Friday, January 29, 2010

Sprouting collaborations

In the last week I have agreed on two major collaborations (with a Harvard professor and the Director of a Max Planck Institute) ordered some tens of thousands of Euros worth of equipment for my own experiments, hired two lab assistants for those experiments and promised my boss that I would perform a significant reanalysis of a set of data I already have in collaboration with another member of the lab. My wife and I also made some very tasty Brussels sprouts with garlic, soy sauce and lemon juice.

Here's the recipe:

Wash the sprouts, peel off any out leaves that don't look good, and cut each sprout in half.

Cut up a head of garlic.

Juice 2 lemons.

Heat a large cast-iron skillet or other frying surface, large enough to fit all the halved sprouts in a single layer. Put on a fair bit of oil and bring to very hot. Pour in the sprouts and use a spatula or fork to flip them over so that the flat side of each is down. Slide them around some so they all cook evenly. Cook them like that until they are somewhat charred on the bottom. Then flip them over and roll them around so that the other surfaces get cooked. They will still be somewhat too hard inside, so pour in a scant cup of water and cover while the water rapidly boils off, steaming the insides. Once the water cooks off, taste a couple of sprouts and if they are still too hard inside, pour on a little bit more water. Once they are done, remove them to a large bowl and put the garlic on to fry. After a minute, pour some splashes of soy sauce over the garlic, and let it cook down a little bit. Mix this with the lemon juice, salt and pepper, and pour it over the sprouts. Serve hot.

Wednesday, January 27, 2010

The flapper in winter

It was -10C this morning, and fresh snow on ice made an unbroken expanse of flat whiteness where the harbor usually is. The small ferry constantly crossing back and forth kept one thin line open, and the water birds congregated around that oasis; compared to sub-freezing air, freezing water is relatively warm. A few birds seemed not to have gotten the memo and instead made lumps in the snow at random points on the ice. One large lump the color of dirty ice seemed bird shaped, and I looked at it on and off seeing if it moved. It was the right size and about the right shape and color to be a juvenile swan, but it could also be a pit of trash or a chunk of refrozen slush someone slid out onto the ice.

My colleague, who also watches birds came into my office to ask if I had noticed it, and if so what I thought it was. He said there were footsteps in the fresh snow near it. He was right. Through my binoculars I could see swan prints leading to where it sat. And that lump on top might be a bit of neck leading to a head tucked entirely under a wing. But it must be dead I thought, why else would it sit so still for so long in such a windy spot on the ice?

I glanced at it occasionally though the morning, and it didn't move. Then some people walking their dog passed by, and the dog made like it was going to run out onto the ice to get the swan. A long gray neck snaked out from under the wing and looked straight back at the dog. The dog must have realized the ice was too thin to hold it. As soon as the dog was gone, the head disappeared under the wing again, and there it stayed.

In the early afternoon a fire department rescue truck pulled down the road to the harbor near the swan. Two guys, one holding binoculars, got out and looked at the swan for a while. I wondered if they thought it was a child. They drove away and came back with a third guy, who threw snowballs near the swan and yelled at it until it got up and walked a few steps. They left again, and the swan sat back in its usual spot, head under wing. The snow got heavier and started to pile up on the windward side of the swan, but it stuck to its spot, and still was there when the sun went down.

Monday, January 25, 2010

Almost finished

I'm about ready to submit this paper, and I have very mixed feelings as to its chances of acceptance. I've shown it to two people who told me they thought it was quite good and that I should send it to the high end journal I'm sending it to, and to a third who said he didn't think it would make it past any reviewer without major rewriting including changing which variables I was analyzing and the whole point of the paper. I've worked the paper over so many times I no longer have any idea if is it brilliant and revolutionary or a pile of misconceived hackary. What I do know for certain is that I am not going to start rewriting it at this point, and I'm going to hope that my friend who suggested I needed to do so just missed the point that the other two saw. The paper is methodologically sound, whatever its other flaws, and if the first journal rejects it I'll send it to lower profile journals until someone thinks it is important enough to print.

Friday, January 22, 2010

I really didn't want to get into discussing testis size.

I'm writing a paper on the choice male primates face between caring for the young they already have, and fighting other males for access to mates so they can have more young. There are, of course, other reproductive strategies they could also be investing in, like trying to impress the ladies without fighting, or impressing the ladies by being such good carers. I didn't want to get into all of these, because it just gets to big and complicated, and the relationship between the variables I have is already complicated and interested enough. But my colleague who read the paper for me thinks it is important to include something on investment in sperm competition. Sperm competition occurs when a female mates with more than one male, but only one of them will end up being the father of each baby she produces. The male with the strongest, fastest, healthiest, most numerous sperm will tend to be the father, and as such will tend to pass on his genes for big healthy sperm to the most sons. And to make lots of big healthy sperm, a male needs big testicles. Testicle size turns out to be closely correlated with how much multiple mating the females do, and in highly promiscuous species, males may dedicate a significant portion of their body mass to testes. And this is how I came to be typing search terms like "bush baby testis mass" and "monkey sperm competition" into Google Scholar. You would be amazed what Google is willing to label as a scholarly article.

Monday, January 11, 2010

Lovers in the snow

The UnterWarnow is frozen, and snow is building up on the ice. Sunset will come 7 hours and 45 minutes after sunrise today. The crows and blackbirds are digging in the snow looking for food, and the birds that usually haunt the harbor all winter are gone, perhaps to the south, perhaps out to the Baltic where the water isn’t solid.

But in the tree in front of my office window, two magpies are carrying fresh twigs into a crook between three branches. There is only one reason I know of why they would be doing this: they are building a nest. Most birds, including magpies, only build nests to lay eggs in, and now is not the time to lay eggs. It is too cold for the eggs to develop (even with mom sitting on them), and if they did hatch , there would be nothing to feed them. Any nest built now isn’t even likely to still be in good enough shape to use come spring. The spot where they are putting the twigs is near the top of the tree, on the branch closest to the river, and shakes whenever the wind blows, which it does frequently.

This raises the question of why? When other birds in the neighborhood are struggling just to keep from freezing or starving, why are the magpies wasting their time and exposing themselves to the cold building a nest they can’t use? Perhaps the cold has driven them mad? Maybe they are pulling food out of the dumpster of the near by grocery store, and having plenty of food, think it is time to breed? A genetic disorder?

There may be some perfectly good reason for this (pair-bonding activity?) but I’m not sure I buy that.

When my colleagues and I were writing a paper on the definition of behavior, many of previously published definitions we came across specified that behavior is adaptive, that it will tend to increase the fitness of the individual performing the behavior. We omitted this from our definition, because there are so many behaviors whose adaptive significance is uncertain, or which seem maladaptive. It is certainly true that most behaviors are adaptive, some, like building a nest in a snow storm, probably are not.

Wednesday, January 06, 2010

Rostock ten day forecast

Mostly Cloudy

I must really love science, as I don't know what else would keep me in this sun-forsaken place.

Sunday, January 03, 2010

Picking sources

My work task for this weekend is making me aware of a gap in my education as a scientist. How does one decide which sources to cite when there are many available with the same information?

I and my assistants at Berkeley classified a significant number of primate species based on how much care fathers give to their offspring. For each species we would search the primary literature for sources documenting if fathers in that species provided care to their offspring, and if so how much. We gathered papers, sometimes dozen for a single species, read the relevant pieces and decided that fathers of that species provided no care, little or incidental care, significant care or were, for at least some part of their offspring's lives, the primary caregivers. This compilation allows me to compare the evolution of paternal care with that of other traits, such as the degree to which males fight for access to females in each species (the prediction being that males will tend to either invest heavily in their offspring or fight intensively for mates, but not both).

But what I have to do now is decide, for each species individually, which paper or papers to say I based my decision on when I publish this compilation. I've not actually studied any live primates myself. The many people who have dedicated years of their lives to documenting the behavior of each species, may disagree with my conclusion on their species (some inevitably will, I hope not too many). Those that do will be prone to dismiss the paper as a whole unless I at least give appropriate references to show I wasn't just making my data up. I feel like somehow I've made it this far without really knowing what rules to follow in documenting my sources. One can't just list every paper one consulted, or pick one at random. Should I reference the first paper to suggest that this species had that trait? Or the one with the strongest evidence, or the review article that states that the evidence for that conclusion is overwhelming? Should I include a reference to the dissenting papers, to show that I am aware of them, even if I disagree? Should I try to include references from the journal I plan to submit to?

What I'm actually doing, which may be the wrong approach, is referencing the papers I find most convincing and relevant, regardless of precedence, author or journal. As long as the reviewers don't object, I'll consider this strategy a success.

Saturday, January 02, 2010

To survive and reproduce in good times and bad

jte asks:

Is there reason to believe, or evidence to support, that the forms of evolution occurring among species during a period of abundant resources is different from the forms of evolution occurring among species during a period of deficient resources?

It seems that a lot of the argument in evolutionary theory is that it takes a lot of energy to grow extra and useless appendages or what have you, so if they really are useless, you'd expect them to evolve away. But if resources are abundant--energy is not a particularly limiting factor--do you then get a scenario in which all kinds of wacky and useless appendages appear and are not attritioned away? Which gives those appendages time to hang around enough to be available when the environment changes and all of a sudden they are useful and confer an advantage?

Or something like that?

I wouldn't go so far as to say the "forms of evolution" are different. In good times and bad evolution acts through natural selection, genetic drift, mutation and all the same basic mechanisms. Rather I would say that selection acts of different traits, or favors different forms of those traits, depending on if times are good or bad. One excellent example of this has been documented by Peter and Rosemary Grant in long term studies of Darwin's Finches on the Galapagos Islands. The climate in the Galapagos is impacted hugely by the El Nino/La Nina climate cycles. In some parts of the cycle, the islands are cool and damp, vegetation grows lush, and there are lots of big seeds to be had. In other parts of the cycle, it is very hot and very dry and only the desert plants with their tiny little seeds are producing. In the good years, the finches with the big bills can eat lots of big seeds, and reproduce like mad. In only a few years the population of one finch species is dominated by big-billed finches. Then when the rains stop, the population starts to crash, and the finches with the little bills good for extracting and opening small seeds are much more likely to survive. After a few years of that, the population of that same species is again dominated by small billed finches. This isn't individuals developing differently depending on the food supply, this is just massive, cyclical natural selection driving the population's genetic make-up around in circles.

On a much larger time scale, generalists are much more likely to survive large extinction events, while specialists often dominate in habitats that have been very stable for millions of years. Consider which of each of these pairs of species is in greater danger of extinction?

German Cockroaches or Lord Howe Island Woodeating Cockroaches
The Black Rat or the Salt-Marsh Harvest Mouse
The Common Pigeon or the Mariana Fruit Dove
The Common Raccoon or the Cozumel Raccoon
Goats or Alpine Ibex
Humans or Sumatran Orangutans

In each case the generalist are doing fine, while their specialized relatives can't cope with change. The fossil record shows multiple examples of large groups going extinct when the coprolites hit the fan, but one or two very generalized species in those groups making it through and giving rise to many new species. The amazing thing is that over and over most of those new species are specialists, evolving to be increasingly good at dominating increasingly narrow sets of resources. Give Rattus rattus a few tens of millions of years and no other mammals on the planet, and they would evolve into many thousands of separate species, filling a vast array of niches, and most of those species would be specialists. If another great collapse came, the ones most likely to make it through would again be the super generalized rat.

As far as the "useless appendages" argument goes, remember that even when resources are abundant, there is still the race to see who can convert those resources into the most offspring the fastest. Plus, the ideal situation rarely lasts very long. Usually within a few generations the population of predators has increased, the food supply has diminished, or population density has gotten so high that pathogens are spread easily. Exponential growth is not to be underestimated. So with the possible exception of humans over the last couple of hundred years, it is almost never the case that a population goes on growing for many generations without selection knocking back those who spend their energy recklessly.

That said, there are traits that are advantageous in bad time and costly in good times, or the opposite. Sometimes species evolve plasticity, such as the ability to grow a thicker coat when the winter is colder, but not waste the protein in mild winters. And sometimes, like Darwin's finches, they just evolve back and forth. The camel's hump is probably something of a hindrance when water and food are plentiful, but it bears that cost because more often than not things will get dry again, and that hump will save its life. If camels lived in an environment where it didn't get dry for some thousands of years, they might end up sans hump, looking more like big llamas. Or they might just die out, vanquished by cows and goats. Camels, after all, are specialists.

Thrice bitten

There is a class of "getting to know each other" games that organizers like to force upon groups of people meeting for the first time, in order to help them start talking to each other. One of these is called something like "Two truths and a lie" in which each person offers three autobiographical facts, and the group has to guess which one is false. My facts when faced with this game were:

1. I have been stung by a Portuguese Man o'War.

2. I have been poisoned by a black widow spider.

3. I have been bitten by a venomous snake.

The third was the one I intended to be false. I have just found out that all three of these are true. The only snakes I have ever been bitten by are those I have picked up, and the only snakes I have picked up are those which I knew to be non-venomous, primarily garter snakes. It turns out though, that garter snakes are venomous, and my knowledge (shared with most of the rest of the world) of their lack of venom was wrong. Mind you, they almost never actually get any venom into a human, and if they do it is not dangerous. But it turns out garter snakes do have venom glands, and of the dozens I've handled I've twice been bitten by them. Once picking up a tiny individual from under a rock, and once rescuing a larger individual from a road. They don't have fangs, or dental groves, or other efficient venom delivery systems, and their venom isn't strong enough to kill even small prey, but apparently if they chew on a prey item long enough some of the poison will work its way into the wound and perhaps help to subdue the food, easing swallowing. I once watched a small garter snake attempt (for about twenty minutes) to swallow a very large frog, and I must say the poison didn't do the snake much good, despite extensive chewing, because the frog escaped after giving the snake a good kicking about the head.

If I'm ever forced into that game again I will have to change my lie to, "I've been bitten by a venomous mammal." I'm not dumb enough to pick up a shrew.

Friday, January 01, 2010

Convergent crocodilians

This attractive individual lives in the Zoo Basel. It shares a large enclosure with these two:

As we gazed upon their toothy serenity, my wife asked me what species they were. I had to admit I didn't know. There may have been a placard somewhere, but in the crowd of humans I didn't notice it. Clearly crocodillians, and not alligators or caimans, but beyond that I couldn't say. Gharials have longer, skinnier snouts for catching fish, and most crocodiles have thicker, heavier snouts for pulling down large terrestrial animals. These seemed to be somewhere in between.

I've looked up what species of crocodilians have snouts like this, and was pleasantly surprised to find out that there are three candidates: the Slender Snouted Crocodile, the False Gharial and the Freshwater Crocodile. All three have similarly shaped snouts and eat a mixture of fish and terrestrial prey. All three are said to bite humans only when harassed, and all three live in fresh water. Each is found on a different continent and they are not closely related to each other. The African Slender Snouted Crocodile, the South Asian False Gharial and the Austrailan Freshwater Croc have apparently evolved into similar niches and therefore converged on similar morphology. Interestingly, despite its numerous crocodilians, the Western Hemisphere seems to lack a similar species.

I found out that these are Australian Freshwater crocs only by looking up which of these three species the Zoo in Basel keeps.

They also hold three of these, Nile Crocodiles:
That's what the above water part looks like. The below water part of the same individual in the same position looks like this:

Notice the much wider, more typical crocodilian snout.

Choughs in the wind.

Pilatus is a minor alp at 2132m (7000ft), but impressive for its sheer ruggedness, and the way it hangs over Lucerne Switzerland and several large lakes and forests. Its peak can be reached by a cog-wheel railroad, except in the winter, when snow and ice block the tracks. In these months, only the aerial cable cars, leaving from Lucerne, reach the top. The large gondola that carried us the last few thousand feet to the peek hung from a great cable with no support between its two ends, excepting one tower, which stood atop a sheer drop of close to a thousand feet. The top half of the mountain was snow covered, with evergreens petering out some hundreds of feet below the top. As we stepped out of the Gondola and into the visitor center on the mountain's top, it began snowing.

Standing outside the visitor center we could see impressive peaks, valleys, lakes and forests stretching far and wide. A stiff wind was blowing, and within two or three minutes we couldn't see much beyond the peak we were on. We went inside and had hot chocolate and pastries. As we sat and sipped, gazing through floor to ceiling windows, visibility continued to drop. We noticed that the staff were starting to close up, which seemed odd, as it was still morning. A smiling suited man with a managerial manner came through announcing something in Swiss German and everyone started moving towards the cables cars. Our friend Annette explained that the wind was picking up so much they were afraid they wouldn't be able to run the cable cars, and they were sending us all down the mountain before that happened. By the time we got down one flight of stairs the wind was too strong, the cable cars couldn't safely operate. We and a couple of hundred other visitor and staff waited perhaps half an hour before the manager came through and announced we would just have to wait the storm out. He invited us all back to the restaurant for free refreshments. So we sat in the big exposed glass walled restaurant consuming free soup, hot beverages, pastries and good bread and watched the blizzard lash the mountain. Chunks of snow the size of small cars broke off the cliffs and were thrown up and out. A wooden bench which had been left outside was hurled into a metal fence hard enough to snap some of the welds. Visibility was perhaps ten meters.

In the middle of this frozen hurricane, this onslaught of white fury, something, no two somethings black and sleek and solid appeared on the edge of visibility and simple hung in the storm. It seemed ridiculous that anything could live on a mountain peek in such a blizzard, but these forms seemed not only unconcerned, but rather playful. Annette and I, both former ornithologists, each had binoculars out and pointed within five seconds. Too slow, for the seemingly magical forms rotated slightly and in unison shot at amazing speed down wind and into the white-out.

"Alpine Choughs!" announced Annette, and several tables-full of other tourists turned around to look for the now vanished birds.

Over the next hours, as the storm slowly passed, we watched the choughs hovering, flipping, clearly playing, in conditions that would kill any normal bird long before it could flee down the mountain. They seemed to seek out the crevices through which wind blew fastest, so as to make their acrobatics all the more impressive. When it finally stopped snowing, we could see dozens of choughs racing and chasing with no apparent goal but to use the still gale force winds to show off for each other. As the winds slowed most of the choughs settled into a snow bank a few meters below the absolute top of the mountain. Their bright yellow beaks and red feet did not hide within their thick black feathers, but stayed exposed to the ice and wind, as though the weather was warm and sunny. They danced on the barbed wire that keeps animals away from the weather station at the peak, swinging in time with the wind.

And with that the manager stopped handing out the free refreshments and herded us down to the cable cars. Our car, rated to hold up to 3000kg, was stuffed with 2985kg of tourists. The wind swung the car side to side as we slid down the cable and over the cliff. It took at least four cars to get everybody down.

Safely back in Germany, I've been reading about the choughs, and they are pretty amazing. They can be found at the tops of high mountains from North Africa to western China, and unlike most other wildlife often do not move to lower elevations in winter. Being corvids (members of the crow family) they are smart and social. They are omnivores, feeding in rapidly moving flocks on insects, seeds, eggs and anything provided by tourists. They eat a lot of berries in winter. They will eat from people's hands at ski resorts and other places where they are fed regularly. Their bills are smaller and their feathers thicker than other crows, but otherwise nothing about their appearance would make one think they were so immune to cold. They likely store food in rock crevice where the cold keeps it good until they want it. They may nest at higher elevation than any other birds. Seeing them play was well worth being stranded on a mountain top for, especially when the stranding was accompanied with free soup, hot chocolate and pastries. I would gladly have shared the pastries with the Choughs, if I wouldn't have had to go out in the storm to give it to them.