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Today is the fiftieth anniversary of manned space flight, which is an anniversary all humankind should celebrate. Now, I’m younger than Yuri Gagarin’s historic flight into space... but older than Neil Armstrong’s trip to the moon. I’m a space age kid.
The Soviets claim the first human in space, but who can lay claim to the first crustaceans sent into space?
All the references to crustaceans in space I have seen talk about good ol’ brine shrimp (Artemia). Why put Artemia in space? There are several reasons. They’re small, for one, which is a prime consideration considering the cost of putting anything into Earth orbit is directly related to mass.
One good scientific reason for putting brine shrimp into space is brought out by Spooner and colleagues (1992). Brine shrimp can put their eggs in tough cysts that can almost entirely dry out, and development stops until they get into salt water again. This means that you can put brine shrimp into space, start them growing, and be sure that all of that development did in fact occur in space. With almost any other animal, you will have a mix of growth on the ground and in space.
Which nation put crustaceans in space first? Wikipedia notes some went up in some of Russia’s Foton missions, which started in 1985. But then, we all know Wikipedia’s shortcomings. With a little digging, I was able to find an earlier spaceflight: Artemia had gone up in Apollo 16 in 1972 (Planel et al. 1974). This record seems to be held by the Americans.
Spooner BS, DeBell L, Hawkins L, Metcalf J, Guikema JA, Rosowski J. 1992. Brine Shrimp Development in Space: Ground-Based Data to Shuttle Flight Results. Transactions of the Kansas Academy of Science (1903-) 95(1/2): 87-92.
Clément G, Slenzka K. 2006 Animals and plants in space. In: Clément G, Slenzka K (eds.), Fundamentals of Space Biology, pp. 51-80. DOI: 10.1007/0-387-37940-1_2
Planel H, Soleilhavoup JP, Blanquet Y, Kaiser R. 1974. Study of cosmic ray effects on Artemia salina eggs during the Apollo 16 and 17 flights Life Sci Space Res 12: 85-89.
Photo by xavipat on Flickr; used under a Creative Commons license.... Read more »
Planel H, Soleilhavoup JP, Blanquet Y, & Kaiser R. (1974) Study of cosmic ray effects on Artemia salina eggs during the Apollo 16 and 17 flights. Life Sci Space Res, 85-89. info:/
When I was in graduate school, my boss went to an IBRO conference that contained a point / counterpoint pair of talks about what triggered the release of chemicals from one neuron that could be picked up by another. One researcher argued that calcium rushing into the neurons was the sole cause of the neurotransmitter release. The other argued that there wasn’t enough evidence to say definitively that calcium was both necessary and sufficient for neurotransmitter release.
A new paper may make both speakers wrong. Shakiryanova and colleagues claim to have found neurons that release neurotransmitter without calcium being involved at all.
My initial thought when I read the title of this paper was, “How silly of me to think that every neuron would have to use calcium to trigger neurotransmitter release. We see so much variation in neurons. Some neurons use calcium instead of sodium for spikes, and some neurons don’t spike at all. Why couldn’t there be a case of some neurons using something besides calcium?”
How do you prove the neurons don’t use calcium? And what do they do instead of calcium?
The basic experiment is very simple. Record from a presynaptic neuron, and target cell – a muscle in this case – and take out the calcium. If the target cell can still do anything in response, there’s your proof, more or less.
Now, the details are much more complicated. Because this is in a fruit fly maggot, they’re using genetically modified flies that have a neuroactive chemical that glows under the right light.
There were two different chemicals that could trigger the neurotransmitter release. One is called forskolin. It activates adenylyl cyclase, which in turn activates cyclic adenosine monophospate (also known as cyclic AMP), and that causes neuroactive chemical release.
The other chemical is something I’m more familiar with: octopamine, which has received a lot of attention for its role in regulating behaviour in invertebrates. For maximum effect, octopamine makes the neuron release calcium stored inside it, and that triggers neurotransmitter release, so calcium hasn’t been completely cut out of the system.
Many of the experiments are... complicated... for anyone who isn’t familiar with Drosophila mutations and cyclic AMP chemistry. This is indirect way of me saying that I struggled to make sense of this paper. This paper is acrotastic, swimming in abbreviations and symbols.
I am left with many questions. It’s not clear to me what the source of either forskalin or octopamine might be in this system. The authors seem to be suggesting that these chemicals are causing a sort of slow, gradual release of neurotransmitter. Some non-spiking neurons release some neurotransmitter tonically, so perhaps this system is a little like those.
If I understand right, calcium is still the only way known to trigger neurotransmitter release from an action potential. But I can’t help but think that it’s just a matter of time before someone finds a neuron where the spike triggers some other ion to rush in and cause neurotransmitter release.
Tangent: The authors call octopamine a “homolog” to norepinephrine. In evolution, “homolog” means “related by common ancestry,” which doesn’t apply to molecules. In molecular biology, “homolog” often means “similar sequences of DNA,” or some other long polymer, which also doesn’t apply here. Anyone familiar with some other meaning of the word I’m no familiar with?
Shakiryanova D, Zettel G, Gu T, Hewes R, & Levitan E (2011). Synaptic neuropeptide release induced by octopamine without Ca2+ entry into the nerve terminal Proceedings of the National Academy of Sciences, 108 (11), 4477-4481 DOI: 10.1073/pnas.1017837108
Photo by Max xx on Flickr; used under a Creative Commons license.... Read more »
Shakiryanova D, Zettel G, Gu T, Hewes R, & Levitan E. (2011) Synaptic neuropeptide release induced by octopamine without Ca2 entry into the nerve terminal. Proceedings of the National Academy of Sciences, 108(11), 4477-4481. DOI: 10.1073/pnas.1017837108
I’ve had one career: scientist.
My dad, on the other hand, has been a musician, mobile home salesman, jeweler, car salesman, Chicken Delight manager, and a few other things besides. But one of his last jobs before retiring was to be a safety officer at the Shell Waterton natural gas plant in the foothills of southern Alberta.
A little while ago, I asked him about one of the biggest safety challenges. I remembered him talking about when he would come home from work, which they usually referred to by the chemical formula: H2S.
Without a doubt H2S is at the very top of the list for the deadliest safety hazard in a gas plant. The H2S is contained in the gas (coming into the plant) before it is stripped out. Should a leak occur, the gas is colourless, odorless and heavier than air, so settles in low spots. The colourless and odorless properties make it extremely hard to detect without proper equipment. Exposure can cause death within three minutes.
Safety people wore H2S detectors and monitors and breathing apparatus and air was available in all buildings. There was an alarm system for the entire plant.
This chemical, hydrogen sulfide, is so nasty because it messes with the energy production in your cells. Your mitochondria get messed up and can’t generate energy. It’s like the power switches in every cell of your body get flipped off, one at a time. Imagine turning off the lights in a big warehouse: one section goes dark. Then another. Then another...
Because all multicellular organisms have mitochondria, hydrogen sulfide in high enough concentrations should be a poison to almost any living creature.
But this unassuming little fish is able to survive levels that would kill almost anything else.
This fish is Poecilia mexicana, a relative of aquarium (and evolutionary biology) favourites like guppies and mollies. As you might guess from the second half of its name, it lives in Mexico – southern Mexico, to be exact, where there are several small rivers with very high levels of hydrogen sulfide. The high levels of hydrogen sulfide are due to the geology of the area: the hydrogen sulfide is in the ground springwater that feeds the rivers.
It’s not only that the hydrogen sulfide levels are high that makes these rivers difficult to live in. Because sulfur reacts with oxygen, the oxygen levels in these rivers are low.
And it’s not the only species; P. sulphuraria also lives in such rivers. In fact, between the two species, it looks like these fishes have invaded these dangerous rivers three separate times. The close relative of these fish do not withstand hydrogen sulfide, so the ancestors of all the locals didn’t have some built-in resistance to the poison.
Given than hydrogen sulfide’s main effect is at the subcellular level, it’s surprising that all these lineages of fish show substantial changes in their body shape: fishes in the high hydrogen sulfide streams have larger heads than those that do not. The selective pressure is probably not the hydrogen sulfide, but the low oxygen in the streams. Larger heads mean more space for bigger gills, which intuitively means more oxygen uptake. This hasn’t been tested physiollogicaly yet, though.
There are also some changes in the fin position in P. sulphuraria compared to their relatives in less toxic streams. This does not seem to have any adaptive significance. They do seem to indicate that this population is off on its own independent evolutionary pathway, however.
Curiously, small fish tolerated the hydrogen sulfide much better than large ones. The reason for this is not discussed in the discussion, and I can’t figure out a reasonable hypothesis for why.
How do these become superfish, impervious to this poison? All animals make some hydrogen sulfide naturally, and so naturally have chemical pathways to get rid of tiny amounts of hydrogen sulfide. Presumably, these pathways have been ramped up to the max in these fish. This remains to be tested physiologically.
Ramping up those defenses against the hydrogen sulfide may not come cheap, though. These are not “superfish,” whose genes are spreading through nearby streams because of their ability to tolerate this poison. The mechanism and the cost of tolerating the hydrogen sulfide remains to be seen. There’s still much to do to understand how these fish were able to make it in these hostile environments.
Tobler M, Palacios M, Chapman L, Mitrofanov I, Bierbach D, Plath M, Arias-Rodriguez L, García de León F, & Mateos M (2011). Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs Evolution DOI: 10.1111/j.1558-5646.2011.01298.x
Photo from Michael Tobler’s own website.... Read more »
Tobler M, Palacios M, Chapman L, Mitrofanov I, Bierbach D, Plath M, Arias-Rodriguez L, García de León F, & Mateos M. (2011) Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs. Evolution. DOI: 10.1111/j.1558-5646.2011.01298.x
Male fiddler crabs spend a lot of time doing this sort of thing:
This is Uca mjoebergi, a colourful crab from south Pacific shores. They're signalling to someone - but to whom?. To their own species? Their own sex? To predators?
I had fun recently giving a talk about fiddler crab signalling at a local nature center. I had seen a decent amount of research on fiddler crabs, but had never had the opportunity to review it and try to pull it into a story before. And while I was doing that, a new paper appeared about fiddler crabs.
While you're preparing talk on something, new research gets published. It's a variation of the law of maximum inconvenience.
One of the problems with signalling is that it implies that there is some sort of intended audience. Spending your time and energy waving a lot can be worth it if your intended audience is always nearby.
In this case, this nicely coloured species, Uca mjoebergi, the males' audience is mainly females of the same species. In most of the range of this species, it's the only fiddler crab in the environment. But in some locations, there are a couple of other fiddler crab species. Some of them look distinctly different to us, but fiddler crabs' eyes don't have the same power as us.
Could the males of this species tell the females apart? Or would they be all, like, "Hey baby... hey baby... hey baby..." to any vaguely crab-like shape that was nearby?
The answer was... it depends.
When single females were released into a colony of U. mjoebergi males, the males waved regardless of whether it was a U. mjoebergi female (smooth moves!) or U. signata female (sorry, but you're not really my type).
Femalesof both species were also presented simultaneously, but in a slightly less natural scenario. Instead of females walking of their own volition through the colony, they were tethered so they wouldn't move out of range of a male's burrow. Booksmyth and colleagues also put up barriers so that males wouldn't be able to see other distractions.
Under these conditions, the males would often wave at both females... but they would wave longer and faster to the females of the same species, and were much more likely to try to mate with the female of the right species. But the match wasn't perfect; some males still tried to mate with the wrong species. Interspecies harassment, if you will.
This suggests that the guys can tell if the girl is the right species. So why don't they, especially if waving is costly?
One possibility is that by having the males generally waving regardless of species, a male colony might become almost like a lek or mating "hotspot" that attracts more females of the right species.
Another interesting one is that the females can tell the males apart better then the males recognize females. The females might "reject" inappropriate males so quickly that the cost to the male is minimized.
Finally, the mix of "right species" to "wrong species" might matter. The "right species" was far more prominent in this area. An interesting follow-up would be to repeat these experiments in a place where the "right species" was in the minority, and males might waste a lot more time and energy courting indiscriminately.
Booksmythe I, Jennions M, & Backwell P. 2011. Male fiddler crabs prefer conspecific females during simultaneous, but not sequential, mate choice. Animal Behaviour: In press. DOI: 10.1016/j.anbehav.2011.01.009
Photo from here.... Read more »
Booksmythe I, Jennions M, & Backwell P. (2011) Male fiddler crabs prefer conspecific females during simultaneous, but not sequential, mate choice. Animal Behaviour. DOI: 10.1016/j.anbehav.2011.01.009
We’re smart. Octopuses are smart. But we have different kinds of smart.
Octopuses don’t process information like us. An octopus can tell -[ from ]-, but has a very difficult time telling < from >. There are plenty of task that we find trivial that are very, very hard for octopuses to do. (Many are shown in Wells 1978).
Gutnick and colleagues were interested in whether octopuses could integrate sight and touch. We do this all the time. Almost the entire video game industry depends upon us being able to do this. But octopuses? They’d probably suck at video games. They can learn to attack a particular object they can see. They can distinguish objects based on touch. Nobody had been able to get them to learn a task that needed both.
These sorts of behavioural puzzles are what led Gutnick and colleagues to build this maze.
To get a food prize, the octopus has to reach up into a tube and grab the food. The octopus can’t use any chemical cues to locate the food, because the food is not in water; the octopus has to lift its arm outside the water to get it. The octopus has to figure out which of three possible locations the food is in by seeing it.
Gutnick and colleagues confirmed that vision is the main cue the octopuses are using by blacking out the arms of the maze and letting the trained octopuses try to find the food. As soon as they do that, octopuses fail, doing no better than blind luck.
This task sounds easy... for a human, it is. But the octopuses in this study had to work a long time to get this down. None learned it in fewer than 60 trials. And one of the seven octopuses never learned the task. (I had similar experiences training octopuses.) And they never got faster at it.
But the point is not that the animals are slow to learn; the point is that they can learn to do this at all. Several previous studies had not been able to get octopuses to integrate their sight and touch in this way. And at the neural level, there is little evidence for the brain of octopuses being arranged in sensory or motor maps like they are in many vertebrates.
The authors speculate a bit on the way that the visual and touch systems might be coordinated. Some octopus arm movements are purely “top down” affairs: the brain sends a command and the arm follows through, and sensory input from the arm doesn’t alter the movement very much.
The authors suggest that the behaviour they are seeing might be too complicated for that, and think that there is an interplay between the sense of sight and the sense of touch. They don't have any strong evidence for that yet, however. This might be testable by modifying the task so that the octopus was only able to see the food for a limited time, or to change the position of the food after the octopus had started to reach into the tube.
So maybe there’s hope that one day, this will be a reality:
Gutnick T, Byrne R, Hochner B, Kuba M. 2011. Octopus vulgaris uses visual information to determine the location of its arm. Current Biology: In press. DOI: 10.1016/j.cub.2011.01.052
Note: The article has a nice 4 minute video that appears to be freely available!
Wells MJ. 1978. Octopus: physiology and behaviour of an advanced invertebrate. Chapman and Hall: London.
Dumbo octopus photo by Anomolous4 on Flickr; used under a Creative Commons license.... Read more »
Gutnick T, Byrne R, Hochner B, & Kuba M. (2011) Octopus vulgaris uses visual information to determine the location of its arm. Current Biology. DOI: 10.1016/j.cub.2011.01.052
Progress happens when people communicate. Otherwise, people waste time re-doing something that has already been done.
Many people are not happy with the state of the teaching of science in universities, particularly the first couple of years of classes. They are often large and can feel impersonal. They are often a mix of people who intend to major in the discipline and those who are taking breadth requirements. And it's fair to say that they are not always viewed as plum tasks by many faculty members.
This paper not only assesses the effectiveness of many different kinds of different strategies for teaching undergraduate classes, but provides great examples of what not to do in reporting your science.
First, the actual teaching stuff. They found positive effects for all manner of innovations, like collaborative learning, conceptually oriented tasks, and used of various kinds of technologies, and all manner of permutations and combinations therein.
The problem is that there is so much smear in the data that it's hard to zero in on which are the most effective techniques. And they note that the better designed the experiment, the smaller the measured effect was. If you randomly assign subjects (i.e., students got into one of two classes at random), a standard technique in experiments biology, psychology, and elsewhere, the effect size was 0.26. If students were not randomly assigned - students self-registered for classes - the reported effect size was bigger, 0.50. But we should maybe have a little more confidence in the actual experiments. After all, this is the level we consider to be appropriate for things like clinical drug testing.
As for the "don't do this" aspect of the paper, the authors say that almost half the studies they looked at couldn't be included in their analysis because of some reporting flaw.
And it's not hard stuff.
For instance, Ruiz-Primo and colleagues note that many papers show p values, but not basic statistical information like sample size. Or the actual means and standard deviation. These are not complicated things to calculate or include.
The authors also slap the journals publishing these papers a little, noting that people have complained about the poor level of science around teaching and education before. Yet, "journals continue publishing these types of papers."
And the moral of the story? Scientists who are interested in teaching need to start bringing the same level of attention to detail to educational experiments that we bring to our other research subjects.
Ruiz-Primo M, Briggs D, Iverson H, Talbot R, & Shepard L. 2011. Impact of Undergraduate Science Course Innovations on Learning. Science 331(6022): 1269-1270. DOI: 10.1126/science.1198976
Photo by THomas Guest on Flickr; used under a Creative Commons license.... Read more »
Ruiz-Primo M, Briggs D, Iverson H, Talbot R, & Shepard L. (2011) Impact of Undergraduate Science Course Innovations on Learning. Science, 331(6022), 1269-1270. DOI: 10.1126/science.1198976
To recap: In early December, NASA holds a press conference relevant to astrobiology, wherein Felisa Wolfe-Simon announces a paper on a very interesting bacteria. The bacteria is indisputably arsenic tolerant, but Wolf-Simon and her eleven co-authors claim that the bacteria is not just tolerating arsenic, but using it in place of phosphorus. Before the weekend is out, strong criticisms of the paper appear on blogs. Wolfe-Simon initially refuses to respond to anything that isn’t in a peer-reviewed journal, but later relents and put up a FAQ on her website.
Now, criticisms are appearing in the peer-reviewed literature, like this one by Rosen and colleagues. The analysis is quite a helpful one in many ways, providing good background information on things like how cells can use arsenate (arsenolipids instead of phospholipids, for instance).
Their summary is that there is no “fatal flaw” in the paper that rules out the possibility of bacteria using arsenic (“no positive data” is how they put it) and that there needs to be more research.
Unfortunately, if you’re hoping to see how they accommodate criticisms from other researchers some argued disproved the notion of arsenic being used in DNA, you’ll be disappointed. This paper not only tries its best to ignore the widespread commentary about the original paper on the blogosphere, it dismisses it. Here’s all they say:
This study has generated significant commentary, often as anonymous electronic communications.
This conflicts with my impression, which was that almost all of the commentary was signed. There was Rosie Redfield and Alex Bradley. Carl Zimmer got a dozen researchers to comment, all with their names in place. There was so much written in the blogosphere about arsenic life, that some of the commentary was pseudonymous (which, as many emphatically point out, is different than being anonymous). But the most prominent critics of the Wolfe-Simon and company paper were certainly not anonymous.
Writing an entire article evaluating the arsenic life paper without any references to what happened on blogs is both disingenuous and bad scholarship. To compress all that online commentary into a single one-liner borders on the unethical, because it so profoundly distorts the events following the release of the paper.
If there had not been such a public thrashing of ideas about this paper online, I doubt a journal have even considered publishing this review of the arsenic life paper (which still hasn’t been officially published yet). So the authors and editor take advantage of the controversy to publish a review, all the while tut-tutting and wagging their fingers at those nasty anonymous bloggers and refusing to do anything but give the most oblique acknowledgment of their role.
I imagine that Wolfe-Simon and some press people at NASA might be happy, though, since this article reinforces the rigid conventions that they promoted in the early days following the release of the paper. But it’s long past time those conventions change.
Rosen BP, Ajees AA, McDermott TR. 2011. Life and death with arsenic. BioEssays: in press. 10.1002/bies.201100012. (DOI link may not be working yet; try http://onlinelibrary.wiley.com/doi/10.1002/bies.201100012/abstract if it isn’t.)
Wolfe-Simon F, Blum J, Kulp T, Gordon G, Hoeft S, Pett-Ridge J, Stolz J, Webb S, Weber P, Davies P, Anbar A, & Oremland R. 2010. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science. DOI: 10.1126/science.1197258... Read more »
Rosen BP, Ajees AA, & McDermott TR. (2011) Life and death with arsenic. BioEssays. info:/10.1002/bies.201100012
Wolfe-Simon F, Blum J, Kulp T, Gordon G, Hoeft S, Pett-Ridge J, Stolz J, Webb S, Weber P, Davies P.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. DOI: 10.1126/science.1197258
Pity poor Hans Berger.
The man changed our understanding of human experience and human consciousness, but didn’t know how he did it, was largely ignored in his life, and committed suicide.
In the mid 1920s, Berger invented the electroencephalagraph (EEG), a technique for measuring the electrical activity of brains. Unfortunately, Berger didn’t understand electricity very well, so didn’t have a clear understanding of what his recordings might mean. But he revolutionized the study of human brains.
Perhaps nowhere was Berger’s invention put to greater use than in the study of sleep. Before that, what did we know of brains while we slept? For all we knew, the brain activity dialed down to almost nothing each night. With the use of EEGs, we discovered the very distinct stages of sleep.
Berger’s invention continues to deepen our understanding of sleep, nearly a century after its invention, as shown by a new paper by KcKinney and colleagues.
McKinney and colleagues claim to have an indicator of how deep asleep you are on a much finer time scale than previously possible.
An EEG signal is a complicated, wavy line. But because it is a wave, you can describe it as a combination of other, simpler waves through a mathematical technique called Fourier analysis or power analysis. McKinney and colleagues say that the waves of one particular frequency, about 8-13 times a second, correlates very closely with how loud a sound has to be for someone to be roused from sleep.
Now, if you could make one of those devices portable so that one person could wear it and broadcast it locally, their partners staying up late would be able to pick the time they were least likely to wake up their snoozing partners.
McKinney S, Dang-Vu T, Buxton O, Solet J, & Ellenbogen J. 2011. Covert waking brain activity reveals instantaneous sleep depth. PLoS ONE 6(3): e17351. 10.1371/journal.pone.0017351... Read more »
McKinney S, Dang-Vu T, Buxton O, Solet J, & Ellenbogen J. (2011) Covert waking brain activity reveals instantaneous sleep depth. PLoS ONE, 6(3). DOI: 10.1371/journal.pone.0017351
We have a burning need to explain what big brains do, because humans have such large brains. “Big brains smart!” is a common idea for why species vary in brain size. But testing this is a fiendish problem. How do you compare widely different species with different ecologies?
Is an osprey smarter than a hummingbird, for example? The osprey is smarter at catching fish than a hummingbird could ever be... but a hummingbird would kick the osprey’s tailfeathers at analyzing flower patches.
One approach is to look not at any one behaviour, but some overall suite of behaviours, and see how different species vary in how many behaviours they produce. This might give a sense of how complex the behaviour of one species is versus another.
William Eberhard has been tackling this problem for a few years now, studying orb-weaver spiders. The advantage of using spiders to study behavioural complexity is that you can use the web as a proxy for the behaviour. The web is long lasting structure, so you don’t have to watch and notate the entire sequence of behaviour. And the spiders vary in size by about a factor of 1,000. Although he didn’t measure brain size directly, I think it’s reasonable to expect that one thousand times bigger body size should be reflected in brain size.
Eberhard used Anapisona simoni (pictured) as his key “small species.” This species weighs about one milligram, compared to other, larger orb-weavers that ranged from 30-40 milligrams as adults. But he did some experiments with A. simoni babies, which register at a barely detectable 5 micrograms!
Eberhard looked for variations in the web structure, working on the hypothesis that small brains might leave the smallest spiders less able to vary their webs in response to different conditions.
A picture might help here. If, when a spider is making a web, it “accidentally” lays down a particularly large space (such as those in the right side marked by the arrow and white rectangles), can it then adjust the other spaces around it to try to even out the spacing?
As it happened, larger spiders made these sorts of compensations more often than the small ones. This is consistent with the notion that small spiders are suffering from behavioural limitations because of their small nervous systems (which Eberhard calls the “limitation hypothesis”).
But in fairness to the small spiders, this is only one of several experiments and studies Eberhard reports on. The majority of studies suggest that small spider species are limited in their behavioural repertoire, but other experiments suggest small spiders are not limited in the behaviour.
This makes for an interesting discussion section in this paper. Eberhard interprets the balance of evidence as rejecting the limitation hypothesis. You can almost feel Eberhard arguing with imaginary reviewers and critics and readers as he points out that you can’t just total up “Experiments with results consistent with the limitation hypothesis” versus “Experiments with results not consistent with the limitation hypothesis” and call it a day. Each experiment provides different information.
For instance, Eberhard points to the alternate web forms that his tiny A. simoni spiders make. They are not common, but Eberhard never saw the larger species make them. And there is certainly an appeal to the argument that something that can make two kinds of structures has a more complex behaviour than something that can only make one.
The discussion is long and nuanced. But what is missing in this discussion of these ideas is one critical data set.
I buy that big differences in body size are reflected in brain size in spiders. But we don’t know just how body size and brain size scales in invertebrates, either during growth or across different species, because there are few good measures or databases of invertebrate brain sizes.
And to make matters even worse, we don’t have information about what regions of nervous systems in spiders are involved in making webs. We know that in vertebrates, some regions of the brain may be bigger than predicted by body size or other regions of the brain if those brain regions are important to the animal.
It might be that when we look at the brains of these tiny spiders, some huge proportion of it is devoted to web-building. And it may be that when we look at the brains of big spiders, a small proportion of it is devoted to web-building, making the differences in body size slightly misleading.
In fairness, Eberhard recognizes this limitation. It seemed worth emphasizing here. Any neuroethologist who wanted to start tackling the neural basis of web-building behaviour would no doubt have more than enough challenges for a long and productive career!
Eberhard W. 2011. Are smaller animals behaviourally limited? Lack of clear constraints in miniature spiders. Animal Behaviour. DOI: 10.1016/j.anbehav.2011.01.016
Spider photo from here; web photo from Eberhard’s Figure 2.... Read more »
Eberhard W. (2011) Are smaller animals behaviourally limited? Lack of clear constraints in miniature spiders. Animal Behaviour. DOI: 10.1016/j.anbehav.2011.01.016
Previously, on NeuroDojo...
Most of the signals running along the neurons in your brain and spinal cord and in the tips of your fingers and the bottom of your bum are started because sodium rushes inside those neurons. The sodium gets in through voltage gated sodium channels. If your voltage gated sodium channels can’t open, neurons can’t fire, and you are done for.
Last week, I talked about a new paper that showed how a little worm, C. elegans, gets along without the sodium channels that we absolutely need. Gao and Zheng claim that the roundworm uses calcium, instead of sodium, to drive action potentials.
There’s another element of this paper that deserves inspection.
There are two ways to make a neural signaling system without using sodium. One is to use another ion, like calcium, to start an action potential. A second way is not to use action potentials at all, but to use graded signals (non-spiking neurons). Graded signals fade as they travel, so they tend not to be the norm.
Something I didn’t emphasize enough in my previous write-up was that Gao and Zheng were working on the muscles, not the neurons. Do the neurons also use calcium to make spikes?
If you were a regular reader with a phenomenal memory, you might dredge out of your memory that about a year and a half ago, I wrote about another C. elegans paper. It claimed that this worm’s motor neurons didn’t generate action potentials at all.
Gao and Zheng, in this newer paper, do several things. First, they are able to replicate the previous finding. They show that the motor neurons are stimulated by increasing amounts of light (described in more detail in the earlier post), there is a graded flow of ions into the muscle. But, these small potentials eventually hit a threshold within the muscle cell, which then triggers the calcium-driven action potentials, which cause the muscle to contract.
They’re also able to provide some evidence that there are two classes of these motor neurons: Excitatory motor neurons, which use acetylcholine as their transmitter, and; inhibitory motor neurons, which use GABA as their transmitter.
“Inhibitory motor neurons?”
I learned that some neuroscientists will blow a fuse at this point. Slip a gear. Spit the dummy.
I once gave a presentation where I mentioned inhibitory motor neurons. There were two prominent researchers in the audience who had co-authored two very successful undergraduate neuroscience textbooks. They were caught flat-footed by the idea of inhibitory motor neurons. They had no idea a nervous system could work that way. They believed that there are only excitatory motor neurons. This is true... for skeletal muscles in mammals. Inhibitory motor neurons are common in invertebrates, like arthropods and C. elegans.
It was a powerful reminder to me about how everyone has their blind spots.
Back to the paper. Here’s a little experiment showing that you can block action potentials in the muscles by putting on a little of the suspected neurotransmitter released by the motor neurons.
Gao and Zhen were also able to show that by stimulating neurons know to contain GABA, they were able to see relaxation of the muscles.
Mammals are use sodium-generated spikes in neurons, and those neurons can only excite muscles, which also use sodium to trigger contraction.
The worm has no spikes in its neurons, and those neurons both excite and inhibit the muscle, which use calcium to trigger contraction.
The physiology of the neurons in C. elegans are so different those of mammals that is is almost perverse that the worm has become a model system for neuroscience. But that it is different presents a wonderful opportunity for all neuroscientists to learn to appreciate the diversity of nervous systems.
Not everything works like a mammal.
Gao S, Zhen M. 2011. Action potentials drive body wall muscle contractions in Caenorhabditis elegans. Proceedings of the National Academy of Sciences 108(6), 2557-2562. DOI: 10.1073/pnas.1012346108
Liu Q, Hollopeter G, Jorgensen E. 2009. Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction Proceedings of the National Academy of Sciences 106(26): 10823-10828. DOI: 10.1073/pnas.0903570106
Photo from here.... Read more »
Gao S, & Zhen M. (2011) Action potentials drive body wall muscle contractions in Caenorhabditis elegans. Proceedings of the National Academy of Sciences, 108(6), 2557-2562. DOI: 10.1073/pnas.1012346108
Liu, Q., Hollopeter, G., & Jorgensen, E. (2009) Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction. Proceedings of the National Academy of Sciences, 106(26), 10823-10828. DOI: 10.1073/pnas.0903570106
Neuroscience is concerned with human, mammals, and vertebrates, in that order. The one example of an invertebrate that appears in many narratives for students learning the field is the squid giant axon, which was used to work out the mechanism underlying action potentials.
From the squid axon, we learned that the action potential, in a nutshell, was:
Sodium in, potassium out.
The electrical signal of a neuron was made possible because charged atoms passed into and out of the cell through channels. These channels opened due to the internal electrical state of the neuron, specifically the voltage. In most species, anything that blocks these voltage-gated sodium channels is nasty stuff indeed. Tetrodotoxin is just one of these toxins, and can be found in many animals, but is most famous as pufferfish poison.
“Sodium in, potassium out” was so common and widespread that you could be forgiven that every animal on Earth does things this way. You’d still be wrong, mind you... but forgiven.
Because one of the most studied organisms on the planet can’t get sodium into its neurons.
Caenorhabditis elegans is a little worm that has two big advantages as model nervous system. It was the first animal in which the connections between every neuron in the body was worked out; it was one of the first organisms to have its genome sequenced.
And when the genome was sequenced, people noticed that there were no genes for voltage gated sodium channels.
Gao and Zhen have a new paper that shows how these worms are managing to run their nervous system without voltage-gated sodium channels. They were focusing on the muscles, which also work with sodium in many critters.
They did several experiments, and the bottom line to them all is that in this worm, it’s calcium in, potassium out. The experiment that’s easiest to explain is that when the calcium concentration surrounding the cell was messed up (no calcium), the spikse were messed up (they stopped).
There are several reasons that this is not a huge surprise. Calcium spikes have been found in other animals. And when channels open, calcium tends to do the same thing, electrically speaking, as sodium: it makes the inside of the neuron more positive. In fact, if anything, it’s a surprise that more cells don’t make calcium spikes, because every calcium ion packs twice the electrical “punch” of a sodium atom.
Alas, examples like this rarely seem to get into neuroscience textbooks.
There’s another piece of this paper that is a nice demonstration of the diversity of nervous systems, but I’ll save that for another post.
Gao S, Zhen M. 2011. Action potentials drive body wall muscle contractions in Caenorhabditis elegans. Proceedings of the National Academy of Sciences 108(6), 2557-2562. DOI: 10.1073/pnas.1012346108
Photo by derPlau on Flickr; used under a Creative Commons license.... Read more »
Gao S, & Zhen M. (2011) Action potentials drive body wall muscle contractions in Caenorhabditis elegans. Proceedings of the National Academy of Sciences, 108(6), 2557-2562. DOI: 10.1073/pnas.1012346108
Textbooks have a lot to answer for.
Textbooks are not the compilation of all knowledge in a field. They are simplified summaries created to teach students new to a field the general lay of the land.
People forget this. Cranks get obsessed with advancing their pet theories by attacking “textbook examples,” because they think the textbook example is all the evidence we have. “If I can show there’s something wrong with the peppered moth example of natural selection, I’ll prove evolution is fake!”
Admittedly, legitimate researchers say, “One day, this will be in all the textbooks!” sometimes, too. It can look self-aggrandizing and egotistical, though.
So this press release titled
Rewrite the textbooksFindings challenge conventional wisdom of how neurons operate
annoyed me and set off my bullshit filter. My annoyance got worse with the first sentence, and continued increasing as I read the press release.
The good news is that the paper is nowhere near as bombastic as the press release. It is a very good paper. It acknowledges the state of the art in the field and does not present itself as revolutionary. The experiments are technically proficient. And the findings are intriguing.
Let’s compare what the press release says and what the paper says.
(T)he basic functional concept is that synapses transmit electrical signals to the dendrites and cell body (input), and axons carry signals away (output).
Paper (my emphasis):
There are exceptions to this, including neurons that lack dendrites or an axon, as well as action potentials propagating from the axon into dendrite. In invertebrates, action potentials can originate in multiple sites, including axon terminals.
What the press release is putting first as the big new finding is not new. It. Just. Is. Not. And the paper’s authors know this and say so in the paper.
In the press release, though, one of the authors, Nelson Spruston, changes his tune:
“Signals can travel from the end of the axon toward the cell body, when it typically is the other way around. We were amazed to see this.”
A neuroscientist amazed by this is either playing to the microphone, or is admitting that he started the project with an ignorance of the diversity of neurobiology. There is certainly no shame in the latter; many neuroscientists concentrate so deeply on one system, they aren’t aware of what else is out there. But playing up, “The signal! It goes backwards! Up the axon!” as something amazing, new, and borderline revolutionary after you’ve admitted in the paper that it happens in other systems is overdoing it.
If I were to rewrite textbooks on this point, it would be to add, “Invertebrates have nervous systems that often work differently than mammals.” Most neuroscience textbooks are far too fixated on humans, mammals, and vertebrates, in that order. If it weren’t for Hodgkin and Huxley’s work on action potentials in squid giant axon, you might have no idea that invertebrates existed.
A deeper understanding of how a normal neuron works is critical to scientists who study neurological diseases, such as epilepsy, autism, Alzheimer’s disease and schizophrenia. ...
This unique neuronal function might be relevant to normal process, such as memory, but it also could be relevant to disease.
Consolidating these results suggests the existence of a previously unknown operational mode for some mammalian neurons. ... The mechanisms responsible for all aspects of this new operational mode are unknown and elucidating them will require extensive work.
These guys care about how cells work. There’s no mention of medical applications anywhere. (They do mention epilepsy, because neurons in animals with epileptic-like conditions do odd things.)
The press release is making empty promises. “What are the practical applications of this?” is a science journalism cliché ranking up there close to “He said, she said.”
“It”s very unusual to think that a neuron could fire continually without stimuli,” Spruston said.
My first reaction was, “Hello! Spruston! They’re called pacemaker potentials and plateau potentials! Both well described in lots of neural circuits!” A pacemaker potential occurs in a neuron that fires over and over again, spontaneously. A plateau potential occurs when a short input causes sustained firing that is much longer than the input; input less than a second could trigger firing for tens of seconds or even minutes.
What Sheffield, Spruston and company have found is something that resembles plateau potentials, but is operating on a different timescale. Plateau potentials are triggered by very distinct, short inputs that depolarize the neuron. The neurons in this paper are getting “set off” by long trains of many events. You need hundreds of potentials (small bottom trace) over many seconds to “set off” these long sets of spikes in response in the downstream cell.
That is different and noteworthy and something I haven’t see quite seen before.
And it’s happening in the axon. Potentials starting in the axon isn’t new, and long periods of firing without stimuli isn’t new, but the combination of those two, plus the long time frame of the trigger (the most truly new and interesting thing in the paper, in my estimation) makes for intriguing combination.
Their studies of individual neurons (from the hippocampus and neocortex of mice) led to experiments with multiple neurons, which resulted in perhaps the biggest surprise of all. The researchers found that one axon can talk to another.
“But... but... but... Axons interacting with axons isn’t new. I learned the term ‘axoaxonic synapse’ from a diagram in a textbook showing two axons connected to each other. Presynaptic inhibition is two axons talking to each other, and Dudel and Kuffler described that in the 1960s.”
Paper: All of the experiments I described above have involved single cells responding to the experimenter. When they were recording from two neurons, they found that occasionally (3 of 19 pairs), when one cell was “set off” into a bout of sustained firing, the partner cell would also go into a long set of sustained firing. This suggests this phenomenon could be a substantial part of the network in this region of the brain (hippocampus).
Finally, Sheffield and colleagues admit they don’t know how these cells are able to generate persistent firing. (This will probably keep this finding out of textbooks until they get the mechanism down. Phenomena without mechanisms are curiosities. Textbooks thrive on neat, complete stories.) Putting on chemical that block gap junctions prevents this sustained firing. But it’s still up in the air as to what gap junctions, where, between what cell, might be involved.
Spruston credits the discovery of the persistent firing in normal individual neurons to the astute observation of Mark Sheffield, a graduate student in his lab.
I say this seriously, with no irony intended: That was a classy thing to say, Dr. Spruston, and good on you. Grad students do not get anywhere near enough credit for being the drivers of discovery that we know they are.
Recently, John Rennie asked science journalists to image what would happen if they didn’t write about papers the same week they were released. This press release was written two months after the pre-print of the paper was published online.
So a cooling off period did not appear to help in this case. The press release is breathless and hyped and oversells a paper that is very admirable and interesting. This paper is like a top notch remix of a song: there’s more old stuff than new material, but the... Read more »
Sheffield M, Best T, Mensh B, Kath W, & Spruston N. (2010) Slow integration leads to persistent action potential firing in distal axons of coupled interneurons. Nature Neuroscience, 14(2), 200-207. DOI: 10.1038/nn.2728
The wedge-tailed sabrewing.
The name sounds like a super top secret stealth fighter jet. The kind that make deep swooshing noises as it flies by that you can barely hear but feel in your bones.
But it’s even cooler than that. The wedge-tailed sabrewing is a tropical American hummingbird. And we know how cool hummingbirds are.
This particular hummingbird species has a couple of extra cool features, though, mostly revolving around mating. The males form leks, loose groups of males that show off for females. They also have elaborate songs, which is quite variable.
We know hummingbirds are quick, but are they quick evolving birds, too? Clementina González and colleagues wanted to find out. They were particularly interested because this bird’s distribution straddles the Isthmus of Tehuantepec in southern Mexico, which is the narrowest point between the Gulf of Mexico and the Pacific Ocean. The isthmus divides two mountain ranges.
The hummingbird populations are not restricted to the high mountain ranges, but they are somewhat separated in the isthmus. For evolutionary biologists, variation of the species and disconnected populations virtually screams, “Allopatric speciation!” Heck, the conditions for these hummingbirds are virtually the definition of allopatric speciation.
When they looked at the DNA of the three subspecies, bird, they were able to cluster them neatly into one eastern and two western populations, on either side of the isthmus. The three different subspecies could also be distinguished by their the songs.
When looking at the bodies of the sabrewings, one of the western subspecies stood out from either of the other two by being larger. The other two were a little more difficult to distinguish based on their body shape, although bill size could pick apart the remaining two subspecies.
With all these different groups of data, they then tried to figure out what caused the differences in these populations. For the differences in morphology, genetic drift alone – random mutations accumulating in one population because they don’t mate with the others – seemed to explain the differences.
The songs, however... they seemed to be not randomly wafting apart as time went on. The changes were such that the authors suggested that selection was occurring to shape the songs of the different populations.
Songs can be shaped over evolutionary time by many different selective pressures. Physics is one. If you move into different habitats with different acoustical properties, different sounds are advantageous. González and colleagues didn’t find any evidence for that, though.
González and colleagues suggest that song evolution is being driven by female preferences for particular songs. This seems plausible on the face of it, but the authors also note that hummingbirds are like humans, songbirds, and parrots: they can learn their vocalizations.
Differences in songs might be better described as changes in learned behaviour (cultural drift, if you will) than evolutionary selection. It’s not clear to me at this instant how you might distinguish between the two alternatives experimentally.
The largest of these three subspecies is also the one in the most danger. It tends to live more in the lowlands, which is being logged for timber.
Gonzalez C., Ornelas J., & Gutierrez-Rodriguez C. (2011). Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis) BMC Evolutionary Biology, 11 (1) DOI: 10.1186/1471-2148-11-38
Come on, let me hear you sing with tailfeathers
Hummingbird photo by jerryoldenettel on Flickr; used under a Creative Commons license.... Read more »
Gonzalez C., Ornelas J., & Gutierrez-Rodriguez C. (2011) Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis). BMC Evolutionary Biology, 11(1), 38. DOI: 10.1186/1471-2148-11-38
A couple of years ago, a paper by Begall and colleagues made a big splash by claiming that cows could detect, and align to, earth’s magnetic field. This report took on a life of its own. I heard it within the last week on one of the science podcasts I listen (though I can’t remember which one).
This paper got attention not only because this was an unusual claim, but for the way that they determined this. Instead of generating their own data, they looked at pictures of cows in Google Earth.
We know that some animals have a magnetic sense; this is pretty much beyond question at this point (for bird, see Ed Yong’s posts here; here; here). But particularly in mammals, we’re not quite sure how they do it.
It’s very unsatisfying when you don’t have a mechanism for a phenomenon. This is why “And how does that work?” is such an incredibly powerful question to ask people selling expensive water that they claim benefits health, holographic bracelets that improve strength, and so on. If you can’t find a plausible mechanism, you don’t have a good understanding of what’s going on.
Hert and colleagues set out to try to replicate the earlier findings, again using Google Earth images.
They found cows were oriented randomly with respect to direction.
And I should add that they also had two sets of data, that were analyzed separately. So it’s not as though this is a one off fluke; maybe a two-off fluke, but not one time happenstance.
Nature abhors a contradiction. How can these two dramatically different results be reconciled?
One possibility is that this study measured the directions of individual cows. The earlier project measured the direction of herds. Begall and colleagues argued:
Cattle of the same heard might not orient independently of each other, and we therefore calculated a single mean vector per pasture that was used in further analysis(.)
There are other subtle differences between the two studies. Begall and company measure to the nearest 5°. Hert and company apparently measured more precisely, but added 4° random “jitter” to the measurements “to account for imprecision in the measurements”.
It’s also important to note that this study doesn’t mean the earlier one was completely wrong. It presented data from three species, and the cows actually showed the weakest trend to northern orientation of the three. The apparently preference for a northern orientation in deer were much stronger.
The good news in all this is that because these data are fairly easy to get (you don’t have to take all those aerial photos yourself!), the fact of the matter should come clear fairly quickly as more people try to find the effect.
The bad news is that if it turns out that there’s nothing to it, unfortunately, there will be a lot of “Did you know cows orient to the north?” out there for a long time...
Begall S, Cerveny J, Neef J, Vojtech O, Burda H. 2008. Magnetic alignment in grazing and resting cattle and deer Proceedings of the National Academy of Sciences 105(36): 13451-13455. DOI: 10.1073/pnas.0803650105
Hert J, Jelinek L, Pekarek L, Pavlicek A. 2011. No alignment of cattle along geomagnetic field lines found Journal of Comparative Physiology A. DOI: 10.1007/s00359-011-0628-7
Photo by clarissa~ on Flickr; used under a Creative Commons license.... Read more »
Begall S, Cerveny J, Neef J, Vojtech O, & Burda H. (2008) Magnetic alignment in grazing and resting cattle and deer. Proceedings of the National Academy of Sciences, 105(36), 13451-13455. DOI: 10.1073/pnas.0803650105
Hert J, Jelinek L, Pekarek L, & Pavlicek A. (2011) No alignment of cattle along geomagnetic field lines found. Journal of Comparative Physiology A. DOI: 10.1007/s00359-011-0628-7
Research on magic has been getting a lot of attention recently, but most of the focus has been on the psychology of the audience.
But what can we learn by studying the performer?
One of the things you need to be a magician, particularly a close-up magician who works with cards or coins, is dexterity. I tried to learn some basic card tricks once, and failed. It requires some very fine motor control, and I didn’t put in enough work to master it.
Many illusions rely on the magician imitating a movement they would make as if they had an object in hand. For instance, some tricks might revolve around pretending to toss a coin from hand to hand, when there is no coin. Peoples’ expectations can be so strong that they will often swear to seeing a coin moving from hand to hand, even when there was no coin.
Are magicians better at this than untrained people? Cavina-Pratesi and colleagues decided to find out.
They recruited experienced magicians and people who were not, and gave them some simple tasks.
See a block on a table, grab it, and move it, or;
See a block on the table, pretend to grab it, and move it.
This was a bit more complicated than it sounds, because the experimenters threw in a twist: you couldn’t see what you were doing.
They used some funky liquid crystal glasses that can switch from transparent to opaque in an instant by applying a little electrical current. This is the same technology used in some new 3D video systems.
People got to see the table, the object they had to pick up and move, but as soon as they started to move their hands, it all went dark, and they had to remember the rest of the move.
When they did this, there were consistent differences across the board between the movements made when people actually picked up and moved an object compared to when they pretended to move the object. Everyone was slower moving their hands when miming, so it isn’t the case that magicians can perfectly mimic their make-believe movements.
On some other factors, the two groups were distinct. Non-magicians tended to hold their fingers together more closely when miming than when they held the real object. Magicians kept their fingers about the same distance apart with both the real and imagined objects.
In a second experiment, people had to do the same sort of task, except in some conditions, there was no object for them to on the table. Instead, they had to imagine moving some familiar object, like a battery.
Without that short-term visual cue and working only from their long-term memory of object size, the magicians did no better than the non-magicians.
There is something different in how magicians are pretending to move things, but what is it? It seems like the magicians are able to use visual information in a different way than non-magicians. The authors put it this way:
(T)he pantomimed actions made by magicians may be indistinguishable from real ones because they have learnt that the best way to fake an action is by performing it “for real”. The talent of magicians therefore lies in their ability to
use visual input from real objects to calibrate a grasping action toward a separate spatial location (that of the imagined object).
Is this skill unique to magicians? Not clear. A follow-up might be to see if other people with lots of motor training perform like the magicians do. Trained mimes or other actors, for instance. Or maybe pianists, who also have highly developed motor control of their fingers, but don’t use use it in creating illusions.
The next logical step in figuring out how magicians are pulling this off is to get a bunch of untalented amateurs, and teach them magic. Then, see what happens as they get better and better. Maybe even throw in a few physiological measurements. Some recordings of muscle activity, or maybe even some brain scans.
That would be an experiment that I totally sign up for. It would be a great excuse to try to learn magic again – for science!
Cavina-Pratesi C, Kuhn G, Ietswaart M, Milner A. 2011. The magic grasp: motor expertise in deception. PLoS ONE 6(2): e16568. DOI: 10.1371/journal.pone.0016568
Magic for dogs
Photo by Christophe Verdier on Flickr; used under a Creative Commons license.... Read more »
“My goodness, Gammarus, what big eyes you have!”
There are a lot of possible answers to Red Riding Hoods question. You might have big eyes to help you navigate in the world, to find resources, mates, and all sorts of things. If you see variation in eye size in populations, it will be tricky to figure out what the selection pressure on eye size is, because eyes do so many different jobs.
In the case of one amphipod crustacean, the answer to Red’s question seems to be:
“All the better to see predators with, m’dear.”
Gammarus minus is a small, freshwater crustacean. Douglas Glazier and Travis Deptola were lucky enough to find five springs where this little bug lives. Two of them were nearly predator free. Amphipod paradise! Three other springs, though, were also home to a fish predator with the suspicious-sounding name of the slimy sculpin. With a name like that, you know that’s a fish up to no good. Two of the springs have quite large numbers of sculpins, and one had sculpins, but far fewer. The sculpins appear to be the major predators in these springs, though the authors note that the two with the highest number of sculpins also had the occasional trout.
Glazier and Deptola went through all five springs in one day, catching sculpins. They standardized the area and time spent looking. Not only did they count all the sculpins they found, they took and weighed them all in the lab.
They also caught amphipods from each stream, took them back to the lab, and measured the size of their eyes and their body length.
The authors show that the eyes are smaller in the spring without sculpins, and in the one with the smallest number of sculpins, than in the two springs with lots of sculpins.
It’s tricky to interpret this result. It would be cleaner if eye size fell right along a “sculpins / no sculpins” dividing line. Instead, you have to start thinking about what the threshold of selection pressure is, how many fish prey upon how many amphipods, etc.
The authors don’t detail any relevant behaviour here, either of the crustacean or the fish. It’s reasonable to think that the amphipods avoid the fish by visual cues, but the authors do say that this sculpin is “relatively inactive benthic fish.” I could imagine some fish would have predation strategies that slightly larger eyes would not help to avoid. A little more detail on how this fish feeds might help persuade that bigger eyes can help the amphipod.
This set of springs is a lovely little natural experiment, but I hope that follow-ups start to bring some more lab experiments to bear on relationship of predation and eye size.
Glazier D, Deptola T. 2011. The amphipod Gammarus minus has larger eyes in freshwater springs with numerous fish predators. Invertebrate Biology. DOI: 10.1111/j.1744-7410.2010.00220.x
Gammarus photo from here. Sculpin photo by Noel Burkhead on Flickr; used under a Creative Commons license.... Read more »
Glazier D., & Deptola T. (2011) The amphipod Gammarus minus has larger eyes in freshwater springs with numerous fish predators. Invertebrate Biology. DOI: 10.1111/j.1744-7410.2010.00220.x
You might not want to fly because of the pat-down, but a bird might not want to fly because it’s hard work. As the old joke goes, “I just flew in from New York, and boy are my arms tired.”
Typically, the faster you want to go, the more energy you have to burn. But it’s not a simple relationship. I can walk home from work, or I can run. But if I’m in a hurry, but not too big of a hurry, is it easier to walk fast, or run slow? Have you ever tried walking as fast as you can? It’s hard! It’s often easier to speed up a little and switch to a slow jog.
The relationship between speed and energy gets even more complicated when you start to look across other animal species. The patterns are different for large quadrupeds versus large birds. Large running birds, like ostriches, have been studied fairly well, but small running birds haven’t been. Small running birds like Lagopus muta here:
This is a ptarmigan, a wide-ranging ground-dweller of a bird. Nudds and colleagues were interested in how these small birds used energy during locomotion, so they put them in treadmills, measured how much oxygen they breathed as they ran, and filmed them so they could see when they were walking or running.
The running is a little complicated, because there are two ways that ptarmigans run. There’s grounded running, where the foot is on the ground more than 50% of the time, and aerial running, where the foot is on the ground less than 50% of the time. It’s faster than grounded running. Buried in the methods is a passing comment that aerial running is also called...
Groucho running. And people think scientists have no sense of humour.
The results are fairly simple to sum up.
The faster the ptarmigans moved, the cheaper it got for them.
Walking used more energy per distance moved than grounded running, which used more energy per distance moved than aerial running.
Ptarmigans are the first birds to show this counter-intuitive result, but they’re not the first animal to show this. Kangaroos show something similar, with the typical explanation that kangaroos are able to use their tendons like springs to store energy. The ptarmigans have some leg tendons that might contribute here, but how big a factor that is remains to be seen.
There are hints of similar patterns of increasing efficiency with increasing speed in roadrunners, but the data there aren’t conclusive. This means either:
Many small running birds may run more efficiently than they walk, or;
Ptarmigans alone can run like a boss.
Regardless of how general the ptarmigan pattern is for small birds, it’s still rather different than most other animals. Even the similarity between kangaroos isn’t very strong, because kangaroo hopping isn’t very similar in form to ptarmigan running.
Why would ptarmigans ever walk or use grounded running? It’s easy to see the advantage of moving slowly for walking. You may want to avoid rapid movement to avoid injury or to avoid drawing attention to yourself.
It’s trickier to know when the animals might prefer to use grounded running, which seems to be the worst of both worlds: slow and more costly than aerial running. An answer to that question probably won’t come from lab studies. It will probably require researchers to go into the field and watch a lot of ptarmigan locomotion.
P.S.—Yes, I wrote the entire post just because I wanted to use that silly ptitle.
Nudds R, Folkow L, Lees J, Tickle P, Stokkan K, & Codd J. 2011. Evidence for energy savings from aerial running in the Svalbard rock ptarmigan (Lagopus muta hyperborea). Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2010.2742
Photo by omarrun on Flickr; used under a Creative Commons license.... Read more »
Nudds R, Folkow L, Lees J, Tickle P, Stokkan K, & Codd J. (2011) Evidence for energy savings from aerial running in the Svalbard rock ptarmigan (Lagopus muta hyperborea). Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2010.2742
You could be forgiven for thinking that there’s no way you could get a useful brain scan of a fish.
First all, if you pay attention to brain scanning, you have probably heard a story about fish in fMRI machines that has become the stuff of scientific legend. The salmon in question being scanned for brain activity was deceased. Pushing up daisies. Size feet under. Joined the choir invisible. In a word, dead.
Yet a brain scan revealed statistically significant brain activity.
Bennett and colleagues were making a point that simple statistics on brain scans could be misleading. But they may have inadvertently dampened other salmon related scanning studies. Brain scans are increasingly being used on small animals. Here, brain scanning gets turned towards studying one of the oldest and deepest questions about salmon behaviour: their ability to return home.
Salmon, like sockeye salmon (Oncorhynchus nerka), are hatched in freshwater streams. From there, they swim out to the ocean, spend years growing and growing, then swim back to the same watershed they were hatched in. That ability to find that original stream, out of the hundreds or thousands pouring into the oceans baffled people for a long time.
Given the complexity of the task, there is probably going to be no single explanation for the salmon’s homing ability, but it seems like smell is playing a large role. There is both behavioural and physiological evidence supporting this.
It’s difficult to build up a cohesive picture of brain activity associated with something like smelling with traditional electrophysiology. You can only record a few cells in a brain at a time. This is where fMRI can shines: looking at the big picture.
You would predict would that the salmon’s brain would show some responses that would occur to pretty much any odour, and a different response to water from the stream a salmon was reared in when it was young.
The trick in an experiment like this is what do you use for a control? Fresh water was used as the “rest” baseline stimulus. To test something that had a definite smell that wouldn’t be associated with a stream, Bandoh and colleagues used amino acids. Amino acids are the building blocks of proteins, and lots of aquatic organisms respond strongly to amino acids in the water. Amino acids are probably the equivalent of the smell this gives off:
The stream water contains amino acids, too, but at concentrations about 20,000 times lower than the amino acid solution used as a control. The experimenters gave the fish fresh water for 10 minutes, an odour for 10 minutes – either the stream water or water laced with amino acids – and then back to non-smelly fresh water for 10 minutes.
The two fluids caused very similar brain activation in the olfactory bulb, which is is basically one step from the nose. If anything, the amino acids activate the bulb more strongly than the stream water.
But things started to differ as the signal went deeper into the brain, through more steps of processing.
When you got into the main part of the brain, the telencephalon, the stream water caused some areas of the brain to activate that the amino acids didn’t. And those regions that were activated by both, the response was stronger to stream water than the amino acid mix.
There are all sorts of interesting questions you could ask with these methods. Could you show that fish that get lost and don’t make it back to their home stream show a weaker signal than those that do? Could you show migrating species have this signal but not non-migrating species? While these could be answered with other techniques, it seems that fMRI might be able to do it a bit more efficiently.
Bandoh H, Kida I, & Ueda H. 2011. Olfactory responses to natal stream water in sockeye salmon by BOLD fMRI. PLoS ONE 6(1): e16051. 10.1371/ journal.pone.0016051
Bennett C. 2009. The story behind the Atlantic salmon. http://prefrontal.org/blog/2009/09/the-story-behind-the-atlantic-salmon/.
Bennett CM, Baird AA, Miller MB, Wolford GL. 2010. Neural correlates of interspecies perspective taking in the post-mortem Atlantic salmon: An argument for proper multiple comparisons correction. Journal of Serendipitous and Unexpected Results 1: 1-5. http://jsur.org/v1n1p1
Bennett CM, Baird AA, Miller MB, Wolford GL. 2008. Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction. Human Brain Mapping 2009. San Francisco.
Salmon picture by toddraden on Flickr; steak picture by Another Pint Please... on Flickr; both used under a Creative Commons license.... Read more »
Bandoh H, Kida I, & Ueda H. (2011) Olfactory responses to natal stream water in sockeye salmon by BOLD fMRI. PLoS ONE, 6(1). info:/10.1371/ journal.pone.0016051
I’ll give you that a massive sword looks cool...
But is it practical? What if you came up against someone with, I dunno, a longbow and you had to run? Things could be worse, though. At least that sword can be dropped. If you’re Xiphophorus helleri, you’re not so lucky: you’re stuck with your sword.
Xiphophorus helleri is a good old swordtail, known to anyone who’s ever been in a pet store. Why does this fish have a sword? The answer seems obvious once you realize that only males have the sword:
Chicks dig it.
Consequently, the role of swords in swordtail courting and mate selection has been well studied. But Baumgarter and colleagues are more interested in what the sword is doing all the rest of the time when a male isn’t trying to catch the eye of fa female.
That long sword could impose a cost on the fish. It might make it harder to swim, particularly when time is of the essence. Swordfish, like many other fish, will escape from a sudden stimulus by bending into a C shape that pulls the head away from the source of the stimulus before the animal swims off. I’ve talked a little about C-starts before (here and here).
Baumgarter and company tested the C-start performance of males with a range of sword lengths, and found no significant differences in their behaviour. They also did before and after experiments where they removed the sword from the tails, and again found no differences in the before and after abilities of the fish to perform C-starts.
That the sword doesn’t impact on this particular behaviour doesn’t mean it’s “free,” though. Those long tailed individuals may have to perform those C-starts a lot more, as the authors note that it’s entirely possible those big, showy tails could translate into more predator attacks.
C-starts are explosive and typically executed in high-risk situations – but they’re rare. Steady swimming is the norm, and the researchers note that long swords seem to make steady swimming more tiring, turning the sword into an ongoing energy sink.
Baumgartner A Coleman S, Swanson B. 2011. The Cost of the Sword: Escape Performance in Male Swordtails PLoS ONE 6(1): e15837. DOI: 10.1371/journal.pone.0015837
Sword picture by DJOtaku on Flickr. Fish picture by mineobskuriteter on Flickr. Both used under a Creative Commons license.... Read more »
Baumgartner, A., Coleman, S., & Swanson, B. (2011) The Cost of the Sword: Escape Performance in Male Swordtails. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0015837
Academic writing is set apart from almost all other writing by its obsession with citations.
Mike Taylor hates numbered references. He notes that numbered referencing saves space in print journals journals where space is at a premium. For journals on the web, there are no space constraints, and thus no reason to use numbered references.
I want to dig down into reference styles a little. I think I can show why professional scientists are more likely to prefer references using author and year (also know as Harvard referencing) than anybody else.
Several people say that the (Author, Year) reference format allows them to evaluate some of the paper’s claims on the fly. “Wait a minute, why are they citing Jones and Peabody 1988? They didn’t show that!”
But this only works if you know the literature extremely well. I’m skeptical of how often people are able to do this. Personally, I constantly have to look up which paper some particular claim was in. Heck, I can barely tell you the years some of my own papers were published. “Hm. Did that one come out in 2005 or 2006?”
But never mind my own shortcomings. The point is:
The more deeply a scientist specializes, the more he or she can recognize papers by the author and year alone.
Another reason professional scientists like the (Author, Year) format is because of the personal branding. If someone cites your paper multiple times, it builds name recognition – particularly if you have a slightly distinctive name in your field. And that can help facilitate networking at conferences and general career development.
Writers of scientific journal articles also have reasons to like the (Author, Year) style, because it’s easier to prepare a reference list. If you insert one reference in the middle of a manuscript, all the references after it have to change. That's why I use name and year references in blog posts; they're quick and easy to do by hand.
I think this also explains why having the full references at the end of the paper more common than footnotes. I shudder to think of doing footnotes on a typewriter.
Nobody doubts that numbered references are shorter that the Harvard style. But the advantage goes beyond saving paper.
Gregory (1992) gives an example where replacing “author and year” references with numbered references reduced 149 words to a mere 22. But he argued that this tremendously improved the readability:
The original passage is unspeakable and unreadable, but neither the author nor the editor is interested in whether anyone reads the paper. Indeed, they prefer nobody reads beyond the summary, or better still, beyond the authors’ names.
I don’t think it’s an accident that most books describing research for a general audience treat references with a light touch. Typically, you’ll find only a list of key references at the end, with very few (Author, Year) intrusions into the text.
The more rigorously documented and referenced a work is, the more difficult it is to read.
Numbered references are fairer to scientific authors than the (Author, Year) format. The tradition is that if you have three or more authors on a paper, the reference in the test is given by the name of the first author only.
If you’re author #2 on a three author paper, you’re screwed. Why should one person get on a large team get such a disproportionate amount of personal advertising by having their name printed throughout the main body of a paper, while the name of author 2 of 3 is only printed once in the literature cited? It’s no coincidence that order of authorship is a common cause of fights and discontent between researchers. More and more papers are being written by larger and large groups of authors, meaning this problem is only going to get worse.
As for the ease of preparing a manuscript, this is why specialty reference manager software exists. We are not living in the age of typewriters any more.
For online journals, technology should be able to provide a “best of both worlds” solution. It should be possible to have numbered references where you could pull up a complete citation in a little pop-up window by hovering the cursor over the number, similar to clicking the magnifying glass icon next to search results on Google.
So the style of referencing actually cuts to a very deep question: Who is a scientific journal article for? One format favours the professionals: the people who are deeply embedded in the literature, and who actively contribute to it. The other favours the readers: those just entering the field and the curious bystanders.
“Open science” is not just about who pays for research and reprints and journal subscriptions; it’s about access in the broadest sense. And something as simple as the reference could raise or lower the barrier to someone reading a research paper, even if just by a smidgen.
I’d much rather the barrier be a smidgen lower than a smidgen higher.
P.S.—I wondered if anyone had ever done any research on the pros and cons of the different reference styles. The only paper I was able to find bore the title, “How the name date (Harvard) reference style in papers shows an underlying interpretivist paradigm whilst numeric references show a functional paradigm.”
That I wasn’t able to find a copy was a relief. Paradigms. I would have been way out of my depth.
Gregory M. 1992. The infectiousness of pompous prose. Nature 360 (6399): 11-12. DOI: 10.1038/360011a0
Oakley P. 2003. How the name date (Harvard) reference style in papers shows an underlying interpretivist paradigm whilst numeric references show a functional paradigm. Systemist 25: 25-30.
Additional: An independent analysis at The Open Source Paleontologist arrives at some similar conclusions.... Read more »
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