Next: Bow Hunter's Syndrome Part 2: What, with a dab of why
Tuesday, January 21, 2020
Bow Hunter's Syndrome Part 1: A Survivors' Support Group of One
Next: Bow Hunter's Syndrome Part 2: What, with a dab of why
Tuesday, June 19, 2012
Field specific meanings
In demography, fecundity means capacity to produce babies and fertility means realized production of babies. In biology, these meanings are reversed.
In demography, EPC means European Population Conference, the largest yearly demography meeting in Europe. In biology, EPC means Extra-Pair Copulation.
Monday, March 12, 2012
Evolutionary biology vs. evolved biology
An example: A couple of years ago I attended a workshop on bioinformatics in aging research. There was a dinner the night before the talks started, and the bioinformaticist organizing the workshop asked me about my training and research. I said, "well I study the evolution of demographic patterns, particularly how constraints on natural selection lead observed demographic patterns to differ from the predictions of evolutionary theory." He replied, "Oh, but you are also trained in biology?" What he meant by this, I discovered, was that I also had some training in the molecular nuts and bolts that to him are biology. Evolution is a process that shapes biology, but in his view, and I think the view of many of the people there, does not in itself count as biology. Asking him if he ever incorporated evolution into his work, he explained that he had, comparing how networks of gene interactions differed between fruit fly and nematode. Fair enough, comparative biology is surely the study of evolution, but his approach to it required no technique or concept from evolutionary theory. He produces good and useful science, and gives no more daily thought to evolution than I give to promoter regions. I am certain that he would not be offended to be described as a good biologist who believes in evolution, but is not an evolutionary biologist.
A definition from wikipedia: "Evolutionary biology is a sub-field of biology concerned with the study of the evolutionary processes that have given rise to the diversity of life." This is somewhat too narrow in my view, but it is close enough given that it is past my bedtime.
This has all come to mind because of the post I wrote yesterday, about weeds evolving resistance to Monsanto's best-selling herbicide, and the failure of Monsanto's biologists to predict this. A good friend of mine, who is deeply knowledgeable about matters environmental and agricultural, responded by asking how Monsanto's biologists could have failed to predict the apparently obvious facts I was pointing out unless they were A, Tools; B, Fools; or C, having their results manipulated by suits. This is a reasonable and interesting question, and I'll venture an answer. My guess is that they were neither A nor B, and that C went on but was not a major factor. Monsanto did have an enormous financial stake in convincing regulators that weeds would not evolve resistance to Roundup, but they also had an enormous stake in having weeds actually not evolve resistance to Roundup. So my guess is they honestly thought it was a highly unlikely outcome.
Why did they think so, despite being smart, honest biologists? Because they weren't trained in, or primarily thinking about, evolution as it occurs in nature. They were plant geneticist and bioengineers, spending many years and countless millions of dollars to unravel the finest details of how Roundup kills plants and how to build a crop that will have resistance to it (without passing that resistance on to its offspring). That was an enormous challenge, and their success was unprecedented. They had achieved what many, even within their own company, must have thought was an impossible SciFi dream.
Surely someone was assigned to think deeply about the problem of whether weeds would evolve resistance, but surely that someone had been involved in the project for years, and was so wrapped up in the grotesque details of the genetic magic they had just achieved that no perspective was possible. In other words, they couldn't see the field for the soybeans. A person highly trained in artificial selection, and used to that way of thinking, will think of the evolution of weed resistance in those terms, despite the fact that natural selection has inherent advantages.
In hindsight, their logical errors are obvious, probably even to them. In foresight, reasonable and well intentioned people frequently fail to think of highly relevant and potentially obvious things. This is particularly likely if those things require a perspective they don't possess, doubly particularly if they are thinking deeply about the problem from a very different perspective. Monsanto had many biologists who knew about evolution, used a particular type of evolution as a tool, and thought about evolution. But my guess is they didn't have any evolutionary biologists.
Sunday, February 12, 2012
Spanning the vastness
Thursday, January 05, 2012
Authorship code
I'm writing a paper with two of my students. Well, I'm writing it with one of them and another one did a lot of work on the statistics. But today we had to straighten out the order that the authors would be listed in on the paper. This can be a contentious issue, and I know of cases in which papers did not getting written at all because the authors couldn't agree on who got to be listed first. Some big multi-author papers simply list everyone in alphabetical order to avoid the fuss, but then Dr. Aardvark always gets to be first author. Some journals have a little section where each author's contribution is described, but they usually end up saying something uninformative and false like "all authors contributed equally."
I came up with most of the ideas in the current paper, put things together, decided who would do what, etc. My student did much of the lab work and is doing much of the actual writing. Given this, most biologists would propose what I did, and what my student objected to: She (as the person doing the writing) should come first, I (as the senior person on the paper) should come last, and everyone else (in this case meaning the statistics student) gets sandwiched in between. This was very counterintuitive for my student; she thought I was trying to minimize my own role by putting myself last. In fact, it is a step up for me to be writing papers in which I am in that last position. I remember this being counterintuitive for me the first time it was explained to me. I was a college student, and a boss said that he'd make me second author on a paper. I said something to the effect that I'd be glad to be even last author, which I thought was being humble, but he took it as me saying the paper had been my idea. We straightened out the miscommunication but I didn't end up being listed as author on the paper. That the last author spot (at least in biology) signifies the senior author is a code biologists internalize, and I had to think back a long way to figure out why my student objected to me being last author. I explained, she reluctantly believed, and now it is settled.
Thursday, December 04, 2008
Journal of Biodemography
I'm just too interdisciplinary for my own good.
Wednesday, August 13, 2008
Stereotyping of students based on intended career
The stereotype goes something like this:
They only care about grades and letter of recommendation, they aren't interested in learning, they have no interest in science but will apply for any and every research position just to put it on their resumes. They will do a desultory job at any task you give them, so you may as well give them menial tasks. They are unpleasant to teach because they aren't interested and they spend all their time grade-grubbing. They are motivated to cheat by their fanatical devotion to getting A's.
This stereotype is, in my opinion, quite destructive. Not to say it has no basis in fact. I have had students who match the stereotype fairly well, both in classes and as lab assistants, and I will admit to finding myself hoping never to find myself or a member of my family in their medical offices. Our campus has both pre-medical and pre-vet undergraduate clubs, and while I have no direct knowledge of the advice these clubs give their members, the students who seem to be living up to the stereotype will occasionally say that they want the A or want the job because their pre-professional society told them so. (See here for my thoughts on how and why undergraduates should get involved in research. One important point, don't apply because your pre-med society told you you should, and if you do, don't admit to it, and if you do, expect menial tasks from most labs.) I suspect that some students really are led astray by receiving advice that emphasizes grades over learning and items on a resume over experience.
But honestly, the best undergraduates, bar-none, I have worked with have been pre-med and pre-vet. When I was a teaching assistant for Animal Behavior last year, the student in my section who asked the best questions, was the most enthusiastic and was the most helpful in explaining the material to her fellow students was a pre-vet student, very active in the pre-vet society. She also happened to get by far the highest grade in the course, but the high grade was clearly not her only reason for being there. My most accomplished lab assistant, whose thesis is nearly ready for publication, just applied to 20 med schools. I will admit to trying to talk her into a career in research, but I also have no doubt she would be an excellent physician. I could give as many examples of excellent pre-med and pre-vet students as I could examples of terrible ones.
Why do I think the stereotype is damaging though, if it is at least sometimes at least partly true? Partly because it colors interactions with undergrads. Some very large portion (well over half, I think) of students taking classes taught by my department are on pre-health career tracks. If one goes into interactions with more than half of one's students assuming that they are uninterested in learning, this affects one's teaching. If one offers only menial lab tasks to more than half of one's students, this affects their opportunity to learn about science. If instructors try to avoid teaching the classes that pre-med students flock toward, that doesn't say anything great about the educations of our pre-med students. It is also damaging if students feel compelled to live up to it. I had a pre-med students say to me that he was not interested in participating in anything that didn't contribute to his grade because that wasn't how pre-med students worked. I had the distinct impression he was striving to be the stereotype.
What actions do I suggest? The first would be for people on all levels of the department to be aware of this stereotype, and the biases it causes, and to be careful about how those biases affect their actions. The second would be for the pre-vet and pre-med clubs to make their members aware of this stereotype, and urge them to avoid being pigeon holed. Just as racism cannot be combated without acknowledging that it exists, I feel that carrerism must be exposed to the light of day.
Sunday, July 13, 2008
Catnip -> Olfaction -> Happy
Pet owners and behavioral scientists alike are fascinated by unique behavioral reactions that cats show in the presence of catnip. These experiments explored the possibility that the catnip reaction might be triggered by chemosensory stimulation of the vomeronasal organ. In the chewing and mouthing of the catnip source, substances might be dissolved in saliva and transported to the vomeronasal organ. The rolling and rubbing during a catnip reaction might be a sexual response activated by the accessory olfactory system since the system projects to parts of the brain involved in mediation of sexual behavior. However, removal of the vomeronasal organ did not attenuate any of the behavioral reactions to catnip. Olfactory bulbectomy immediately eliminated catnip responding, revealing that the chemosensory stimulus evoking the catnip reaction is undoubtedly mediated through the main olfactory system. Catnip activates behavioral elements associated with several species-specific behaviors, including sniffing and chewing as associated with oral appetitive behavior, rolling and rubbing characteristic of female sexual behavior, batting the catnip source characteristic of play behavior, and a type of kicking associated with predatory behavior. These behavioral reactions occur randomly and intermittently.
The moral of the story seems to be that:
A. Cats respond to catnip through their olfaction, the type of smelling that humans do fairly well, rather than through the vomeronasal organ, the part of smelling that humans don't seem to do at all.
B. Catnip elicits from cats behaviors associated with almost every active things cats enjoy (eating, playing, sex and hunting). Catnip does not elicit the calming and resting behaviors such as self-grooming and napping that cats also enjoy. Catnip also does not elict behavior associated with things cats don't enjoy (fighting, danger, housechoirs).
Based on this, and my own observations, it seems likely that catnip is a quick-acting stimulant, extremely pleasant to the cat and absorbed through the olfactory epithelium.
Stefanie Schwartz, in her book "Psychoactive Herbs in Veterinary Medicine" list some other useful facts. Catnip response is not associated with any know histological or physiological effect, (meaning that while it certainly does something in the body, it is something subtle) catnip is not toxic even at relatively high doses, and the physiological and psychological effects are very different in cats than in humans. In humans, catnip is mild sedative, and smoked catnip is said to have similar psychtrophic effects to smoke marijiana. In cats, it is clearly a stimulant. In neither species does it have any known side effects.
Nepetalactone, the active ingredient, is also aparrently a powerful insect repellant, driving off both lice and cockroaches many times more powerfully than does DEET.
Friday, April 18, 2008
Dying for Sex
There has been limited support for this hypothesis, and most of the others, because so many hypotheses make the same predictions that one can rarely conclude that a particular factor is at play unless one ignores all the other possibilities (which seems to be the standard practice.)
This paper from Proc.Roy.Soc.B. takes an interesting new tack, looking not at whether males that are shorter lived than their mates are taking more risks, but rather at whether their short-livedness can be explained by increased mortality during the season of risk taking.
Here is the abstract:
Abstract
Male excess mortality is widespread among mammals and frequently interpreted as a cost of sexually selected traits that enhance male reproductive success. Sex differences in the propensity to engage in risky behaviours are often invoked to explain the sex gap in survival. Here, we aim to isolate and quantify the survival consequences of two potentially risky male behavioural strategies in a small sexually monomorphic primate, the grey mouse lemur Microcebus murinus: (i) most females hibernate during a large part of the austral winter, whereas most males remain active and (ii) during the brief annual mating season males roam widely in search of receptive females. Using a 10-year capture–mark–recapture dataset from a population of M. murinus in Kirindy Forest, western Madagascar, we statistically modelled sex-specific seasonal survival probabilities. Surprisingly, we did not find any evidence for direct survival benefits of hibernation—winter survival did not differ between males and females. By contrast, during the breeding season males survived less well than females (sex gap: 16%). Consistent with the ‘risky male behaviour’ hypothesis, the period for lowered male survival was restricted to the short mating season. Thus, sex differences in survival in a promiscuous mammal can be substantial even in the absence of sexual dimorphism.
Wednesday, April 02, 2008
Non-scatological poo
This afternoon, I was considering the question of why we evolved to have our anus placed such that feces, after leaving the rectum, have ample opportunity to contact the surrounding skin, which then need to be cleaned. And then I began trying to imagine other places a human's digestive tract couple potentially end, and what the advantages and disadvantages would be. What would it be like, for instance if our genitals were behind, rather than in front of, our anuses. And, taking a comparative approach, I thought about what I know about the anal anatomy of other species, and how they clean themselves, or avoid the need to do so. And all in a purely intellectual context, without the slightest feelings of revulsion, shame or titillation. Yet somehow, I knew that one is expected to keep that sort of speculation to one self. Unless one is a biologist. And even so, I probably won't bring it up to my neighbor on the train tomorrow.
Monday, March 17, 2008
Rotifers, sex and locomotion: fast males, slow females
1. Oh! so that's what I've been seeing all this time.
2. Damn they're so tiny compared to the females
3. Golly-gee-willackers they move fast.
To give you a sense of this, observe the following Youtube video I came across. The little bizarrely fast ones are the males.
The males are short-lived, have no digestive system or foot (meaning they can't eat or anchor in one place). They hatch from an unfertilized egg, carry their mothers' genes to other females, and die.
I was discussing this with a friend of mine, who asked, "what good are the males anyway?"
"They're just swimming sperm packets." I replied. But then I thought about it more, and realized the question could be viewed another way. There are plenty of invertebrates that are hermaphroditic. A single individual has both ovaries and testes. I fertelize you while you fertilize me. No need to build a whole separate individual to deliver the sperm. So why go to all the expense of pumping out fleets of males?
Maybe, I thought, it was that speed. The smaller a rotifer is, the faster it can swim. This is the result of the fluid dynamics of how they swim. I don't know a thing about fluid dynamics, so I won't try to explain that, but the data show that swimming speed is predicted with great accuracy by size.
Having fast moving sperm deliverers could have two benefits that immediately occur to me. First, one can spread one's genes much further by producing small, fast males and sending them off in all directions, than by having one big slow female swim around. Especially considering that the female's immediate neighbors have a good chance of being clones of herself, to make sexual reproduction worthwhile, she needs to get get her sperm far away. That may require speed.
Second, maybe being fast is useful in the competition for mating. If the females are not just willing to mate with every rotifer that wanders along, perhaps being fast increases the chance of fertilizing her eggs.
These are all just hypotheses, but they are testable ones, and perhaps some day I will get to testing them.
Thursday, January 24, 2008
Life. Life. What is it?
In high school biology, I was told that viruses are not alive. They are like pieces of paper that say "Photocopy me!" They cause themselves to be replicated, but they don't actually self replicate. They don't grow. They don't exchange gasses. They don't take in low entropy material and put out high entropy material. They don't have a membrane.
Prions, misfolded proteins which cause other similar proteins to misfold in the same way, are even further from the traditional definition than are viruses. Viruses at least have their own genetic material. Prions don't. Therefore, not alive.
But we must be careful about phenomenological definitions. If we define Zebra as "an equid with stripes" then we can make any horse into a zebra by painting stripes on it, and an albino foal born to a zebra mother and zebra father would not a zebra. But an albino zebra is a zebra, and so while stripes are a prominent characteristic of zebrasity they are not a defining one.
So we must be wary of defining things in ways that they have to have some arbitrarily chosen us-like characteristic to qualify. Anthropocentrism is so uncool, and so limiting. Why does life need to have cells bounded by membranes? When earth is invaded by aliens who's tissues don't consist of cells bounded by membranes, are we going to insist that they aren't alive? I hope not. If on Mars we find some manner of critter that self replicates, exchanges gases and takes in low entropy matter/energy in order to maintain a low internal entropy state, but is without genetic material, are we going to say, "damn, we thought we might have life here, too bad?" No. We would say how amazing yet expectable it was that Martian life does it differently than we do.
So I don't quite know what life is, but looking again at that list from my high school biology class, there are certain criteria that make more sense than others. The "cells bounded by membranes" criterion is foolish, based only on the fact that we have only ever observed one related group of living things. It is like defining humans as light skinned after a visit to one family in Norway. The "has genetic material" criterion makes a bit more sense. I would rephrase it as "makes offspring that are more similar to themselves than would be expected randomly." The "grow and reproduce" thing is really two criteria. Growth, I think, is like the zebra's stripes. If we found beings that were built at full size by their parents, and then went on to make offspring that at the beginning of their lives were also full sized, but had high alivitude in every other way, I think we would recognize them as alive. Reproduction, on the other hand, seems a necessary component of a living system. Individuals who don't reproduce can be alive, but it is difficult to imagine a system in which life persists without reproduction. The "exchange gasses with their environment" malarkey is pure chauvinism. Most living things we know do, but is this a defining characteristic? No. "Maintains internal order by taking in low entropy mass/energy and putting out high entropy mass/entropy" is I think, inescapable for any lifeform.
So biology is (maybe) the study of entities or phenomena which make offspring that are more similar to themselves than would be expected randomly (in other words reproduce) and maintains internal order by taking in low entropy mass/energy and putting out high entropy mass/entropy. I'll have to think about this definition and see if I can think of counter-examples.