NeuroDojo

07 July 2010

Sending signals is subtle: Killifish’s favourite colours

Making a clear visual signal is tricky. Consider this traffic signal:

(I totally thought I was going to have to photoshop a stop sign, but no.)

Whether this signal is effective depends on a lot of factors. What's the visual environment like? Some colours stand out better in some lighting conditions than others.

More critically for this discussion, what’s the experience of the person the signal is aimed at? And I mean the term broadly. Is the person colour blind? Has the person grown up in a place with blue stop signs everywhere?

Fuller and colleagues are interested in this question of colour signal, and are studying it in bluefin killifish (Lucania goodei). These fish live in lots of different habitats, ranging from water that is very clear, letting in lots of short-wavelength blue and ultraviolet light, to water that they describe as “tea-stained.” (In one of their experiments, they actually dump instant tea into an aquarium to make the water the right colour.)

The fish are quite brightly coloured, and the males vary in their colours. Fuller and company are trying to work out what factors influence those colours. Is it purely the physics of the environment – certain colours are just more visible in particular light regimes? Is it an innate preference of other fish (mainly females) that matter? Do all the ladies love red fins, say? Or do fish reared in a certain light environment develop a preference for one colour?

Rather than trying to sort this out one at a time, the researchers embarked on carrying out one of the most complicated experimental designs I’ve seen in a long time. Four genetic crosses of parents, two rearing environments, and two testing environments... 16 combinations of variables right there. They measured both the visual pigments expressed by the fish and a feeding-related behaviour: the tendency of the fish to pick at small coloured discs.

That’s not going to be easy to summarize, but let me try.

Visual pigments were affected by the environment the fish were raised in (i.e., clear or tea coloured).

Pecking was also affected by the environment: the fish were raised in; fish raised in clear water liked the yellow more than those raised in tea-stained water.

You’re probably thinking, “A-ha! The changes in the visual pigments explain the differences in behaviour!” Surprisingly, no. The differences in visual pigment expression explained a paltry 3% of the behavioural variation. The important changes are probably hidden somewhere in the visual centers of the brain.

There were also some effects of the setting the fish were tested in, which interacted with the rearing conditions. The authors say that the interactions between where the fish were raised and where the fish were tested is the “unique finding of this study” that is “striking.”

But there’s a problem for the reader in figuring this out. Here’s the graph they present plotting the behaviour (their Figure 5). Look for the open diamonds and the crosses.

That’s right: There aren’t any in the plotted data. D’oh! It snuck past the reviewers, editors, and proofreading authors! ~~(Caveat: Hurricane Alex has curtailed my access to the paper, and it’s possible that the final version has been fixed.)~~

Of course, one of the problems with this experiment is that while part of the avowed reason for doing it is to explain mate choices, they didn’t measure mating preferences. I’m sure that’s coming. But you need these data on non-sexual stimuli to tell you whether females like certain colours all the time or just for mating.

For instance, human females are often thought to prefer pink. But will that enhance the dating opportunities for this man?

Reference

Fuller, R., Noa, L., & Strellner, R. (2010). Teasing Apart the Many Effects of Lighting Environment on Opsin Expression and Foraging Preference in Bluefin Killifish The American Naturalist 176(1): 1-13. DOI: 10.1086/652994

Stop sign ohoto by Chris Pirillo on Flickr. Man with cat by aBbYhaLO on Flickr. Both used under a Creative Commons license.

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.

24 June 2010

Headline Hogwash, Part 1

Head over to Carin Bondar’s site for a double dose of extra examination of heaving headlines.

She and I will be doing a few of these, and I can’t wait!

A virtual camera lucida

Sometimes, the scientific literature sucks at getting information to you.

I was looking at the table of contents of a new issue of The Journal of Crustacean Biology and saw an article about how to photograph soft-bodied crustaceans. Hm, I wonder why photographing soft-bodied crustaceans is difficult, I thought.

And the abstract mentioned software to deal with short focal planes by merging several pictures. The software is Helicon Focus.

Yes, I should be happy that I have found something useful, but... dagnabbit, why didn’t I know about this years ago?

For instance, here’s part of Figure 3 from a paper a few years back (Espinoza et al. 2006) on the left, compared to a new picture processed with Helicon Focus (click to enlarge).

These are neurons stained through a technique called backfilling. The best backfills are really superb, and you can see a lot of detail. But they’re often in thick tissue, and neurons go all over the place through it, making it hard to see all the relevant detail. The way people usually got around this was to get a camera lucida attached to a drawing tube through a microscope, then trace the axons as you focused up and down.

I was actually very pleased with the pictures in Figure 3 as published, which had dark cells against a very clear background. But the one shown here on the left shows the problem of getting all the relevant detail in the shot. The cell bodies on the right are okay, but the ones down a little deeper in the ganglion on the left and their axons are already blurring out.

The processed version on the right is better.

Having played with this a bit, sometimes there are things you can see in the individual frames that do get lost in the processed version. The biggest problem is when there is some detail underneath something else. You can often see it under the scope and in the individual frames, but not so well in the composite image.

This was so startling and so useful to me, I briefly entertained the thought of trying to turn this into a neuroscience methods paper. Then I looked and found short references that it had been used in the invertebrate neurobiology literature a couple of years ago (Scanell et al. 2008) in a journal I read. D’oh! Another shrewd Faulkes scheme bites the dust.

But at least I can spread the word through a blog post. A slightly more recent paper by Berejnov and company (2009) has nothing whatsoever to do with biology, but gives a better example of what you might get from this kind of software.

As I was writing this, I read an interview with Neil Gaiman, where he said this, mostly in relation to book publishing in particular genres:

Information used to be gold: hard to find, expensive, the equivalent of going off into the desert and coming back with a perfect lump of gold. Now, it’s the equivalent of going off into the jungle, in which there is information everywhere and what you are trying to find is the piece that is useful, while ignoring the noise.

I do wish the process of finding useful things was a little less jungle-like.

References

Berejnov, V., Sinton, D., & Djilali, N. (2010). Structure of porous electrodes in polymer electrolyte membrane fuel cells: An optical reconstruction technique Journal of Power Sources 195 (7), 1936-1939. DOI: 10.1016/j.jpowsour.2009.10.050

Espinoza SY, Breen L, Varghese N, Faulkes Z. 2006. Loss of escape-related giant neurons in a spiny lobster, Panulirus argus. The Biological Bulletin 211: 223-231. http://www.biolbull.org/cgi/content/abstract/211/3/223

Hegna, T. (2010). Photography of Soft-Bodied Crustaceans via Drying, Whitening, and Splicing Journal of Crustacean Biology 30(3): 351-356. DOI: 10.1651/09-3253.1

Scannell, E., Dell'Ova, C., Quinlan, E., Murphy, A., & Kleckner, N. (2008). Pharmacology of ionotropic and metabotropic glutamate receptors on neurons involved in feeding behavior in the pond snail, Helisoma trivolvis Journal of Experimental Biology 211(5): 824-833. DOI: 10.1242/jeb.011866

23 June 2010

Vendetta

A new website for neuroscience called The Third Reviewer has been generating some comment in the blogosphere (DrugMonkey’s and Dr. O’s blogs, among others).

One of the things that bugs me it is that commenting is anonymous. My position: Anonymity doesn’t improve things (see here and here). The ostensible reason it is the way it is because people “fear reprisals.”

Has science become that much like the mob?

Are we as a group that thin-skinned, petty and vindictive that we’re going to put out a hit someone’s grant or whack another scientist’s pub because they didn’t think we used the right statistical test?

And if the answer is yes, we should start asking ourselves why that bad behaviour is tolerated, and how we can get rid of it.

Besides, anyone who believes they can safely remain anonymous on the web is fooling themselves. Own every word you speak.

Personally, I doubt I’ll be commenting on papers on The Third Reviewer website, for much the same reason John Stewart doesn’t use Twitter: He has a TV show. I have a blog. If I have something substantive to say, I’ll say it here.

I wish the guys behind the site luck, because I think they’ll need it. The history of researchers commenting on published papers is... not encouraging. Many papers on, say, PLoS ONE don’t even a star rating, which is also anonymous, but much easier than writing a specific comment.

Profs don’t text

Why can’t course management systems send text messages? (Or am I just ignorant and there one of them does?)

Because email’s going away.

I read some time ago that phone text messages were the most common means of communication in the world, by a wide margin, surpassing email. It’s increasingly obvious to me in the way I use my own computer. I have my RSS reader and Twitter running all the time in addition to my email.

I want to be able to type a text message, click the mouse button, and have it sent to all the students in the class who want to receive texts.

I hacked a crummy solution in the spring semester: I created a list of students in Google Voice. The problem was, I could only send one message to one person at a time. So I had to cut and paste and send for each student. The list was short, so it didn’t take up that much time, but it took minutes when it could have taken seconds.

If anyone has a solution... yeah, I’m a dinosaur, email me.

Photo by neutralSurface on Flickr, user under a Creative Commons license.

22 June 2010

Razor-sharp teeth and venom: The bacteria love it

A bite from a Komodo dragon would take you down. They have large teeth that are very sharp. And their salivary glands secrete venom.

For a long time, people sort of overlooked those two factors. The teeth were obvious, but the venom wasn’t. Instead, people suggested that one of the ways that the slow moving monitor lizards were able to take down large prey was because their mouths contained so many bacteria, that the bitten prey animal got infected, quite quickly, and went down from the bacteria.

The discovery of venom seemed to put the kibosh on that particular story – the prey die too fast for bacteria to be the cause of death. But it doesn’t change the fact that the mouths of Komodo dragons are loaded up with very nasty bacteria.

Bull and colleagues take a totally different approach to this question. Rather than asking what the bacteria do for the Komodo dragons, they ask what the Komodo dragons do for the bacteria.

They hypothesize that the way to view the relationship is using a disease model. Bacteria are spreading from dragon to dragon in an epidemic fashion. The bacteria spread from dragon to dragon by growing on the large kills that dragons make, which are often fed on by several different individuals. The dragons’ prey almost becomes an intermediate host; a means of spreading from dragon to dragon.

They are not suggesting that the bacteria are harming the Komodo dragons or causing them to become sick, which seems a bit of a strange bending of the word “disease,” but at least they warn us.

It’s an interesting way of looking at the problem. There’s no experimental evidence presented here that it allows you to make better predictions about the bacteria or the dragons, though.

Related post

The birth of dragons

Reference

Bull, J., Jessop, T., & Whiteley, M. (2010). Deathly Drool: Evolutionary and Ecological Basis of Septic Bacteria in Komodo Dragon Mouths PLoS ONE: 5(6): e11097. DOI: 10.1371/journal.pone.0011097

Texas Higher Education and Creation Research, Part 36

The National Center for Science Education is reporting that the Institute for Creation Research’s (ICR) lawsuit has suffered a powerful defeat.

But being rules that they brought no actual evidence was not enough. (Hey, since when has a lack of evidence ever bothered a creationist?) If you read previous entries in this series, you may recall that documents submitted by ICR as part of the lawsuit were described by external observers as “gloriously insane” and “20 pages of non-stop, thigh-slapping hilarity.”

I am sorry, but I have little sympathy for the ICR, and enjoy this part of the judgement against them.

It reads best if you imagine a dramatic pause where each comma sits in the sentence:

Plaintiff is entirely unable to file a complaint which is not overly verbose, disjointed, incoherent, maundering, and full of irrelevant information.

BOOM!

That’s got to sting. Just a little. Even for people with notoriously thick hides.

Tuesday Crustie: Terminal

A close up of the very last appendages of a stomatopod, the uropods of Hemisquilla californiensis. Stompatopods can probably appreciate more of this colour than we can, having the most complex eyes in the animal kingdom.

Photo by Michael Bok on Flickr, used under a Creative Commons license. Michael also blogs at Arthropoda; check it out!

21 June 2010

The rational crayfish, Procambarus economicus?

You might expect a paper whose title starts with “Neural control” to include neurons.

This new paper by Liden and collegues doesn’t. It’s straight behaviour paper in the style of classic neuroethology. It starts by explicitly trying to tie itself to a hot new field: neuroeconomics. Neuroeconomics is about value assessment and decision making in humans. In many cases, this means doing brains scans of people while they play with experimenter’s money.

Liden and company argue that humans are far too complicated (which is true), and the way to go about understanding how you make decisions is by looking at an escape system. Escape systems are reasonably simple in terms of neurons, and they definitely control a decision: Fight or flight? Or, in the case of crayfish, freeze or tailflip?

When crayfish see a large dark object looming over them, they can freeze, or perform an escape tailflip. The experimenters put crayfish in a tank, and passed shadows over them. They did record from the giant pair of escape neurons that trigger visual escape responses, but they way they used those recordings was as a marker for whether an escape tailflip occurred.

Not surprisingly, when you change the stimulus the crayfish gets, the behaviour changes. Speed the shadow up, and the crayfish is more likely to freeze. But if the crayfish does tailflip, it “decides” to do so in less time.

The big finding that has the authors tooting the neuroeconomics horn is that if you put a strong smell of food in the water, the animal is more likely to freeze than if there’s very little smell of food. This, the researchers argue, means that the crayfish moderating the use of its escape behaviour due to the presence of the food, because the escape would be costly in that it would take the animal away from the food it wants.

But. This effect happens only at one of two shadow speeds that they tested. The effect does not appear to be very robust.

There are just two two problems with integrating this sort of study into the fold of neuroeconomics:

The neurons.
The economics.

As for the neurons, the title of this paper implies that it’s found how these neurons make decisions, but this paper only suggests what to look for. It doesn’t give new discoveries at the neuronal level. There are no new neurons or synapses or neurotransmitters described here.

And the search isn’t going to be easy. The main neurons that make the escape decision in these cases are medial giant (MG) neurons. While the MG axons are well known (they run throughout the crayfish’s body), the bit where all the interesting integration is going on – the place where sensory neurons and interneurons are connecting with the MGs – are nearly a complete mystery, tucked away inside the crayfish’s brain. A while ago, I went looking in the scientific literature for any good picture or diagram of the MG cell bodies and dendrites in the brain – and came up empty handed.

I’m glad that the authors are working with the MG-mediated escape responses; they’re overdue for attention. But make no mistake, the low level of information about them is a bug, not a feature, for crayfish escape as a neuroeconomics model.

As for the economics, it seems difficult to assign values in this situation. Human economics is pretty easy: $20 is better than $10, but not as good as $50. Having a standardized interval scale makes some of the most interesting neuroeconomics research possible.

But what is the value of the smell of food? What is the cost of tailflipping? An escape tailflip is very brief, and it doesn’t take the animal very far from the food. The authors point out that crayfish who win fights gain access to food – which is true – to argue how important food resources are to crayfish. What they don’t mention is that will crayfish fight in the complete absence of food or any other resource. The advantages that crayfish gain through fighting are subtle enough that it took several decades of research before people figured out that there were any resource advantages gained by winning fights.

It’s also worth noting that these experiments are very similar to some theoretical models about the regulation of crayfish behaviour. Don Edwards (a former supervisor of senior author Jens Herberholz) wrote a paper discussing how a crayfish might choose between different behaviours (getting food, escaping a predator) back in 1991. The results of that computer model feel very much like the results presented here.

Indeed, thinking back to the 1990s, there were a lot of important papers on how crayfish escape responses were modulated via changes to the lateral giant (LG) interneuron circuit (e.g., Yeh et al. 1996). The changes were caused by social interactions, so this was pitched as a model for... human aggression!

All these little moments of “spin” in this paper seem to have carried through to how the paper has been promoted. This press release, from the interesting (albeit sometimes dodgy) Science Direct is a testament to good marketing. There’s another press release here. Here’s a snippet from one:

(A) new line of research that may help unravel the cellular brain activity involved in human decisions.

Yeah, and if I don’t clean out my fridge, I may help develop a new antibiotic.

This is good research. But to say that it’s going to help us understand human decision making? Not yet. Not by a long shot.

P.S. – I have to bust the authors and reviewers’ and editor’s chops for letting this get into the paper:

(D)ifferences were not statistically significant although only marginally(.)

A p value is either significant, or it is not. It is not legitimate to treat the p value as some sort of direct indication of the “reality” or the size of an effect; see Schmidt (2010) for more.

Shameless self-promotion! For those who might want more information on the crayfish escape system, I wrote a review on this, focusing on the evolution and diversity of the behaviour and the underlying neurons responsible for it (Faulkes 2008).

References

Edwards DH. 1991. Mutual inhibition among neural command systems as a possible mechanism for behavioral choice in crayfish. The Journal of Neuroscience 11: 1210-1223. http://www.jneurosci.org/cgi/content/abstract/11/5/1210

Faulkes Z. 2008. Turning loss into opportunity: The key deletion of an escape circuit in decapod crustaceans. Brain, Behavior and Evolution 72(4): 351-361. http://dx.doi.org/10.1159/000171488

Liden, William H., Phillips, Mary L., & Herberholz, Jens (2010). Neural control of behavioural choice in juvenile crayfish Proceedings of the Royal Society B: In press. 10.1098/rspb.2010.1000

Schmidt, F. (2010). Detecting and Correcting the Lies That Data Tell Perspectives on Psychological Science 5(3): 233-242. DOI: 10.1177/1745691610369339

Yeh, S., Fricke, R., & Edwards, D. (1996). The Effect of Social Experience on Serotonergic Modulation of the Escape Circuit of Crayfish Science 271(5247): 366-369. DOI: 10.1126/science.271.5247.366

Homo economicus by keystricken on Flickr; MG picture by rustyheaps on Flickr. Crayfish showdown picture by ratterrall on Flickr. All used under a Creative Commons license.

19 June 2010

Conquest of the land, a la Chubby Checker

Now this is wild:

It’s a fish. It jumps.

This picture was not taken in an aquarium filled with water; it’s in air.

The fish is a blenny, Alticus arnoldorum, and a new paper introduced me to this fish that barely deserves to be called a fish. According to the author, Shi-Tong Hsieh, this fish spends so much time on land that it actively defends territory on land. It can stay out of water indefinitely, as long as it stays moist.

That blows my mind.

Hsieh was interested how blennies were able to be so agile on land, so she recorded high speed video of several species and did detailed analysis of the movement. The leaping blenny above is the most active on land.

The big finding is that these terrestrial blennies are able to rotate their tail. That it, they can move it clockwise or counterclockwise relative to the axis of their bodies, not simply move it back and forth. When these fish jump, they are pushing off with the side of their tails, not the bottom.

The terrestrial blennies are able to jump about twice as far as their aquatic relatives, which can’t twist the tail. Although there isn’t enough evidence to say that this ability to rotate the tail caused the performance increase, it certainly is mighty suspicious.

Hsieh suggests that this jumping behaviour may be related to C-starts, which are fish escape responses I’ve mentioned before here and here. This would be tricky to test: the neurons are huge, but active behaviours like jumping make it difficult to record the activity.

An easier follow-up would probably be to start looking closely at the musculature and innervation of these terrestrial blennies to figure out exactly what has changed in the skeleton and / or muscles that allow them to do the twist.

Reference

Hsieh, S. (2010). A Locomotor Innovation Enables Water-Land Transition in a Marine Fish PLoS ONE, 5 (6) DOI: 10.1371/journal.pone.0011197

18 June 2010

I’m a pebble in the avalanche

I wasn’t going to do any more blogging today, but damn, this makes me mad. There’s posts on DrugMonkey and Female Science Professor that also take this apart.

This seems to me like a coded argument to thin the competition for resources by deciding, a priori, that certain kinds of research are “a problem.” It’s balkanization (see also here).

By their argument, whole swathes of scientific endeavor should just... go away. Do we really want nothing but cancer research? Because that’s the kind of thing that would happen under their scheme. Biology would become medical research and not much else.

Arguing that certain kinds of research aren’t worth doing is arguing for ignorance. Sorry, but as far as I am concerned, knowledge is better than ignorance.

ARGH! (If you were in my office, you’d be hearing the greatest hits of “What is your favourite curse word?” from the Pivot questionnaire.)

Now, please excuse me. I have to go back to destroying science by writing my latest manuscript.

Traffic on the net and traffic on the road

Although I’ve been blogging a long time, it’s only in the last couple of years that I’ve started to get serious about it, and social media (as these various channels have become known). I have developed a little online network of people I like to follow, and who, I would like to think, find at least some of what I have to say useful.

Yet as I’ve grown this online network, I’ve become more and more aware of the physical isolation of where I live. As I like to put it, “South until there ain’t more south to go.”

Twitter has probably been the biggest contributor to this increased awareness of isolation. Because Twitter is conversational, it is surprisingly spatial. People talk about where they are going to, who they are going to meet, and so on. Watch long enough, and you start to see some of the people you know crossing paths with each other.

Watching that traffic of information on the net emphasizes the long time I would have to to spend in traffic on the roads to have the face to face interactions others talk about. And I’ve noticed people in other parts of the country sometimes don’t understand the distances involved. “No, you don’t get it. I would have to get up early and drive all day to do that.”

Sure, now I can blog, tweet, and do other sorts of things from where I am and try to create involvement with my research colleagues in ways that I never could have before.

But damn it, there’s still nothing like face to face interaction. Face to face is about the joy of spontaneity, whereas online is about the admiration of the composed.

Related post

Are scientists lonely?

17 June 2010

The downsides of meritocracy

Academia is supposed to be a meritocracy: You rise through the ranks because your work (and, by extension, you) is better than someone else’s. I think this emphasis on merit might be doing people a disservice, in a couple of ways.

The entire process de-emphasizes happenstance and luck. People chase and chase and chase after those grants and high impact publications, figuring that if they just work that much harder, they must get them. Particularly in tight financial times like these, where there are more proposals and papers submitted than can be published, you’re essentially playing a lottery. There is just no way to be that much more outstanding than all the other bright people to ensure success.

And I think this can be very demoralizing for people. Academics are usually very bright people. For much of their lives, things have often been relatively easy for them academically. They do well in school, through their undergrad degree, grad school, and so on.

But then they start reaching the point where things aren’t working as well as one would hope. They get a job at an undergrad university instead of that major research university you’ve been working towards for a decade or more. They don’t get the grant. Again. You can’t get the publications in the journals you want. And when these things happen? There’s that little niggling voice in the back of your head saying, “Well, it’s a meritocracy, so you deserve what you get. Loser.”

From reading a lot of other academic blogs, and comments thereupon, I sense that a very particular path of success in research is presented to students that utterly buys into the meritocracy model and utterly discounts the lottery-like aspects of the career.

It could impede science more generally. People could be pursuing that last experiment, that last piece of data so that they can get it in a “better” journal, rather than publishing something that is perfectly interesting in its own right for others to see. People can get to be afraid of shipping.

For a supposed left-wing institution, academia often has some of the competitive elements associated with right-wing politics.

16 June 2010

Armored car parents

“Helicopter parents” refers to adults who hover relentlessly around their kids at times when the kids should probably be trying to do things for themselves.

I propose there is a more advanced stage of this syndrome.

Armored car parents n. Parents who attempt to transport their children from one secure point to another throughout life, abandoning any pretense of the offspring moving through life independently.

I arrive at this definition from this quote (from here), which disappoints me on so many levels.

(M)any evangelical parents seem to ask, “Is there someone in the virtual sphere where I can send my child where they can transition directly from a home-schooled environment into a collegiate environment and never leave the home?”

One of the undervalued aspects of schools, both grade schools and universities, is that they usually force you to meet people who are different than you. Who have different backgrounds, different ideas, different experiences, and who may (gasp!) actively disagree with you. For some people, school may be the only time in their lives they are actively challenged to articulate and justify their positions.

And some parents aren’t comfortable with that and want to take it away. Talk about living in a bubble.

Taking that experience away will leave those kids much duller and less prepared for that inescapable reality: There is more than one kind of person out there. And you’d better make some effort to get along with them.

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