NeuroDojo

06 July 2010

In which ScienceBloggers suddenly realize they're supported by ads

ScienceBlogs, the portal published by Seed magazine, introduced a new blog today, called Food Frontiers. It's a blog by PepsiCo. Response has been swift and mostly negative. Let's see.

http://scienceblogs.com/ethicsandscience/2010/07/welcome_to_inescapable_conflic.php
http://scienceblogs.com/whitecoatunderground/2010/07/rethinking_blog_networks_and_e.php
http://scienceblogs.com/grrlscientist/2010/07/sucking_corporate_dick.php
http://scienceblogs.com/goodmath/2010/07/seed_conflicts_of_interest_and.php
http://scienceblogs.com/myrmecos/2010/07/enjoy_a_nice_cold_pepsi_today.php
http://sciblogs.co.nz/code-for-life/2010/07/07/scienceblogs-adds-pepsico-sponsored-blog-sparks-debate/
http://twitter.com/search?q=%23scibloxymorons
http://twitter.com/search?q=%23scibloxymoron

I can probably go on, but be that as it may. What does Ambassador Kosh say about the situation?

You have always been here.

“You’re not Riptide the Barbarian... You’re Bob.”

The question of anonymity has been a bit of a recurring issue for me lately. So it’ll be interesting to see what happens when the makers of MMORPGs ditch anonymity.

Myers is right: Someone could do some great research with this.

Additional: Reaction begins.

Tuesday Crustie: Nothing rhymes

A pistol shrimp (Alpheus villosus). Love all the setae covering the claws and body!

Photo by Saspotato on Flickr, used a Creative Commons license.

05 July 2010

Abusing scientists

The Guardian reports on just how much abuse is being thrown at climate scientists. It’s frightening. Here’s a small selection of things climate scientists have been told:

I was hoping I would see the news that you’d committed suicide. Do it, freak.

Go gargle razor blades.

Dear Communists, know that you will fail.

I think these sort of directed threats is going to have long-term knock-on effects on climate science, and maybe in other fields. A lot of students could look at this and think, “This is not what I want to sign up for.”

July 2010 carnivals

Circus of the Spineless #52 goes up at Kind of Curious. Arranged from beautiful to “Ick! OoooOOoooooh..."

Carnival of Evolution #25, the Silver Anniversary, is running at Culturing Science. Featuring original art!

Carnival of the Blue #38 is hosted by Water Words That Work.

Island getaway, or: A lizard in a life-boat

Bermuda. Famous for its sun. Sand. Surf. Shorts. Triangles. Lizards.

Okay, maybe not the lizards. Not yet.

Islands and lakes hold a special place in the heart of evolutionary biologists (here’s a few examples from this blog: sticklebacks, crickets). As Jerry Coyne likes to say, island biogeography provides evidence for evolution so strong that most creationists simply ignore it.

View Larger Map

Bermuda formed about two million years ago. It’s small and a long way from the mainland, and has almost certainly never been connected to any other landmass. That Bermuda appeared very recently (in geologic terms) and that it is so far away from potentially invasive populations means that anything that lives only in Bermuda has probably evolved pretty darn fast.

Plestiodon longirostris is a skink that is found on Bermuda and nowhere else on earth. There aren’t many animal species living on this island at all, which is not surprising, given how remote it is. There are, however, other members of the genus, many of which live on the mainland of North America.

We’ve gotten fairly good at using DNA to generate hypotheses about relationships between species, and, to a lesser degree, the time of divergence. Using that, Brandley and company found that Plestiodon longirostris split from its closest relatives...

Pop quiz!

How old would you expect the Bermuda skink lineage to be? “Well, the island’s only two million years old, so it's got to be younger than that.”

That's a perfectly sensible answer. But wrong.

Brandley and company estimate that this lizard split from its relatives about 16 million years ago. This means that the line leading to this particular skink diverged way, way before Bermuda formed.

These data don’t, alas, give many clues to when the skink’s ancestors got to the island, or how. Nor do we know how its relatives on the mainland went extinct. But what it does say is that islands are not only important centers for evolutionary experimentation, they can also act as centers for preservation. Or, as the authors put it, islands can be a “life raft” for species that make it to their shores.

Reference

Brandley, M., Wang, Y., Guo, X., Nieto Montes de Oca, A., Fería Ortíz, M., Hikida, T., & Ota, H. (2010). Bermuda as an evolutionary life raft for an ancient lineage of endangered Lizards PLoS ONE, 5 (6) DOI: 10.1371/journal.pone.0011375

Lizard picture from here.

Additional: Another take at Natural Selections.

04 July 2010

Headline Hogwash, Part 2

My collaboration with Carin Bondar continues with the second of our look at the headlines and the papers they were based on! Head on over to her site to check it out!

And if you haven’t seen part 1, you can find it here.

Fish in an electric maze

For many, this is the most familiar image of animal behaviour:

The rodent in the maze is such a well-known image, you can find countless cartoons alluding to it. And with good reason: we've learned a lot by teaching animals to perform these kinds of maze running tasks. By tweaking the task, we can learn much about the kinds of cues that animals pay attention to in learning.

Walten and Moller put a new spin on this old classic by using a different kind of animal: electric fish. Fish do not have reputations as being good at navigation. You only have to think about the old, busted myth that goldfish only have a 5 second memory. But, to some degree, it might make a certain amount of sense if fish were bad at the navigating: after all, there aren't that many permanent positions in the water.

With many animals, the trick is finding a task that motivates them. This species, Mormyrus rume, doesn't like to be out in light and bare tanks, much preferring small, dark, hidey-holes. Indeed, the authors say that the animal has a home base that it roams away from, and has to learn its way back. When an electric fish was placed at one end of an open tank with a nice dark spot they could escape into, they quickly learned how to get there.

The interesting thing here is that the electric fish sees the world though a few different sense, including one for which we have no equivalent. The fish can see the maze. The fish can also sense the way electricity "flows" through the maze.

The authors trained the fish, letting them use either vision or electrosense during the learning phase.

The maze was dead simple; we really wouldn’t even consider it a maze, given that there were no turns or decision points where the fish had to remember, “Do I got left, or right?” Basically, the maze was just a long corridor that went back and forth.

In some versions of the maze, the authors added extra visual cues: big “signs” sitting outside the tank. In others, they made the maze more distinct electrically by placing aluminum or plastic cubes at key points in the maze.

To test what they fish were doing, they “knocked out” one sense at a time. They removed vision by letting the fish do the maze in the dark. With a little surgery, they could knock out the fish’s electosense.

After the fish learned the maze (intact animals got to about half a minute within 3 days; those ), they took the walls and the shelter away. There literally wasn’t a maze any more – the fish could just swim straight to the place the hole had been if they wanted to.

These are a few possibilities as to what the fish might do.

It might just swim straight towards the place where “home” used to be; this would indicate it had a sort of mental “map” of the tank.
It might actually do the whole turning back and forth, indicating it had memorized a pattern of movement.
It might be completely discombobulated and not be able to find anything.

When the visual cues were left outside the maze, the fish still tended to meander a bit. If you moved the starting point, though, the fish would not meander – they would treat it as a new situation. All of which suggests the fish, even though they can see, aren’t paying attention to those visual cues.

When the electrical cues remained in the maze, the fish tended to use them. If the authors threw in some new ones, the fish got very lost. The most interesting situation was when the electrically important cues were removed: the fish zipped straight to the target. This suggests that the fish had formed a map, but only fell back on it when the old dependable cues weren’t available any more.

Suffice to say, what’s going on when these fish are learning these mazes is fairly complicated. They fish mostly use electrosensing, but learn better if they can see. They will use electrical cues if they’re there, but have other ways to find their way if they don’t. I’ve left out a batch of other variations and controls and such that Walton and Moller performed.

The maze learning behaviour is just the first tip-toe to looking at the neurobiology, though. The authors don’t have some very specific hypotheses about a new form of protein kinase C that they expect to find in the brain of these fish...

Reference

Walton AG, & Moller P (2010). Maze learning and recall in a weakly electric fish, Mormyrus
rume proboscirostris Boulenger (Mormyridae, Teleostei) Ethology : 10.1111/j.1439-0310.2010.01807.x

Rat photo by 19melissa68 at Flickr. Used under a Creative Commons license.

02 July 2010

Persuasion and other failures of will (but trust me on that sunscreen)

You don't have to read this. You could stop at any time. Couldn't you?

Everyone is going to say "Yes" to that question. We love to think that we are masters of our fate, captains of our destiny, our choices are ours alone. That notion is crucial to the ethical concept of agency, legal matters of intent, and much more.

But I'm sure everyone has had a moment like in video below. It starts at 1:58 and runs to 3:00:

It's that moment where you stop yourself, and go, "What am I doing?"

We don't always know why we do what we do. This idea probably got its biggest push from Sigmund Freud. Freud has a lot to answer for, because so much of his psychology is wrong, but his notions about the unconscious were revolutionary . Two articles have recently appeared that both lend support, in broad strokes, to the important of unconscious decisions.

I'll start with the empirical, by Falk and colleagues, who looked at what happens in the brain when you try to persuade somebody of something. They took a bunch of volunteers, and tried to get them to use sunscreen every day. This research was done in sunny California, so it's relevant for the people there.

I'm not sure that was the exact material they used, but you get the idea.

While showing their educational material to 20 subjects, the authors took fMRI brain scans, paying particular attention to the medial prefrontal cortex. Falk and company also asked their subjects if they planned to used more sunscreen.

After a week, they asked the subjects back, and checked on their sunscreen use.

What people said they were going to do was not significantly correlated with what they did do. This might be called the "New Year's effect."

The fMRI signal in the medial prefrontal cortex (remember, taken beforehand) was significantly correlated with what people actually did. The brain scan was a better predictor of actual behaviour than people's own statements about their intentions.

The researcher do note that they are taking the subject's word that she or he used sunscreen. They argue, though, that people would probably tend to report using sunscreen consistent with their stated intention, so if anything, the relationship between the initial intention and sunscreen use - which was not significant in the first place - was inflated.

The brain scan explains about 25% of the behavioral variation, so the effect is not huge. But still, this experiment is important is that it's part of a larger emerging enterprise that chips away at the notion that our conscious decisions cause, or are independent of, neural activity. You can't argue that very well when the neural activity precedes conscious decision and predicts it better.

Along these lines, a new review by Custers and Aarts argues that everything a human being need to create and act towards a goal can all occur unconsciously. This paper deal more with psychology than neuroscience. Interestingly, it seems to suggest that subliminal messages - once oversold, now largely ignored - can have some effects on behaviour under some circumstances.

Reference

Falk, E., Berkman, E., Mann, T., Harrison, B., & Lieberman, M. (2010). Predicting Persuasion-Induced Behavior Change from the Brain Journal of Neuroscience, 30 (25), 8421-8424 DOI: 10.1523/JNEUROSCI.0063-10.2010

Custers, R., & Aarts, H. (2010). The Unconscious Will: How the Pursuit of Goals Operates Outside of Conscious Awareness Science, 329 (5987), 47-50 DOI: 10.1126/science.1188595

01 July 2010

The elephant and the shrew, an axonal story

The world is different for small animals and big animals. J.B.S. Haldane said it best:

To the mouse and any smaller animal (gravity) presents practically no dangers. You can drop a mouse down a thousand-yard mine shaft; and, on arriving at the bottom, it gets a slight shock and walks away, provided that the ground is fairly soft. A rat is killed, a man is broken, a horse splashes.

What does scale mean for neurons? As an animal gets bigger, it’s going to take longer for neural signals to get from one part of the animal to another – all other things being equal. But, typically, not all things are equal. You can speed up how fast a signal travels down the length of a neuron by making that neuron larger. just like water current can flow faster through a bigger pipe, an electrical current can flow faster down a larger axon.

There’s more going on in this paper by More and colleagues (so it’s literally More going on), but that gives you a starting point for the rationale here. If you take the teensiest mammal you can find, and one of the biggest mammals you can find, how different are those axons, and how fast they can send their signals, going to be?

To test this, they did neurophysiology and neuroanatomy on the neurons of a least shrew and an Asian elephant. These two animals are about as different in size as mammals can get. The shrew’s mass measures in milligrams, and the elephant’s measures in megagrams – tonnes!

But because you don’t want to draw a line using only two data points, they also went into the existing literature for mammalian neuroanatomy, and got equivalent measures for about nine other species of mammals.

The axon sizes scaled – bigger animals had bigger axons – but much, much less than the animal’s size. I mentioned mass before, but distance is the more relevant measure, though less impressive. An elephant’s leg is about 100 times longer than a shrew’s, but the elephant’s axons are only about twice as big. That’s about as close to scale-free a relationship in biology as you’re likely to find.

Okay, the neurons may be about the same size, but maybe there’s some other mechanism that might make the actual speed of the signals a better match to the animals’ proportions. Nope. A similar story held when they stimulated the nerves electrically and measuring the delay to the muscle twitch.

All of this means that big animals are going to be slower to detect and react to the world around them. It’s a real cost to being massive, which are no doubt compensated for by other factors. Like being able to sit anywhere you want.

Unfortunately, More and company point out that all this means that dinosaurs and other large creatures probably weren’t as as agile as they are often portrayed.

Reference

More, Heather L., Hutchinson, John R., Collins, David F., Weber, Douglas J., Aung, Steven K. H., & Donelan, J. Maxwell (2010). Scaling of sensorimotor control in terrestrial mammals Proceedings of the Royal Society B: Biological Sciences : 10.1098/rspb.2010.0898

Additional: Brian Switek also summarizes this paper here.

Comments for second half of June 2010

Prof in Training points out that it’s not only couples who have problems with work-life balance in academia. I recount a story of actual, perhaps not discrimination, but definitely thoughtlessness, concerning one of my single colleagues.

The Scholarly Kitchen asks how PLoS ONE was able to create an enviable impact factor in its first go (something I’ve wondered myself). Actually promoting the journal might have something to do with it.

Hank Campbell also looks at the PLoS ONE impact factor, and raises many of the same questions above. The publication fee comes up, and I ask what a reasonable figure is.

Both SciCurious and I blogged about the Komodo dragon bacteria paper. But she gets more commenters than me. Heck, even I’m a commenter there.

And to reverse the flow of commentary for a second, the joint article Carin Bondar and I did on headlines gets mentioned in this Seed column.

30 June 2010

Alex

Lots of rain today, on and off. Enough to close some roads. Not much wind, so we're unlikely to lose power of suffer much damage.

Preemptive strikes

I had a quick peek at Chris Mooney's paper, "Do scientist understand the public?" Worryingly, examples where he holds out where the relationship between the two seem to be working out reasonably were all cases were engagement occurred right at the start when the scientific information was just starting to trickle out.

In at least one of those cases (vaccination), there may have been no way for scientists to get out an engage in advance. Indeed, science had won. Vaccination was accepted as routine for decades. Then, panic emerged in the 1990s or so in various forms. And again, there's little discussion of how to deal with such flare-ups: "crisis communication" gets about half a paragraph.

Maybe those are good models. But it's still incredibly frustrating that they provide no insight on how to resolve issues where the science is as clear as it ever gets, and large numbers of nonscientists simply discount it. You know the issues: evolution, vaccination, climate change, etc. On subjects like these, Mooney all but throws in the towel:

Battle lines have hardened... and it may be far too late to “fix” the situation.

The word "fix" didn't need scare quotes in that sentence. The disconnect is a problem, and it does need to be fixed.

Additional: I rather like some of the commentary made by Evil Monkey here.

29 June 2010

Working at home

Tropical storm. probably soon to be Hurricane, Alex is heading our way. The previous hurricanes that have had this sort of trajectory haven’t really done much more than a thunderstorm, so I’m not terribly worried. The university, though, decided to close. The initial announcement was for three days, although that was earlier in the day when the project ed path was straight on top of us.

We’ll see. Minimally, I’ll be ~~playing Wii games~~ working at home for tomorrow at least.

A bull in a bear market: Social media and the scientist “shortage”

Joshua Ward thinks scientists have to embrace social media.

Okay. As a blogger, someone on Twitter, and so on, I guess I can’t disagree with that.

But almost didn’t get to that point, because I just about did a spit-take when I read:

In the face of basic scientist shortages in many of the leading fields(...)

Shortage? What shortage? I rarely read about institutions unable to find good people. I read a lot about institutions with bona fide research positions that are swamped by applications.

Creating many high quality job opportunities is what will convince students to enter a scientific career, not having a Facebook page.

Reference

Ward, J. (2010). Recruiting future talent in ecology and evolutionary biology Trends in Ecology & Evolution. DOI: 10.1016/j.tree.2010.06.002

Tuesday Crustie: Claw eat claw world

A crab (Macrophthalmus abbreviatus) makes a meal of a ghost shrimp (species unknown).

Photo by Changua Coast Conservation Action on Flickr, used under a Creative Commons license.

28 June 2010

Vendetta, Part 2

Several people disagreed with my previous post about academic reprisals. So it seemed to me worth trying to explore the problem further.

It seems to me scientists fear reprisals because there are two things that they want:

Publication in high visibility journals, the “glamour mags.”
Grants.

Those two resources have two features that make the threat of reprisal genuine:

Anonymous peer review.
Scarcity.

Dealing with fear of reprisals at the level of the scientific community is a multi-part problem, each with different solutions.

The publishing model for journals is changing under our feet right now, and I think many of those changes are going to be good for breaking the prospect of reprisal. There are more and more venues where someone can publish, and it’s unreasonably to think a rival can block them all.

Journals are also promising targets for change because each one is independent. One dedicated editor or publisher can change how that venue works. There may be some limits to that, as Medical Hypotheses showed, but overall, editorial boards could really be change agents on this issue if they want to be.

Grants... much harder. This may be a situation where (gasp!) the politicians force change in federal funding. Transparency and accountability are fairly big issues for governments. Listen to this story (Part 2) about the G8/G20 and listen for how often “transparency” and “accountability” are mentioned.

Obviously, I advocate far more transparency in the review process. Just this morning, the editor-in-chief pf the British Medical Journal argued that the lack of accountability in peer review was a problem. This is the overwhelming direction the rest of the world is taking, governments and business and non-governmental organizations alike.

To that end, I’m giving up reviewing anonymously. And I’ve already started. I submitted some reviews over the weekend, and I signed them. I don’t know if the person in charge will keep my name on them, but there’s not a lot I can do about that.

I realize that I’m in an unusual situation that makes it easier for me to try to put my money where my mouth is. I don’t need six figure grants to do my research. I’m probably never going to have a paper in one of the fancy journals. I’ve sort of self-selected myself out of the rat race.

(But I’m still a rat!)

26 June 2010

Mondo boffo scary boo!

Someone who is certain can be scarier than someone who is crazy.

25 June 2010

Building a bigger brain

How does one species get a bigger brain than another?

A while ago, I wrote about a paper that argued that genes that define boundaries in the nervous system seemed to be responsible for differing brain structures in cichlid fish. This seemed to explain the data better than a competing hypothesis, which was that the differences in brain size were caused by the length of time the brain spent forming neurons (neurogenesis). A forthcoming paper by Charvet and Striedter suggest a third possibility.

Bobwhite quails (pictured) have kind of small brains. But that’s okay, because they’re kind of small birds; they’re smaller than a chicken.

But despite the chicken having a bigger brain, the chicken goes from fertilization to hatching faster than the bobwhite quail.

Proportionately, both the quail and chicken start neurogenesis at about the same time. The chicken has a slight edge, but the extra 5% of time the chicken spends doing neurogenesis isn’t enough to explain that the chicken’s brain ends up being 100% bigger than the quail’s. When neurogenesis starts, the chicken’s brain is already 100-200% bigger than the quail’.

Before neurons form, the chicken’s cells are diving great guns. The whole cell cycle, everything mitosis related, is ramped up and going at a much faster clip in chicken than quail. They tested this using bromodeoxyuridine (BrdU), a chemical that cells incorporate into themselves if they’re actively dividing. The more a cell divides, the more BrdU it takes in. They couldn’t test all the way through development, but at around 11% development, chicken are showing cell division going about 100% faster than quail. After neurogenesis begins, though, that difference is almost nil.

To sum up: The chicken makes a mess of cells real fast, real early.

The other two mechanisms are more about changing the relative proportions of regions within a brain: enlarging over here, shrinking over there. This mechanism allows you to make brains that are different sizes, but that are otherwise structurally similar.

The unanswered question, though, is why do chickens need such large brains?

Ever wonder what chickens do when you’re not looking?

Reference

Charvet, C., & Striedter, G. (2010). Bigger brains cycle faster before neurogenesis begins: A comparison of brain development between chickens and bobwhite quail Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2010.0811

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

Now that’s just harsh.

For those who don’t follow international politics, this man was the Prime Minister of Australia at the start of the week. Now he, um, isn’t.

He’s actually shown up in this blog before.

Spotted on The Age.