Administrative Danglish

A few examples:

Censorship- Grading, examining
"Will this class require external censorship?"

Confrontation Hours- The time an instructor spends actually face to face with the students, contact hours
"You are responsible for 160 confrontation hours."

Critical Situation- Emergency
"A critical situation has occurred. A critical situation has occurred. A critical situation has occurred."

Dimensioning- Downsizing, rescaling
"The department will undergo dimensioning, as the government has determined there is too much competition for the jobs our graduates seek."

Economy- Accounting, bookkeeping, purchasing, etc.
"Mads handles our economy."

Licitation- bidding (as for a construction contract) or bid
"The licitation on the new station was higher than we expected."

Referent- The person who takes minutes at a meeting, secretary
"Are you the referent for this class?"

Taxameter- I have not yet figured out what this one means.  Something to do with fees or tuition.

. . . by any other name . . .

I'm sure it makes a difference to the worms, but to me 'cattle manure,' 'cowdung,' 'cowshed manure' and 'cattle solid waste' are all the same experimental growth medium.

Apozygotic agamospermic apomictic agamospory

I'm making a table. Not the tisch, bord, tavolo, mensa kind. I'm making a table of comparisons of offspring viability between sexually and asexually produced offspring. This is polychallenging. Part of it is that the literature is scattered, so it takes a lot of hunting around, but that is a usual and interesting sort of challenge. Part of it is that I want to include lots of different kinds of organisms, and find basically comparable comparisons for each, and the measure one might use for offspring viability for a lizard is necessarily different than that used for an insect, plant or mold, but this is arises from the real diversity of biological process, and so is also interesting. The part that I am finding frustrating and difficult is the choking miasma of obfuscatory terminology. Some terms, like amictic, are used to mean different things by different authors. Clear concepts (e.g., what portion of seeds open and something live comes out) are referred to by a dozen different terms. Frequently a single author or group of authors will have a term that does not seem to be defined anywhere and isn't used by anyone else. Apozygotic, for example, seems to be used only by eastern European sugar beet scientists to mean agamospermic, which is a term botanists use to describe reproduction via diplospory, apospory or nucellar embryony, which are all (I think) non-automictic kinds of agamospory, which is close to what a zoologist would call apomictic parthenogenesis, which basically means that offspring are coming out of eggs (or seeds or spores) produced without any genetic recombination or changes in chromosome number along the way. There are various places in the literature or on the web where good intentions have tried to straighten all of this out and discard the duplicate or ambiguous terms, but of course they come to different conclusions and are frequently ignored.

Immortaly Tomfoolery

Their is a saying among scientists that the more you know about the scientific subject a journalist is writing about, the less of what he writes makes any sense. There is a long new article in the New York Times magazine about a hydrozoan jellyfish, Turritopsis dohrnii, which the author claims holds the key to immortality. As someone who happens to work on hydrozoans, and on aging, I can assure you that not a bit of it makes any sense. The title, "Can a Jellyfish Unlock the Secret of Immortality?" should be a dead giveaway that this is magical thinking with a whitewash of pseudoscience. The argument behind the article, striped of its misunderstandings and untruths,  goes something like this:

1. There is this jellyfish that can develop back from the medusa phase, which we normally think of as the adult, to the polpy phase, which we normally think of as the juvenile. It can then develop into the medusa phase again.
2. We are going to assume that this is the only know case of an organism that does not show a human-like pattern of aging.
3. We are going to assume that this non-human like pattern is equivalent to immortality.
4. We are going to assume that if we understood the mechanisms behind this assumed immortality, we would know how to make humans immortal.
5. We would know by now what makes them immortal except that we are going to assume that the one researcher I talked to extensively for the article who studies the species is the only one doing so.
6. We are going to assume that this one researcher is unfunded and working alone not because he is considered a crackpot, but because the rest of science is just too blind and lazy to see the importance of this man and his work.
7. We are going to assume that when he has learned a little bit more, we will achieve immortality.

I do not recommend that you read it, and mention it only because I have been asked about it, and because I would like to speak briefly about the word immortality. Immortality is defined as immunity from death. Immortal beings cannot be killed. Turritopsis dohrnii can very easily be killed. Put one out of water for a few minutes, feed it to a predatory snail, heat it, freeze it, slice, dice or frappe it, and it will be dead. Ergo not immortal. However the journalists are not to blame for the misuse of the word. A very good recent paper in PNAS from a very good careful research group is titled, "FoxO is a critical regulator of stem cell maintenance in immortal Hydra." They use the word immortal as many people in bio-gerontology do, to mean that the risk of death does not increase with age. My general impression is that using the word in this way is misleading, but that it is a lot flashier than 'nonsenescing' and therefore widely used.

When animals aren't 'animals.'

I know a guy who has fishing licenses in about ten states. He doesn't fish, but he does study salamanders, and according to the fishing regulations in many states, salamanders are fish and you need a fishing license to mess with them. Salamanders are of course not fish, unless you are a hard-core cladist who thinks that all vertebrates are fish. State fishing officials are not generally hard-core cladists, just people who write and enforce regulations and don’t really care if salamanders aren’t fish.
A similar situation arises when it comes to laws governing ethical animal research. If a scientist wants to passively observe a bunch of animals in the wild, she needs to go through all kinds of ethics boards and paper-work to make sure she is complying with these laws. If another scientist wants to slowly dissolve a bunch of live insects in acid, he just needs to buy some acid, because legally, invertebrate animals aren’t ‘animals.’ Animal ethics laws generally don’t apply to them. I say generally because their are particular exceptions. Switzerland and Norway consider lobsters and their relatives to be animals, so you can’t just drop them in boiling water (at least not in a scientific context), you have to kill them humanely. England extends animal protection laws to the Common Octopus, but apparently not to other less common octopuses, so it pays to be common.

For a researcher like myself, who studies invertebrates in the lab, this is a very convenient absurdity. It means that when I want to feed live brine-shrimp to my hydra, I don’t have to ask any committees to review whether the feeding is humane to the brine-shrimp or the hydra. I don’t need to get official approval for the size of container I keep barnacles in.
I approve of laws, regulations, forms and committees that require the ethical treatment of animals in research, and I try hard to follow the principles they are intended to enforce. I am also very glad I don’t personally have to deal with the red tape.

Field specific meanings

In demography, the phrase "historical demography" means studying the population processes of human populations of which we have historical records. In population genetics and other subfields of biology, it means trying to estimate past changes in population sizes based on the genetic patterns of current populations.

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.

Evolutionary biology vs. evolved biology

Once, during a medical exam, the doctor asked me what I did. I said I was an evolutionary biologist, to which he replied, "oh, so not a creation biologist?" His tone of voice made it clear he thought it was funny that I had to specify evolutionary, as though a biologist in Berkeley could possibly not believe in evolution. Considering where his hands were at the time, I didn't stop to explain to him what the term "evolutionary biologist" means. Every biologist knows, or should, that Theodosius Dobzhansky wrote, "Nothing in biology makes sense except in the light of evolution." The vast majority of biologists, of all disciplines not only know about evolution, but accept it as a necessary part of any complete explanation for the things they study. But a large portion of biologists don't regularly think about evolution; it is not the part of the explanation they are interested in. A large (and I think increasing) proportion of biologists study the interactions of atoms, molecules, organelles, genes, cells, etc. And while they may connect their work to evolution in some way, they are not basically asking questions about evolution, but about the details of the proximate mechanisms which make organisms work. That these mechanisms are the result of evolution is often not particularly relevant to the present question.

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.

Who's a demographer?

I tend to find religious fundamentalists, whatever the religion, hard to listen to. One of the habits I find objectionable is the tendency for fundamentalists of a religion to argue that others who practice the same religion differently aren't really practitioners of that religion at all. This tendency has recently been popping up in the news as Christian fundamentalists in the US argue that because Mitt Romney is a Mormon, he isn't really a Christian. I have no fondness for Mitt Romney, and frankly suspect he would claim to be a Pastafarian if he thought it would get him elected. That said, the Mormons declare themselves to be Christians (they do talk about Christ a lot), and I can't see as anyone has the authority to tell them they aren't. It is just hubris to go around telling people that you can describe their religious beliefs better than they can.

This is all a roundabout way of getting to the question of who is a demographer. Ask a demographer what is the largest annual scientific meeting for demographers, and she will probably say The Population Association of America (PAA). I consider myself a demographer as well as a biologist, but I think most PAA members would say the stuff I do isn't demography. This is for the simple reason that I mostly study non-human populations, and the PAA defines demography as the study of human population processes. Studying the same processes in non-humans is, by this definition, not demography. Last year they had a session on evolutionary demography, but all the accepted papers were on humans. This year they don't even have such a session. I think that inserting the word 'human' into the definition of demography is roughly akin to saying that anyone who doesn't follow the teachings of a particular Rabii isn't really Jewish, so I call myself a demographer.

I was recently surprised to find myself in a conversation in which the tables were turned. A colleague was arguing that most PAA members are not really demographers, but sociologists. His argument was that many human-focused hard-core demographers feel out of place at the PAA. After their meetings this spring several colleagues complained that most talks at PAA meetings are really quantitative sociology rather than demography. The distinction is a fine one, but basically classical demography has a core set of questions and methods, and these have certainly been supplanted to a considerable degree by questions coming out of sociology, mostly approached with methods that don't require the quantitative machinery of formal demography. My colleague told me, "All the talks are full of regression tables, and most of the regressions aren't even done well."

So is it fair to say that my colleagues and I, who apply classical demographic methods to non-humans are more demographery than the quantitative sociologists at the PAA? I'm afraid not. We can no more revoke their demographer label than they can revoke ours. However, since the social demographers who control the PAA aren't interested in evolutionary demography, and most of their presentations frankly aren't that interesting to us (there really are a ridiculous number of regression tables, mostly demonstrating the relationship between fertility and female education for yet another population), I'm going to let my membership lapse. I'm thinking I'll join the British Ecological Society instead. They have lots of evolutionary demography at their meetings. I don't even feel the need to call myself an ecologist.

name for a principle?

There is a principle that I want to refer to in an upcoming talk, but I can't find a name for it. Someone must have named it after themselves by now. It is related to Ockham's razor, and to parsimony, but is distinct.

The principle is that an explanation for a pattern should preferably be applicable as broadly as the pattern is observed, but not more broadly. For example, an evolutionary explanation for group living that can be applied to all the group-living insects is preferable to an explanation that works only for one species of ant. The explanation should preferably not explain the pattern more broadly than it occurs. For example, an explanation for the fusion reaction of the sun merely in terms of the presence of hydrogen would also tend to predict fusion in many other contexts where it does not generally occur, making this explanation less desirable than a more complex one which also specifies the need for the physical conditions which encourage the hydrogen to fuse.

This is the sort of logical statement that is so obvious as to rarely need to be said, yet I need to say it for this talk. If you know what I should call it, please let me know.

What is EvoDemo?

The question has arisen how we should define Evolutionary Demography, such that we can decide if someone's work qualifies. I have offered 2 short definitions, into which I haven't yet put a lot of thought.

Short definition 1 : Scientific study which combines evolutionary biology and demography.

Short definition 2: The study of the evolutionary history, function, variation and relevance of demographic traits.

These are both broadly phrased. I don't like constraining definitions to the traditional terrain. A zebra found outside Africa is, in my opinion, still a zebra. As such, I haven't included anything about what traits, methods, etc. evolutionary demographers usually consider.

My question to you, dear readers, is: Can you think of anything that should be considered evolutionary demography that doesn't qualify under these definitions, or anything that shouldn't qualify that these definitions let in?

neologistic challenge

In demography, we spend a lot of time thinking about how the risk of dying increases with age. Economics calls itself the dismal science, demography is the morbid science. Anyway, we call the increase in mortality risk with age in adults "senescence", from the Latin root senex (old). I prefer to think and write about the fact that mortality rate decreases with age in those who are not yet adults. My problem is that there is no word equivalent to senescence that mean this, so I have to invent one.

So I want a word that can be defined as "the decline in mortality risk with age from conception to maturity." A root that means improvement, growth, blossoming, development, growing up, or something along those lines would be best. Twelve points for whoever comes up with the best term.

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.

conflation

Word of the day: Conflate (v)- to mistake two or more separate things as being only one thing, generally in a way that leads to further logical flaws.

from Latin con- (together) -flate (blow, as in inflate).

I'll give you a few examples of conflation:

There was, some years ago, a debate as to what to call that portion of the American electorate who wanted the US government to be run according to the precepts of the right-wing evangelical clergy in the US. Should they be the Evangelical voters, the Christian Right, the Values Voters? It seemed to many on the political left that we should simply use the word which by definition means, "those who advocate for government according to the rules of a particular religion." This word of course is "theocrats.' Leaders of this movement for Christian government, when asked about the term theocrat would reply that this word comes from Greek theos, meaning god and kratos, meaning rule or regime, and therefore theocracy is direct rule by God, and so they weren't advocating for theocracy, merely rule in the name of and in line with their understanding of the will of God. It is a common trick by those who wish to redefine a word for political or rhetorical purposes to conflate etymology with denotation.

In another example from the news, a large species of Atlantic ray, the flapper skate, has been fished nearly to extinction. It had been conflated with the blue skate, a smaller, faster breeding distinct species, such that for several decades we thought the two species were one, with the flapper skates merely being the larger individuals. As the number of larger individuals declined, no legal protections were put in place, as the relatively numerous smaller individuals indicated reproduction was still sufficient to maintain the population. Oops. Now that the two species have been deconflated, we know that the flapper skate is all but gone.

Finally, on this thanksgiving day, let us not conflate sweet potatoes, which are commonly eaten in North America, with yams, which are not. Whether orange or white, they are sweet potatoes.

So what, you might ask is the difference between conflation and confusion? The answer is that conflation is a specific type of confusion, one that is worth being aware of in its own right. Having a name for a logical flaw, in my experience, makes it easier to spot it.

Extinction is evolution

I often enjoy Olivia Judson's science blog on NYTimes.com. She has an actual science background, and gets the science badly wrong far less often than most other reporters of science.

Her most recent post is more in line with what I expect from science journalism. Without recapping her whole argument, she writes, "But if [evolution] has that much potential — how come organisms keep going extinct in nature? In other words, why does evolution keep failing?"

She then goes on to make a big deal about how evolution fails each time a population fails to evolve. But in so doing she fails to admit the distinction between evolution on the one hand and adaptation on the other.

Evolution is genetic change in lineages with time. Adaptation is the process by which the genetic makeup of a population is altered in a way that helps individuals of that population be more successful in their environment. Adaptation is one mechanism, and result of, evolution. It happens to be the best known mechanism, and the one that in the popular imagination defines evolution. But evolution has lots of other mechanisms. Genetic drift for example. Imagine you have a small population of squirrels on an island, some gray, some black. A disease comes through and kills a significant portion of the squirrels, and even though they are all equally susceptible to the disease, through the randomness of epidemiology more grays than black catch it and die. After the disease, the population has a higher proportion of black alleles than before. The population has evolved, because the proportional genetic makeup of the population has changed. But this is not an example of adaptation, because the genetic change was not caused by one version of the color gene conferring a selective advantage over the other. The allele frequencies "drifted" without being pushed by selective considerations. The next time the disease comes though more black squirrels could happen to catch it, and the allele frequencies could drift back.

So adaptation is not the be all and end all of evolution. Much of the evolution that happens is non-adaptive. And another important mechanisms of evolution is extinction. Imagine now that the disease killed not just some, but all of the squirrels on the island. That population is extinct. They are no longer represented in the genetic diversity of squirrels more generally, of rodents more generally, of mammals more generally. The remaining diversity, through the removal of that population, has changed. The extinct population has ceased evolving, but through their removal the larger group is left genetically less diverse. The genetic makeup of the larger lineage has changed, so evolution has occurred. It is also possible that the residual populations are more fit than the pre-epidemic average, because they are resistant to that particular disease. Whether or not this qualifies as adaptation depends on the fine details of the definition of adaptation you prefer. There is no standardly accepted definition, or rather different groups of biologists prefer different definitions. But all evolutionary biologists, save those who have crossed over into journalism, agree that extinction is an example of, not a failure of, evolution.

Individuality

The central question of interest here in the Laboratory for Evolutionary Biodemography is: how does evolution determine demographic patterns (usually individual lifespan) and, secondarily, how do demographic patterns (again usually individual lifespan) influence the evolution of other traits? This questions leads to all manner of difficult sub-questions. One of these, that comes up surprisingly often is, "what is an individual in this case?"

One colleague has been pondering this question in the context of eusocial insects. Eusocial means that some individuals do all the reproducing, and others don't reproduce at all, they just work to increase the survival and reproductive success of the breeders. Queen ants and their workers are a good example. It seems pretty easy to count ants, they have separate little bodies and they are genetically distinct "individuals" but because they don't breed (usually) from the viewpoint of propagating genetic material, their only role is to perform their appointed task within the colony, in order to aid the queen. This has led some ant experts to refer to the ant nest as a super organism, with the queen functioning as the reproductive organ, and the workers, like the cells in our intestines, as merely the body that supports this reproduction. In many organisms reproductive cells can last the whole lifetime, which intestinal cells are disposable, and frequently replaced. Likewise, queens live as long as the colony does, greater than 30 years in some species, while workers usually last only a few weeks or months. So is the colony a single organism, and therefore the workers its sub-parts, or is each worker an individual, and therefore the colony a multiplicity?

Another colleague is studying the demography of hydra, small mostly sessile cnidarians. Hydra are among the most demographically bizarre organisms. For starters, no one has been able to prove that hydra age at all, despite multiple long term attempts. Second, their primary means of reproduction is through budding, where a bump on the side of the organism gradually elongates, grows tentacles, forms a digestive cavity and takes on the form of a fully formed and functional (but somewhat small) hydra before detaching and becoming a separate individual. Add to this that if you mash them up to separate their cells from each other, each cell has the capacity to grow into a new hydra. Yesterday, I spent a few minutes watching through a microscope as a hydra with a large bud sticking off the side, about half the size of the main body, wiggled in a perti dish. Both sets of tentacles, both digestive systems worked, like conjoined twins. As I watched, I wondered if I was looking at one individual, or two, or hundreds. Each cell had the capacity to found a new colony, build a new hydra, and therefore each cell was in a sense an individual. Each stem could be called an individual, by the loose analogy to humans. Or the whole genetically identical, physically attached, coordinated being could be an organism. Depending on what unit we call the individual, we get very different answers as to the lifespan.

A final example I've been wondering about is the giant redwood tree. A single trunk of a redwood seems to the casual observer to be one huge individual. But redwoods bud prolifically from the base, and multiple trunks can grow out of the same stump, the same root system. Large groups of huge trees can be genetically identical, save for the mutations accumulated in their growing tissues over thousands of years of growth. If we consider one stem to be the individual, redwoods can live for thousands of years. But if we consider everything derived from one seed to be the individual, I don't know of any reason not to consider redwoods, like hydra, effectively immortal. Sequoia sempervirens indeed.

So I'm posing the question to you dear reader, what is an individual? What operational rule should be applied? How do we find the individual in a hydra, or in a redwood forest?

Ego boost of science.

There is a very flattering article in tomorrow's New York Times science section, by Natalie Angier, about our article on the definition of behavior. (There is also an online quiz associated with it.) It has, to be honest, many fewer errors than I generally expect from science journalism. The main one that will jump out at most of my peers is her statement that, "neither that textbook nor any other reference he consulted bothered to" define behavior precisely. We found lots of definitions, they just didn't agree with each other, or with what we or other biologists thought the word meant. That said, I think this NYTimes article is much better than most science reporting on the accuracy front. And of course, it is nice to have one's work described as "provocative and crisply written" in a large circulation newspaper.

She did neglect mention my two favorite things about the article; the title is, "Behavioral biologists do not agree on what constitutes behavior," and; in a biological article in a peer reviewed journal, we quote both Supreme Court Justice Potter Stewart's opinion on pornography and Conan-Doyle's Sherlock Holmes mystery of the dog that did nothing in the nighttime. I amuse myself heartily.

Behavio(u)r defined.

Published in this month's Animal Behaviour. British spelling.

Behavioural biologists do not agree on what constitutes behaviour

Daniel A. Levitis, William Z. Lidicker Jr. and Glenn Freund

"Behavioural biology is a major discipline within biology, centred on the key concept of ‘behaviour’. But how is ‘behaviour’ defined, and how should it be defined? We outline what characteristics we believe a scientific definition should have, and why we think it is important that a definition have these traits. We then examine the range of available published definitions for behaviour. Finding no consensus, we present survey responses from 174 members of three behaviour-focused scientific societies as to their understanding of the term. Here again, we find surprisingly widespread disagreement as to what qualifies as behaviour. Respondents contradict themselves, each other and published definitions, indicating that they are using individually variable intuitive, rather than codified, meanings of ‘behaviour’. We offer a new definition, based largely on survey responses:

Behaviour is the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal and/or external stimuli, excluding responses more easily understood as developmental changes.

Finally, we discuss the usage, meanings and limitations of this definition."

Binning Algorithms for Metagenomic Sequencing

One of my assistants, SM, who is at least as smart as me and twice as hard working, wrote to ask my advice.

SM: Do you know of any good binning algorithms for metagenomic sequencing?
DL: Huh? What does, "binning algorithms for metagenomic sequencing," mean?

SM has not given me an answer. Either she assumes I am joking, and actually do know (which I don't) or she assumes it would take far too long to explain it to me (which I will pretend to resent.) So now I shall try to reckon out what "binning algorithms for metagenomic sequencing" means on my own.

Metagenomics, according to my sources (Wikipedia) "is the study of genetic material recovered directly from environmental samples." So, you take a pinch of garden dirt, extract all the DNA in it and then set out to study it in some way. You are metagenomisizing.

Sequencing, in the context of genetics, means figuring out the sequence of DNA bases (A's, T's, G's and C's) that make up part of the genome of an organism. So metagenomic sequencing presumably is taking the DNA from your pinch of dirt, then trying to figure out the sequence of DNA bases that made up all the genomes of all the organisms whose DNA are jumbled together in that dirt. A pinch of dirt, I am guessing, has DNA from hundreds of types of bacteria, a huge number of types of fungi, various protozoans and whatever else has dropped seeds, pollen, poo, tissue or hair in that vicinity in the recent past. And much of that DNA isn't going to be whole chromosomes, but whatever bits and pieces are still mostly intact after all that pooing and shedding and biodegrading. You'll have a real mishmash.

This, I suspect, is where the "binning algorithm" comes in. Binning is any process where you have a large number of elements and you want to separate them into a smaller number of categories. A binning algorithm would be a set of rules one uses to make those decisions on categorization. In the context of metagenomics, I'm guessing that each bin represents a species. You have a snippet of DNA and you need to assign it to an organism, so you don't just think that every bit of DNA is another organism, and you want to get a sense of how much representation you have of each species. So the set of rules you use to assign snippets of DNA extracted from your pinch of dirt to different species is your Binning Algorithms for Metagenomic Sequencing. I think.
My friend DS works on this kind of stuff. I'll write to him and ask.

UPDATE:
I wrote to SM and DS and asked:
Will one of you tell me what "binning algorithms for metagenomic sequencing" means?
I know what each word means, but I could come up with three or four very different guesses as to what the whole phrase means. What does each bin represent?

DS writes: [Bins represent] Taxa. In metagenomic sequencing, you get a soup of reads from all the strains of microbes present in your sample. "Binning" is the process of trying to guess which species each read comes from (or genus, or kingdom for that matter).

All methods in the literature so far are "supervised", meaning that you can only assign a read to a taxon bin if you know something about that taxon in advance (e.g., you have an isolate genome). However, environmental samples may contain previously unknown taxa: new bacterial divisions are still being discovered fairly rapidly, and at the strain level of course nearly everything is novel. A supervised binning process ought to throw up its hands at sequences from novel taxa, since they don't match any known bins. An "unsupervised" process would create new bins on the fly, in order to lump together reads that seem to be related to each other, independent of reference sequences. No published methods do that yet, though.

The accuracy of binning varies dramatically depending on the complexity of the community, the read length, the phylogenetic resolution you're asking for, and many other parameters.

Hope this helps,

-ds

What I'll be talking about at ABS.

The concept of "behavior" is central to the activities of the Animal Behavior Society and its members, but do we know what we mean by this term? Most published sources either do not include a definition of the word "behavior", or have definitions that both contradict each other or are either too broad or too narrow to be applied operationally.

We examined the range of available definitions, and finding no consensus, polled members of ABS as to their understanding of the term. Here again, we found surprisingly widespread disagreement as to what qualifies as behavior. This paper highlights the areas of agreement and disagreement, and proposes a definition intended to be operational and as free as possible of taxonomic bias.

Plant Behavior

There is a scientific society dedicated to the study of almost anything. But until recently (2005) there was no society dedicated to the study of the behaviors of plants. Enter The Society of Plant Neurobiology. which states on its website:

"Plant Neurobiology describes a newly named, but also old and fascinating field in plant biology addressing the physiological basis of adaptive behavior in plants. Perhaps this field could be called "Sensory Biology in Plants" or something similar. However, these names don't quite cover topics like plant cytology and anatomy, adaptive plant behavior, signaling and communication in symbiosis and pathogenesis, or newly emerging topics like for instance plant immunity, plant memory and learning, plant-plant communication, as well as plant intelligence."

This is very convenient for me, as I am currently writing a paper on, among other things, taxonomic bias in definitions of the word 'behavior.' Having gotten input from member of the Animal Behavior Society and the International Society for Applied Ethology, I am thrilled to be able to get the viewpoints of botanists interested in behavior. I emailed the chair of their steering committee, asking her to forward a link to my "what is behavior?" survey to their membership. If she is sympathetic, this could be really cool.

I learned of the existence of SPNb through this article on NYTImes.com. Check out the video of the parasitic plant sniffing for prey and pouncing on the unsuspecting tomato vine.