to do to break a world record in altitude, either for SCUBA or finding new species:

That’s 5,946 metres above sea level. This means crustaceans in these kinds of environments tend to have eggs that encyst, and can remain dormant for long periods until water returns, or be taken up and dispersed by birds. That this is particular species reproduces sexually also suggests that several cysts were introduced to the area by birds.

What’s slightly nerve wracking is that, as you can imagine, pools like this tend to come and go. This particular species is known only from the one collection in the one pool, and the authors suggest it might have evolved and speciated only in that pool. That makes it a good thing that it’s so high up, humans are unlikely to mess with it.

Reference

Hegna, T., & Lazo-Wasem, E. (2010). Branchinecta brushi n. sp. (Branchiopoda: Anostraca: Branchinectidae) from a Volcanic Crater in Northern Chile (Antofagasta Province): A New Altitude Record for Crustaceans Journal of Crustacean Biology 30(3): 445-464 DOI: 10.1651/09-3236.1

Energy disasters

Following up on yesterday’s comment, I got to thinking about energy disasters.

The BP spill in the Gulf of Mexico is just one of many disasters with oil.

Coal mining is dirty and dangerous.

Nuclear power has had at least two memorable accidents.

Hydroelectric dams can fail and flood.

Wind power can be dangers to flying animals, but I’m having hard time imagining a a failure that would endanger so many human lives and jobs as to rate as a “disaster.”

I am having a hard time imagining a solar power failure that could threaten anyone. Burns from steam if you were using concentrating mirrors is about as close as I’ve come.

Fuel outrage

I made a comment earlier today on Twitter:

If people were serious about their outrage about the Gulf oil spill, they wouldn't stop buying from BP, they'd try to stop buying gasoline.

Got a lot more attention and retweets and such than most things I put out (I think anything with BP is getting auto-tagged).

Note the use of the word, “try.” I know we’re in a fossil fuel economy and a lot of people can’t quit gasoline and still make a living. It would just be nice if people acknowledged that the demand for fossil fuels makes things like oil rigs possible, and that if it wasn’t BP out in the Gulf, it’d be someone else.

A little later, I found an article about boycotting BP that looks at the issue of boycotting BP.

My less than calm take on this is that listening to people hoping that BP goes bankrupt is like listening to addicts who want to find a better class of dope peddler.

“Ogle me, ogle me!” orders the opistobranch

The problem with writing about sea slug colouration is that they are so spectacular, so lovely, that you are tempted to turn the whole post into a photo gallery just to show off the pictures.

The bright colours are not there for just the benefit of lucky SCUBA divers. As I’ve noted before, sea slugs mollusks are perhaps the most appealing targets imaginable for a predator. When your entire body plan is essentially a predator’s “meals on wheels,” you might think the last thing you would want to do would be to draw attention to yourself.

Except that seas slugs are not as helpless as they might seem. They use chemicals extracted from the food they eat to make fairly nasty new chemicals. Predators do not like ingesting these chemicals, and some may well be toxic enough that if you ate one of these slugs, the predator might die.

Of course, making a predator sick after you’re in said predator’s digestive gland doesn’t do the slug any good, either. And that’s the problem with deterrents: they only work when everyone knows about them. (Corollary: If you ever develop a doomsday device, don’t keep it a secret.)

The theory that these bright colours are honest signals is more often intuited that tested. Just because SCUBA divers find sea slugs easy to see doesn’t mean that other animals do. Every animal has different sensory abilities, a different umwelt than humans. For instance, some fish see ultraviolet; many crustaceans are insensitive to red. And just because they seem very bright in an aquarium doesn’t mean they’ll stand out in the wild, where shades of the rainbow drop out the deeper you go.

You also have to reckon that at some point, there is going to be a point of diminishing returns. Even if you have a deterrent, there’s a point where you will draw so much attention to yourself that predators will attack either because they’re naive or starving or in error. (Corollary: Don’t go around being an ass even if you know kung fu, because sooner or later someone will wail on you anyway for being a jerk.)

Cortesi and Cheney keep quite a few of these balls in their air in this paper to figure out if, in fact, sea slugs’s bright colours are warning signs as predicted. They collected twenty sea slug species from their natural habitats, and took high quality images, including the ultraviolet, of both the slug and the environment it was found in.

To test whether this combination of colours of the slug on the background were conspicuous to fish, they used models of the kinds of colours that a couple of different fish species can see. The triggerfish (here) sees in the blue-green range; another species tested sees up into the ultraviolet. The authors admit that these species were chosen because we know about their visual systems, not because we know for certain that they eat all twenty of these sea slug species. Somewhere down the road, it would be nice if someone did behavioural tests with known sea slug predators.

The theory is that the most conspicuous sea slugs should be the ones that are the most toxic. To test toxicity, the authors ground up slugs, and put the extract in with brine shrimp eggs. Brine shrimp are pretty tough little creatures, but development is fairly fussy, and shrimp will be killed off by sea slug chemicals.

One of the most toxic is Sagaminopteron ornatum, shown here. Hypselodoris obscura, below that, is near the bottom of the toxicity list; the very bottom one I couldn't find a picture of searching the photo database as I usually do. I guess it’s just that plain-looking that nobody can be bothered to take a picture of it.

There is a correlation between conspicuousness and toxicity, regardless of what fish visual system they used to model this. There is a lot of variation, though, with the correlation explaining only about 7-12% of the variance.

The authors talk about several explanations to the rest of the variance. They talk about sexual selection, developmental variation, and the necessary simplification of the rampantly wild colour patterns into a more tractable measure of contrast. They also point out that while they measured toxicity, toxicity may not be as relevant a measure as palatability. There are plenty of foods that wouldn’t kill me or even make me sick, but I sure wouldn’t choose to eat voluntarily.

One of the other factors that they don’t raise is that there may be mimicry going on. Typically mimicry is considered to be between a pair of, or small number of species. But maybe there’s an element of bluffing that could be effective.

The authors also don’t discuss the possibility of individual variation. The methods are a bit vague on just how many individuals they used to test the toxicity. Considering that the chemical defenses are diet based, it’s entirely possible that toxicity fluctuates not only between individuals, but within an individual over time, as well.

Additional: Forgotten I’d bookmarked this lovely gallery from National Geographic. Like I said, you can’t help but end up making a slideshow.

Reference

Cortesi, F., & Cheney, K. (2010). Conspicuousness is correlated with toxicity in marine opisthobranchs Journal of Evolutionary Biology DOI: 10.1111/j.1420-9101.2010.02018.x

Picture credits

Chromodora splendida picture by taso.viglas on Flickr.

Chelidonura varians by Allerina & Glen MacLarty on Flickr.

Rhinecanthus aculeatus picture by zsispeo on Flickr.

Sagaminopteron ornatum by saspotato on Flickr.

Hypselodoris obscura by doug.deep on Flickr.

All photos used under a Creative Commons license.

Video link I want to embed, but can't.

But I’m hungry!

Seen in the building this weekend:

Even if you did happen to crave jalapeno flavoured Cheetos, a closer look reveals you’re still screwed:

I pity the person who was trying to get the last thing in the machine. That must have been frustrating. So much for “lucky last.”

There’s a fail in here somewhere, but I just can’t figure out what it is.

Why science writing differs from every other form of writing

A bane of many professional writers is people asking, “Will you read my...?”

If the pro has one whit, one iota, one remaining pair of neurons to fire together, the answer will be no.

And probably not a polite “No,” either.

Robert J. Sawyer is one of the more polite authors on this score. But most of the time, the response is much more likely to be something like Josh Olson’s essay, “I will not read your fucking script.” David Gerrold’s response may not be blunt as Olson’s but  is much more... thorough:

The only proper response when an amateur attempts to hand you his manuscript... is to take an axe to his laptop, follow him home, burn down his house, and salt the ground.

But even more fun is Harlan Ellison reading a poem about why he will not read your fucking script. (In fact, this post is an elaborate contrivance to link to Ellison reading this poem.)

Scientists get far fewer amateurs asking them read things; I suppose that occasionally mathematicians have to put up with people claiming to be able to trisect an angle (i.e., cranks). But scientists are not only asked to read their colleagues’ work (sometimes by strangers), but they tend not to pull out the torches and pitchforks when they are asked. I'm not just talking about peer review; I'm talking about pre-submission work. I think the difference is that scientists are not paid directly for their writing, but only indirectly through "prestige," which may later generate grants and such.

Mimics without models: Allopatric Batesians

I was imitating Jean Chrétien a while ago to tell an anecdote to one of my students.

I could have done the greatest, most perfect, most spot-on, hysterical impersonation of Chrétien ever.^* It all would have been lost on this student. An American undergraduate would be unlikely to recognize a Canadian prime minister, no matter how distinctive his speaking style was. (And it was. Oh, how it was.)

That’s the problem with imitation: it only works if both parties recognize what’s being imitated.

There’s imitation in the natural world, too, although it’s better known as mimicry. Almost everyone knows the example of the viceroy butterfly: tastes fine, but looks like the monarch butterfly, which tastes awful, so birds leave both alone because they can’t tell them apart. Thus, the viceroy gains an advantage. This is Batesian mimicry, named after Henry Bates. (Sean Carroll has a great bio of Bates in his book Into the Jungle.)

What if the viceroy butterfly and the monarch butterfly never met? Imagine that there was no overlap in their distributions at all? Now that would be a puzzle.

Those two butterflies do overlap, but a new review paper by Pfennig and Mullen argues that there are many cases where a mimic species occurs where the species its imitating does not. There are no cases where the mimic is completely isolated from the species it is mimicking, but the range of the mimic is often much greater than those of of the species being mimicked.

Pfennig and Mullen give examples of mimicking snakes that occur hundreds of kilometers away from the range of the model species. For the most part, there are only able to give crude estimates of how often the mimic is found without the model: basically, at this point, we’re unable to say little more than, “It happens.”

The paper lists several ways that we might be able to explain these distributions.

The first possibility is that mimicry really isn’t Batesian mimicry. For example, a species thought to be harmless might turn out not to be harmless (Müllerian mimicry). Alternately, both species have hit upon some sort of signal independently that predators avoid (convergent evolution).

Second, distributions of species are very dynamic. Just because the two species don’t overlap in some location now doesn’t mean that they have never done so. I like this idea, because it reminds us that things have a history.

Third, they discuss the possibility of hybridization leading to expansion for genes related to mimicry into new populations. Hybridization seems to occur quite a bit in butterflies, which are important models for mimcry, but this may not happen much in other species.

Fourth, the authors note that if a mimic is rare in arts of its ranges away from the model, it may not incur much of a cost, because many predators avoid feeding on unfamiliar foods. If anything, this paper underestimate the role that the predators could play in establishing the mimicking situation. If a long-lived, fairly smart predator feeds on the distasteful model at site A, it may remember that even if it encounters the mimic at site B very much later.

This review paper is a nice example of a review that tries to push the state of the art forward, and not just summarize.

Reference

Pfennig, D., & Mullen, S. (2010). Mimics without models: causes and consequences of allopatry in Batesian mimicry complexes Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2010.0586

Photo by ~K~ on Flickr, used under a Creative Commons license.

^* It wasn’t, but it could have been. Work with me here.

Balkanizing small universities

Our university had a 5% budget cut, an now is facing a 10% budget cut on top of that. Our situation is the new normal, according to a news piece in Nature that looks at the effects the financial crisis is having on universities. Also worth reading is an article on the financial benefits of investing in research (harder to prove than you might think).

One section, though, bugs me.

Diane Auer Jones... thinks budget pain should make smaller state schools rethink their research ambitions... (A)dministrators have been spending too much on programmes besides undergraduate education. Faculty members are rewarded on the basis of their research portfolios, and teaching gets mere lip service.

Not surprisingly, I disagree strongly with Jones (who also has an opinion piece in the issue).

First, if undergrad institutions are putting “too much” emphasis on research at the expense of teaching, what does that say about the heavily research intensive universities? They have far more notorious reputations for ignoring everything but research on tenure decisions.

Second, this advice reeks of something that “have” research universities would say. They would probably love to have less competition for money and resources.

I don’t believe for an instant that telling faculty that they should abandon their research and balkanizing undergraduate universities the way forward.

I believe it’s called “consumer resistance”

OoooOOOOOoooh, now this is going to be interesting.

Nature Publishing Group, which publishes one of the two “flagship” journals for science, Nature, announced that it was going to quadruple subscription prices for the University of California system.

The University of California system, which is massive by any account, has basically said, “Negotiate, or we’re out.”

Let’s see who blinks first.

Additional: Nature Publishing Group isn’t blinking yet, according to this entry.

Academic titles as lubrication

I hate formality.

It’s one of the many deep flaws in my character. This may seem strange for someone who actively puts his title in the name of his main website and uses it as part of his Twitter name, but I realize that many people like formalities much more than I do. Robert Heinlein, so often good for a quote, wrote:

Moving parts in rubbing contact require lubrication to avoid excessive wear. Honorifics and formal politeness provide lubrication where people rub together. Often the very young, the untraveled, the naive, the unsophisticated deplore these formalities as “empty,” “meaningless,” or “dishonest,” and scorn to use them. No matter how “pure” their motives, they thereby throw sand into machinery that does not work too well at best.

A little note on academic formalities, then, for students, particularly those applying to a program or a grad school.

If you don’t know if a person should be addressed as “Doctor” or not, you haven’t done your homework.

It used to be easy to claim ignorance of someone’s academic credentials, but now, it’s hard to do so. You can usually uncover people’s academic credentials with a little Google stalking, particularly for people running programs.

Not everyone insists on being addressed by their title. I don’t (see above). But still, correct use of titles can be a signpost for several things.

One of my colleagues, who had a doctorate, told me that students – almost invariably male students – would refer to her as “Miss” or “Ma’am,” but would then turn around and refer to a male instructor as, “Doctor.” Even after this was pointed out to them. These were cases of macho bullshit, as far as we could tell.

And another thing, students: Never use “Dear Sir or Madame” in your email to your potential supervisor. If you can’t even figure out whether I’m a man or a woman, I sure as hell don’t want you in my lab.

As a gleeful thrower of sand, I never insist on formality. As a scientist, though, I almost always insist on accuracy.

Photo by russelljsmith on Flickr, used under a Creative Commons license.

Tuesday Crustie: Beach circles

Imagine walking along a beach, and coming across something like this:

Beautiful little designs, radiating outward. A closer inspection reveals them to be tiny balls of compressed sand, with a small hole at the center.

This is something I have never had the good fortune of seeing on the beaches I’ve worked on. But now, if I was lucky enough to find this, I’d hazard a guess that it was the work on one of several species of crabs called sand bubbler crabs.

This sand bubbler crab was identified by the photographer as Dotilla fenestrata.

Beach picture by Edi Weissmann on Flickr; bubbles picture by Stewf on Flickr; Dotilla picture by Moon Fish on Flickr; all are used under a Creative Commons license.

Carnivals for June, 2010

Circus of the Spineless #51, the circus for all things invertebrate, is up at Deep Sea News.

Carnival of the Blue #37, for all things salty and aquatic, is hosted by blogfish this month.

Normally, I’d also be plugging the Carnival of Evolution, but I kind of already did by hosting it.

Paper trail, or: Did they say that? Peer-reviewed journal edition

Everybody makes mistakes. But the peer-reviewed scientific literature tries to reduce mistakes by having fairly rigorous rules for citation. Citing original sources increases transparency and greatly facilitates fact-checking.

For instance, in one of our recent papers, we pointed out that a reference given in another paper did not support the point being made (as far as we could tell). Probably most practicing scientists have a story like that. But how common is that sort of error?

A new paper by Todd and company claims that the error rate for peer-reviewed scientific journals in marine biology is about one in four.

That’s a bit of a surprise.

To come up with this number, they looked at one reference given in support of a claim from three articles of two issues of 33 journals (198 references total – pity they couldn’t have found a way to squeeze in two more to make it an even number). The authors say the reference was selected at random, but they didn’t really, because they only picked assertions that were supported by one reference, so a bit of selection is going on.

Although the title of the article claims one quarter of citations is “inappropriate,” the picture is not as bleak as the title suggests. In fact, only 6% of references did not support the claim being made; a figure closer to one in twenty than one in four.

The “one in four” comes from their claim that 75% of reference support the claim in the paper making them. The remaining 25% that they deem “inappropriate,” however, fall into several categories, and not all of those categories are equally problematic.

About 10% of citations are ambiguous, although the Todd and colleagues say they tended to give benefit of the doubt to those doing the citing. Annoying, but perhaps not damaging to the scientific literature.

The remainder of citations (7.6%) they deem “inappropriate” are cases where the claim is not supported by original data in the paper being cited, but in another paper that the cited paper itself cites. These are almost certainly people citing review articles. Todd and company argue that this is “inappropriate,” but this is surely debatable. Off the top of my head, here are some positive reasons to cite reviews:

• Review articles often more cohesive than original articles
• Easier to read text with a single citation than a long list of citations
• Saves space
• Can save time and effort for readers to track down only one article instead of a long series

Todd and company did look at impact factor of the journal the original paper doing the citing appeared in, with the unstated hypothesis being that “good” journals (i.e., higher impact factors) would have fewer inappropriate citations than “bad” journals. No relationship, which I think goes to show reviewers, and the review process, is a pretty homogeneous lot. (Every journal has a reviewer 2 who hates the paper.)

When initial discussion of this broke out on Twitter, Carin Bondar’s initial response was, “Impact factor is screwed!” I don’t think so. Impact factor would screwed only if there was some sort of systematic bias in which journals are being inappropriately cited. As far as I can tell, everything in this paper seems to suggest the errors are occurring at random. (Impact factors can be abused, but they provide a rough measure for authors to figure out if a journal has any credibility, which is a major problem in this day of experimentation in scientific publishing.)

Journal editors and reviewers should be the gatekeepers here. Reviewers should have some understanding of the relevant literature for the paper they are reviewing. But there are too few people to review too many papers, and it may be unreasonable for reviewers to do more than just a spot check. Maybe journals, particularly those of published by some of the extremely profitable academic publishers, could hire professional fact checkers. That a journal that had full-time fact checkers could easily be a selling point as a good impact factor.

That this article shows how easy it is to go and fact check these things shows, more than anything else, that the citation system works. We just don’t take enough advantage of the opportunities.

Reference

Todd P, Guest J, Lu J, & Chou L. 2010. One in four citations in marine biology papers is inappropriate. Marine Ecology Progress Series 408: 299-303. DOI: 10.3354/meps08587

Photo by gadl on Flickr, used under a Creative Commons license.

Why is this taking so long?

Are American scientists twice as good as British scientists?

Because the Americans are spending about twice as long working on the doctorates then the Brits are.

DrugMoney said the length of a doctorate has fluctuated from five and a half to seven years. I asked if this was U.S. data, but haven’t seen an answer yet. Those kind of numbers are also typical of Canada, too.

But the typical length of a doctorate in the U.K. is about three years. That kind of length is typical for Australia, too.

DrugMonkey also said:

I'm willing to accept that 4 years may be too short of an interval(...)

I’m not willing to accept that. Because I don’t automatically think my colleagues who got degrees in other countries with shorter doctorates are crummy half-rate scientists.

I didn’t exactly rush to finish my own degree (I was pretty happy as a graduate student, and I had a lot to learn), but I don’t think that the expectation that a degree should take that the better part of a decade is healthy. It reminds of the report I talked about before that talked about “maintaining incentives for entry into scientific careers as the training phase extends” rather than shortening the training phase.

The disconnect between policy and ground truth was represented in a recent presentation to some U.S. lawmakers. Not surprisingly, they didn’t know what things are like for incoming scientists:

The members of Congress seemed surprised and, according to Miller, “deeply concerned” and “disappointed” by this and other testimony – which indicates how effectively the viewpoints of the research universities and today's established scientists have dominated the discussion and how little attention tomorrow's scientists' concerns have received.

The lawmakers, two of them UC alumni, all expressed chagrin. Miller in particular seemed flummoxed by Tyler’s presentation. He mentioned briefly that what she revealed appeared to contradict the widely assumed scientist shortage. “It’s almost as if we’re toying with some of the brightest, most talented, and skilled people in our society,” he mused in dismay.

As far as I can tell, the length of expected training for scientists before they can start an independent research career – particularly post-docs – has very little to do with actual amount of training to be done, and a lot more with the strangled job market for researchers.

Photo by ATIS547 on Flickr, used under a Creative Commons license.

The all-seeing eye gazes upon the land of crickets

It’s good to be omniscient.

Only a few natural studies have been able to approach that level of all-knowing knowledge. Peter and Rosemary Grant come fairly close in some seasons studying finches on the smaller Galapagos Islands. A new paper must must surely be a contender for god-like knowledge of a population of animals.

Rodríguez-Muñoz and colleagues basically became all-seeing and all-knowing to figure out what evolutionary pressures were being brought to bear on a population of crickets (Gryllus campestris). In other words, who’s getting it on with whom? Who’s being eaten? Those sorts of things.

To do this, they pulled off a rather astonishing video recording set-up of over 60 infra-red cameras that allowed them to monitor between 150-200 crickets all the time.

Let me say that again.

Every. Single. Cricket.

All. The. Time.

And lest you think this is in a controlled lab setting? No! This is a field in Spain! And lest you think this is just a series of snapshots of the population? No! They tagged each individual so they were able to identify them by name! And lest you think was some a few days? No! This was over two summers! And, just to top put a cherry on top, they did DNA work to identify parents and offspring.

And some say they did it while keeping six plates on rods spinning simultaneously and telling jokes.

Once you’ve got thousands of hours of video of crickets... what do you want to know? Because you probably have a good shot at answering the question, almost regardless of what it is.

A classic prediction in evolution and ethology is that most females have some reproductive success, but males tend to vary wildly in their success, with some being “super winners” and some being “super losers” (It’s rather like research.)

They did indeed find this pattern, but a surprise was that the female success was not as uniform as expected: many females had no offspring. They also found that the females had more offspring when they mated with multiple males. This is an effect that has been suggested in other research, but the comprehensive nature of this study makes this one of the best examples for the phenomenon to date. Indeed, females tended to have as many mates as males.

Another surprise was that dominant males had fewer offspring than subordinate males. The authors don’t have a ready explanation for why this is, more or less shrugging and saying, “Dominance doesn’t always predict mating success.”

Are there similar surprises waiting in survivorship? The story doesn’t seem to be as well fleshed out as the mating story. For instance, there’s not a major breakdown of the causes of death; mostly it’s just lifespan information.

The main behaviour that appeared to be linked to lifespan was singing in the males. Longer-lived males had sung more over their lives. This suggests that the ability to sing a lot is a good indicator of general health. And, for short-lived males, this was also correlated with more offspring. Oddly, though, there was no correlation between the amount of singing and amount of offspring for long-lived males.

With so many surprises, I’m sure there will be other papers to emerge from this massive recording session. And it will be interesting to see if other researchers can apply this high level of surveillance to other species that are larger or more mobile.

Reference

Rodriguez-Munoz, R., Bretman, A., Slate, J., Walling, C., & Tregenza, T. (2010). Natural and sexual selection in a wild insect population Science 328(5983): 1269-1272. DOI: 10.1126/science.1188102

Third picture by Gilles San Martin on Flickr, used under a Creative Commons license.

To have and have not. Mostly not.

The Scientist has a must read article about the disparity in funding across institutions and states.

This article resonates with me, because I’m in a “have not” institution with ambition. While Texas as a state isn’t faring badly, Texas is a big state, and some regions, like southern Texas, don’t fare as well.

My mind boggled from this quote from Ian Blair, who runs a proteomics core facility at University of Pennsylvania:

“My view is that mass spectrometers are like handbags,” he says. “You can’t have too many.”

The article uses North Dakota and South Dakota as examples of “have not” states, and describes several things that people do to keep noticed:

Kevin Young, a UND professor, says he wears a North Dakota t-shirt when attending meetings, since people always remember the guy from North Dakota. “It’s like going to see a panda.”

Ultimately, however, if push ever comes to shove, you know what side you’re on in the race:

There’s no way the school can fairly compete with major players, (Van Doze) says. “They’ve got tanks for weaponry, and we’ve got BB guns.”

BB guns? Count yourself lucky, good sir! Or we shall come after you with our pointed sticks!

Judging brain scans

I knew the day would come, but wasn’t sure when.

Yesterday, a court ruled against using fMRI data as a lie detector as evidence in a criminal case (see also here).

Several other commentators elsewhere seem pleased with this ruling; I’m tempted to say overly so, at times.

A couple of things are worth noting.

First, fMRI was being used as a lie detector in this case. But fMRI’s potential scope reaches was beyond just lie detection. There are many reasons why information gleaned from a brain scan could be relevant in a court setting. For instance, check out this example of a mock court case where a brain scan is used, not to determine the truth of falsehood of specific statements, but to suggest something about a defendant’s ability to control and plan.

Second, the research on fMRI is ongoing, as are technical improvements. While this ruling says that fMRI as a lie detector is not admissible for now, I wonder when, if ever, people will have another go at getting it admitted.

3 Quarks Daily contest update

Voting has started for this contest. Lots of good reading there. Please vote as you will, but the important thing is to vote.

I self-nominated a post of my own. Not sure it’s necessarily my best, but it was one that I was kind of fond of.

Carnival of Evolution #24

Welcome to the June edition of...

Hm. You know, something’s not right here. That logo could use a little something... extra. (Click to enlarge.)

There. That’s better.

Scandalous

Probably the biggest story in evolution in May was the publication of the much ballyhooed Neanderthal genome. You know, the one where everyone overlooked the phenomenal technical achievement of getting a complete genome of an ancient species... and headed straight for the sleaze.

The question on every headline writer’s lips was, “Did humans have sex with Neanderthals?” If you think the answer is yes, you owe it to yourself to read “Nerdy” Christie Wilcox’s fine analysis of the question.

Speaking of scandals, a paper on oral sex in fruit bats was at the center of a personal dispute that got called, inevitably, fruitbatgate. Regardless of your opinions on that matter, the science is definitely worth looking at, which Jason does at The Thoughtful Animal. (And not in a pervy way.)

And we're still not done with scandals. A creationist claimed biologists “don’t have a clue” about the evolutionary origin of bone. This would be a scandal... if it were true. Which provides a nice segue into...

Connective

I am shocked, shocked, I say, to learn that – contrary to creationist claims – we have many interesting clues about the origin of bone in vertebrates. (Regular readers of this blog may have already seen this post.)

Bones aren’t the only way to hold an organism together. Kevin Zelnio looks at decidedly un-spongy sponges: the glass sponges, and how they evolved the ability to make their silica skeletons.

But if you go down to even finer levels of detail, you might want to know how cells keep connected to each other. Thoughtomics examines how a molecule that was thought to serve primarily to hold cells together has been discovered in a solitary cell.

Annoying

The Agricultural Biodiversity blog takes a look at the perpetual pest problem: They evolve to things we throw at them. This time, it’s a cotton pest.

And I rather suspect that many readers of this carnival will also found certain creationist arguments irritating (see above). Pleiotropy examines creationist claims made some organisms too incredible to have evolved.

(The brains are coming. Trust me.)

Artistic

Art can be evidence for evolution, particularly when it’s ancient Australian rock art. A piece of aboriginal art thought to be an emu might be something much more interesting. (And congrats to GrrlScientist for this piece being put up on Slashdot!)

Hill-Stead’s Nature Blog brings us reminds us of the (very loose) link between biology and destiny.

Biochemical Soul is back with a new depiction of the K-T extinction.  It looks like this:

Hm. You know, something’s not right here. That artwork could use a little something... extra. (Click to enlarge.)

There. That’s better.

Uncategorizable

Leave it to protists – and by extension, protist bloggers – to mess up any categorical system.

Skeptic Wonder tackles convergent evolution between big protists and tiny animals. Some good examples of how something that was once thought to have evolved one time was much more common.

And now, the moment you've all been waiting for:

Brainy

We are fortunate to have two posts on sign language this month, both inspired by a recent fMRI study examining brain activity for people who use sign language. 360 Skeptic starts the boll rolling,, and AK’s Rambling Thoughts picks it up and runs with it.

While on the topic of language, which is one of the most distinctive human skills, Jerry Coyne examines whether humans evolved to fill a particular cognitive niche.

Evolutionary changes in brains must often force evolutionary changes to occur in other structures, not the least of which for the vertebrates in the skull. The complex relationship between brains, faces, and skulls in primates is discussed over at A Primate of Modern Aspect.

The Thoughtful Animal asks, “Can observing animal behaviour tell us anything about brain evolution?” Make sure you haven’t reached your cuteness threshold for the day before you see the answer.

The Weird Things blog looks at the case for convergent evolution in brains and... computer chips?

And I’m going to pull rank as host, and end with a post of my own, completed just under the wire for today’s carnival: It’s a look at how genes that establish boundaries in developing embryos may be critical to explaining the brain diversity in cichlid fishes.

Denoument

Thanks for visiting the Carnival of Evolution! Next month, Culturing Science will be hosting the 25^th edition. Blog about something silver or something Canadian. Either will be considered appropriately thematic.

Submit your article to the next edition of Carnival of Evolution using the submission form. Past posts and future hosts can be found on the index page.

P.S. – And a great big boo to the three four five six seven eight nine ten eleven twelve thirteen fourteen fifteensixteen seventeen people who felt compelled to submit posts to the Carnival that had nothing to do with evolution. This is a carnival, not a spam channel. Idjits.

Picture credits

Glass sponge picture by smallislander on Flickr, used under a Creative Commons license.

Sign language picture by Elyse Patten on Flickr, used under a Creative Commons license.

Comments for second half of May 2010

Research Explainer picks up on the theme that scientists are bad communicators. The examples used, though, may not be indicative of just bad communication skills.

The Scholarly Kitchen looks at a now infamous slide from the military, and concludes it may not be as bad as the mockery would indicate.

BenchFly looks at how to work with undergraduate students. I say it’s the same as working with anyone.

drdrA at Blue Lab Coats asks what cranky reviewer phrases people have encountered.

The Prodigal Academic describes the process whereby 210 applications for tenure-track positions get cuts down to about five for on-site interviews. We do a step they don’t.

The Faculty of 1000 started up a new poster archive, and well, since I run a poster blog, I made a comment about the need to show off, not just the best science, but the best graphics.

Mental Floss reviews the question of crab pain, citing some research I’ve talked about here before, but discussing some more recent stuff (i.e., mine).

Not exactly comments, but I somehow got involved in a Twitter contretemps that became known as bacon blog wars. You may see my name kicked around in relation to that...

Tuesday Crustie: Insect cousin

Speleonectes tanumekes is a remipede. The remipedes are an interesting group of crustaceans for many reasons. They were, for many years, known only from fossils, but, like the coelocanth, were discovered years later alive and well. (Such species are sometimes called “Lazarus taxa” because they “rose from the dead.”) That they were not known to have survived before this could perhaps be excused, because they now only live in underwater caves.

They have started to attract much more attention recently with a paper on arthropod relationships, which suggests that remipedes are the closest living relatives to insects. You can read more about this here and here.

Remipedes also boast one of my favourite genus names in the animal kingdom: Godzillius. It was the name given to a remipede of “monstrous” size: a little over 40 millimetres.

Unfortunately, many of these remipede species are only known from a very restricted number of caves, making them very vulnerable.

Picture from here.

The painless thesis competition

Almost every grad student experiences a certain amount of pain in pulling together their thesis. But does it have to be that way? Boris Gorelik says no!

Boris writes the blog In the Haystack, and is holding a competition for the best tips to help make writing a thesis painless. Boris asked me to help judge the entries, and I’m pleased to do so.

The rules are easy. Post your advice for painless thesis writing on Twitter with the #painlessthesis tag.

You still have several days left to enter; competition closes at the end of the week (6 June 2010). You can read all about it here.

The winner will receive a copy of Presentation Zen Design; I’ve reviewed this book at the Better Posters blog; Boris reviews it here.

I think I got called on to judge this competition for three reasons. First, I’m our department’s grad program coordinator, so I’m always trying to help students with their theses. Second, the prize is Presentation Zen Design, and well, you know what my name is. Third, I recently co-authored a paper on crustaceans’ lack of nociception, so I guess that makes me an expert on painlessness.

Laying down boundaries for brain evolution in cichlids

Walter Garstang famously said that ontogeny creates phylogeny: you need to understand the development of a structure to understand the diversity of that structure across species.

There are a few different ways to change the way a structure is put together. Research on the development of limbs has tended to view morphological changes as being caused by changing boundaries that delineate different regions of the embryo. If you want a bigger forebrain, shift the boundary between the forebrain and the midbrain backward.

Neurobiologists, however, have sometimes suggested that brains differ due to the amount and duration of neurogenesis that goes on during development. If you want a bigger forebrain, make neurons for a longer time in the forebrain than in the midbrain.

A new paper by Sylvester and colleagues tries to look at the relative importance of these two developmental mechanisms in brain evolution. To do this, they looked at the brains of cichlid fishes. Cichlids are renowned among evolutionary biologists for their diversity and the speed at which it was achieved, and this diversity extends to their brain morphology. They chose six species to study; Cynotilapia afra and Copadichromis borleyi are shown here (click to enlarge). The former is a mbuna, a rock-dwelling fish, and the latter is a sand-dweller; the authors had three species of each.

The brains of the mbuna and non-mbuna differ in their proportions: the mbuna have smaller forebrains (strictly speaking, purists would say the telencephalon) than the non-mbuna.

Sylvester and colleagues visualized the cichlid brains using several that are well-known to be involved in development, like sonic hedgehog (shh), and Wnt and found that the pattern of expression of these did indeed differ in these species, typically following the mbuna / non-mbuna split.

To test whether these genes caused the differences in brain sizes, the authors exposed embryos of the mbuna species Labeotropheus fuelleborni (right) to lithium chloride, which affects the Wnt pathway. When they did this, they found that the L. fuelleborni brains were looking rather more like non-mbuna brains, which proportionately larger telencephalons.

Sylvester and company argue that this suggests the very early expression of genes that lay out patterns in the nervous system are key regulators of brain evolution. Considering that they sort of set up timing of neurogenesis as an alternate hypothesis in their introduction, however, it’s worth pointing out that they didn’t actually measure neurogenesis or try to manipulate it in a manner similar to what they did for these patterning genes and proteins. It’s possible that neurogenesis is playing a role in shaping diversity of brains in other ways than tested here.

Additional: The journal is publishing a commentary on this paper. While the original article is open access, the commentary, alas, is not.

Reference

Sylvester, J., Rich, C., Loh, Y., van Staaden, M., Fraser, G., & Streelman, J. (2010). Brain diversity evolves via differences in patterning Proceedings of the National Academy of Sciences 107(21): 9718-9723. DOI: 10.1073/pnas.1000395107

Photo of Cynotilapia afra by Calwhiz  on FLickr; photo of Labeotropheus fuelleborni by Lee Nachtigal on Flickr; photo of Copadichromis borleyi by Petrichor on Flickr. All used under a Creative Commons license.

Global warming, ocean acidification, and KO’d crayfish

What do global warming, ocean acidification, and KO’d crayfish have in common? Carbon dioxide.

A forthcoming paper by Biewbower and Cooper caught my eye because it incidentally supports a contention in the last paper I co-authored on crustacean nociception (Puri & Faulkes 2010). We couldn’t find any evidence that crustaceans responded to acids.

The new paper isn’t actually interested in acids; it’s all about what carbon dioxide does to crayfish. The first question is, can crayfish detect changes in carbon dioxide concentrations at all?

The authors ran crayfish through a Y-maze: one arm with high CO₂ concentrations, and one without. The higher the carbon dioxide concentrations, the more the crayfish tended to avoid that end of the maze, suggesting that yes, the crayfish can detect carbon dioxide in water. They also found that when placed in a pool containing high levels of carbon dioxide, crayfish would leave the water to cross in the air to a chamber with lower levels.

Another possible interpretation is that the crayfish aren’t detecting carbon dioxide in these experiments, but a lack of oxygen. It could also be low pH. When you ramp up the concentration of carbon dioxide in water, create carbonic acid. This is why burning fossil fuels is leading to ocean acidification. Crayfish could have avoided the end of the maze because they detected the low oxygen or low pH rather than the carbon dioxide specifically.

Consequently, they created two control conditions in addition to regular water. First, they created a low-oxygen water by bubbling nitrogen through it. Crayfish did not discriminate between the nitrogen laden water and the regular water. Second, they made one end of the Y maze with normal CO₂ concentrations, but acidic pH; about 4.85.

And the crayfish walked right into it.

No difference between the regular water and the acidic. So their study supports ours: decapod crustaceans seem to be mostly ignorant of changes in pH.

Another interpretation might be that the animals are responding to low oxygen; to control for that, the authors also had a control condition with very high nitrogen concentrations in the water, which lowered oxygen, and again, the crayfish didn’t distinguish between that and regular water.

Bierbower and Cooper also found that at high concentrations, carbon dioxide does a number on the crayfish, effectively putting them out of action stopping their heart and ventilation (“breathing,” more or less).

Why are crayfish repelled by high levels of carbon dioxide? Not clear. Bierbower and Cooper suggest that high levels of carbon dioxide might be a cue that an environment is toxic. That said, these are swamp crayfish (Procambarus clarkii), and they probably have a pretty high tolerance for low quality water. It would be interesting to see if crayfish that favour highly oxygenated streams might be more sensitive to carbon dioxide concentrations.

While very interesting to me because of its relevance to a story I’ve been working on (crustacean nociception), this paper might have limited interest to others. Both the introduction and discussion are very general, and don’t convey a strong sense of where this fits into a broader research picture.

References

Bierbower, S., & Cooper, R. (2010). The effects of acute carbon dioxide on behavior and physiology in Procambarus clarkii. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology DOI: 10.1002/jez.620

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

The unread masses of scientific literature

Canadian Girl Postdoc resumes her look at slow science. She asks:

Although I’ve heard the common refrain from faculty that some members of a search committee do look for quality, I wonder how many of them have actually read any of the papers from the job candidates. And if that assessment of quality is based on the journal’s impact factor or the faculty member's own assessment of the candidate's science?

Speaking just for me as a search committee member, I haven’t read papers by job applicants. First, it takes more time than I’m willing to give, and we tend not to have the problem of triple digit numbers of job applications.

Second, we are routinely hiring outside of areas that I am qualified to judge the technical proficiencies of the science. Heck, in many cases, we’re get applications from people whose science I almost literally do not understand at all.

I judge the research of job applicants largely by the number of publications, the titles of their articles, and their research statement, and yes, there’s a tiny little bit of journal “quality.” Taken together, those provide an overview of the kind of research someone is doing, and the questions they are asking.

Journal “quality” based on a very general perception. I don’t look up impact factors. More often, there’s someone on the search committee who knows about the journals people have published in, and weighs in with, “That’s a good, solid, international journal,” or, “Not so good.” Journal titles can reveal a lot about their scope, so you probably don’t want to publish in the Chinese Journal of Irreproducible Crap.

What about the whispers that a job applicant must have a “SNC” (Science, Nature, Cell) paper to be competitive? Obviously, a Science or Nature paper is a nearly universally known entity, so it helps, but it has never been a determining factor in our searches, or even a large factor. A consistent record in strong disciplinary journals has worked for us.

But you know what’s worse than me not reading the papers of our tenure track job candidates?

I rarely even read the papers of my own friends.

I know about the science of people in my department, or the ones I hang out with at conferences from talking to them in the hallways, not from reading their papers front to back.

I don’t read them for a lot of the same reasons I don’t read papers from job candidates: takes a lot of time, their research is far afield from mine, and I have other ways of learning what they’re doing.

I suppose the thing that makes it okay is that I know that they don’t read mine, either.

Save the Stazione Zoologica Anton Dohrn

I received the following email from Roberto Di Lauro, president of Stazione Zoologica Anton Dohrn.

The Stazione Zoologica Anton Dohrn of Naples is at risk of being closed by the Italian Government.

If you agree in signing the petition reported below, please go to http://www.szn.it click on "sign the petition" and fill in the form.

We learned that the Stazione Zoologica Anton Dohrn di Napoli will be suppressed according to the Decree-Law adopting urgent measures on financial stabilization and economic competitiveness, that the Italian Government is in the process of final approval.

The Stazione Zoologica, founded 130 years ago by Anton Dohrn, is among the most prestigious Italian Research Institutes. It acts in the field of marine biological research and is known for the multidisciplinary nature of its activities and for the excellent scientific output.

Current research activities, international and national collaborations, exchanges with scientists of different nationalities, and participation in numerous scientific projects in Europe and worldwide are a clear sign of the nature of the Stazione as an international research institution.

The Stazione Zoologica coordinates the project EMBRC, the only European infrastructure in the biomedical sciences coordinated by an Italian Institution and involving 14 institutions from seven European countries. The EMBRC project is a clear testimony of how the international spirit of the Institute is still alive and present.

Active participation of distinguished scientists, including three Nobel Laureates, as members of the Scientific Council of the Stazione is another demonstration of the relevance of the Institution among the international scientific community.

We manifest our serious concern for the suppression of the Stazione Zoologica, which would greatly reduce the impact of the Italian presence in the international scientific community.

We therefore ask that the Stazione is maintained as an autonomous structure. It is the autonomy, uniqueness, diversity and freedom of research that allowed the Stazione Zoologica to reach its present level of excellence in science and will continue to be among the flagships of the Italian research in the world.

Data underload: Correlation of mood and precipitation, according to Garbage

For those who don’t get the reference...