Janet Stemwedel is about to submit her tenure dossier. She describes the process and the dossier on Adventures in Ethics and Science [A postcard from academe: my tenure dossier]. It's worth a read to see how the process works. Note that Janet has included a section on blogging and her department recognizes that as a legitimate academic pursuit.
One of the most persistent myths of evolutionary biology is that random genetic drift only occurs in small populations. You'll find this myth everywhere you look, even in textbooks that should know better. A few minutes ago I was looking for a simple way to explain this in the comments section of P-ter Accuses Me of Quote Mining when I came across this explanation in Modern Genetic Analysis by Anthony Griffiths, William Gelbart, Jeffrey Miller, and Richard Lewontin (1999 edition). This is the offspring of a textbook that David Suzuki started many years ago [ 17. Population and Evolutionary Genetics].One result of random sampling is that most new mutations, even if they are not selected against, never succeed in entering the population. Suppose that a single individual is heterozygous for a new mutation. There is some chance that the individual in question will have no offspring at all. Even if it has one offspring, there is a chance of 1/2 that the new mutation will not be transmitted. If the individual has two offspring, the probability that neither offspring will carry the new mutation is 1/4 and so forth. Suppose that the new mutation is successfully transmitted to an offspring. Then the lottery is repeated in the next generation, and again the allele may be lost. In fact, if a population is of size N, the chance that a new mutation is eventually lost by chance is (2N − 1)/2N (For a derivation of this result, which is beyond the scope of this book, see Chapters 2 and 3 of Hartl and Clark, Principles of Population Genetics.) But, if the new mutation is not lost, then the only thing that can happen to it in a finite population is that eventually it will sweep through the population and become fixed. This event has the probability of 1/2N In the absence of selection, then, the history of a population looks like Figure 17-17. For some period of time, it is homozygous; then a new mutation appears. In most cases, the new mutant allele will be lost immediately or very soon after it appears. Occasionally, however, a new mutant allele drifts through the population, and the population becomes homozygous for the new allele. The process then begins again.This is an important conclusion. It shows that alleles are fixed in large populations by random genetic drift. I'd like it a lot if people would stop saying that drift only occurs in small populations.
Even a new mutation that is slightly favorable selectively will usually be lost in the first few generations after it appears in the population, a victim of genetic drift. If a new mutation has a selective advantage of S in the heterozygote in which it appears, then the chance is only 2S that the mutation will ever succeed in taking over the population. So a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.
The fact that occasionally an unselected mutation will, by chance, be incorporated into a population has given rise to a theory of neutral evolution, according to which unselected mutations are being incorporated into populations at a steady rate, which we can calculate. If the mutation rate per locus is μ, and the size of the population is N, so there are 2N copies of each gene, then the absolute number of mutations that will appear in a population per generation at a given locus is 2Nμ. But the probability that any given mutation is eventually incorporated is 1/2N so the absolute number of new mutations that will be incorporated per generation per locus is (2Nµ)(1/2N) = µ If there are k loci mutating, then in each generation there will be kμ newly incorporated mutations in the genome. This is a very powerful result, because it predicts a regular, clocklike rate of evolution that is independent of external circumstances and that depends only on the mutation rate, which we assume to be constant over long periods of time. The total genetic divergence between species should, on this theory, be proportional to the length of time since their separation in evolution. It has been proposed that much of the evolution of amino acid sequences of proteins has been without selection and that evolution of synonymous bases and other DNA that neither encodes proteins nor regulates protein synthesis should behave like a molecular clock with a constant rate over all evolutionary lineages. Different proteins will have different clock rates, depending on what portion of their amino acids is free to be substituted without selection.
There are many adaptationists who recognize that random genetic drift exists. They will, when pressed, admit that neutral alleles can be fixed in a population. However, these adapationists pften maintain that visible phenotypes cannot be neutral with respect to survivability. Thus all visible phenotypes, with rare exceptions, are adaptations.I have tried to show that adapatationism can have virtues as well as faults. But this chapter's main purpose is to list and classify constraints on perfection, to list the main reasons why a student of adaptation should proceed with caution. Before coming to my list of six constraints on perfection, I should deal with three others that have been proposed, but which I find less persuasive. Taking first, the modern controversy among biochemical geneticists about "neutral mutations", repeatedly cited in critiques of adaptationism, it is simply irrelevant. If there are neutral mutations in the biochemist's sense, what this means is that any change in polypeptide structure which they induce has no effect on the enzymatic activity of the protein. This means that the neutral mutations will not change the course of embryonic development, will have no phenotypic effect at all, as a whole-organism biologist would understand phenotypic effect. The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's 'neutral mutations' are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.Natural selection is the only explanation we know for the functional beauty and apparently "designed" complexity of living things. But if there are any changes that have no visible effect—changes that pass right under natural selection's radar—they can accumulate in the gene pool with impunity and may supply just what we need for an evolutionary clock.
This certainly seems to place Dawkins as an "adaptationist", one who thinks that all differences in phenotypes are adaptations. I was a little surprised by this, but the quote seemed clear, and I wasn't going to take the time to find my original.The next lines P-ter is referring to is the beginning of a new paragraph ...
Luckily, another commenter pointed out that The Extended Phenotype is searchable at Google Books [The Extended Phenotype]. And funny, the very next line after Moran stops quoting is possibly relevant:
He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral.P-ter then continues with ...
Dawkins goes on to express some skepticism about some arguments for evolution by drift, but he's certainly not an "adaptationist" in the Moran sense.This is a very serious charge. I'm accused of deliberately distorting Dawkins' position by selective quotation. According to P-ter, Dawkins does not believe what he says in the quoted paragraph. (And elswhere, I might add.) According to P-ter Dawkins believes that mutations with a visible phenotype can be neutral. (We're not talking about one or two exceptions here, we're talking about the generality that applies to a significant percentage of mutations.)
I suppose I'm somewhat naive: distorting someone's argument through selective quotation is a classic creationist tactic, and Moran has written a bit about the propaganda techniques used by that crowd. Little did I know his familiarity is not of an entirely academic sort.
[1] As opposed to "pluralists", as he likes to call himself. For someone who (rightfully, in my opinion) is disdainful of "framing" (the view that scientists need to spin their results in order to resonate better with the public), he certainly knows how to frame.
He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral. But mathematical calculations such as those of Fisher (1930b) and Haldane (1932a) show how unreliable human subjective judgement can be on the "obviously trivial" nature of some biological characters. Haldane, for example, showed that, with plausible assumptions about a typical population, a selection pressure as weak as 1 in a 1000 would take only a few thousand generations to push an initially rare mutation to fixation, a small time by geological standards. It appears that in the controversy referred to above, Wright was misunderstood (see below) ...A careful reading of Dawkins shows that the objection to his claim doesn't stand because people misunderstood Wright. Thus, according to Dawkins, characters that appear to be neutral really aren't.
Today's molecule (in red) is part of a larger complex. There are two view of this complex in the figure. You have to supply the common name of this molecule—the one colored red in the complex. There's a direct connection between this molecule and Wednesday's Nobel Laureate(s).
Tomorrow President Mahmoud Ahmadinejad of Iran will speak at Columbia University. There are some who argue that universities should not invite controversial speakers. There are some who argue that Iran is the "enemy"—a member of the axis of evil—and once an enemy has been identified, and vilified, you must never allow them to speak in their own defense. It's especially horrible, according to these people, to allow a publicly-funded university to sponsor such a person.I would like to add a few comments on the principles that underlie this event. Columbia, as a community dedicated to learning and scholarship, is committed to confronting ideas—to understand the world as it is and as it might be. To fulfill this mission we must respect and defend the rights of our schools, our deans and our faculty to create programming for academic purposes. Necessarily, on occasion this will bring us into contact with beliefs many, most or even all of us will find offensive and even odious. We trust our community, including our students, to be fully capable of dealing with these occasions, through the powers of dialogue and reason.If you don't understand this then you don't understand anything about the purpose of a university and the importance of listening to the other side.
I would also like to invoke a major theme in the development of freedom of speech as a central value in our society. It should never be thought that merely to listen to ideas we deplore in any way implies our endorsement of those ideas, or the weakness of our resolve to resist those ideas or our naiveté about the very real dangers inherent in such ideas. It is a critical premise of freedom of speech that we do not honor the dishonorable when we open the public forum to their voices. To hold otherwise would make vigorous debate impossible.
That such a forum could not take place on a university campus in Iran today sharpens the point of what we do here. To commit oneself to a life—and a civil society—prepared to examine critically all ideas arises from a deep faith in the myriad benefits of a long-term process of meeting bad beliefs with better beliefs and hateful words with wiser words. That faith in freedom has always been and remains today our nation’s most potent weapon against repressive regimes everywhere in the world. This is America at its best.
Skeptico reports that Merck has just pulled a new AIDs drig because tests were showing that it didn't work [When will CAM do this?]. That's the way the system is supposed to work.Homeopaths pulling (say) Belladonna for the treatment of urinary tract infections, because they determined it doesn’t work for that.
Jena is a small town in Louisiana. It was named for Jena in Germany, the site of a famous victory by Napoleon in 1806. I'm a (very amateur) student of military history so I'm familiar with this battle [Battle of Jena-Auerstedt].
The Committee on Culture, Science and Education of the Parliamentary Assembly, Council of Europe has issued a report on The dangers of creationism in education. One of the most interesting parts of this report is that the committee does not back away from labeling Intelligent Design as a form of creationism. For example, in the opening paragraphs the report says,Creationism in any of its forms, such as “intelligent design”, is not based on facts, does not use any scientific reasoning and its contents are definitely inappropriate for science classes.Later on they define creationism using a great deal of common sense.
However, some people call for creationist theories to be taught in European schools alongside or even in place of the theory of evolution. From a scientific view point, there is absolutely no doubt that evolution is a central theory for our understanding of life on Earth.
The Assembly calls on education authorities in member states to promote scientific knowledge and the teaching of evolution and to oppose firmly any attempts at teaching creationism as a scientific discipline.
Creationists question the scientific character of certain items of knowledge and argue that the theory of evolution is only one interpretation among others. They accuse scientists of not providing enough evidence to establish the theory of evolution as scientifically valid. On the contrary, they defend their own statements as scientific. None of this stands up to objective analysis. ...I will continue to refer to Intelligent Design Creationism as an accurate representation of the views of people like Dembski, Behe, Phillips etc. Their allies, like Denyse O'Leary, are also creationists by my definition. They aren't Young Earth Creationists, they are Intelligent Design Creationists.
Creationism has many contradictory aspects. The “intelligent design” idea, which is the latest, more refined version of creationism, does not deny a certain degree of evolution but claims that this is the work of a superior intelligence. Though more subtle in its presentation, the doctrine of intelligent design is no less dangerous.
[Hat Tip: Panda's Thumb]
I've encountered many critics of the Mixed Member Proportional system who are uttering the same mantra. It includes the phrase "Belgium has 33 parties." I think this is meant to be a criticism of the MMP system. Those who mention the mantra often associate it with the fact that Belgian politicans have had trouble forming an effective government since the June 10, 2007 election.
Maclean's magazine has the story by Patrick Graham [How George Bush became the new Saddam].It was embarrassing putting my flak jacket on backwards and sideways, but in the darkness of the Baghdad airport car park I couldn’t see anything. “Peterik, put the flak jacket on,” the South African security contractor was saying politely, impatiently. “You know the procedure if we are attacked.”
I didn’t. He explained. One of the chase vehicles would pull up beside us and someone would drag me out of the armoured car, away from the firing. If both drivers were unconscious—nice euphemism—he said I should try to run to the nearest army checkpoint. If the checkpoint was American, things might work out if they didn’t shoot first. If it was Iraqi . . . he didn’t elaborate.
Arriving in Baghdad has always been a little weird. Under Saddam Hussein it was like going into an orderly morgue; when he ran off after the U.S.-led invasion of March 2003 put an end to his Baathist party regime, the city became a chaotic mess. I lived in Iraq for almost two years, but after three years away I wasn’t quite ready for just how deserted and worn down the place seemed in the early evening. It was as if some kind of mildew was slowly rotting away at the edges of things, breaking down the city into urban compost.
[Hat Tip: Jennifer smith Best Cover. Ever]
