Why are fish brains so small?

I’ll take “questions I didn’t realize I was interested in”. The deeper you go in the ocean, the smaller brains get. From the abstract:

Here, we test three hypotheses of brain size evolution using marine teleost fishes: the direct metabolic constraints hypothesis (DMCH), the expensive tissue hypothesis and the temperature-dependent hypothesis. Our analyses indicate that there is a robust positive correlation between encephalization and basal metabolic rate (BMR) that spans the full range of depths occupied by teleosts from the epipelagic (< 200 m), mesopelagic (200-1000 m) and bathypelagic (> 4000 m). Our results disentangle the effects of temperature and metabolic rate on teleost brain size evolution, supporting the DMCH. Our results agree with previous findings that teleost brain size decreases with depth; however, we also recover a negative correlation between trophic level and encephalization within the mesopelagic zone, a result that runs counter to the expectations of the expensive tissue hypothesis. We hypothesize that mesopelagic fishes at lower trophic levels may be investing more in neural tissue related to the detection of small prey items in a low-light environment.

In other words, there are metabolic constraints at lower ocean depths over and above the temperature-dependence. And interestingly, fish that are lower on the food chain (trophic levels) have relatively larger brains; possibly because it requires more difficult sensory/etc computations to find their prey in a sensory-deficient environment:

Although encephalization in marine fishes of the mesopelagic was partially explained by trophic level (Tables 2 and 3), this finding disagrees with expectations under the expensive tissue hypothesis. Rather than finding an increase in encephalization at higher trophic positions, our analysis supported an inverse relationship. This trend of increased brain size relative to body size at lower trophic positions may be partially explained by the increased sensory needs of planktonic feeders at depths below 200 m… Plankton feeders in particular tend to have greater eye and lateral line modifications in order to detect more minute prey quantities (Bleckmann, 1986; Coombs et al., 1988). While changes in brain morphology have been associated with epipelagic fishes living in turbid water…

(ht Neuroskeptic)

Whither experimental economics?

When I was applying to graduate school, I looked at three options: neuroscience, computer science, and economics. I had, effectively, done an economics major as an undergrad and had worked at an economic consulting firm. But the lack of controlled experimentation in economics kept me from applying and I ended up as a neuroscientist. (There is, of course, a very experimental non-human economics which goes by the name of ecology, though I did not recognize it at the time.)

I profess to being confused as to the lack of experimentation in economics, especially for a field that constantly tries to defend its status as a science. (Well, I understand: incentives, existing capabilities, and all that.)

A recent dissertation on the history of experimental economics – as opposed to behavioral economics – is enlightening:

“We were describing this mechanism and Vernon says, “You know, I can test this whether it works or not.“ I said, “What do you mean?“ And he says, “I’ll run an experiment.“ I said, “What the heck are you talking about? What do you do?“ And so he hauls seven or eight graduate students into a classroom. He ran the mechanism and it didn’t work. It didn’t converge to the equilibrium. It didn’t produce the outcomes the theory said it would produce. And I thought, okay. So back to [doing] theory. I don’t care; this doesn’t bother me.

It bothered Vernon a lot because we sat around that evening talking and he says, “Oh, I know what I did wrong.“ And he went back the next day and he hauled the students back in the room, changed the rules just a little bit in ways that the theory wouldn’t notice the difference. From our theory point of view, it wouldn’t have mattered. But he changed the rules a little bit and bang that thing zapped in and converged.“

The difference between the two experiments was the information shared with the test subjects. The first time around, the subjects wrote down their number on a piece of paper and then Smith wrote them up on the board. Then he asked the subjects to send another message and if the messages were the same twice in a row he would stop, since that stability would be interpreted as having reached equilibrium. But the messages did not stop the first time Smith had run the experiment a day earlier…

The fact that the experiment did not converge at the first attempt, but did at the second with a change of only one rule (the information structure available to the participants) not required by theory to make its prediction made a lasting impact on Ledyard.

And this is exactly why we do experiments:

[T]he theory didn’t distinguish between those two rules, but Vernon knew how to find a rule that would lead to an equilibrium. It meant he knew something that I didn’t know and he had a way of demonstrating it that was really neat.

In psychology and neuroscience, there are many laboratories doing animal experiments testing some sort of economic decision-making hypothesis, though it is debatable how much of that work has filtered into the economic profession. What the two fields could really use, though, are economic ideas about more than just basic decision-making. Much of economics is about markets and mass decisions; there is very animal experimentation of these questions.

(via Marginal Revolution)

Richard Lewontin: some perspectives on the sociology of ecology

There’s an interesting interview with Richard Lewontin over at the Evolution Institute.

First, he slags off Steven J Gould a bit:

RL: Now I should warn you about my prejudices. Steve and I taught evolution together for years and in a sense we struggled in class constantly because Steve, in my view, was preoccupied with the desire to be considered a very original and great evolutionary theorist. So he would exaggerate and even caricature certain features, which are true but not the way you want to present them. For example, punctuated equilibrium, one of his favorites. He would go to the blackboard and show a trait rising gradually and then becoming completely flat for a while with no change at all, and then rising quickly and then completely flat, etc. which is a kind of caricature of the fact that there is variability in the evolution of traits, sometimes faster and sometimes slower, but which he made into punctuated equilibrium literally. Then I would have to get up in class and say “Don’t take this caricature too seriously. It really looks like this…” and I would make some more gradual variable rates. Steve and I had that kind of struggle constantly. He would fasten on a particular interesting aspect of the evolutionary process and then make it into a kind of rigid, almost vacuous rule, because—now I have to say that this is my view—I have no demonstration of it—that Steve was really preoccupied by becoming a famous evolutionist.

And then his former advisor:

RL: Now, historically one of the most interesting—now I want to talk a little about the sociology of our science—Theodosius Dobzhansky, my professor and then greatest living evolutionary biologist…

DSW: Mr. “Nothing in biology makes sense except in the light of evolution…”

RL: Yeah, right. He was a very bad field observer. Theodosius Dobzhansky never, in his entire life, nor any of his students, me included—I would go out in the field with him, actually–ever saw a Drosophila pseudoobscura in its natural habitat…We didn’t know where they laid their eggs. We couldn’t have counted the number of eggs of different genotypes. How did we study Drosophila in the wild? We went out into the desert, into Death Valley, we moved into a little oasis, we went first to the grocery store, and bought rotten bananas. We mushed up the bananas with yeast till they fermented a bit, we dumped that into the paper containers, put it out in the field and the flies came to us…If I wanted to study evolutionary forces acting on some genetic polymorphism in Drosophila, I would go and look for some species of Drosophila where I could actually look at, perturb, and work with the actual breeding sites and egg laying sites and pick up larvae in nature and so on. And in fact there is such a group of Drosophila. They the cactophilic ones. There is a group [of scientists] from Texas and other places that studies the cactophilic Drosophila in an ecologically sensible way of going to the rot pockets and perturbing them, getting larvae out of them and so on. That group never acquired the prestige associated with the Dobzhansky school because—I don’t know why.

Lewontin is not normally my cup of tea, but this view is very interesting.

The unappreciated animals of science

Would you believe it – I actually forgot that I had a blog for a few of weeks. I guess I was busy?

If you don’t work on a particular organism, you tend to forget that each has its own history outside of the laboratory. Catherine Dulac has a great video wild-caught mice: whereas laboratory strains are sedentary, moseying about their cage without a care in the world, wild-caught mice are little ninjas, running around and jumping off the sides. These ain’t the same creatures.

eLife has a good series on the natural history of model organisms. Right now they have C. elegans, zebrafish, and E. coli, though I expect there will be more.

On nasty E. coli:

In 1884, the German microbiologist and pediatrician Theodor Escherich began a study of infant gut microbes and their role in digestion and disease. During this study, he discovered a fast-growing bacterium that he calledBacterium coli commune, but which is now known as the biological rock star that is Escherichia coliE. coli‘s relationship with a host literally begins at birth. Newborns are typically inoculated with maternal E. coli through exposure to her fecal matter during birth and from subsequent handling. Although perhaps disconcerting to ponder, this inoculation seems to be quite important. Indeed, E. coli becomes more abundant in the mother’s microbiome during pregnancy, increasing the chances of her newborn’s inoculation…

The external world was long thought to be so harsh as to preclude E. coli‘s growth outside of its host. While a tiny minority might eventually reach a new host, most cells were expected to eventually die. This is the basal assumption behind using the presence of E. coli as an indicator of fecal contamination. However, recent studies have shown that E. coli can, in fact, establish itself as a member of microbial soil, water, and plant-associated communities

On fishies:

Field observations of zebrafish behavior are few and anecdotal, and so much of what zebrafish do in nature has to be inferred from their behavior in the lab…Interestingly, wild-caught and lab fish (both previously imprinted on the ‘wild type’) have similar preferences for prospective shoaling partners…Lab strains of zebrafish spawn all year round, but breeding in the wild occurs primarily during the summer monsoons, when ephemeral pools appear; these presumably offer plenty to eat and some shelter from currents and predators.

Analyses of wild zebrafish suggest a reason for the discrepancies: these fish have a major sex determinant (WZ/ZZ) on chromosome 4—which has features similar to sex chromosomes in other species—yet this determinant has been lost from lab strains (Wilson et al., 2014). This suggests that founder effects, or domestication itself, led to seemingly ad hoc systems employing multiple sex determinants, probably of small original effect in the wild.

On wormies:

This species was originally isolated in rich soil or compost, where it is mostly found in a non-feeding stage called the dauer. More recently, feeding and reproducing stages of C. elegans have been found in decomposing plant material, such as fruits and thick herbaceous stems. These rotting substrates in their late stages of decomposition provide abundant bacterial food for the nematode…Population demographic surveys at the local scale in orchards and woods indicate that C. elegans has a boom-and-bust lifestyle. C. elegans metapopulations evolve in a fluctuating environment where optimal habitats are randomly distributed in space and time… Over the year, in surveys performed in France and Germany, C. eleganspopulations in rotting fruits typically peak in the fall, with proliferation possible in spring through to early winter…

If not with E. coli, it is noteworthy that C. elegans shares its rotting fruit habitat with two other top model organisms, Drosophila melanogaster and Saccharomyces cerevisiae…A specific association is actually found between another Caenorhabditis species and another Drosophila species: this nematode species, C. drosophilae, feeds on rotting cactus in desert areas and its dauer juveniles use a local Drosophila species as a vector to move between cacti.

Orchid mantis: more interesting than cryptic mimicry


I know, I know, you read the title and exclaim: what can be more exciting than cryptic mimicry?! Well, listen to this:

On the face of it, this is a classic evolutionary story, and a cut-and-dried case: the mantis has evolved to mimic the flower as a form of crypsis – enabling it to hide among its petals, feeding upon insects that are attracted by the flower…

O’Hanlon and colleagues set about systematically testing the ideas contained within the traditional view of the orchid mantis’ modus operandi. First, they tested whether mantises actually camouflage amongst flowers, or, alternatively, attract insects on their own…

However, when paired alongside the most common flower in their habitat, insects approached mantises more often than flowers, showing that mantises are attractive to insects by themselves, rather than simply camouflaging among the flowers…Surprisingly mantises did not choose to hide among the flowers. They chose leaves just as often. Sitting near flowers did bring benefits, though, because insects were attracted to the general vicinity – the “magnet effect”.

But wait: there’s more!

As an aside, I’ve heard that Preying Mantis’ make great pets. They are social creatures that will creepily watch you everywhere you go, but also kind of ignore you. They’re like insect-cats.

(Photo from)

Neanderthal neurograstronomy

There is a genetic basis to the food that we enjoy eating. Some people – which I call strange people – think cilantro has a strange, soapy taste at least partially because of a particular polymorphism in a odor receptor gene (OR6A2).

soapy cilantro

The question of why we enjoy certain foods and flavors is not solely a genetic one, but also a conceptual one. Take the questions of why we like spicy food. Other animals do not: they will eat spicy food but would rather prefer not to, thanks. If you ask people what the best spiciness level is, they will tell you that it is whatever is right below their pain threshold. A smidgen too much and it is unbearably hot. A smidgen too little and it is bland as they come. The molecule that gives something its spiciness is capsaicin which stimulates the same receptors that give information about the warmth of food. It is possible, then, that this is a byproduct of our adaptation to prefer cooked food. Food that has been roasted is digested more quickly and provides more calories.

But knowledge of genetics can give us insight into those we do not have direct experience with. We now have genomic sequence data from one Denisovan and two Neanderthals. Do they experience food similarly to modern humans?

In many ways, yes. One change that probably occurred after the invention of cooking is a reduction in certain masticatory muscles. Once you can cook, your needs to chew really really hard are reduced. And a gene responsible for this, MYH16, is expressed in chimpanzess (no fire) but not in humans (plenty of fire). It turns out that MYH16 is also not expressed in the Denisovan and Neanderthal samples.

We can also look at a taste receptor, such as TAS2R38 which responds to phenylthiocarbamide (PTC). This is a flavor that, depending on your genetic makeup you either cannot taste at all, or that tastes very bitter. There is variation across populations: 98% of people indigenous to the Americas can taste it while only 42% of those indigenous to Australia and New Guinea cannot. Interestingly, chimpanzees can also taste it but they do so in a different manner.

None of the Denisovan or Neanderthals had the human mutation that allowed PTC-tasting. But that shouldn’t stop them from tasting it: one of the Neanderthals had a different mutation from either humans or chimpanzees on the gene. This is convergent evolution at work, people.

Even more interestingly, the AMY1 is a gene responsible for the enzyme that starts the digestion of starch. Starch is responsible for something like 70% of the calories in human agricultural population. The more copies we have of this gene, the more of the enzyme we have in our saliva. Chimpanzees have two copies: humans have around 6 or 7 of them. And these Denisovans and Neanderthals? Only two!

You are what you eat, and what you eat is influenced by what you are. It’s pretty fun that we can get at what a Neanderthal enjoyed eating by looking at the genetics of their taste receptors…


Perry, G., Kistler, L., Kelaita, M., & Sams, A. (2015). Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data Journal of Human Evolution DOI: 10.1016/j.jhevol.2014.10.018

We are already cyborgs

You could see this as the impotence of separating our ‘selves’ from our choices and environment. You could also see this as how integrated technology already is into our bodies, even though we usually don’t realize it.

Biss says we are doubly bound: to nature and to technology, neither system we can either comprehend or reject completely. The cyborg scholar Chris Hables has written that many of us are “literally cyborgs, single creatures that include organic and inorganic subsystems.” The inorganic subsystem, Hables explains, is the “programming of the immune system that we call vaccination.” The vaccines are made by corporations, but corporations are made by people, and both the immune response and the antibodies it produces—to wit, the organic subsystems—are made by cells. Yet cells are so numerous, so automated that they resemble, in a way, corporate drones.

From an article on our complex, churning, learning immune system.

Hand-to-hand combat between animals and cells

eosinophils and c elegans



From an article on white blood cells (eosinophils) attacking nematodes, it is like something out of a horror movie. What is amazing about this is that these cells are attacking an animal with a nervous system and exist on roughly the same size scale! It kind of blows my mind that nervous systems and single cells coexist in this manner. Which returns to the question of: why does something at that size need a nervous system at all?

Here’s a new research program for you –  the neurological correlates of hand-to-hand combat with single-celled organisms…

[via reddit]

Behavior is as much about environment as it is about cognition

Over at TalkingBrains, Greg Hickok points to a review on embodied cognition that has several neat examples of how distinct behavior arises just by placing an agent in the correct environment:

Robots with two sensors situated at 45 degree angles on the robot’s “head” and a simple program to avoid obstacles detected by the sensors will after a while tidy a room full of randomly distributed cubes into neat piles:


Female crickets need to find male crickets to breed with. Females prefer to breed with males who produce the loudest songs… Female crickets have a pair of eardrums, one on each front leg, which are connected to each other via a tube. It so happens that the eardrums connect to a small number of interneurons that control turning; female crickets always turn in the direction specified by the more active interneuron. Within a species of cricket, these interneurons have a typical activation decay rate. This means that their pattern of activation is maximized by sounds with a particular frequency. Male cricket songs are tuned to this frequency, and the net result is that, with no explicit computation or comparison required, the female cricket can orient toward the male of her own species producing the loudest song. The analysis of task resources indicates that the cricket solves the problem by having a particular body (eardrum configuration and interneuron connections) and by living in a particular environment (where male crickets have songs of particular frequencies).

(Emphasis added.)

This, of course, is a perfect example of why we need ethology in order to understand the nervous system – behaviors only make sense in the context of the ecology that they operate in!