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Brains, behaviour, and evolution.

Zen Faulkes
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April 27, 2012
08:00 AM
105 views

Turn on your shark light

by Zen Faulkes in NeuroDojo

Sharks! Feared ultimate predator of the sea! Striking terror into... ah, no can’t say it with a straight face when the shark in question is this:

This is the smalleye pygmy shark. It may be tiny, but it has a cool trick that few fish have.

You’ve probably noticed that the belly of fishes are lighter than their top sides. The typical explanation for this is countershading. We often see fish in tanks, with light coming in from all directions. But in water, the only source of light is above. This means the underside of the fish is in shadow. Having a lighter underside than top makes the fish blend into it surrounding, making it harder to see.

But the problem is that light varies in intensity as you go up and down in the water. It would be an advantage for a fish to be able to change how bright its underside was.

The smalleye pygmy shark (Squaliolus aliae) pulls this trick off thus:

Its underside lights up.

A decent number of fish are bioluminsecent, but this little shark is a bit different. Some fish, like the flashlight fish, generate a glow using bacteria. To turn the glow on and off, they cover or reveal the patch.

In this shark, the glow is generated by light generating organs called photophores. And the shark controls the brightness more directly. It’s a little bit closer to the way a cephalopod changes colour, but not as fast.

Claes and colleagues have been studying photophores in sharks for a few years now. In this new paper, they looked at how the shark controls the brightness of its photophores. It’s a neat system.

The shark switches its light “on” using a hormone: melatonin. Melatonin is a widespread chemical, and so not surprising that it would be found in these sharks.

The shark switches its light “off” using neural control: the neurotransmitter GABA will turn the light off... eventually. It’s a very slow decline, and GABA never shuts the light off entirely. The authors showed this by bath applying the GABA. Ultimately, I would like to see neural stimulation turning off the glow, but this is a good start.

I was a bit frustrated with the writing here. The story is simple, but the prose is complicated. For instance, the very first sentence starts with an exception:

Except Dalatias licha, a benthopelagic shark that can attain almost 2 m in total length (TL)...

This caveat not so important that it needs to be the first thing on the page.

A nifty finding, though. I can think of cases where a single organ has both endocrine and neural input for fast and slow changes, but I can’t think of another effector where the two opposing effects are controlled by two different organ systems off the top of my head.

Reference

Claes J, Ho H, Mallefet J. 2012. Control of luminescence from pygmy shark (Squaliolus aliae) photophores. Journal of Experimental Biology 215(10): 1691-1699. DOI: 10.1242/jeb.066704... Read more »

Claes J, Ho H, & Mallefet J. (2012) Control of luminescence from pygmy shark (Squaliolus aliae) photophores. Journal of Experimental Biology, 215(10), 1691-1699. DOI: 10.1242/jeb.066704

April 25, 2012
08:00 AM
64 views

Dear Americans for Medical Progress

by Zen Faulkes in NeuroDojo

Dear Americans for Medical Progress,

As a pro-research, pro-science advocacy group, I'd like to think you take facts seriously.

On your FAQ, on the very first question justifying animal research, you write:

For instance, sharks are immune to cancer. By studying their biological system, scientists hope to understand what mechanism prohibits shark cells from mutating into cancer cells, and from this information, create a medicine that mimics that mechanism to prevent cancerous cells from forming in humans and animals.
Let’s look at those two sentences in turn.

“Sharks are immune to cancer.”

This is a myth. Christie Wilcox wrote a fantastic blog post debunking this. The title says it all: “Sharks DO get cancer!” Here’s the key quote (my emphasis):

(I)n 2004, Dr Gary Ostrander and his colleagues from the University of Hawaii published a survey of the Registry for Tumors in Lower Animals. Already in collection, they found 42 tumors in Chondrichthyes species (the class of cartilaginous fish that includes sharks, skates and rays). These included at least 12 malignant tumors and tumors throughout the body. Two sharks had multiple tumors, suggesting they were genetically susceptible or exposed to extremely high levels of carcinogens. There were even tumors found in shark's cartilage! Ostrander hoped that this information would finally put to rest the myth that sharks are somehow magically cancer-free.

The second sentence claims that there are researchers who are actively studying cancer in sharks. That sharks do get cancer does not mean that there would be no researchers on them, so this is a completely separate claim. This is also not true, as far as I have been able to find.

A PubMed search for “cancer” and “shark” reveals a fifteen articles with those words in the title. None reveal any researchers using sharks to study cancer. Most of those papers bemoan the use of shark cartilage as quackery, and a few test the shark cartilage treatment (it failed). Another search for “tumor” and “shark” finds a few papers that are testing shark derived products on cancer. But testing a shark product for anti-cancer properties is not the same as studying sharks.

I can find nobody doing the type of research you describe in your answer: studying the cellular biology of sharks. I may be wrong on this, and would like to knowing what researchers are actively studying tumorigenesis in sharks.

The combination of these two claims may give people the false impression that there is something the quack science concerning treatment of cancers using shark cartilage. This is also not true, and contributes to severe overfishing of sharks (also addressed in Christie Wilcox’s post).

Beside, using sharks as an example misses the point that concerns most people. Most people are concerned about the use of mammals in research. You should address that directly and use mammals in answering the question.

One alternative would be to naked mole rats in the example. There is ongoing research on tumorigenesis in this species; references are below. Frankly, an example of information gained from a more common lab animal, like a mouse, would be even more convincing.

I hope you will consider changing your FAQ. As a researcher, I am very concerned about issues surrounding animal care. Errors like this can damage the credibility of everyone who has to use animals in research.

Yours truly,

Zen Faulkes

Additional: I emailed this to AMP this morning, and received an email back from them in about five hours. They plan on reviewing their FAQ and should have a revised version up soon.

Hooray!

References

Seluanov A, Hine C, Azpurua J, Feigenson M, Bozzella M, Mao Z, Catania K, Gorbunova, V. 2009. Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proceedings of the National Academy of Sciences 106(46): 19352-19357. DOI: 10.1073/pnas.0905252106

Liang S, Mele J, Wu Y, Buffenstein R, Hornsby P. 2010. Resistance to experimental tumorigenesis in cells of a long-lived mammal, the naked mole-rat (Heterocephalus glaber). Aging Cell 9(4): 626-635. DOI: 10.1111/j.1474-9726.2010.00588.x

Shark picture by PacificKlaus on Flickr; used under Creative Commons license.... Read more »

Seluanov, A., Hine, C., Azpurua, J., Feigenson, M., Bozzella, M., Mao, Z., Catania, K., & Gorbunova, V. (2009) Cozzarelli Prize Winner@;DELIM@;From the Cover: Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proceedings of the National Academy of Sciences, 106(46), 19352-19357. DOI: 10.1073/pnas.0905252106

Liang, S., Mele, J., Wu, Y., Buffenstein, R., & Hornsby, P. (2010) Resistance to experimental tumorigenesis in cells of a long-lived mammal, the naked mole-rat (Heterocephalus glaber). Aging Cell, 9(4), 626-635. DOI: 10.1111/j.1474-9726.2010.00588.x

April 20, 2012
01:00 AM
100 views

Red returns: What women wear for wild times?

by Zen Faulkes in NeuroDojo

Note: This paper in this post is also being covered by the mighty Scicurious in her weekly Friday Weird Science!

Last week, I wrote about women and red. To recap: Men think that women wearing red look smokin’ hawt. (That’s the technical term.)

There’s a lot of questions you can ask about that fact. Last week's paper tried to figure out if red was sexy because it reminded men of the colour of female sex organs. (No.) Another question, tested here, is whether women use red to show their interest in sex.

This new paper by Elliot and Pazda has some similarities to the hypothesis of the previous paper. The authors imply that red is a sexual signal because of biology more than culture. The paper's first sentence is:

Females in many primate species, such as baboons and chimpanzees, display red on their body (e.g., chest, genitalia) near ovulation.
(Because of lead time, Elliot and Pazda don’t mention the paper from last week. They couldn't have known that the “red makes men think of women’s sex organs” hypothesis was not supported.)

The authors did three studies, all online. But I am frustrated by a lot of missing details. The authors mention their own website, and other existing “dating websites,” and we aren’t told anything else about them.

See, here's the thing. The Internet? It's a big place. (I live in Texas. “Big” is kind of a local obsession.) If you want to argue that the effects you’re seeing are biological rather than cultural, we need to know something about the particular websites used. What was the primary language of the website, for instance? I’m almost willing to bet that these were English language sites based in the United States.

That sort of detail could make a big difference in the strength of the interpretation. It’s hard to rule out or control for confounding factors, particularly good old culture (as Sci notes). This research would be much stronger if it had a cross-cultural component. For instance, in China, red is associated with good fortune... and I don’t mean “getting lucky.” Elliot and Pazda do note that they had a mix of ethnic groups in their first experiment, but not their nation of origin.

In the first experiment, they asked women hypothetically what they would show in a profile pic on a dating website, and varied the instructions as to whether there is a mention of casual sex or not. When casual sex was mentioned, “red” was the most popular colour chosen by women, and it was was a significantly more common choice than when casual sex was not mentioned. Blue was the most common colour when casual sex wasn’t mentioned.

Things get more complicated on the existing, functioning dating websites. On these websites, mostwomen were wearing black – more than red and blue and green combined. Those women who indicated an interest in casual sex were more likely to be wearing red in their picture, which is consistent with the hypothesis. But the popularity of black doesn’t make for a straightforward interpretation.

Maybe these were dating sites for goths?

We just don’t know!

In the discussion, Eliot and Pazda do add nuance. They still seem to favour a biological interpretation of their results, with some references to primate literature. They admit, however, that they can’t rule out the cultural explanations. They also talk about whether red is simply a signal to men, or whether it is also intended as a signal to other women (that is, potential competitors).

I do find it odd that this paper frames its discussion from a heterosexual perspective. There is no speculating on whether red would be used by people of other orientations in the same way. This seems a curious omission, because Elliot and Pazda mention that their first two studies contained women who identified themselves as bisexual.

Maybe I’ve been spoiled. Frankly, OK Cupid did this kind of stuff better. Their OKTrends blog posts were often much more detailed and rich than this paper, and I’d love to have seen them tackle this question. I imagine they wouldn’t just have data on what the women wore, but they’d have data on how often men responded to those profile pics where women wore red. And how gay women responded to pics with red. And bi women. And so on.

I’d like to know how women wearing red would answer, “Do you like the taste of beer?”

Now that you’ve reached the end of my post, don’t forget to read Scicurious!

Reference

Elliot A, Pazda A. 2012. Dressed for sex: red as a female sexual signal in humans. PLoS ONE 7(4): e34607. DOI: 10.1371/journal.pone.0034607
... Read more »

Elliot, A., & Pazda, A. (2012) Dressed for Sex: Red as a Female Sexual Signal in Humans. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0034607

April 17, 2012
08:00 AM
105 views

Tuesday Crustie: Obscure

by Zen Faulkes in NeuroDojo

I recently described myself as a “crustacean biologist” for a project I was working on. But whenever I do, I feel like such a sham, because I barely have a clue about critters like these...

I look at these and have a hard time believing that some of these are even animals.

These are examples of tanaidaceans. Haven’t heard of them? Don’t worry. I was at best only vaguely aware of their existence, too.

A recent paper by Blazewicz-Paszkowycz and colleagues is a nice little introduction to this little known group. They are almost all small burrowing animals living in sediment. They have almost zero ability to disperse, and so they become isolated and for mew species frequently as they become isolated. There are about 1,200 species known, but the rate of discovery has consistently increased. The authors estimate that for every known tanadacean species, there may be nine undescribed ones awaiting discovery.

Reference

Blazewicz-Paszkowycz M, Bamber R, & Anderson G (2012). Diversity of Tanaidacea (Crustacea: Peracarida) in the world's oceans – how far have we come? PLoS ONE 7(4): e33068. DOI: 10.1371/journal.pone.0033068... Read more »

Blazewicz-Paszkowycz M, Bamber R, & Anderson G. (2012) Diversity of Tanaidacea (Crustacea: Peracarida) in the world's oceans – how far have we come?. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0033068

April 11, 2012
08:00 AM
115 views

Will you split or steal my Golden Balls?

by Zen Faulkes in NeuroDojo

The prisoner’s dilemma is a classic problem of cooperation. You’ll find lengthy and erudite academic discussions of it in many fields of academia, from evolution to behavioural economics.

I wouldn’t have pegged it as a staple for a television game show.

Golden Balls is a UK game show that always ends with a prisoner’s dilemma decision. Burton-Chellew and West took advantage of this to study the prisoner’s dilemma respond “in the wild.”

Golden Balls goes through several rounds; I have a whole episode in links below. Early rounds give players ample reason and opportunity to lie. The penultimate “test your psychic powers” segment has players randomly selecting balls, which determines the final total they will play for in the end. In the final round, two players are left, and they have to make a decision: split or steal?

Both players make independent decisions. If they both choose “split,” they the pot of money is split 50-50%. If one chooses “Steal,” that player gets all the money (twice what they’d get by splitting) and the other gets nothing. But if both pick “steal,” neither gets anything.

Here is an example of a final, high stakes decision, for “life-changing” money (as the presenter is fond of calling it):

Not all the stakes are quite so high, though:

By watching every episode of the show on DVD, Burton-Chellew and West found there was no overall pattern to splitting or stealing; it was almost exactly split down the middle. This was a bit of a surprise to me, as I’d understood that people tended to cooperate more.

Lots of factors were correlated with the decision, but one of the biggest ones was the amount of money at stake. With more money at stake, contestants were more likely to steal. People got greedy.

The earlier rounds, where players often had to lie, did affect the decisions of the contestants. There were hints of retribution. Lies about the amount of cash the player had made their opponent more likely to steal.

There are few cases where a player will admit to planning to steal the jackpot. Were there ways to tell who was being honest? One signal that seemed to be an honest signal was laughter. Another was reciprocal physical contact. But if only one player touched the other... it was more likely there would be stealing. Sadly, although both of these seemed to be somewhat honest signals, there was very little evidence that players picked up on these reasonably reliable cues from their opposite number!

One limitation of this study is that game show contestants are hardly selected at random. The producers may well have screened their contestants to get both strategies about equally represented in the game. This makes some of the other demographic information (i.e., that women split more) problematic. The authors address the non-random selection, but they focus more on the possibility of certain personalities wanting to be on TV, more than active choices by producers.

Further, game shows are a very strange situation. People may be inclined to think, “What happens on the game show, stays on the game show.”

Still, if you’re wondering if you can trust someone, asking yourself if whether he or she makes you laugh might be a good first question to ask.

Golden Balls episode

Part 1
Part 2
Part 3
Part 4
Part 5

Reference

Burton-Chellew M, West S. 2012. Correlates of cooperation in a one-shot high-stakes televised Prisoners' Dilemma. PLoS ONE 7(4): e33344. DOI: 10.1371/journal.pone.0033344... Read more »

Burton-Chellew M., & West S. (2012) Correlates of cooperation in a one-shot high-stakes televised Prisoners' Dilemma. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0033344

April 10, 2012
08:00 AM
112 views

Tuesday Crustie: Wheeeeeeeeeeee!

by Zen Faulkes in NeuroDojo

This week, the focus is not so much on what a crustacean looks like as what it can do.

Waach this little speck – a copepod – faced with being eaten by a fish.

According to Gemmell and colleagues, when a copepod leaps out of the water this, only one fish out of all they tested was then able to catch the escaping crustacean.

And here is is in high speed. It’s too bad that it’s so fast that you can’t get in any closer, because the beast would immediately have it go out of focus.

For more, check out the story from the indefatiguable Ed Yong: “Flying plankton take to the air to flee from fish.”

Reference

Gemmell B, Jiang H, Strickler J, Buskey E. 2012. Plankton reach new heights in effort to avoid predators. Proceedings of the Royal Society B: Biological Sciences: In press. DOI: 10.1098/rspb.2012.0163... Read more »

Gemmell B, Jiang H, Strickler J, & Buskey E. (2012) Plankton reach new heights in effort to avoid predators. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2012.0163

April 9, 2012
08:00 AM
151 views

Red is sexy but not sexual

by Zen Faulkes in NeuroDojo

The Methods section of most papers is the least read part of the paper. You can see this in how some journals print the Methods in a tiny point size. Others have taken to putting the section at the end of the paper, so as not to disrupt the narrative flow with details.

Occasionally, you get a paper – usually in your field – where you need to read the Methods section closely to understand a paper enough to criticize or replicate.

Rare indeed are papers where the story is so unusual that I think, “I have absolutely got to read that Methods section!”

A new paper by Johns and colleague marks the first time I thought, “I have to read those Methods,” and “These Methods should come with an NSFW warning.”

It’s about the colour red.

Red seems to affect us in a way that other colours don’t (Elliot et al. 2007, Hill & Barton 2005). Case in point:

These head-turning dresses would not be the show-stoppers they are if they were beige.

Red is sexy.

If that picture doesn’t convincing you, check out Elliot and Niesta, 2008 and go through the data to your heart’s content.

Johns and colleagues test an hypothesis for why red on women looks so attractive to me. The hypothesis is that red is sexy because it reminds men of... lady parts.

An obvious objection to this idea is that t external sex organs of women are not red in the way that the dresses above are red. The hypothesis is a more subtle, however. One version of the hypothesis is that as females are approaching ovulation, the vulva becomes more red than is is at other points in the cycle.

If this “red is code for female sex organs” hypothesis is true, you might predict that men would judge female genitals as more attractive as they became more red.

The Methods section does not disappoint.

Explicit images of anatomically normal, un-retouched, nonpornographic, similarly-orientated female genitals were surprisingly difficult to obtain... We selected photographs that ... did not contain other, potentially distracting, objects (fingers, sex toys, piercings etc.) and were hairless to account for current fashion.
Ah, scientific prose, you’re at your most amusing when you’re trying to act coy.

They showed their pictures to 40 males. Most of the men were in their 20s, and they asked the participants about factors like their sexual orientation (they all reported themselves to be straight) and number of sexual partners. The men rated the attractiveness of each image.

The ratings of attractiveness were the exact opposite of those predicted by the signalling hypothesis. The reddest images were rated the least attractive.

The authors are then tasked to come up with an hypothesis as to why redness is less attractive. Their suggestion is that red is suggestive of menstrual blood. I'm not sure how one would test this hypothesis.

The results also showed that there was no difference in the judgments of men depending on their sexual experience. I learned from the Methods section of this paper that... shhhh, don’t spread this around... one can find pictures of female genitalia on the Internet. Is is possible that the men in this study knew this and might have looked at pictures of ladybits before participating in the study? I know, it’s incredibly unlikely, am I right? But if they did, it might explain why they found no difference in attractiveness ratings according to number of partners the men had.

This study is useful in that it tries to test an adaptive hypothesis experimentally. But it is frustrating because it is a limited study and hard to interpret.

First, there were few stimuli used. Only four pictures were used (then coloured four shades of red, for a total of 16).

Second, and more importantly, for an hypothesis that is all about sex, the authors seemed determined to make everything as clinical and detached and, well, unsexy as possible. First, the pictures were substantially cropped. They didn’t show the labia minora or the clitoris. As mentioned in the quote above, they didn’t want to use images had any sort of sexual nature (non-pornographic). The female equivalent of this task might have been to evaluate penises for attractiveness from pictures that only showed half a flaccid member.

Perhaps not surprisingly, the men didn’t find images of lady parts alone to be very attractive. On a scale of 1 to 100, the average was around 40, except for the reddest, which was rated 35.

I’m curious as to whether the authors would expect to see the same effect with homosexual women.

Finally, there is a great opportunity for further research. The authors note:

Surprisingly little is known about the range of variation in morphology and colour of the external genitalia of normal women of reproductive age, however, and further research is necessary in this area.
I think this could be the chance for someone (not me) to create the best citizen science project ever. “Ladies, all you need to contribute to science is privacy and a camera.” We need data!

Reference

Changizi MA, Zhang Q, Shimojo S. 2006. Bare skin, blood and the evolution of primate colour vision. Biology Letters 2(2): 217-221. http://dx.doi.org/10.1098/rsbl.2006.0440

Elliot AJ, Maier MA, Moller AC, Friedman R, Meinhardt J. 2007. Color and psychological functioning: The effect of red on performance attainment. Journal of Experimental Psychology: General 136(1): 154-168.

Elliot AJ, Niesta D. 2008. Romantic red: Red enhances men’s attraction to women. Journal of Personality and Social Psychology 95(5): 1150-1164.

Hill RA, Barton RA. 2005. Psychology: Red enhances human performance in contests. Nature 435(7040): 293-293. http://dx.doi.org/10.1038/435293a

Johns SE, Hargrave LA, Newton-Fisher NE. 2012. Red is not a proxy signal for female genitalia in humans. PLoS ONE 7(4): e34669. 10.1371/journal.pone.0034669

This article is made possible thanks to Helen Lewis, who compiled covers of book on female sexuality for New Statesman.... Read more »

Johns SE, Hargrave LA, & Newton-Fisher NE. (2012) Red is not a proxy signal for female genitalia in humans. PLoS ONE, 7(4). info:/10.1371/journal.pone.0034669

April 6, 2012
08:00 AM
126 views

Brainbrawl round-up

by Zen Faulkes in NeuroDojo

Columbia University hosted a debate between Tony Movshon and Sebastian Seung last Monday, “Does the brain’s wiring make us who we are?” This became known informally as “brainbrawl.” I watched it livestreamed through the Radiolab site, and someone had the wherewithal to grab the video below (which Radiolab said they weren’t planning on archiving). Radiolab did archive the live chat here.

Where’s the fight?

As I predicted, it was a much more sedate affair than the “brainbrawl” moniker suggested. Seung set the tone in his first comments by pulling back from the big claims that he has made previously. Instead of discussing the nature of human identity (his TED talk) or immortality (his book), he was much more circumspect in outlining what a connectome could do for us. Near the end, he said, “All I want to do is map some connections!”

I liked this, actually. It is a far more sensible view of the promise of connectomes than we’ve sometimes seen. But yes, it would have been more fun if Seung had swung for the fences anf salked about uploading consciousness. At the end, co-moderator Robert Krulwich was apologizing for the lack of blood on the floor and the modesty of the speakers.

The fight (to the extent that there is a fight), then, is not about whether connectome research is feasible or useful, but about grand challenges and resources. Movshon nailed it when he said people are looking for “gigascience” projects, and that neuroscience has been a “cottage industry.” While nobody said it directly, “gigascience” is often about making a sales pitch. People want to be at the forefront of establishing big projects, because the prospect of money is there. Someone made a comment about keeping score, and Movshon said, “The NIH is.” Krulwich asked Movshon, “What’s your recruiting pitch? What do you tell the young mavericks to bring them into the field?” (Krulwich occasionally seems to confuse science with the Wild West; also here.)

It seems to me like Seung talks about connectomes as a way to pitch his research, which involves developing techniques to do high-throughput neuroanatomy (e.g., Jain et al. 2010). Faster, more automated electron microscopy would be a godsend. But I doubt Columbia UNiversity would have hosted a debate on, “Should we develop better EM?” One commenter on Twitter said:

I haven't heard alternatives to connectome that generate comparable ideas/excitement
I’m not sure we need it. It’s not as though neuroscience is suffering for people; remember, we hold the biggest scientific meeting in the world. personally am unconvinced that we need grand challenges in science. The history of science shows that the way you answer the big questions is by answering the small questions.

The invertebrate in the vertebrate brain

Invertebrates came up in the discussion a couple of times. Good circuit descriptions of the mammalian retina are actually fairly far along, and may be the first part of the brain for which we have a connectome. Seung commented, however, that the retina was like an invertebrate brain contained within a vertebrate brain. I think he was referring to several of the retinal cells being non-spiking, which is also true of the worm Caenorhabditis elegans.

On Twitter, Noah Gray said he didn’t think C. elegans informed the connectome debate at all, because it has non-spiking neurons. I disagree, but at the very least, it does point out the importance of the intrinsic properties of neurons. Movshon suggested that the reason that C. elegans had non-spiking neurons was that it was small. This is too simple an explanation. In crustaceans, you can find both spiking and non-spiking proprioceptive sensory neurons (e.g., Paul and Wilson, 1994), and there seems to be no readily apparent functional reason to favour one or the other.

As I’ve mentioned before, we have a connectome of C. elegans, and there was discussion about how useful it actually it. In his book, Seung admitted that the connectome hadn’t solved all the neurobiological research problems for that animal, but that it might be a special case. Seung tried to argue that C. elegans posed technical problems in recording from the neurons, but Carl Zimmer pointed out that if his hypothesis was true, that wouldn’t matter. I do think the moderators, and possibly Movshon, were too dismissive of what we have learned from the connectome of C. elegans. Seung is correct that the connectome is very important to guiding research in the nervous system of the animal.

What occurred to me, though, was that there might be another invertebrate example that shows the usefulness of determining neuronal circuits: the eye of the horseshoe crab.

Haldan K. Hartline won the Nobel prize for his work on horseshoe crab vision. Hartline was able to map connections between the photoreceptors in the crab’s eye. He had the advantages that the photoreceptors were spiking neurons (unlike in mammals), and that there was only one type of photoreceptor. That is, each was an interchangeable widget, and the properties of the neuron were largely determined by connections with other neurons. By figuring out the simple circuit in the eye, he showed how lateral inhibition was able to enhance contrast of edges. This is important because the horseshoe crab eye has very low resolution.

Many years later, Robert Barlow and colleagues used a connectome-like model to build a biologically realistic model of the horseshoe crab retina and the signal it sends to the brain (Passaglia et al. 1997; Barlow et al 2001). When it was published, it was the largest biologically realistic model that had been built. They showed that some previously puzzling features of the synapses, like neurons inhibiting themselves, did things like filter out flicker in the environment.

If the mammalian retina is an invertebrate nervous system trapped in a vertebrate brain, the horseshoe crab retina may be a vertebrate nervous system in an invertebrate brain.

Other tidbits

I liked Movshon’s comment that the brain is not a multi-purpose computer, but a specific purpose computer. That is, brains are the products of natural selection and need to do specific things very well. This contrasted with his earlier argument against studying connectomes by using a well-worm software analogy, used my many cognitive pyschologists: "Studying the hardware doesn’t tell you anything about the software.” True for your desktop computer, but the brain is not an electronic computer, as Seung noted.

The audience asked some very smart questions. I wished they’d had a chance to ask more.

References

Barlow R, Hitt J, Dodge F. 2001. Limulus vision in the marine environment. The Biological Bulletin 200(2): 169-176. DOI: 10.2307/1543311

Jain V, Seung HS, Turaga S. 2010. Machines that learn to segment images: a crucial technology for connectomics. Current Opinion in Neurobiology 20(5): 653-666. DOI: 10.1016/j.conb.2010.07.004

... Read more »

Barlow R, Hitt J, & Dodge F. (2001) Limulus vision in the marine environment. Biological Bulletin, 200(2), 169. DOI: 10.2307/1543311

Jain V, Seung HS, & Turaga S. (2010) Machines that learn to segment images: a crucial technology for connectomics. Current Opinion in Neurobiology, 20(5), 653-666. DOI: 10.1016/j.conb.2010.07.004

Passaglia C, Dodge F, Herzog E, Jackson S, & Barlow R. (1997) Deciphering a neural code for vision. Proceedings of the National Academy of Sciences of the United States of America, 94(23), 12649-54. PMID: 9356504

Paul DH, & Wilson L. (1994) Replacement of an inherited stretch receptor by a newly evolved stretch receptor in hippid sand crabs. The Journal of Comparative Neurology, 350(1), 150-160. DOI: 10.1002/cne.903500111

April 4, 2012
08:00 AM
156 views

Science careers: fair play or field of bullets?

by Zen Faulkes in NeuroDojo

Yesterday, Elizabeth Sandquist posed an hypothesis:

You can't just be good to succeed in #science, you have to be exceptional. Any thoughts?
NeuroPolarBear replied with a post, and Drugmonkey pulled out an older post.

But my post will be the best, for I shall cite peer-reviewed data in the primary literature.

As it happened, Petersen and colleague published a paper yesterday looking at career success in physics. Appropriately enough, even though it’s a career paper, it feels very much like a physics paper: lots of equations and models and phrase like “leptokurtic but remarkably symmetric.” Hoooookay...

The authors tracked 300 physicists through about 20 years of their careers. They fell into three groups: phsyicists who were eminent (h -index of 61); productive and highly cited (h-index of 44), and early career assistant professors (h-index of 15). In that data from real scientists, Petersen and colleagues see that there are time when physicists are “shocked.” The shocks can be positive (“Wow, I just made this totally great discovery by accident!”) or negative (“Uh oh, they found that paper where I manipulated data.”)

They also look at career productivity, and the ability of researchers to build collaborations.That’s the “ground truth” that Petersen and colleagues use to create models of research career trajectories. This lets them play with some of the parameters.

The models indicate that as competition increases, many people can be taken out of the career pathway by... blind, stinking, clueless, doo-da luck.

Those that survive the field of bullets reach a point where they can start generating collaborative networks, and that builds even more success.

But the competition turns out to be very important in this model; and that relates to tenure. Many people want to see tenure replaced with a series of recurring short-term contracts. The authors imply that the short-term model could be harmful for the development of science. A failure in one short-term contract could derail a productive researcher, since early career shocks can ripple throughout a scientist’s career.

I think Petersen and colleagues would say that you do not have to be exceptional to make it in science. More important is the ability to tough out the early weeding out period, which doesn’t necessarily have a lot to do with your talent.

Reference

Petersen A, Riccaboni M, Stanley H, Pammolli F. 2012. Persistence and uncertainty in the academic career Proceedings of the National Academy of Sciences 109(14): 5213-5218. DOI: 10.1073/pnas.1121429109... Read more »

Petersen A, Riccaboni M, Stanley H, & Pammolli F. (2012) Persistence and uncertainty in the academic career. Proceedings of the National Academy of Sciences, 109(14), 5213-5218. DOI: 10.1073/pnas.1121429109

April 2, 2012
08:00 AM
126 views

Brainbrawl! The Connectome review

by Zen Faulkes in NeuroDojo

Recently, I wrote a post discussing connectomes. (Recap: Connectomes are descriptions of every synaptic connection between neurons in a brain.) In it, I referred to a paper by Cornelia Bargmann and argued that the amount of enlightenment we will gain about ourselves through connectomes is being oversold. I used several quotes from Sebastian Seung as examples, and mentioned his book on the subject.

Sebastian Seung noted that I had not read his book. Fair enough. I was not trying to single out Seung, but I can see that my post uses his examples enough that it seems like I am reviewing the book without reading the book.

I bought the book and read it.

The timing has turned out to be good, for today, Carl Zimmer and Robert Krulwich are moderating a debate between Seung and Anthony Movshon at Columbia University. The formal title of this debate is, “Does the brain’s wiring make us who we are?”

The Twitter hashtag? #brainbrawl. Much more fun, although I worry it promises more sparks than one will probably get from an academic debate about neuroscience. For example, The description of the #brainbarl debate ends with the question, “Are brain maps the future of neuroscience or an empty promise?” I doubt anyone will argue that describing connectomes will yield nothing. As I said, even though I think the enterprise will fail, on some level, it will fail in an interesting way.

Additionally, Seung was recently profiled in Discovery magazine by Carl Zimmer and Wired.

Early in the book, Seung says:

This book proposes a simple theory: Minds differ because connectomes differ.
I read through, making notes, and was caught off guard in the last chapter. After spending all this time making arguments for his connectome theory, I was surprised that in the last chapter, Seung surrenders the war.

Yet Seung remains optimistic that he can win one battle.

In Chapter 4, Seung argues that the function of a neuron is determined primarily by its connections with other neurons. Take a neuron from one region of the brain, stick in into another part of the brain, hook up the input and output synapses the right way, and away you go.

To put it another way, Seung initially treats neurons as interchangeable widgets.

At this point, I was getting ready to start a big long list of reasons why neurons are not interchangeable. There are not only neurons that generate action potentials, there are neurons with graded potentials, pacemaker potentials, and plateau potentials. There are the the passive electrical properties of the dendritic tree. These are just a couple of examples of the long list of intrinsic properties of neurons that make them distinguishable by far more than their connections to other neurons.

These are all in addition to changes of neuronal physiology introduced by neuromodulation.

Seung addresses the intrinsic properties of neurons in the book's last chapter:

In principle, every neuron is unique in its behavior, owing to the unique configuration of its ion channels. This is a far cry from the weighted voting model, according to which all neurons are essentially the same. But it sounds like bad news for brain simulation. If neurons were infinitely diverse, how could we ever succeed at modeling them? Measuring the properties of one neuron would tell you nothing about another.

There is one hope for escaping the morass of infinite variation: neuron types.
The concept of neuron "types" is initially introduced in Chapter 10. Seung initially want to categorize the neurons by their connections.

If two neurons are connected to similar or analogous partners, they should be grouped in the same type.
Seung then makes an extrapolation that is plausible, but I would say not yet proven: neurons with similar anatomical connections will have similar physiology and other intrinsic properties.

(N)eurons of the same type generally exhibit the same electrical behaviors. This is presumably because their ion channels are distributed in the same way. If this is the case, then neural diversity is actually finite.
By this point, Seung has described the only complete connectome of any animal, that of the 302 cell nervous system of the worm, Caenorhabditis elegans. I expected that this would be used as the flagship case of how connectomes can help us understand behaviour.

Instead, Seung declares defeat.

He estimates that of the 302 neurons in C. elegans, there are about 100 different types of neurons. And that proportion of distinct neuronal types is too high for a purely connection-based model to explain the worm's behavior.

As you read this section (emphasized sections are mine), recall that he's been repeated the mantra, "You are your connectome," for the previous 14 chapters. Now, in the very last chapter, an important missing piece gets added.

Thus the earlier claim should be revised to say, “You are your connectome plus models of neuron types.” (Let’s assume that a connectome is defined to specify the type of each neuron.) But the models of neuron types are likely to contain much less information than the connectome, as most scientists agree that there are far fewer neuron types than neurons. In this sense, “You are your connectome” would remain a very good approximation.

So “You are your connectome” would be a terrible approximation for a worm, even though it might be almost perfect for us.
If Seung is not convinced that the connectome theory yields meaningful information for C. elegans, I am skeptical that the ratio of neuronal types to the total number of neurons in a human brain* is going to be more favourable to connectomes explaining the mind.

At the very least, we have to acknowledge that there is a continuum.

One one end, we have circuits in which activity is dominated by few types of neurons, in which understanding the synaptic connections explains a large proportion of the function. Escape circuits are excellent examples, such as those in crayfish and fishes.

On the other end, we have circuits that are composed of many personalities, and where the intrinsic physiological state of the neuron matters a great deal to the function. Seung suggests C. elegans falls into this category, and I'll suggest the crustacean stomatogastric nervous system as another.

It is not clear to me where regions of human brains may fall on this continuum. When I visited the Neuroscience department at the University of San Antonio recently, and was discussing my previous post, several people indicated to me that those interested in connectomes placed special emphasis on the cerebral cortex, apparently because those neurons are a little closer to the "interchangeable widget" end of the scale than other brain regions.

Having lost the war - the ability of connectome theory to explain large parts of behaviour in many species - may not matter for Seung, however.

For Seung, like many neuroscientists, the only battle worth fighting is the one for human minds. Near the end of the book, he writes:

(T)here is only one truly serious problem in science and technology, and that is immortality.
The last sections of the book deal with topics like transhumanism, immortality, and putting consciousness into computers. These are a very distinct group of pre-occupations, all revolving around human consciousness.

As a neurobiologist, I want a theory that can explain how nervous systems generate all the behaviours of all the diversity in the animal kingdom. A theory that only explains the human mind is a small and paltry thing.

Connectome theory reminds me of Anne Elk's theory:

In one sense, the theory is trivially true. But in another sense, the theory omits so much that it doesn't end up telling us anything we wanted to know.

Reference

... Read more »

Seung S. (2012) Connectome: How the Brain's Wiring Makes Us Who We Are. Houghton Mifflin Harcourt, 1-384. info:other/978-0-547-50818-4

Neuroscience

March 21, 2012
08:00 AM
234 views

The myth of fingerprints

by Zen Faulkes in NeuroDojo

Could you have made a mistake?

If you are a fingerprint examiner in court giving testimony, the answer was once, “No,” according to Mnookin (2001).

(T)he primary professional organization for fingerprint examiners, the International Association for Identification, passed a resolution in 1979 making it professional misconduct for any fingerprint examiner to provide courtroom testimony that labeled a match “possible, probable or likely “rather than “certain.”
(I’ve been unable to find is this is still true.)

This paper by Ulery and colleagues is a follow-up to a paper published last year on fingerprint analysis. The previous paper found 85% of fingerprint examiners made mistakes where two fingerprints were judged to be from different people, when in fact they were from the same person (false negative). There was much more analysis, but you get the idea.

The researchers wanted to see how consistent the decisions were after time had passed. For this paper, they used some of the same fingerprint examiners that had been tested before (72 of 169 from he previous paper). It had been seven months since the fingerprint examiners had seen these prints. They were all prints that they’d seen for the previous research, but Ulery and colleagues didn’t tell them that.

Because the experimenters wanted to see if examiners who had made a mistake before would make the same mistakes again, the choice of what pairs of fingerprints to make was somewhat complicated. But all examiners saw nine pairs fingerprints that were not matched (from different people) and sixteen pairs that were matched (same people). And it’s also important to note that the fingerprints chosen were chosen in part because they were difficult.

In the original test, the fingerprint examiners only rarely said two fingerprints were from the same person when they weren’t (false positives). On the retest, there were no cases of false positives, either repeated mistakes from the previous test or entirely new mistakes.

The reverse mistake, the false negatives, were more common. Of the false negative errors made in the previous paper, about 30% were made again in the new study. And the examiners made new mistakes that hadn’t been made before.

There is some good news here, however. One piece of good news in this paper is that in some cases the examiners’s ratings of the difficulty were correlated with probability they would make the same decisions as before. But he examiner’s ratings of difficulty, however, only weakly predicted the errors that they made.

Another important finding is evidence that the best way to reduce errors is to have fingerprints examined by multiple people, rather than multiple examinations by the same person. The authors write:

Much of the observed lack of reproducibility is associated with prints on which individual examiners were not consistent, rather than persistent differences among examiners.
Nevertheless, even with two examiners checking fingerprints, Ulery and colleagues estimate that 19% of false negatives would not be picked out by having another examiner check the prints.

These papers all concern decisions made by experts, which is obviously the logical place to start from a policy and pragmatic point of view. As an exercise in seeing how expertise develops, tt would be interesting to see if beginners showed the same types of patterns in decision making.

References

Mookin JL. 2001. Fingerprint evidence in an age of DNA profiling. Brooklyn Law Review 67: 13.

Saks M. (2005). The coming paradigm shift in forensic identification science Science, 309 (5736), 892-895 DOI: 10.1126/science.1111565

Ulery B, Hicklin R, Buscaglia J, & Roberts M (2012). Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners PLoS ONE, 7 (3) DOI: 10.1371/journal.pone.0032800

Photo by Vince Alongi on Flickr; used under a Creative Commons license.... Read more »

Saks M. (2005) The coming paradigm shift in forensic identification science. Science, 309(5736), 892-895. DOI: 10.1126/science.1111565

Ulery B, Hicklin R, Buscaglia J, & Roberts M. (2012) Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners. PLoS ONE, 7(3). DOI: 10.1371/journal.pone.0032800

March 8, 2012
08:00 AM
175 views

Overselling the connectome

by Zen Faulkes in NeuroDojo

In the last few years, there has been much discussion about the prospect of tracking the neural connections of mammalian, and particularly human, brains at very high levels of detail.

One of the major proponents of this effort has been Sebastian Seung, who you can see giving a TED talk here. He sells the idea that understanding the human connectome will help us understand human identity. In his talk, Seung encourages his audience to say along with him. “I am my connectome.” He’s written a new book on this subject, Connectome: How the Brain’s Wiring Makes Us Who We Are.

This is an ambitious research project that will no doubt yield highly improved techniques to get anatomical information and analyze it. We will learn a lot.

And it will fail.

The allure, promise, and shortcomings of the connectome approach are yesterday’s news to neuroethologists. In the 1960s and 1970s, neuroethologists put in a lot of effort to crack partial connectomes of several species. These were usually referred to as “circuit” or “wiring diagrams.” (“Connectome” only appeared when neuroscientists got genome envy.) We made good progress on these. For example, we can explain escape behaviour in fishes and crayfish by the main synaptic connection between the critical neurons. That said, escape systems were chosen specifically because they were unusual behaviours. They are very sterotyped, very fast, and dedicated to one single task.

As other circuits were cracked, they revealed a much more subtle story.

A new paper by Bargmann details the case histories of a few of the species that neuroethologists have basically cracked the circuit. And contrary to some expectations, getting the complete set of synaptic connections did not solve the problems of understanding behaviour. I’m very glad that Bargmann wrote this paper, because it saves me the trouble of writing a much longer blog post.

For example, the nematode worm Caenorhabditis elegans has 302 neurons, and all the connections between them are known. Bargmann writes:

At a more profound level, however, the wiring diagram was and remains difficult to read. The neurons are heavily connected with each other, perhaps even overconnected – it is possible to
chart a path from virtually any neuron to any other neuron in three synapses. ... Circuit studies suggest a reason for this failure: there is no one way to read the wiring diagram.
One of the major lessons that emerged in the 1990s from the study of these small circuits where we knew all the synaptic connections was the importance of neuromodulation. Neurons’ functions were not set only by their anatomical connections. They were profoundly influenced by a cocktail of neuroactive chemicals that could change the physiological responses of neurons.

Bargmann breaks it down. First, she shows that only rarely can you link single neurons to single behaviours. Then, she shows how one behaviour can result from several circuits, how one neuromodulator can influence several behaviours. And she notes that given how neuromodulation has appeared pretty much in every nervous system where we’ve looked, there’s every reason to expect it’s going to be a major factor in determining human neural activity, and thus, human identity.

In his TED talk, Seung draw an extended metaphor that the connectome is like the bed of a river.

I would like to propose a metaphor for the relationship between neural activity and connectivity. Neural activity is constantly changing. It's like the water of the stream; it never sits still. The connections of the brain's neural network determines the pathways along which neural activity flows. And so the connectome is like bed of the stream; but the metaphor is richer than that, because it's true that the stream bed guides the flow of the water, but over long timescales, the water also reshapes the bed of the stream. And as I told you just now, neural activity can change the connectome. And if you'll allow me to ascend to metaphorical heights, I will remind you that neural activity is the physical basis – or so neuroscientists think – of thoughts, feelings and perceptions. And so we might even speak of the stream of consciousness. Neural activity is its water, and the connectome is its bed.
Knowing the bed of the river still doesn’t tell you everything. The same river bed can have a trickle one day, and a flash flood the next. Neuromodulation is a bit like a dam partway along the river. It can regulate whether you have a torrent or a trickle.

Bargmann and I agree that connectome projects are very useful. But they alone will not solve the question of human identity.

Reference

Bargmann C. 2012. Beyond the connectome: How neuromodulators shape neural circuits BioEssays DOI: 10.1002/bies.201100185... Read more »

Bargmann C. (2012) Beyond the connectome: How neuromodulators shape neural circuits. BioEssays. DOI: 10.1002/bies.201100185

February 28, 2012
04:01 PM
202 views

Not every radical idea is right

by Zen Faulkes in NeuroDojo

It’s too hard to do groundbreaking science. Hutchinson, who self identifies as a student (though what level is not clear) argues in forthcoming paper in BioEssays that the reason it’s hard to do original science is all because of how science is funded.

As it stands, our current system may work well in weeding out technically flawed proposals and advancing incremental work, yet truly novel ideas will rarely be funded or even tolerated.
This is not a particularly new insight. I’ve written about it from time to time; see here. I think we disagree on the value of incremental work, though. I think most scientific progress comes from incremental work, while Hutchinson seems to think we get progress from “out of the box” thinking. Hutchinson asks:

If, historically, most new ideas in science have been considered heretical by experts, does it make sense to rely upon experts to judge and fund new ideas?
It is true that some now accepted ideas in science were disputed at first, but Hutchinson does not seem to consider that not every “novel idea” is ultimately vindicated. Case in point:

The emphasis on being liked by the scientific community as a prerequisite to survive as a practicing scientist subsequently limits critical exchange in science. This is the case with Peter Duesberg who went from a prestigious 7-year outstanding investigator grant from the NIH to grant-less ever since because he questioned the role of oncogenes in cancer and the role of HIV in AIDS.
You’re going to use HIV denial to build your case? Seriously? In a spectacular “own goal,” Hutchinson inadvertently demonstrates exactly why funding agencies are conservative: because there are some people out there who have ideas that are just wrong. There are ideas that are not worth pursuing.

And I did a double take when I read this in the acknowledgements:

I thank Peter Duesberg (UC Berkeley) for useful comments and suggestions(.)
It might not be best form to use someone who gave you feedback on an article as an example of someone who’s been treated unfairly. This is in an article that complains about how “who you know” is contaminating science.

Hutchinon says:

The novelty of an idea can be measured by how many ideas and people it contradicts.
Alas, the insanity of an idea can be measured in precisely the same way.

At the end of the article, Hutchinson proposes a couple of ways out of dealing with fuddy-duddy old boys’s network of granting agencies. One is to incorporate more non-scientists into the review process. I might argue that we’ve seen some of the outcomes of non-scientists getting involved in the scientific process whenever we hear about politicians ragging on certain projects as “wasteful.”

Another solution, Hutchinson argues, is crowdfunding. Having been involved in a crowdfunding project (SciFund), I’ve heard concerns that cranks will use crowdfunding to get money for their goofy projects. I think that crowdfunded research projects should have some form of peer review to keep out the crazies.

Reference

Nicholson J. 2012. Collegiality and careerism trump critical questions and bold new ideas: A student's perspective and solution. BioEssays: in press. DOI: 10.1002/bies.201200001... Read more »

Nicholson J. (2012) Collegiality and careerism trump critical questions and bold new ideas: A student's perspective and solution. BioEssays. DOI: 10.1002/bies.201200001

February 23, 2012
08:00 AM
214 views

Walk up to that bear

by Zen Faulkes in NeuroDojo

“See that bear?”

“That one there? Yeah.”

“Go walk up to it.”

“What?”

“Go on. Just walk up to it.”

“Um...”

That’s the sort of dialogue I heard in my head with I read the title, “Behaviour of solitary adult Scandinavian brown bears (Ursus arctos) when approached by humans on foot.”

Large mammals and humans often don’t get along well, and this is true of bears, too. Bears are a threat to humans, and humans are a threat to bears. This particular bear species is not doing so well in the wild, with several countries having a few hundred to a few thousands.

The researchers located 30 bears that had been given radio collars. That way, the positions of the bears were known to the people walking towards them. Many, if not all of the bears, were approached multiple times, but those were at least two weeks apart. One to four people started almost a kilometer away from the bear. The observers’ path was always upwind of the bear, so the bear would have scent cues coming from the people and would be less likely to be surprised.

As part of the objective was to simulate hikers, the observers were keep a normal hiking pace and talk to each other. The authors noted, though:

When just one observer approached the bear, this person talked to him- or herself.
I imagine some poor bear sitting in the forest thinking, “Hoooooo boy. That one’s crazy.”

Most of the time, even knowing where the bears were, people only managed to see them about 15% of the time. Typically (80% of the time), the bears walked away from where they had been. None of the bears ever showed any signs of aggression towards people.

It’s good news that humans have little to fear from these bears. I do worry, though, that the bears might have a bit more to worry about from humans. I used to work in Waterton Lakes National Park in Alberta (one of my favourite places on the planet, by the way), and hikers were always being warned about bears. The black bears and grizzlies in the region, while not aggressive, are not exactly retiring, either. And humans in those parks have gotten themselves into all sorts of trouble by doing stupid things around bears. I do worry that if people think that Scandinavian bears are mostly harmless, people might do incredibly stupid things around the bears (trying to get a picture, and so on.)

Reference

Moen G, Støen O, Sahlén V, Swenson J. 2012. Behaviour of solitary adult Scandinavian brown bears (Ursus arctos) when approached by humans on foot PLoS ONE 7(2): e31699. DOI: 10.1371/journal.pone.0031699

Picture by ucumari on Flickr; used under a Creative Commons license.... Read more »

Moen G, Støen O, Sahlén V, & Swenson J. (2012) Behaviour of solitary adult Scandinavian brown bears (Ursus arctos) when approached by humans on foot. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0031699

February 15, 2012
08:00 AM
207 views

Miniature chameleons: beyond the “Squee!”

by Zen Faulkes in NeuroDojo

The discovery of several new tiny species of chameleons is making the round in science news this week. When I heard about them, I went to the paper and to see the pictures of them. And they are amazing! Look at juveniles in B and C – they are irresistible.

You went, “Squee!”, didn’t you?

This is Brookesia micra, the smallest of the new species. There are four species described in this paper, shown below:

From top to bottom, they are Brookesia tristis, Brookesia confidens, Brookesia micra (which you saw above), and Brookesia desperata.

But as I was browsing through the paper, I hit this. And it stopped me cold.

It’s the description of the name of one of the species, Brookesia tristis.

Etymology.— The species epithet is an adjective derived from the Latin “tristis” meaning “doleful”, “sad”, “sorrowful”, and refers to the fact that the entire known range of this species (Montagne des Français) suffers from severe deforestation and habitat destruction despite recently being declared as a nature reserve.
I just found this so sad. The authors are so pessimistic about the chances for the survival of this marvelous little species, they have

Another species, Brookesia desperata, has a similar section describing the rationale for its name:

Etymology.— The species epithet is an adjective derived from the Latin “desperatus” meaning “desperate”. Although the known range of the species is within a nature reserve established decades ago, its habitat is in truth barely protected and subject to numerous human-induced environmental problems resulting in severe habitat destruction [41], thus threatening the survival of the species.
I am glad that one species gets a more optimistic name:

Etymology.— The species epithet is an adjective derived from the Latin “confidens” meaning “confident”, “trusting”. The known range of the species is supposedly a well protected nature reserve with apparently limited habitat destruction. Furthermore, this area might benefit from natural protection by the tsingy limestone formations which are difficult to access, thus giving hope for the species’ survival.
A lot of the news coverage is focusing on the tiny size and the cuteness of these animals (io9, Gizmodo, Gizmodo Australia, MSNBC, Our Amazing Planet). Only one of the stories I have seen so far have mentioned the extreme pessimisn about the species’ continued survival. And – surprise! it’s The Daily Mail, which I mocked a while back for their headline hogwash. Their story says:

The new additions to the chameleon species are only found in an area just a few square miles in size.

Experts believe they may be especially sensitive to habitat destruction.
A big part of the discussion section of this paper is about “microendemism” This is the fancy way of saying that these chameleon species, and their relatives in this genus, all appear to have very small, restricted ranges. Presumably, they are just not able to disperse from location to location, so even minor geographic barriers becomes insurmountable to these creatures.

I’m actually terribly worried now that someone will look at these, see only the cuteness, and try to go collect them for the pet trade. That could be devastating to this species.

I wish more articles that tell people about these marvelous little animals would use the opportunity to tell people that if we’re not careful, we could lose them before we even get to know them.

Reference

Glaw F, Köhler J, Townsend T, & Vences M (2012). Rivaling the world's smallest reptiles: discovery of miniaturized and microendemic new species of leaf chameleons (Brookesia) from Northern Madagascar PLoS ONE, 7 (2) DOI: 10.1371/journal.pone.0031314... Read more »

Glaw F, Köhler J, Townsend T, & Vences M. (2012) Rivaling the world's smallest reptiles: discovery of miniaturized and microendemic new species of leaf chameleons (Brookesia) from Northern Madagascar. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0031314

February 13, 2012
10:09 AM
236 views

How Pompeii worms take the heat

by Zen Faulkes in NeuroDojo

This is the Pompeii worm (Alvinella pompejana), and it is a record-holding animal.

Its record is not for the most unlikely animal (though you have to admit, it is a bit odd looking). You are looking at the animal that is able to withstand higher temperatures than anything else in the animal kingdom. The Pompeii worm routinely withstands scalding 80°C water. Not only that, it can routinely go outside of that to water that is more like room temperature, at 20°C.

That this worm is able to take high temperatures makes sense when you consider where these animals live. These are one of the deep sea vent animals that live near water hot enough to melt lead. As I described recently, the animals themselves don’t venture into the superheated water, but stray close enough that temperature is a consideration for them. And when they move away from the water erupting from the bottom of the ocean floor, they can face temperatures that are only a few degrees above freezing.

Most organisms cannot go into temperatures that high, because their proteins, including all the vital enzymes that catalyze almost every reaction in every cell, should be coming apart at the seams. Proteins are long, strand-like molecules, and they work because that strand is folded into complicated shapes. Those shapes are held together by a whole bunch of complex chemical bonds. But high temperatures can break chemical bonds. You see this process in action every time you cook an egg: the high temperatures break the chemical bonds holding the proteins in their particular shapes, and you get new shapes with different properties. This is why eggs go from runny and clear to more solid and white.

A new paper, authored by Jollivet and team, tries to work out just how the proteins in the Pompeii worm are able to hold together in conditions that would turn ours all sproggly (that's the technical term). They do this by a lot of molecular biology to look at the structure of the proteins in the worms en masse. They note two things.

First, the proteins in the Pompeii worm are do not like to dissolve in water (hydrophobic). I don’t pretend to exactly understand how that stabilizes the protein, but it seems to be a trends that is also seen in bacteria that thrive in hot springs and the like.

Second, the proteins in the Pompeii worm have a lot of ionized bits. This made a little more intuitive sense to me, as I could imagine how having lots of positive and negative charges in the proteins would allow for the formation of more ionic bonds (salt bridges) along the length of the protein. More bonds within the protein should mean more stability. Ionic bonds are reasonably strong (weaker than covalent bonds, stronger than hydrogen bonds and Van der Waals forces).

The authors take this analysis one step further, and look not only at the Pompeii worm, but a relative (Paralvinella grasslei; alas, it seems to have no common English name), which is nowhere near as tolerant of those high temperatures. Jollivert and company found that many of the changes they saw were not unique to the Pompeii worm; P. grasslei showed some of the same trends. Both worms seemed to have a trend to hydrophobic proteins compared to other species. The authors suggest that the common ancestor of the two may have been more like the Pompeii worm in liking hot water, and that Paralvinella grasslei migrated back into cooler waters during its evolution.

Hot worm. Cool science.

Reference

Jollivet D, Mary J, Gagnière N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O, Lecompte O. 2012. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm PLoS ONE 7(2): e31150. DOI: 10.1371/journal.pone.0031150
... Read more »

Jollivet D, Mary J, Gagnière N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O.... (2012) Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0031150

February 7, 2012
08:00 AM
251 views

Tuesday Crustie: What’s bigger than a giant?

by Zen Faulkes in NeuroDojo

This picture was making the rounds last week after being reported by the BBC:

The BBC did not mention a species name, and the infographic below suggests that it’s an unknown. On the CRUST-L listserver, however, the general agreement was that this was Alicella gigantea, the biggest known amphipod. This is a deep water, rarely seen species.

This infographic prompted Rebecca Watson to quip:

If you’re wondering how big Superprawn was, this image clearly shows he was about half the size of New Zealand.
Not a heck of a lot is known about its biology, though all signs point to it being a scavenger. The few times its been photographed, its often been on bait. Its mouth is shaped to take in large bites of food, and about 90% of its innards consists of the midgut. Many of the specimens have been retrieved from the guts of fish, so these animals aren’t big enough to escape predators.

Alicella gigantea is collected in the Atlantic, too. It’s thought that they are the same species, but to my knowledge, no DNA work supports that. Several people on the Crustacean discussion list were explicitly skeptical of the idea that something this wide-ranging would be the same species. Indeed, one person noted that differences between the Atlantic and Pacific populations were noted some time ago.

References

De Broyer C, Thurston MH. 1987. New Atlantic material and redescription of the type specimens of the giant abyssal amphipod Alicella gigantea Chevreux (Crustacea). Zoologica Scripta 16(4): 335-350. DOI: 10.1111/j.1463-6409.1987.tb00079.x

Barnard JL, Ingram CL. 1986. The supergiant amphipod, Alicella gigantea Chevreux from the North Pacific Gyre. Journal of Crustacean Biology 6: 825-839.... Read more »

Broyer C, & Thurston M. (1987) New Atlantic material and redescription of the type specimens of the giant abyssal amphipod Alicella gigantea Chevreux (Crustacea). Zoologica Scripta, 16(4), 335-350. DOI: 10.1111/j.1463-6409.1987.tb00079.x

February 6, 2012
08:00 AM
268 views

Be eaten, make glowing fish poo, profit!

by Zen Faulkes in NeuroDojo

Why glow if you don’t have eyes to see?

Glowing takes energy. Down in the deep ocean, energy is in short supply, so why would bacteria do this? Bacteria don’t have eyes. It’s not like they’re going to be able to use it to find stuff. And these bacteria are not living in another organism, so it’s not as though they’re glowing in some sort of mutual trade with a host.

These bacteria only glow when they’re in large numbers, close together (quorum sensing), however. This gives a clue to what might being going on. A new paper by Zarubin and colleagues conducts several experiments to test the hypothesis that these deep sea bacteria are glowing because they want to be eaten.

You might think getting eaten is not a productive thing to do. The idea is: bacteria light up when they’re in large enough numbers to signal decent food. The bacteria themselves might not be the food, so much as the article they’re attached to.

The bacteria use the insides of their consumers as a way to disperse themselves throughout the ocean. It’s already been shown that a fairly large number of these glowing bacteria can survive passage through the gut. But that alone doesn’t provide enough a strong test of the hypothesis that the bacteria glow to advertise themselves as bait.

First, the team tested whether animals preferred glowing bacteria by putting two bags in a big tank of predators. One bag contained glowing bacteria; another contained same species, but with a mutation that prevented the glowing. Decapod and mysid crustaceans went almost all for the glowing bacteria. But it’s not a universal attractor; copepod crustaceans ignored both bags of bacteria.

Brine shrimp (Artemia) would start to glow after swimming in these bacteria, and their guts started to glow after the shrimp ate the bacteria.In the picture below, you can see Artemia in plain light, and after 30 second in the dark. The light is dim, but they do indeed glow.

There is a problem here, though: they switched species. They don’t say whether they tested if Artemia were attracted preferentially to the glowing bacteria. You can show a plausible chain of events, but to “close the loop” on this story, you’d have to use the same bacteria eaters all the way through. The authors justify this partly by convenience (Artemia are easy to rear in large numbers) and partly by saying that this allows them to see the effect better. Brine shrimp don’t have escape behaviour. Thus, this removed possible confounds of an interaction between the glowing and any movements caused by escape responses. They also say that one of the mysids glows after contacting the bacteria. They don’t show data for that, or give any citations, however. Their convenience came at the cost of ecological plausibility.

The glowing Artemia are much more likely to be eaten by fish – about ten times more likely. They tested this by putting Artemia in tanks with ring-tailed cardinal fish (Apogon annularis, pictured), which is nocturnal. And after the cardinalfish eat these brine shrimp, the bacteria do fine. They make it all the way through the fish’s digestive system, and they make the resulting feces also glow (though probably not brightly). The authors also tested the feces of other bacteria eaters – the Artemia and mysids – and they also tend to glow.

What I’d like to see next is some indication of whether the zooplankton are getting any nutritional value from eating these bacteria. Are the bacterial consumers being tricked into wasting time consuming “empty calories” that will just pass through their guts without benefit? If so, why haven’t the zooplankton wised up to this? I mean, how embarrassing would it be to be punked by bacteria? Or is these a “selfish herd” sort of situation, where a small proportion of group members are lost, but the risk to individuals is so low? And is there any manipulation of the plankton behaviour by the bacteria, similar to the way large parasites often work?

Reference

Zarubin M, Belkin S, Ionescu M, Genin A. 2012. Bacterial bioluminescence as a lure for marine zooplankton and fish Proceedings of the National Academy of Sciences 109(3): 853-857. DOI: 10.1073/pnas.1116683109

Apogon annularis picture from here.... Read more »

Zarubin M, Belkin S, Ionescu M, & Genin A. (2011) Bacterial bioluminescence as a lure for marine zooplankton and fish. Proceedings of the National Academy of Sciences, 109(3), 853-857. DOI: 10.1073/pnas.1116683109

February 3, 2012
08:00 AM
289 views

Jumping spiders still have use for muscles

by Zen Faulkes in NeuroDojo

You can’t push on a rope.

This is why you typically need two muscles to get things done. Muscles only shorten; if you flex a joint, you can’t expand your muscles to push that joint back to its original position. You have to pull a different muscle, with different insertion points, to get that limb back to where it was. For instance, you have biceps to flex your forearm, and triceps to extend it.

Spiders have always been something of a puzzle, because many of their limb joints have unpaired muscles. This is particularly true of the joints far from the body; the joints close to, and on, the body have more usual paired muscles.

On the face of it, this should mean that their joints should only be able to go int one direction. But spiders are agile predators and their limbs are moving back and forth rapidly.

Many spiders use hydraulic pressures to snap their limbs back into position after a muscle has moved it. This has been quite well investigated in a few small species, but Weihmann and colleagues reckoned it was worth re-investigating in a larger spider. They took a big spider species, Ancylomete concolor (pictured), and studied the forces the legs exerted when this spider jumped.

Some of the math and methodology is a little hairy (no pun intended), but this picture helps:

In short, if the spiders are using hydraulics (as small spiders do), the forces from the tip of the leg should be directed forward. If the spiders are mainly using the paired muscles in the joints close to the body, the forces should be directed much more upward.

Wiehmann and company find that their results are much more in line with the jump being powered by muscular contraction than hydraulic pumping. They’re not saying it’s entirely muscle, though, just that muscles are contributing more than the hydraulic factors.

The team briefly takes a stab at the bigger question: why mess around with all the hydraulics in the first place? Why do spiders not have paired muscles all the way through their legs, like sensible insects and crustaceans? Weihmann and company speculate that because spiders are obligate, active predators, that the loss of extensor muscles means that there’s more room for big, powerful flexord muscles – just the things to grab and grapple and subdue prey.

Reference

Weihmann T, Gunther M, Blickhan R. 2012. Hydraulic leg extension is not necessarily the main drive in large spiders. The Journal of Experimental Biology 215(4): 578-583. DOI: 10.1242/jeb.054585

Photo from here.... Read more »

Weihmann T, Gunther M, & Blickhan R. (2012) Hydraulic leg extension is not necessarily the main drive in large spiders. The Journal of Experimental Biology, 215(4), 578-583. DOI: 10.1242/jeb.054585

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