Fun while it lasted

My many months of enjoying a Top 10 listing in Brain, Behavior and Evolution for my last review article have abruptly come to a close this month. My review article is nowhere to be seen...

I do think that the creation of a new section – Highlights and Perspectives on Evolutionary Neuroscience &ndash that is not paywall protected may have had something to do with the sudden reorganization of the top 10 this month from the previous months. The free stuff will undoubtedly dominate the top 10.

Doing ethics like science?

Earlier this year, Sam Harris gave a talk at TED, which was just released, and given the title of “Science can answer moral questions.”



Having watched it, and read its follow-up, I have to say I’m a bit puzzled. I don’t see anything controversial or novel here. And I think the title is wrong.

Harris writes:

(I)t is taboo for a scientist to think such things, much less say them public.

I have good news for you, Sam: nobody thinks of you as a scientist.

Everyone thinks of you as a writer. I know you do neuroscience, which is ostensibly my field, but I don’t know what kind of research you do. I had to look, and I had to look pretty hard. You have a grand total of two peer-reviewed publications containing original data listed on your website (here’s one, and here’s the other). Sorry, but your list indicates that even you don’t think of yourself as a practicing scientist.

On to his points, and why I see them as trivial.

First, Harris attacks ethical relativism, and makes a big deal of his proposition that there are definite answers to moral questions. I have never met a philosopher or ethicist that seriously proposes or defends any form of ethical relativism. Harris claims to have met them, and I am sure that they exist. But the point is, this is not contentious or particularly insightful on Harris’s part.

Second, Harris says that point of ethics is to promote human flourishing. This sounds one heck of a lot like utilitarianism. Utilitarianism is a well-described and argued moral theory. Again, nothing controversial or new.

Third, I don’t see how Harris thinks science can answer moral questions, in this sense. Practicing scientists are always harping on about how science is a process. But Harris is, as far as I can see, mum on what processes we could use to answer moral questions.

Should we do double blind, ramdomized control experiments? Do we demand one group take a particular course of action, demand the other group not take this action, and measure them again at some point to see which group has undergone more flourishing? Because that’s empiricism, and that’s the way we do science. Maybe this is a good way to go (though I have doubts). But Harris doesn’t say.

If you want to say “science can do this,” you have to outline a research program. Harris doesn’t.

Tuesday Crustie: Scrawny

An arrow crab, Stenorhynchus seticornis. One of the most uneven ratios of exoskeleton to everything else you’re likely to find in the crustacean world.

Photo by baltus15 on Flickr. Used under a Creative Commons license.

Is Texas’s textbook buying power all that and a bag of chips?

The Texas Tribune reports that the much ballyhooed Texan influence on K-12 textbooks may be exaggerated.

(S)ince the mid-1990s and the rise of the state curriculum standards and testing movement, publishers have increasingly been forced to customize their books for different states, as well as for larger school districts in the roughly 30 states without statewide adoptions. Simultaneously, advances in publishing and printing technologies allow far more customization at lower cost, much like large newspapers that issue several geographically customized editions every day.

What’s more, rapidly shifting politics and the digital revolution in instructional materials promises to dilute the power of state school boards even further — both here in Texas and nationally.

On this point, a blog in Newsweek reaches a somewhat similar conclusion, and concludes with this cynical observation:

Besides, it's not like high-schoolers pay any attention to their textbooks anyway.

Open Lab 2010 ready for your choices

The Open Lab 2010 submission form is now live! Get cracking, people, you’ve already had almost a third of the year go by! There should be a couple of hundred prospective posts up there now!

Hat tip to Nerdy Christie and Greg Laden’s blog.

Desperado crickets

In Texas field crickets (Gryllus texensis), males come in two types: a flying long-winged form, and a non-flying short-winged form. These crickets’ forms are correlated with their interests in reproduction: short-wingers court females much more than fliers do. In this new paper, Guerra and Pollack predict the different interest of males in reproduction would be reflected in their willingness, and ability, to fight with other males.

Doesn’t that sound like a simple thing to test? You might think all you gotta get some crickets, put them together, watch them fight, and you’re ready to write up the paper! Not so fast, speedy. Watch the factors pile up, and you’ll get a sense of how performing a behavioural test of even a simple hypothesis can be trickier than you think.

Unfortunately, what appears to be a simple test is complicated by the flying males losing their ability to fly. So instead of a simple face-off between the mobile “colonists” and the flightless “desperados,” you have a more complex set of nine match-ups: each morph against the other two, and a control set of fights against the same morph.

There’s also the chance that the act of flight itself would affect the males’ aggression, because that had been shown to influence courtship.

To make things even more complicated, tn most studies of animal aggression, the number one factor in determining who wins and loses is not morph, but size. So the authors also have to track body size and account for it.

Ooooh, and hormones affect aggression, so testes size better be a variable to consider, too.

The results are tricky to summarize, since not only are there a lot of different match-ups, but fights are measured in different ways: Who starts the fight? Who wins the fight? How intense was the fight?

The trends, however, were that the short-winged males tended to be the most aggressive ones in terms of the initiation of aggression and the level of aggression, as predicted.

As to the question they might ask in the movies, “Are you going to bet on the man with the big muscles or the man with the big cajones?” I’m not sure about men, but in crickets, it was the case that both mattered. Indeed, those factors mattered more than the type of wings and flight capability the animals had.

Flying changed aggression levels of the long-winged males, but, surprisingly, not the probability of winning. This paper suggests that fighting can affect mating success, although there are no direct tests in this paper. There’s still a lot to work out in this system, not least of which is how all these variations are going to result in greater or lesser reproductive success. Is this a stable system? Or ar their conditions under which the colonists might out compete the desperadoes, and vice versa?

Reference

Guerra, P., & Pollack, G. (2010). Colonists and desperadoes: different fighting strategies in wing-dimorphic male Texas field crickets Animal Behaviour DOI: 10.1016/j.anbehav.2010.02.002

No hurry

Because some days, you’re just all blogged out.

Publishers and citation managers

I use a citation manager. Currently, it’s EndNote X3. I ♥ EndNote, and have told more than one person it was one of the best purchases I’ve ever made as a career scientist. And nobody paid me to say that, incidentally. (Other reference managers are available. Please sing their praises, but don’t be disappointed if I don’t convert.)

But I’ve noticed something weird. Most journals have a “download to citation manager” or “export citation” option for their articles, and most will specifically give you the option of downloading to EndNote.

Almost none of them gets the friggin’ digital object identifier (DOI) right.

I love DOIs. I love the idea of each scientific article having a uniform and permanent ID number, so that I don't have to constantly update my links or go trolling through Google Scholar when publishers rearrange their websites.

ScienceDirect journals put the doi in the “Type of article” field instead of EndNote’s “DOI” field. And they put, “doi: DOI:” before the actual DOI number.

Nature Publishing Group journals put the DOI under "Type of article", and put the link to supplemental information in EndNote’s DOI field .

Wiley Interscience journals stick the DOI under the “legal note” field.

What about that bastion of new ways of publishing and article level metrics including citation downloads, the Public Library of Science? PLoS journals don’t export a DOI into any field in EndNote, making me have to go cut and paste from the webpage.

Highwire Press seems to be the only one who gets it right. So there – it is possible!

Next time: And what about those keywords...?

Research with undergrads

Last week, I was at an undergrad research meeting in Washington, D.C. On the whole, the trip was not highly useful, but I did get a lovely view from my balcony:

It was depressing to hear multiple people say that a lot of undergrad research mentors don’t benefit from working with undergraduates. They see it as a duty that they do somewhat reluctantly. Sort of like cleaning the toilets after a party. The mentors don’t even work directly with the students in some cases, leaving it to grad students and post-docs. I wonder how many students apply to a program and think they’re going to work with a faculty member, only to discover you’re going to get very little face time with the “listed” mentor.

Interestingly, most of the grants go to research intensive universities. A discussion about publishing with undergraduates, though, indicated that the ones at the mainly undergraduate institutions might have better success in publishing papers.

There was no discussion about long term career prospects; i.e., whether all these undergraduate researchers are going to be able to have career prospects at the end of this. To some degree, some people addressed this by asking, “If a student goes on to become a science teacher, is that as much a success as a student who goes into a Ph.D. Program?”

While at the meeting, someone asked if there was any drug violence around the region. I said I wasn’t aware of any, but little did I know that waiting on my iPod was a story from The Current about violence in Reynosa, which is right across the border from us.

I did have some time after the meeting to walk around the mall. I stuck to the outside exhibits rather than going into the Smithsonian museums, several of which had long lines and wanted me to check my bag. I did see the signs for a new hall on human origins in the Natural History Museum (right). As I was walking past, I saw one man point at the banners and say to his friend, “That’s where they try to tell you we came from monkeys,” and laugh. (More commentary on the exhibit by Jerry Coyne.)

Going through security was much less annoying than I expected. I got some useful data mining done on the flight between Memphis and McAllen, so I’m glad I brought my netbook after all.

Unfortunately, I seem to have walked past someone who had a virus either in DC or in an airport. I’ve been feeling a little woozy since getting back.

Tuesday Crustie: Racing stripes

Not identified on the webpage, but based on some similar looking pictures, I think it’s Lysmata amboinensis. Lovely whatever its species!

Photo by David Panevin from Flickr, used under a Creative Commons license.

Research Blogging winners...

...are listed here. Congrats to Scicurious at Neurotopia blog for kicking my butt in the best neuroscience blog category!

Beware, predator, I have ink!

If you were a predator trying to design the perfect food source, you’d probably want something that was slow moving, reasonably large, and had no annoying hard bits that you couldn’t really eat. In other words, it would probably looks something like an opisthobranch mollusk. Opisthobranch are also known as sea slugs or sea hares, and at first glance, they look like snack packs for predators.

Of course, opisthobranchs don’t take this lightly. Rather than physical defenses, they put up chemical ones. Besides any chemicals that they keep inside, many sea hares release chemicals, too. Sea hares have two chemicals they will squirt out in the presence of a predator: ink and opaline.

To test for how these two different chemicals affect predators, Nunsbaum and Derby looked at the inking behaviour of the California sea hare (Aplysia californica – a species well-known to neurobiologists for the many studies on memory that have been conducted on it; pictured above). They used blueheaded wrasse (Thalassoma bifasciatum; pictured right) as a predator.

The sea hare is a Pacific species (hence the species name “californica,” as in California) and the wrasse is an Atlantic species, so the authors obviously can’t mimic ecological interactions with 100% realism. The choice of species is almost certainly one of convenience, but you might expect that these chemicals and such are general enough that the exact species wouldn’t matter. That said, it does open up some possibilities to check whether there might be “arms races” where species in the same region have different inks or behavioural responses to animals they live with versus animals they don't.

To test the effect of the ink or opaline alone, without the actual sea hare in the tank to possibly confound things, Nunsbaum and Derby made “shrimp cubes” as a food item for the fish. They released them simultaneously with ink between the food and the fish. Ink made the fish less likely to get the food, but opaline didn’t, indicating that the ink is acting as a deterrent, partly visual.

Previous work had suggested that ink / opaline was a distraction to a predator, which would mistake it for food. They found that fish wouldn't eat alginate cubes, cubes with ink, cubes with opaline, but would eat pellets that had the amino acid components contained within ink and opaline.

What about when the ink and opaline are presented with actual food? Put any ink in it, and the fish wouldn’t eat it. Literally none. Zero. Put opaline alone in it, and the fish will eat it. All of them. 100%. This experiment (plotted right) is significant by IOT^*. The more complex stats just seem like going through the motions...

When ink was around, fish took longer to get to food; this got shorter if the nose was blocked. This indicates that ink has some sort of olfactory blocking in addition to being a visual distraction.

Opaline appears to have no effect on fish at all. Curious. But this paper doesn’t speculate on what its job might be. A likely story is that opaline is a deterrent to non-fish predators, but the sea hares either can’t or don’t distinguish between predators bothering them enough to cause ink and opaline release.

^* IOT = inter-ocular test. It’s something so obvious, it hits you right between the eyes.

Reference

Nusnbaum, M., & Derby, C. (2010). Ink secretion protects sea hares by acting on the olfactory and nonolfactory chemical senses of a predatory fish Animal Behaviour DOI: 10.1016/j.anbehav.2010.01.022

Wrasse picture by algaedoc on Flickr. Slug picture by user wanderinggnome on Flickr. Both are used under a Creative Commons license.

Are big brains better for long trips?

For many birds, migration is a major component of life. You'd expect think that migration would have a whole cascade of effects on those birds, including the nervous system. But which way?

On the one hand, migration might be correlated with large brains to handle the the complex navigation tasks. On the other hand, migration might be correlated with small brains that are energetically efficient.

Sol and colleagues compared over six hundred species of birds (measuring over 4,000 skulls). Species ranged from non-migratory, to some members of a population where migratory, to some that were extensively migratory. They found, as had previous authors, that migratory birds tended to have smaller brains than non-migratory birds. Unsurprisingly, there is a substantial amount of variation from species to species. For instance, corvids (e.g., crows and allies) don't show this effect.

But what these authors are really trying to figure out is not the correlation, but the direction of causation. Do lineages become migratory because their small brains allow it, or does migration cause brains to become smaller, as neurons as jettisoned over evolutionary time for efficiency?

And here, there's a lot of math. It's not easy going for someone who doesn't do these kinds of models routinely, and I don't. Sol and colleagues argue that the models they tested indicate that migration causes brain size to reduce, rather than the other way around. Again, however, a good chunk of variation appears to be due to factors that were not included in the model. They also suggest that some brain areas may be more subject to selection pressures, and it's more complex than just the overall brain size alone.

When people think about the evolution of brains, the most common thing that leaps to mind is brains getting larger. Maybe that's just because that's such a major aspect of human evolution. This work is a nice example of selection pressure working to reduce brain size.

Reference

Sol, D., Garcia, N., Iwaniuk, A., Davis, K., Meade, A., Boyle, W., & Székely, T. (2010). Evolutionary Divergence in Brain Size between Migratory and Resident Birds PLoS ONE, 5 (3) DOI: 10.1371/journal.pone.0009617

Picture from user philip.bitnar on Flickr. Used under a Creative Commons license.

The scientific-industrial complex

At the [citation needed] blog, Tal Yarkoni wrote about a recent fMRI paper (mphasis added):

I really do think that the prevalence of long author lists in a discipline are an important sign of a discipline’s maturity, and that the fact that you can get several dozen contributors to a single paper means you’re seeing a level of collaboration across different labs that previously didn’t exist.

I’m increasingly understanding how mom and pop shops felt about Wal-Mart, and how local booksellers felt about Barnes & Noble.

“I’m going to get crushed.”

This has been on my mind for almost five years now, if not longer: the effect of automation and increasing efficiency in data collection. Indeed, this has been going on for a while in biology. For instance, the amount of attention paid to model organism is an early indicator of this, even when there were many labs working independently.

But the argument above is that ever increasing numbers of authors on scientific papers is good, and as far as I can see, the reasoning is that economies of scale start to kick in. The result? I expect that you will increasingly see the same kind of positive feedback loop that you see in business. Small, independent businesses mostly lose to large corporations.

Of course, it’s long been the case that certain labs and universities outcompete all others in the question for federal funding. But I supposed that when a lot of labs had personnel numbering in the single digits, it seemed like a more even match in resources. And somehow, I never thought of the emergence of huge, multi-author papers as a sign of “maturity” of a research field.

As more and more papers have 50 authors or more, will researchers with small labs that don’t generate terabytes of data will have to sell their land to the cattle barons (so to speak)? Close up shop and join the factory (to use another metaphor)?

I’m terribly worried that the kind of biology I love, like neuroethology, is irrelevant. (I’m not so worried about myself, since I’ve known my place in the research world for a good long while.)

And, on another note, the increasing prevalence of papers with 50 or more authors really points to the need for reform of authorial credit.

Related posts

Science is a doozy
Long live the scientific method

Tuesday Crustie: Glam

She’s arguably the hottest star in the music world right now, thanks to her amazing dance beats and wilder than life stage persona, and now, Lady Gaga brings crustaceans to the limelight...

Much cooler than the last crustacean-inspired headwear.

Spotted at The Daily Mail.

Why science loses in the short term (but usually wins in the long term)

Over the last few months, there has been much weeping and wailing and gnashing of teeth about strategy and tactics over how to communicate with non-scientists, and how to regain public trust over issues like climate change. A good example of this was a recent email exchange between Matt Nisbet and Randy Olson.

Nisbet:

When scientists... take action by responding with tit-for-tat attacks on climate skeptics, it... feeds a downward spiral of “war” and conflict rhetoric that appears as just more ideological rancor to the wider public.

Olson:

There comes a point where the public DOES want to see the science community stand up for themselves.

People arguing that scientists are losing to denialists in areas like climate science because they have taken a poor approach to communication are perhaps mischaracterizing the problem. The problem of what approach scientists use to communicate with non-scientists is a real problem, but it is minuscule in these cases.

Scientists have to, you know, do science in addition to communication with non-scientists. Denialists, as far as I can tell, can devote 100% of their time to communication.

If scientists want to win, we need to find a way to support a dedicated crew of people whose job is to do nothing else but do public relations. Why don’t national academies and organizations for the advancement of science have full-time, professional communicators?

The only organization that I can think of that is even close to the sort of “think tank” person who seems to be so routinely called for media interviews is the National Center for Science Education. They do a heroic job, but there’s only sixteen people listed on staff, including some whose job is in no way related to science.

Allocation of resources is a major problem, and time is a 100% non-renewable resource. People who can devote time to that will, in the short term, win.

The good news may be that because scientists are responsible for generating new knowledge, that can help in the long term. Ultimately, denialists cannot create anything new.

Image from here.

Comments for first half of March 2010

Canadian Girl Postdoc has a great post about how power relationships filter into conversations in the academic blogosphere.

Miriam at Deep Sea News talks about how fact-based science communication is failing. Facts are good; a plan is better.

FlowingData shows the “How genetics works” picture, which should be called, “How genetics was thought to work in the eighteenth century or so.”

Biochem Bell asks if a bird in the hand is worth two in the bush. Or something. Doctor Becca then takes this and runs with it some more. (Actually, they’re both concerned with high prestige journals.)

David Crotty at The Scholarly Kitchen examines a wonky paper on science blogging, and asks, “If you knew people read your blog, would you blog differently?” (I’m paraphrasing there...)

Jeff Jarvis at BuzzMachine asks, “In the Google age, what is the point of teaching memorization?” An excellent question, and one I also struggle with.

Sheril Kirshenbaum asks at The Intersection what readers want to know about energy. I’m perpetually confused by nuclear power generation and whether it’s worth it or not.

Armin Schneider, in a book review in PLoS Biology, says neuroscientists must not be interested in the history of their field, because the aren’t a lot of people in the history poster sessions. He neglects to mention that the history posters are displayed all week long, while regular posters are only up for four hours. Visits to the history posters are going to be more spread out.

Nancy Duarte wanted feedback on the cover for her next book. It’ll be called Resonate, and I guarantee you I’ll be buying it whichever cover ends up on it.

I’ve been trying to stay out of this

Yes, it’s about the Texas State Board of Education and the Texas K-12 education standards. Again. I’ve tried to limit my comments to stuff related to science, particularly biology, because that’s what I feel competent to make comments about.

As a faculty member at a university that has about 85% Hispanic students, however, I feel obligated to highlight this bit from a New York Times article yesterday. It concerns the ongoing review of the state’s social studies standards.

Efforts by Hispanic board members to include more Latino figures as role models for the state’s large Hispanic population were consistently defeated, prompting one member, Mary Helen Berlanga, to storm out of a meeting late Thursday night, saying, “They can just pretend this is a white America and Hispanics don’t exist.”

Ms. Berlanga is the representative for the area that includes my institution, by the way.

There’s much more of interest in the Times piece.

Lab equipment love #3

Last equipment post for a while, but by no means least. Finally, something a little bit more high tech than forceps and a microscope.

A 60 cycle noise eliminator, the HumBug.

To understand how marvelous this little box is, I have to explain a little about electrophysiology.

Everything you’re using to read this blog post runs off a powerline. So do lights and other electrical appliances. Those electric powerlines generate noise, or a “hum,” that cycles 60 times a second in North American, and 50 times a second in Australia and, I think, the U.K. This “60 cycle” is picked up by recording electrodes, like those used to record neural activity.

Since biologists are interested in the biology and not power mains, the 60 cycle just gets in the way of seeing the actual biological signal. So eletrophysiologists have to spend huge amounts of time trying to eliminate that 60 cycle noise by grounding, using Faraday cages, tinfoil, alligator clamps, and offerings to minor deities.

Worse, it’s incredibly unpredictable. A set-up that is perfect one day may have horrible 60 cycle the next day.

Thus, anything that helps combat 60 cycle is a beautiful thing. And that is what this clever little device does. I had no idea it existed until I went to the annual Neuroscience meeting the year I was hired, and discovering it alone made the trip worthwhile.

One degree of separation between fellow nerds

I had never met Carin Bondar until I followed her on Twitter. Only after that did I learn that we have several colleagues in common, so there is absolutely no “old boy’s club” networking behind her decision to put me in Nerd Corner this week.

Nerd Corner? It’s like a regular corner, only, you know, nerdier.

Actually, Carin thought I might be interesting enough to interview. I sure fooled her.

Carin has a great website, with lots of other interviews, career resources, and more. Tell her Zen sent ya!

P.S. – She’s not related to Canadian astronaut Roberta Bondar.