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Associate Professor of Biology at The University of Texas-Pan American.

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February 13, 2012
10:09 AM
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How Pompeii worms take the heat

by Zen Faulkes in NeuroDojo

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

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

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

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

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

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

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

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

Hot worm. Cool science.

Reference

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

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

February 7, 2012
08:00 AM
76 views

Tuesday Crustie: What’s bigger than a giant?

by Zen Faulkes in NeuroDojo

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

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

This infographic prompted Rebecca Watson to quip:

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

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

References

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

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

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

February 6, 2012
08:00 AM
64 views

Be eaten, make glowing fish poo, profit!

by Zen Faulkes in NeuroDojo

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

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

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

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

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

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

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

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

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

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

Reference

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

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

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

February 3, 2012
08:00 AM
95 views

Jumping spiders still have use for muscles

by Zen Faulkes in NeuroDojo

You can’t push on a rope.

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

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

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

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

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

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

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

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

Reference

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

Photo from here.... Read more »

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

January 26, 2012
08:00 AM
91 views

Once more into the cave

by Zen Faulkes in NeuroDojo

Caves. There’s a whole series of things that tends to happen in creatures that become cave-dwellers. Over and over and over again, animals that live exclusively in caves tend to be blind compared to their closest living relatives.

This makes cave species great for studying evolution, because each cave is a “natural experiment.” Mexican cave fish are a particularly cool case, because we have in the same species both cave dwellers, which are blind, and surface fish, which are not. And they can interbreed.

This new paper looks purely at the genetics of these cave fishes, trying to figure out just how many times they have invaded caves and lost developed the “cave” phenotype. This new paper by Bradic and colleagues is an extensive crunching of gene samples, and concludes that while there were two ancestral populations, those ancestral populations in turn invaded caves several times: a total of five introductions to caves, all told.

Furthermore, although these animals can interbreed in the lab, this seems to be unlikely in nature. Their results indicate low gene flow between the surface population and the cave populations. Still, while low, it’s not zero, suggesting that there is a genuine fitness advantage to the blind cave-dwelling form.

Reference

Bradic M, Beerli P, Garcia-de Leon FJ, Esquivel-Bobadilla S, Borowsky RL. 2012. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evolutionary Biology 12: 9. DOI: 10.1186/1471-2148-12-9

Photo by Joachim S. Müller on Flickr; used under a Creative Commons license.

Links

Turning light and going blind: A tale of caves and genes
... Read more »

Bradic M, Beerli P, Garcia-de Leon FJ, Esquivel-Bobadilla S, & Borowsky RL. (2012) Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evolutionary Biology, 9. info:/10.1186/1471-2148-12-9

January 25, 2012
08:00 AM
122 views

Males have bigger brains than females, if those males are sticklebacks from Iceland

by Zen Faulkes in NeuroDojo

This supershort paper contains an interesting fact: there is a population of male stickleback fish out there with big brains. The males fish that have brains 23% larger than the females of approximately equal size.

This is a bit of an unfair characterization. The paper does talk a little bit about how the look for differences in brain size according to the local eco-type that they found the fish and: mud or lava. the nails from allow the environments have bigger brains than those from muddy environments, but there is no such difference in the females.

This is an interesting difference, because so few animals have differences in brain size mispronounced between males and females. Kotrschal and colleagues say that this is the biggest difference in overall brain size in males and females to date.

What are we to make of this one interesting fact? The team speculates that this might be because the males make complicated nests, and compete for females through courtship displays. But it seems that there are many other animals that have similar differences in behavior without the differences in overall brain size. Maybe the real question is not why male brains are so big, but why are female brains in this fish so small? The authors speculate that this might be because the females are investing energy in egg production. Again, it doesn’t really answer why it should be so specifically strong in this particular population of this particular fish when all sorts of females invest energy in making eggs.

While the fact that this paper presents is interesting, a fact in isolation is mainly a curiosity, to borrow a phrase from psychologist Ernst Hilgard. I would’ve liked to have seen this fact presented slightly longer paper with a few more experiments and a little more context. There will surely be some interesting follow-up studies to do.

Reference

Kotrschal A, Räsänen K, Kristjánsson B, Senn M, Kolm N. 2012. Extreme sexual brain size dimorphism in sticklebacks: a consequence of the cognitive challenges of sex and parenting? PLoS ONE 7(1): e30055. DOI: 10.1371/journal.pone.0030055

Photo by Noel Burkhead on Flickr; used under a Creative Commons license.... Read more »

Kotrschal A, Räsänen K, Kristjánsson B, Senn M, & Kolm N. (2012) Extreme sexual brain size dimorphism in sticklebacks: a consequence of the cognitive challenges of sex and parenting?. PLoS ONE, 7(1). DOI: 10.1371/journal.pone.0030055

January 24, 2012
08:00 AM
108 views

Tuesday Crustie: Fresh ink

by Zen Faulkes in NeuroDojo

Keeping with last week’s hydrothermal vent crustaceans...

This is another hydrothermal vent shrimp, Alvinocaris komaii. The tattoo belongs to one of the authors who formally described it for science, Kevin Zelnio of Deep Sea News. It was completed last week at the Science Online 2012 conference, by Dogstar Tattoo.

This shrimp lives near hydrothermal vents just north of New Zealand, where they normally are found on beds of mussels. They are probably generalist feeders.

One of the recurring questions with hydrothermal vent animals is that given that the vents are so separated, how do the animals living at them disperse from vent to vent? The paper alludes that that when it discusses the relationships between the shrimps in this genus. The geographic locations of the species don’t seem to make well with the relationships, which would be consistent with animals that have to disperse widely and live in short-lived habitats.

It’s interesting to compare this artistic rendition to the formal figure from the paper:

Reference

Zelnio K, Hourdez S. 2009. A new species of Alvinocaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vents at the Lau Basin, Southwest Pacific, and a key to the species of Alvinocarididae. Proceedings of the Biological Society of Washington 122(1): 52-71. DOI: 10.2988/07-28.1... Read more »

Zelnio K, & Hourdez S. (2009) A new species of Alvinocaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vents at the Lau Basin, Southwest Pacific, and a key to the species of Alvinocarididae. Proceedings of the Biological Society of Washington, 122(1), 52-71. DOI: 10.2988/07-28.1

January 23, 2012
08:00 AM
100 views

The disembodied tail

by Zen Faulkes in NeuroDojo

When things are bad, and I mean really bad, horribly you-are-in-the-jaws-of-death bad, sometimes you have to let go of something.

Like a tail.

This leopard gecko (Eublepharis macularius) can, when hassled, have its tail fall off. Losing a limb (autotomy) is not a particularly unusual trick for this species. Lots of animals can drop legs and tails if necessary. But this one is noteworthy because if it does so, the tail doesn’t just come off, but it will continue to twist and writhe for up to several minutes after the tail has been separated from the rest of the body.

We’re not just talking about simple twitching here. We’re not talking about something regular, like a horror-show heart that beats after removal from the body. Higham and Russell show that that the tail is doing at least two things. One is a slow, rhythmic swinging, and occasionally, much faster contortions that made the tail flip or jump around. The flips tend to fade out faster than the slower swinging, though.

When we think about vertebrates movements, we normally think that the brain is involved somehow. But here, the tail has been completely severed from the brain, so how are these movements generated and controlled?

Taking the information from the muscle recordings they made from the tail, Higham and Russell think that the slower rhythm is generated by neurons left in the spinal cord of the tail. We’ve known for a long time, probably since the 1970s, that the spinal cord in vertebrates holds a lot of the neural circuitry needed to generate basic locomotor motions.

Higham and Russell argue that the gecko’s tail the faster movements are more interesting. They marshal a few pieces of evidence for their hypothesis. First, they note that the flips only occur for a couple of minutes after the tail’s been removed, whereas the slow movements continue for up to half an hour. Second, the flips are extremely variable compared to the slow movements, even after you take into account the fact that they’re shorter. Third, when a flip occurs, the muscles along the tail are active simultaneously, compared to the slow movements, where the muscles along the tail are activated one after another.

They don’t know yet what the mechanism of these fast flips might be. Higham and Russell note that working on the neural basis of this behaviour has an advantage: you can do neurophysiological experiments on the spinal cord without having to kill the animal. I’m sure that the gecko appreciates this, but I still bet it will miss that beautiful tale it used to have. They never grow back as nice as the original one.

Reference

Higham T, Russell A. 2012. Time-varying motor control of autotomized leopard gecko tails: multiple inputs and behavioral modulation The Journal of Experimental Biology 215(3): 435-441. DOI: 10.1242/jeb.054460

Photo by A. Jaszlics on Flickr; used under a Creative Commons license.

sciseekclaimtoken-4f1c30b1b9dfe... Read more »

Higham T, & Russell A. (2012) Time-varying motor control of autotomized leopard gecko tails: multiple inputs and behavioral modulation. The Journal of Experimental Biology, 215(3), 435-441. DOI: 10.1242/jeb.054460

January 18, 2012
08:00 AM
112 views

Delivering postcards supercars: big neurons and information transfer

by Zen Faulkes in NeuroDojo

In the world of neurons, bigger may not be better, but it is usually faster – which is almost as good.

The wider an axon, the faster a signal travels along it. You can see this readily by playing around with a computer simulations. This is the traditional explanation for why the largest, fattest neurons are almost always found in escape circuits. Escape systems push neurons to the limit of what is physically possible to shave off every possible microsecond in the response time, because every single one could make the difference between life and death.

But when you get away from these largest neurons, what explains the differences in the axon diameter? Can everything be explained just by the need for speed?

Perge and colleagues look at the issue of axon size (which, for reasons unclear, they call “caliber”) across lots of different structures. For the most part, they use mammalian brains. They didn’t include motor neurons, because the problems motor neurons are largely forced by the distance to a muscle. They are more interested in the differences in sizes within tracts contained within the central nervous system, where all the neurons are more or less starting and stopping in the same place.

Their hypothesis is that the differences in axon size within a brain are related not to speed so much as to the ability of a neuron to convey information. The smallest axons convey information at the lowest rates, according to their discussion. Big axons can transfer information at higher rates, they argue, because there is less “jitter” in their timing. Plus, a big neuron can send a signal to many more cells downstream than a small one.

The problem, though, is that big neurons are expensive. Smaller neurons, with lower rates of spiking, convey information less rapidly, but do so more efficiently. It’s like using a Bugatti Veyron to deliver a postcard: it’s fast, but it’s an absurd extravagance. To reduce the time signals spend traveling along the axon, the authors argue that brains typically try to minimize the distance the signal has to travel instead of increasing the size of the axon.

I was also interested to see a little aside about the amount of mitochondria in neurons. Neurons are famously energy hungry cells. They noted that nonspiking neurons have fewer mitochondria than myelinated spiking neurons, and unmyelinated spiking neurons typically have the highest fractions of mitochondria.

They don’t provide any of their own original recordings of spiking rates here. The new data are all anatomical, based on electron microscope sections. Their data serves, almost incidentally, as a nice little review of neuronal diversity.

I always find papers discussing “information” to be a bit tricky, and this one is no exception. But it’s a useful paper to get you thinking about “how neurons work.”

Reference

Perge JA, Niven JE, Mugnaini E, Balasubramanian V, Sterling P. 2012. Why do axons differ in caliber? The Journal of Neuroscience 32(2): 626-638. DOI: 10.1523/JNEUROSCI.4254-11.2012

Sculture photo by nicoleversetwo on Flickr; used under a Creative Commons license.

Veyron photo by Philipp Lücke on Flickr; used under a Creative Commons license.... Read more »

Perge JA, Niven JE, Mugnaini E, Balasubramanian V, & Sterling P. (2012) Why do axons differ in caliber?. The Journal of Neuroscience, 32(2), 626-638. info:/10.1523/JNEUROSCI.4254-11.2012

Neuroscience

January 17, 2012
08:00 AM
162 views

Tuesday Crustie: Hot or not?

by Zen Faulkes in NeuroDojo

This shrimp is a new species that is mentioned in a new paper on a new hydrothermal vent community by Connelly and colleagues.

The Daily Mail recently ran this story on this discovery with the headline:

So how on Earth do you cook THIS? The shrimp that lives in water four times hotter than boiling point
Time for a classic facepalm.

I can see how this headline got cobbled together, but still... sigh. No. No, no, no, and again, no. These are not invulnerable super shrimp.

Time to become... a TRUTH VIGILANTE! Quick! To the Truthmobile!

The original paper the news story is based on makes no claim that the shrimp can tolerate super-hot temperatures. But it helpfully shows the change in water temperature as you descend into the sea in Figure 2. By the time you get to below 1000 m, the water temperature is only a couple of degrees above freezing. And these vents are almost 5,000 m down. It’s freakin’ cold down there – except where there are hot vents.

It’s like having a campfire in the winter.

According to the logic of this article, the person who took this picture should have been burned alive. Fires are hot! And the middle of the fire is hot and will burn you.

But step back a little ways, and you can be very cold. You have to find the sweet spot where the warmth from the fire is just counteracting the surrounding cold. (The optimal spot for your hot dogs and marshmallows is rather closer.)

The exact same thing happens at these hydrothermal vents. You have superhot water emerging from the vents, but it’s surrounded by very cold water under very high pressure. The shrimp have to do a constant dance to find just the right distance, darting in and out near the turbulent high temperature plumes to avoid getting cooked.

Oddly, the Daily Mail article gives the shrimp a name, Rimicaris hybisae, which is nowhere to be found in the scientific article in Nature Communications. I hope they have the paper describing this species accepted, because otherwise, these reports might end up jeopardizing the name.

Reference

Connelly D, Copley J, Murton B, Stansfield K, Tyler P, German C, Van Dover C, Amon D, Furlong M, Grindlay N, Hayman N, Hühnerbach V, Judge M, Le Bas T, McPhail S, Meier A, Nakamura K, Nye V, Pebody M, Pedersen R, Plouviez S, Sands C, Searle R, Stevenson P, Taws S, Wilcox S. 2012. Hydrothermal vent fields and chemosynthetic biota on the world's deepest seafloor spreading centre. Nature Communications 3: 620. DOI: 10.1038/ncomms1636

Classic facepalm by Alex E. Proimos on Flickr; campfire photo by mismisimos... Read more »

Connelly D, Copley J, Murton B, Stansfield K, Tyler P, German C, Van Dover C, Amon D, Furlong M, Grindlay N.... (2012) Hydrothermal vent fields and chemosynthetic biota on the world's deepest seafloor spreading centre. Nature Communications, 620. DOI: 10.1038/ncomms1636

January 12, 2012
08:00 AM
120 views

Error bars

by Zen Faulkes in Better Posters

Comparing averages should be one of the easiest kinds of information to show, but they are surprisingly tricky.Most people know that when they show an average, there should be an indication of how much smear there is in the data. It makes a huge difference to your interpretation of the information, particularly when glancing at the figure.For instance, I’m willing to bet most people looking at this...Would say, “Wow, the treatment is making a big difference compared to the control!”I’m likewise willing to bet most people looking at this (which plots the same averages)...Would say, “There’s so much overlap in the data, there’s might not be any real difference between the control and the treatments.”The problem is that error bars can represent at least three different measurements (Cumming et al. 2007).Standard deviationStandard errorConfidence intervalSadly, there is no convention for which of the three one should add to a graph. There is no graphical convention to distinguish these three values, either. Here’s a nice example of how different these three measures look (Figure 4 from Cumming et al. 2007), and how they change with sample size:I often see graphs with no indication of which of those three things the error bars are showing! And the moral of the story is: Identify your error bars! Put in the Y axis or in the caption for the graph.ReferenceCumming G, Fidler F, Vaux D 2007. Error bars in experimental biology The Journal of Cell Biology 177(1): 7-11. DOI: 10.1083/jcb.200611141A different problem with error bars is here.... Read more »

Cumming G, Fidler F, & Vaux D. (2007) Error bars in experimental biology. The Journal of Cell Biology, 177(1), 7-11. DOI: 10.1083/jcb.200611141

January 9, 2012
05:51 PM
157 views

ESA still not supporting open access

by Zen Faulkes in NeuroDojo

The Ecological Society of America drew attention to itself last week for a statement regarding open access for scientific publication. Jonathan Eisen covered it here.

I posted the link to Eisen’s post this on ESA’s Facebook page, and today, there was this comment:

ESA’s recent letter in response to OSTP’s Request for Information has generated discussion in the social media realm. This is perhaps a good example of the inherent conflict between the interests of those who believe research publications should make their content freely available to all and the reality that there are significant costs associated with publishing scholarly research journals. This topic will continue to be one with which the scientific community must grapple and one that will continue to evolve.
My response was that they seemed to be confusing “access” with “profit.” PLoS ONE has proved that open access journals can be profitable. Other publishers (Brill; see here) have recognized this.

If journals are worried about losing their subscriptions, I suggest this: Keep the technical articles free and print other, original content that people will pay for.

For instance, let’s go back the the journal Science, which I suggested would be a good target to convert open access. Only a small fraction of the original technical articles in Science are going to be relevant to any particular reader. As it stands, a subscriber to Science is getting a lot of non-targeted articles that are irrelevant to them.

What Science has been really good at is providing news and commentary. That is much more widely relevant to a broader spectrum of readers. I think if all the technical articles were still free, people would probably still be willing to pay money for all the other original writing. The conference reports, the policy analysis, and so on. That original work by professional writers is something that people realize should not be free. At least, the arguments for making it free are different than the usual ones used to justify open access, that is that publicly funded scientists are doing all of the intellectual work.

But oddly, the tendency for general journals has been to do the exact opposite. Journals have tended to make a few of their comments freely available, while locking down all the original science.

So, ESA, if you want people to stay members of your society, to give them reasons to do so besides original journal articles. I doubt it’s the main reason that most people join scientific societies. In fact, ESA, you yourself have surveyed why people joined your society.

The number one reason given in a membership survey for joining ESA was, “Supporting the field of ecology.” For young members, under the age of 35, “opportunities to present or publish my work” was third in the last but that's difficult to interpret because it includes presenting at conferences and not just the journals. Regardless, it's not just for the journals you publish.

When they asked lapsed members what might make them rejoin the society, the three main reasons were for information and career development. These were things that require more than just original journal articles. For example, the first item on the list was, “Help me stay abreast of developments in my field.” Sure, that is something that is partly about original research, but good original analysis and news reporting would also seem to be valuable to members. So why not give it to them?

Reference

ESA. 2012. ESA membership survey, February 2011 summary of results Bulletin of the Ecological Society of America 93(1): 13-23. DOI: 10.1890/0012-9623-93.1.13... Read more »

ESA. (2012) ESA membership survey, February 2011 summary of results. Bulletin of the Ecological Society of America, 93(1), 13-23. DOI: 10.1890/0012-9623-93.1.13

January 9, 2012
08:00 AM
144 views

Hidden potential, and the concept of syngeny

by Zen Faulkes in NeuroDojo

There’s much excitement about a new paper in Science that shows how ants have hidden potential. In short, there are a few species of ants that can produce “supersoldiers”. Other ant species, however, can also make supersoliders when they are experimentally give the right dose of hormone.

Crudely, it looks like the ants’ ancestors had the ability by changing the hormone levels, but the pathway that was sensitive to the hormone remained. When species started to evolve differences in hormone levels again, the supersoldier body type “re-emerged” after a long period of suppression.

Ed Yong covers it here and here. One of the authors talks about it on Quirks & Quarks.

I wanted to talk not about the paper so much as a concept it illustrates that I don’t think has gotten enough attention in the evolutionary biology literature.

Homology is a critical concept in evolutionary biology. A generally used definition is a feature that two different species share because they inherited it from a common ancestor. But homology can be tricky, because a “feature” or “trait” isn’t a single thing. Features have different levels of organization: genes, cells, tissues, organs, and so on. And each level can evolve long a different path than the others.

Plus, the concept of homology was first proposed first by Richard Owen, who rejected the idea of evolution by natural selection. And it was widely used before we had learned a lot about the subtleties of genetics.

For instance, we’ve learned that just because you have a gene doesn’t mean it’s expressed. Much like the supersoldier ants, you can imagine a scenario where a gene (or gene network, etc.) is present in an ancestral species, but not expressed. The species diversifies, and diversified, leaving many daughter species with the unexpressed genes. Then, independently, several of the daughters of the original ancestor start expressing the genes, and the trait pops up in distantly related species.

From the point of view of the phylogeny, that feature doesn’t look homologous, even though there is evolutionary continuity at the genetic level from a common ancestor.

Butler and Saidel recognized this scenario some time ago. They coined the term “syngeny” to describe a feature arising from genes that are present, but rarely expressed. I heard Butler discuss this at a JB Johnston Club meeting, citing a particular fish brain structure that appears only in a few not closely related species. The idea was great.

What the ant story brings that they didn’t have at the time was the ability to bring their feature back through an experimental manipulation. It’s likely that many cases of syngeny are not going to be as easy to show in the lab as in the ants.

Rajakumar and colleagues, the authors on the ant paper, call what they’re seeing parallel evolution, but syngeny might be a better description.

References

Butler A & Saidel W. 2000. Defining sameness: historical, biological, and generative homology BioEssays 22(9): 846-853. DOI: 10.1002/1521-1878(200009)22:93.0.CO;2-R

Rajakumar R, San Mauro D, Dijkstra MB, Huang MH, Wheeler DE, Hiou-Tim F, Khila A, Cournoyea M, Abouheif E. 2012. Ancestral developmental potential facilitates parallel evolution in ants. Science 335(6064): 79-82. http://dx.doi.org/10.1126/science.1211451... Read more »

Butler A, & Saidel W. (2000) Defining sameness: historical, biological, and generative homology. BioEssays, 22(9), 846-853. DOI: 10.1002/1521-1878(200009)22:93.0.CO;2-R

Rajakumar R, San Mauro D, Dijkstra M, Huang M, Wheeler D, Hiou-Tim F, Khila A, Cournoyea M, & Abouheif E. (2012) Ancestral developmental potential facilitates parallel evolution in ants. Science, 335(6064), 79-82. DOI: 10.1126/science.1211451

January 8, 2012
08:00 AM
110 views

“The scientists are coming, run!”

by Zen Faulkes in NeuroDojo

Animals on some islands are famously unafraid of humans (click here to watch an example). In almost every case, this tameness hasn’t lasted long, ending either with the animals become very wary or harvested to extinction.

A new paper by Delibes and colleagues tells a story about the behaviour of an island animal, but it’s too early to tell if this one will have a better ending. Delibes and company were collecting lizards, the orange-throated whiptail (Aspidoscelis hyperythra). As you can seen, these guys are not large, and a bit cryptically coloured.

The research team decided that they could treat themselves as predators, if you will, and would chase lizards until they caught them or the lizard got away. They did this on the Baja Peninsula and on eight islands just off the peninsula.

More than half the lizards on the islands (~58%) got away. But not even 15% of the lizards living on the mainland were able to get away from the scientists.

This is the reverse of the standard “island animals are less concerned by people” story we normally hear.

The authors examine and discard a few hypotheses to explain this unusual pattern. The presence of cats on the islands is considered, but not all of them had cats. They looked at the tails for signs of regeneration from failed predation attempts, but those were about the same on the islands and the mainland (although the authors do say that is tricky to interpret, though).

It seems to come down to the humans. Now, the islands are not inhabited, so one possibility is just that the lizards on the mainland are used to humans and don’t view them as threats. As noted when I started, however, this is rather the opposite of what is often seen.

They think that the lizards have learned to avoid the scientists.

Delibes and colleagues argue that researchers are significant collectors of the island lizards. As you can imagine, this is a fairly difficult thing to prove, and the team has only circumstantial evidence. They note that a couple of papers involved collecting anywhere from 47 to 160 lizards from these small islands. (Some of them are so small, the dot showing the location of the island covers the entire island.) They also have anecdotes from locals, who told them about the “relatively frequent groups of students who rent boats to travel to the various islands”.

The authors discuss whether this is a learned response, or whether it is an evolutionary change. Unfortunately, it’s not easily testable with the data they have. Certainly, however, human harvesting has caused many species to change behaviours. Lobsters, for instance, used to strand themselves in tide pools. They don’t do that anymore, because they kept getting picked up there by hungry humans. What would be unusual is if researchers alone are more or less responsible for this change.

The curiosity about why the lizards are becoming better at escape rather pales next to the possibility that scientists may be chasing these populations, perhaps not to extinction, but down roads that the lizards wouldn’t have otherwise trekked.

The researchers who wanted to study these lizards’ evolution of these lizards might now be the major drivers of it.

Reference

Delibes M, Blázquez M, Soriano L, Revilla E, Godoy J. 2011. High antipredatory efficiency of insular lizards: a warning signal of excessive specimen collection? PLoS ONE 6(12): e29312. DOI: 10.1371/journal.pone.0029312

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

Delibes M, Blázquez M, Soriano L, Revilla E, & Godoy J. (2011) High antipredatory efficiency of insular lizards: a warning signal of excessive specimen collection?. PLoS ONE, 6(12). DOI: 10.1371/journal.pone.0029312

January 6, 2012
08:00 AM
188 views

Calling Nemo

by Zen Faulkes in NeuroDojo

Everyone knows clownfish are pretty. Almost everyone knows they live among the tentacles of anemones. But I’m willing to bet fewer people know that clownfish are noisy.

Fishes make noises for the same sorts of reasons that other animals make noise. Sometimes, it’s to say, “This is what species I am!” Sometimes, it’s to say, “Listen to how big I am!” All kinds of important signals can be contained in sounds. Such behaviours can become important drivers in evolution. Certain kinds of sounds might be considered “sexy” in different groups, and start driving differences in mate choice, and ultimately speciation.
The team of Colleye and colleagues listened to 14 different species of clownfish, most of which were in the genus Amphiprion (A. ocellaris and A. frenatus are shown here). They predicted that if these sound signals were important in the evolution of this group of fishes, they should see lots of diversification in the signals, and not much overlap between them.

This turned out not to be the case. The sounds were quite similar, perhaps because clownfish all make sounds by snapping their jaws together.

The sounds clownfish make are excellent signals of fish size. Big fish make longer and lower sounding pulses in their calls than small fish. The correlations are tighter than most that you see in biology. (The r values are 0.98 and -0.99! See here for more on correlations.)

This doesn’t support the idea that the sounds are important as way
to isolate different species, except incidentally if the species differ
in size.

But these signals could be critical to the dynamics between individuals within a group a clownfish, because breeding in groups is dependent on size. If you are the biggest clownfish in your group, you are a reproductive female. If you are the second biggest fish in your group, you are a reproductive male. If you are the third biggest fish in your group... you are a male who doesn’t get to reproduce until one of of the top two go missing. (Yes, clownfish undergo sex changes.)

When your reproductive success depends on size, being able to recognize the information about size in other group members could be critical.

Reference

Colleye O, Vandewalle P, Lanterbecq D, Lecchini D, & Parmentier E. 2011. Interspecific variation of calls in clownfishes: degree of similarity in closely related species BMC Evolutionary Biology 11(1): 365. DOI: 10.1186/1471-2148-11-365

Amphiprion ocellaris by Joachim S. Müller on Flickr; Amphiprion frenatus by brian.gratwicke on Flickr; both used under a Creative Commons license.... Read more »

Colleye O, Vandewalle P, Lanterbecq D, Lecchini D, & Parmentier E. (2011) Interspecific variation of calls in clownfishes: degree of similarity in closely related species. BMC Evolutionary Biology, 11(1), 365. DOI: 10.1186/1471-2148-11-365

December 26, 2011
04:52 PM
187 views

Sand crab shrinkage?

by Zen Faulkes in NeuroDojo

I spent the day in my office working on two talks I have to give next month. One is for the Subtropical Biology meeting we are hosting (13 January), and one is a public talk at the South Padre Island Birding Center (28 January).

It was lovely to just have the day to think about how to do these talks. Nobody else around. No interruptions. Just a chance to think about how to explain the science in a (hopefully) engaging way.

And along the way, I solved a puzzle that lets me fix a 25 year old error in the scientific literature. Even more satisfying.

The talks I am giving are both about one of the local species of sand crabs, Lepidopa benedicti. There’s not a lot of papers on any sand crab, including this species. But there is a nice paper that describes how thee little ones grow and develop, which is relevant to my talks.

Sand crabs, like many arthropods, have a larval stage. The adult sand crabs are dedicated diggers, and are rarely seen above sand, but the babies (zoea) are adrift in the waves. They spend the first few weeks of their life as plankton, up in the water. This might give them a chance to drift away, so that populations can colonize brave new beaches, where no sand crab has dug before. Because they are tiny and tasty, many crustacean larvae have spines of one sort or another to try to keep themselves out of the mouths of predators.

Then, the larvae undergo metamorphosis into a stage the looks much more like the adult (the megalopa) and they settle out into the sand.

I wanted to put all the different larval stages together on a single slide, all to the same scale, so that people could see the growth. But when I grabbed the pictures and rescaled them all to a single size, I got this:

I was confused. Why was the second stage smaller than the first one? And the third stage was still about the same size as the first. Typically, animals, you know, grow. Not shrink.

My first thought was I’d made a mistake. Rescaling things can be tricky, with lots of multiplications and divisions, especially since these all had different size scale bars (one was a bar for 1 mm, another was for 1.5 mm, and so on). (This led to some slightly goofy efforts of me holding up rulers to my computer screen to try to measure the sizes of the pictures ad scale bars from the PDF.) But no, it didn’t seem to be a math mistake on my part.

I went back to the text, and found there was something weird going on. Stuck and Truesdale had measurements of the size listed in the text, and they weren’t in line with the pictures. Even accounting for the fact that they probably didn’t draw an “average” larvae, there was no way they could be right: the most of the stages were about half the size in the pictures that the text said they should be!

Based on the measurements in the text, the sizes should be more like this:

Ahhhhh. That makes more sense.

Now I have my slide, and I have, in a very small way, perhaps helped there be just a little less error in the world. Even though it is no be a big deal, it’s still satisfying. Like pushing that jutting book back into place on the shelf.

Reference

Stuck KC, & Truesdale FM (1986). Larval and early postlarval development of Lepidopa benedicti Schmitt, 1935 (Anomura: Albuneidae) reared in the laboratory. Journal of Crustacean Biology 6(1): 89-110. DOI: 10.2307/1547933... Read more »

Stuck KC, & Truesdale FM. (1986) Larval and early postlarval development of Lepidopa benedicti Schmitt, 1935 (Anomura: Albuneidae) reared in the laboratory. Journal of Crustacean Biology, 6(1), 89. DOI: 10.2307/1547933

December 16, 2011
08:00 AM
470 views

When bluebells aren’t blue: Pollinator pulling power for flowers

by Zen Faulkes in NeuroDojo

Why do flowers have such beautiful colours? The quick answer that you’ll probably think of is, “To attract pollinators.”

This New Zealand bluebell (Wahlenbergia albomarginata) is – despite the name – usually mostly white. There is variation in this species, though; you can see some of this in the picture at right. Most of the related species are blue, and the typical explanation for why this species is white is that the pollinators that visit the flower dislike blue.

Campbell and colleagues argue that the hypothesis of pollinator preference for colours is often not very well tested. This surprised me since, like you, I’d hear the story about flowers being brightly coloured to attract pollinators so often. They set out with a very thorough series of experiments to test the relationship of pollination to colour.

The researchers’ first step was simply to observe. No experimental manipulations of any sort; they just watched pollinators visit flowers. They found no difference in visits to flowers based on colour, though they saw a preference for size.

Then they busted out experimental manipulations. They painted the flowers. The native bees showed no preference for white or blue, speaking against the hypothesis. Flies disliked the blue, which was consistent with the original hypothesis.

But... about 90% of pollen transfer (depending on flower colour) was by bees (who didn’t mind the blue) rather than flies. And pollen export (as estimated with dyes) correlated highly with bee visitation, but not with fly visitation.

The team didn’t find any difference in moving pollen from plant to plant that was associated with the flowers’ natural colour.

Finally, they did some larger scale experiments. The results were a bit complicated. The pollinators’ choices changed, depended on how much variation in colour the pollinators got to see, and on how big the flower beds were.

When the pollinators had a natural range of colours, they still showed no preference.

When the experimenters enhanced the colours by painting some bluebells even brighter blue, the pollinators show no preference in a small plot of flowers, They finally showed a preference for a flower colour in a larger plot of flowers!

Except it was in the the wrong direction: a preference for blue, not white.

All in all, you’d expect there to be a lot more blue flowers in this species.

The authors explored some alternative hypotheses that were unrelated to pollination. One was a possibility that there was some sort of thermal advantage to differences in colour, but there were no temperature differences between the blues and whites.

Another possibility was that there was some selective pressure from herbivores, but the team found (say it with me) no differences in how much the plant-eaters were chomping on the blues and whites.

Having eliminated a lot of functional explanations related to the bluebells’ ecology, the authors suggest that the flower colour is incidental, and there's some other factor under selection that is linked to flower colour by genetic happenstance. They’re betting on proteins, anthocyanins, that are related to both colour and to temperatures stress.

Campbell and the rest are busy breeding a bright blue and a white strain for new experiments and comparisons. Watch this space.

Reference

Campbell D, Bischoff M, Lord J, Robertson A. 2011. Where have all the blue flowers gone: pollinator responses and selection on flower colour in New Zealand Wahlenbergia albomarginata. Journal of Evolutionary Biology: in press. DOI: 10.1111/j.1420-9101.2011.02430.x

Photo by Mollivan Jon on Flickr; used under a Creative Commons license.... Read more »

Campbell D., Bischoff M., Lord J., & Robertson A. (2011) Where have all the blue flowers gone: pollinator responses and selection on flower colour in New Zealand Wahlenbergia albomarginata. Journal of Evolutionary Biology. DOI: 10.1111/j.1420-9101.2011.02430.x

December 8, 2011
08:00 AM
223 views

Burn your tables

by Zen Faulkes in Better Posters

A new paper provides empirical evidence for something that many people, like Edward Tufte, have been saying for years: graphs and figures are better than tables.Cook and Teo took the results of statistical simulations, and presented them to people in the form of graphs or tables. Everyone were able to answer questions about the data more quickly using a graph. Less experienced people (i.e., undergraduates compared to postgraduates) were able to make more accurate statements about the results when presented in a table rather than a graph.They note that many journals print tables that make matters even worse. Tables often have far too many significant digits, and readers are often asked to make comparisons horizontally, rather than vertically.If you are thinking of putting a table on your poster: burn it.ReferenceCook A, Teo S. 2011. The communicability of graphical alternatives to tabular displays of statistical simulation studies. PLoS ONE 6(11): e27974. DOI: 10.1371/journal.pone.0027974Photo by cranky messiah of Flickr; used under a Creative Commons license.... Read more »

Cook A, & Teo S. (2011) The communicability of graphical alternatives to tabular displays of statistical simulation studies. PLoS ONE, 6(11). DOI: 10.1371/journal.pone.0027974

November 30, 2011
08:00 AM
308 views

Aerobics grows your brain, but does it make you smarter?

by Zen Faulkes in NeuroDojo

Here’s what looks to be a straightforward claim:

Increased hippocampal volume translates to improved memory function(.)
But a simple line in the Discussion section may not convey the trickiness of the analysis in the Results section.

This paper, by Erickson and company, is looking for ways to prevent or reverse cognitive decline as people age. The hippocampus is part of the brain critical to the formation of memory, something we’ve known from many unfortunate people like Henry Molaison (known in the scientific literature as HM) or Clive Wearing who have suffered damage to their hippocampi. There’s good evidence that the size of the hippocampus can be affected by experience in humans.

The experiment had two groups. One group did aerobic exercise, the other did stretching exercises. They tested people after six months of exercise, and again after a year.

People who did the aerobic exercise had an anterior hippocampus that was a couple of percentage points larger than when they started. This is pretty cool, because hippocampus size decreases with age. The authors estimate that this is the equivalent of “rolling back the clock” by one or two years. The pattern they saw with the people doing stretching exercises was more typical: their hippocampi, on average, shrank.

Hippocampus is involved in forming new memories. Aerobic exercise makes your hippocampus bigger, as shown in this paper. So the statement I quoted at the top seems to follow, not just logically, but inevitably.

But here’s my problem. In the Results, the authors write:

Both groups showed improvements in memory(.)
Wait. Both groups got better at the memory task? That’s not what I would predict if hippocampus volume relates to memory function. After all, the hippocampi of the stretching control group decreased in size. You might think, “Well, okay, maybe both groups improved, but the aerobic exercise group must have improved more than the stretching control group, right?” Wrong.

(T)he aerobic exercise group did not improve performance above that achieved by the stretching control group(.)
Wait. What? How can you claim that bigger hippocampus volume translates into better memory, when people whose hippocampi are shrinking perform just as well at the memory task as those whose hippocampi are growing? Erickson and colleagues make this claim based on an analysis of the people in the aerobic control group only, and show that there’s a correlation between the amount of increase in the hippocampus and the improvement on the memory task.

Am I missing something blindingly obvious? I don't see how you can claim bigger hippocampus means better memory when you only analyze the test group and not the control.

This paper is very cool in what it shows about flexibility of brain size, but I am not sure what the take-home message is about whether aerobics can keep your memory sharp.

Reference

Erickson K, Voss M, Prakash R, Basak C, Szabo A, Chaddock L, Kim J, Heo S, Alves H, White S, Wojcicki T, Mailey E, Vieira V, Martin S, Pence B, Woods J, McAuley E, & Kramer A. 2011. Exercise training increases size of hippocampus and improves memory Proceedings of the National Academy of Sciences, 108 (7), 3017-3022 DOI: 10.1073/pnas.1015950108

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

Erickson K, Voss M, Prakash R, Basak C, Szabo A, Chaddock L, Kim J, Heo S, Alves H, White S.... (2011) Exercise training increases size of hippocampus and improves memory. Proceedings of the National Academy of Sciences, 108(7), 3017-3022. DOI: 10.1073/pnas.1015950108

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