Saturday, November 29, 2008
Some people have pointed out a major problem with the rendering of this website on IE. I think I fixed the stylesheet issue. Since the site was fine in IE until recently I'm pretty sure it was a Microsoft update of some sort. If you notice anything similar with IE, just email me. I only use IE for Netflix. This only applies to IE 7.
Thursday, November 27, 2008
You probably already know this, but in case you don't, I'm somewhat involved in a new website, Secular Right. Heather Mac Donald, Derb and Walter Olson are current contributors. My own postings there will be mostly about philosophy, history and data analysis, as opposed to rapid response to other weblogs or commentary on current politics.
From time to time I give links to those of my old posts that may still be worth reading. Previous guides are here: 1, 2, 3, 4.
It is over two years since the last update. In that time most of my posts have been on the history of population genetics, and especially on the 'founding fathers', R. A. Fisher, J. B. S. Haldane, and Sewall Wright. I recently finished a long series of Notes on Sewall Wright, so this is a convenient time to take stock.
Most of these posts are long, and aimed not so much at day-to-day readers as at people searching for specific topics.
Notes on Sewall Wright
On Reading Wright gave an overview of the planned series of notes, and includes some general reflections on Wright's reputation.
Before continuing with the series as planned, I realised that I needed to cover an additional topic, Wright's Method of Path Analysis This note is especially concerned to clarify the concept of a path coefficient, and the relationship between Wright's method and multiple regression.
In preparing the note on path analysis, I wanted to refer to some source containing the material on the statistical theory of correlation and regression that would be needed to understand Wright's work. I could not find a suitable source, so I decided to write it myself, using notes I have made on the subject over the years.
Notes on Correlation, Part 1 covers the general concepts of correlation and regression, and the justification for using them (which, like much in the foundations of statistics, is a moot point). Part 2 proves some key theorems on the correlation and regression of two variables, and discusses problems of interpretation. Part 3 outlines the theory of correlation and regression for more than two variables. This is particularly important for the understanding of Wright's path analysis.
After the note on Path Analysis I got back on the series as planned, with the following notes.
The measurement of kinship tries to explain Wright's approach to this, by contrasting it with the now more familiar methods of Gustave Malecot. The essential point is that Wright's kinship coefficients are in principle correlation coefficients rather than probabilities of identity (as in Malecot's system). A consequence of this is that kinship (or relatedness, or inbreeding) is relative to a specified population. The kinship between randomly selected individuals within such a population, relative to that population, is on average zero. This has implications for Hamiltonian inclusive fitness. Another implication is that Wright's kinship coefficients can be, and often are, negative (unlike Malecot's probabilities).
Wright's F-statistics. Wright devised a series of statistics known as F-statistics for measuring relationship and diversity within or between populations. The best known of these is FST, which is widely used as a measure of the genetic divergence between sub-populations of a species. My note traces the evolution of the F-statistics in Wright's work.
Genetic drift.. This note was originally going to be called 'Inbreeding and the decline of genetic variance', but that is not a very catchy title. I try to clarify the connection between genetic drift, inbreeding, and the decline of heterozygosis (a measure of genetic diversity). The note includes a detailed commentary on Wright's proof that heterozygosis tends to decline by 1/2N per generation.
Population size. I discuss the concept of effective population size and point out that Wright overlooked an important class of cases where effective population size is much larger than the current number of breeding adults.
Migration. Migration is important to Wright's theories because even very low rates of migration suffice to prevent subpopulations of a species diverging by genetic drift. The note traces Wright's work on the subject including his famous article on 'Isolation by distance'.
The adaptive landscape. Wright is closely associated with the concept of the adaptive landscape, though as far as I can find Wright himself never used this term. My note especially aims to explain the concept of a selective peak, and why Wright believed that there are a multitude of distinct selective peaks, usually of different fitness. In a related post on the Adaptive Landscape: Miscellaneous points, I discussed some issues not directly concerned with Wright, such as Stuart Kauffman's NK model, the relationship between selective peaks for genotypes and for gene frequencies, and the accessibility and stability of peaks.
The shifting balance theory of evolution.
This final note in the series is split into two parts. Part 1 examines the origins of Wright's famous shifting balance theory, and analyses the contents of the original version of the theory, as published in 1929-31. Part 2 explores subsequent developments in the theory, some of which are very important. Notably, as early as 1932 Wright abandoned his insistence that only genetic drift in small populations could take a population away from a suboptimal selective peak, as he now accepted that environmental fluctuations could have the same effect. In my view this removed much of the rationale for Wright's emphasis on population structure in evolution, though Wright himself never fully absorbed the implications of the change, which many biologists have overlooked.
Altogether, this series of posts would come to over 100 print pages. That's very nearly a book's worth! Alas, even if there were a market for such a boring book, I don't have the time, energy, or expertise to research and write it to the necessary standards, but I hope that anyone making a serious study of Wright will find something useful in my posts.
R. A. Fisher
My various notes on R. A. Fisher are mainly attempts to correct misunderstandings of his views which I have come across from time to time.
Fisher and Wright on population size (and here). These two notes were written shortly before I started my series of notes on Sewall Wright. Fisher is sometimes thought to have believed that entire species are randomly mating single populations. As this is palpably false, it is worth examining what Fisher really thought. In my first note I show, using Fisher's publications and letters, that he believed that migration between districts was usually frequent enough to offset their divergence by genetic drift. This does not imply that species are literally random mating (if they were, migration would be irrelevant), but only that for many purposes they can be treated as if they were. In the second note I examine what Fisher says about the actual population size of species. An Addendum is here.
Fisher on epistasis. It is sometimes claimed that Fisher ignored epistatic gene effects or considered them unimportant. My post shows that Fisher took account of epistasis in a variety of ways. Two further posts produce additional evidence: here and here.
Fisher on the adaptive landscape Following my note on Sewall Wright's adaptive landscape concept, I wrote this post on Fisher's views on the subject. Notably, he believed that environmental change, particularly in the biotic environment, made the idea of a constant landscape inapplicable.
Fisher on inclusive fitness
In this short post I draw attention to a passage by Fisher which contains a general anticipation of Hamilton's concept of inclusive fitness.
J. B. S. Haldane
I have written much less about Haldane than about Fisher and Wright. This is not because Haldane was less important or original. Haldane probably originated more of the basic results of population genetics than either of the others. But I tend to write posts mainly on issues that are obscure or controversial, whereas most of Haldane's results are clear and uncontroversial.
I have however devoted two posts to Haldane: one on Haldane's Dilemma, which examines Haldane's pioneering attempt to quantify the amount of genetic change possible by natural selection in a given period (see here for some corrections), and Haldane's Selection Theorem which comments on Haldane's proof that the probability that an individual favourable mutation will be successful is 2s, where s is the coefficient of selection.
Odds and ends
Finally, a few posts cover other issues.
Good Point? arises from a study by the economists Samuel Preston and Cameron Campbell. If intelligence is partly inherited, and less intelligent people on average have more children, it seems to follow that the average intelligence of the population will decline from one generation to the next. Preston and Campbell use an elaborate mathematical model to show that this is not necessarily the case. My post examines the argument, using a much simpler model due to the statistician I. J. Good. Briefly, I conclude that the argument is mathematically possible but biologically unrealistic. The case illustrates the danger of using sophisticated mathematics without properly considering the underlying assumptions.
Heterosis and the Flynn Effect looked sceptically at claims that heterosis (reduced inbreeding) might explain the long term increase in IQ scores.
Origins of the British is a piece examining the evidence on the ethnic origins of the people of the British Isles, following the recent book by Stephen Oppenheimer.
Group Selection and the Wrinkly Spreader takes a look at a recent defence of group selection by E. O. and D. S. Wilson, by examining in detail an example (the 'wrinkly spreader' variant of a certain bacterium) that they claim is a good case of group selection in action. It isn't.
Ethnic Genetic Interests Revisited looks at the new edition of Frank Salter's book Ethnic Genetic Interests, which includes comments on my own critique of the first edition.
Genophilia traces the origins of the term 'genophilia', which has been wrongly attributed to Francis Galton.
Wednesday, November 26, 2008
I thought I knew a fair amount about monkeys already, but a BBC wildlife documentary last night still had some surprises for me. The documentary is ouststanding even by the BBC's usual standards for this kind of thing. I dare say it will be broadcast in most countries sooner or later, but meanwhile it can be seen online here (iplayer or equivalent required).
Monday, November 24, 2008
From Henry Harpending:
This is from a 1984 paper, citation below the figure. The genetic data were 6 red cell antigens, 9 electrophoretic systems, and HLA and HLB. The context was the authors' effort to set up a big population genetic and demographic database of Mormons, which was criticized because the Mormons were thought to be derived from a small isolated inbred group. They wrote this paper to show that Mormon allele frequencies were generic northern European. Another paper the followed this showed that Amish and Mennonites were indeed off in another dimension, but not Mormons.
I made a minor modification to the figure, which is courtesy of Lynn Jorde.
Sunday, November 23, 2008
I recently posted a note on an anticipation of Hamilton's concept of inclusive fitness by R. A. Fisher in the Genetical Theory of Natural Selection.
As I pointed out, in that passage Fisher did not quantify the effect of what he called 'indirect effects of natural selection', so he did not state what we now call 'Hamilton's Rule' (though later in GTNS he came close to it in his discussion of distasteful insects).
However, I have noticed the following passage in a letter from Fisher to Leonard Darwin dated 27 June 1929, which states Hamilton's Rule for the special case of parental care:
The reproductive value at different ages must determine the extent to which parental care pays. If all ages were of equal reproductive value, a species would tend to benefit its offspring up to the point at which the offspring gains double the advantage which the parent loses, but no further. Of course immature offspring are usually worth much less, and so should be cared for only at a cheaper rate still. But if crocodiles were able to recognise their mature offspring, I suppose they would co-operate with them not only on terms of mutual advantage, but on terms of joint advantage so long as the loss of either did not exceed half the gain of the other. Hence society starts with the family. - Natural Selection, Heredity and Eugenics: Including selected correspondence of R. A. Fisher with Leonard Darwin and others, edited by J. H. Bennett (1983), p.104-5
The important qualification about the maturity of the offspring is probably also in Hamilton somewhere, but I can't immediately find it. Dawkins makes a similar point in his '12 Misunderstandings of Kin Selection'.
Added: I had another skim through Hamilton's papers, but I still couldn't find a discussion of the maturity point. However, I imagine Hamilton would have said that differences of maturity should be taken into account in quantifying the 'benefit' to an offspring of a given amount of parental care. So, for example, in a species with very high infant mortality, the benefit of a given amount of resources to an immature offspring, measured by the expected number of its own future offspring, would be less (other things being equal) than to an offspring who has already reached sexual maturity. Against this, 'other things' are seldom equal, and the benefit of a given amount of resources (e.g. food) to a newborn may be much greater than to an older offspring which can already fend for itself.
In the comments below Susan C asks an interesting question:
I'm still surprised that this works as well as it does, given that there were mass movements of people during the nineteenth and twentieth century.
An interesting point. Some levels of immigration and movement have always been part of European history. Think about the outflow of Huguenots after the revocation of the Edict of Nantes. The trade and migration between the Low Countries and the eastern shore of Britain. The immigration of Spaniards, Poles and Italians to France in the 19th century. The relocation of Saxons to Romania, Russia, etc.
1) Many of the immigrants, like the Huguenots, settled disproportionately in cities and towns (the Volga Russians are an exception obviously). French in Berlin, British Puritans in Amsterdam, Jewish industrial workers in East London, Asian sailors in Cardiff. And cities until recently were powerful relative population sinks. So modern European cities might be affected by past immigration (e.g., in changing the accent on dialects) culturally, but they are far less reshaped genetically than you would expect.
2) Many of the immigrants were from nearby regions. Spanish and Italian immigration to France was far higher than Polish. So the affect would be more to subtly shift the positions and centers of gravity, as opposed to rearranged the expected spatial relationship.
3) Aside from France, there wasn't much migration as a proportion of the population. The ancestors from Aberswyth and Krakow are very salient because of their exoticism. This is just subject to the same dynamics as disappearing English phenomenon.
4) They sampled from only a few locations within each nation, so the clumping is exaggerated, and combined with #3, the migration effect wasn't strong enough to change your impression. Perhaps they also generally don't sample ethnic minorities in these studies; e.g., avoiding Hungarians and Saxons in Romania.
5) Some migrations, like the expulsion of Germans from Eastern Europe after World War II, rolled back the obscuring effects of earlier movements.
I was thinking about following the notes and what not and see where the samples came from, but I'll leave it to enterprising readers. I'm sure that can answer some of these questions.
Saturday, November 22, 2008
Currently I'm compiling my own dataset of international cognitive test scores. Right now I'm moving on to China. China contains nearly 20% of the human species, with every province being the size of a large country, so it would be nice to get a fuller picture for China than other places. The good news here is that Chinese scientists have engaged in a good deal of intelligence testing. The bad news (for me) is that most of these studies are confined to Chinese language journals.
I'm looking for a temporary collaborator who can read Chinese to help me find and extract data from Chinese language studies. Ability to read Chinese and curiosity about the subject are all you really need.
If you are interested, please contact me by clicking my name above.
Also if any readers are at an institution with electronic access to many Chinese journals (such as the following) and are willing to share the wealth, please contact me as well.
This week's To The Best Of Our Knowledge interviews George R. R. Martin. If you have iTunes just subscribe to their podcast and you'll see it on the list of shows (I don't know where to find it streaming online). I was talking to an owner of a local science fiction bookstore, and we agreed that many angry fans are going to break down the gates of hell and tear him to pieces if Martin does a Jordan. Apropos of which the proprietor mused how worrying it was that the 60 year old Martin is corpulent (also, he resented the fact that Martin took vacations!). On the other hand, we agreed that there's no way Brandon Sanderson would ever be commissioned to complete A Song of Ice and Fire.
Friday, November 21, 2008
I pointed to the paper at my other weblog, but since ScienceBlogs has a narrow page width, I've put the important charts below the fold.
Table 4 - Each horizontal line in the table shows the proportions of test samples originating from a given country that were assigned to each possible target country. I made a few edits, see paper for original.
The Audacious Epigone has two interesting posts up right now. Conservative men more intelligent than conservative women; Liberal women more intelligent than liberal men and Politics and IQ; Conservative Democrats and liberal Republicans least intelligent. The titles are self-evident, but, I would add that with hindsight it might make sense that liberal Republicans aren't too bright. If you're a liberal Republican you are probably just in denial, or, confused and dull. When I think liberal Republican I think Tom Campbell or Chris Shays, but these may simply be elite examples who don't reflect the fact that most ideological outliers in parties are just individuals who don't think deeply. For example, someone who was born into a "Republican family," and doesn't reflect much about ideology and so continues to vote Republican despite being liberal. I don't feel I need to explain conservative Democrats, as it seems to me that political exemplars of this class are generally duller than liberal or moderate Democrats.
Note: I know this is kind of a political post, but I'm going to be strict about not letting the comment thread degenerate immediately. So don't get offended if I don't let you through the mod-queue even if I normally do.
Thursday, November 20, 2008
OK, not really, but I have a new piece in The Guardian's Comment Is Free on polygamy.
One of the implicit assumptions of a book like Albion's Seed is the "First Settler Effect," (FSE) whereby the groups which originally settle a region have a disproportionate effect on its cultural character in perpetuity. Obviously there are boundary conditions, the first settlers might be totally replaced demographically rapidly, or, superseded by a cultural complex which views itself as dominant and superior. But in the cased of the United States the best illustration of FSE is linguistic dialect. In New England the tendency to drop the final "r" in words like "car" (non-rhoticity) is a South English linguistic development, and is traced to the East Anglia bias of the original Puritan settlers. This tendency is today strongest in the regions around Boston. Of course, this is probably the area where the Irish Catholics overwhelmed the Yankee Protestants to the greatest extent, showing the strength of FSE ("r" was kept longer, or, is, in Irish and Scottish English, making the illustration of FSE symmetrically persuasive in this case).
But many of the arguments in favor of FSE are rather impressionistic. They are impressions filtered through the eyes of historians, though sometimes they are backed up by quantitative data (New England remains the smartest American region, as it was in 1700). Luckily for us, New England is one of the Census Divisions in the GSS, and so one can explore the differences between Protestants and Catholics, which would roughly map onto the division between original stock and later white ethnic immigrants, and compare them to the McCain Belt whites. Like New England, the East South Central Division of the GSS regions is nice and compact, and correspondences with a relatively homogeneous cultural area.
What are the religious breakdowns of New Englanders?
This looks about right checking with the Pew Religious Survey. I'm not totally sure about the representativeness of the GSS in terms of within New England balance, but since I'm interested in comparing New England Protestants and Catholics and McCain Belt whites I'm not too worried.
Earlier I said that the proportion of people with "No Religion" in New England probably was going to be disproportionately Yankee. I'm not so sure. The two tables below have rows which add up to 100% for religion and ancestry respectively.
If the Irish and English & Welsh are the canonical white ethnics vs. Yankees, it seems secularization hit them both to the same extent. Since 88% of whites in the East South Central Division are self-identified Protestant, I won't even give a breakdown by religion for that region. From now on I'll refer to Yankee for Protestant New Englander, and White Ethnic, for Catholic New Englander, and the McCain Belt. Remember that I'm excluding those who put religion down as "None" for New England.
Instead of an impression based on impressions, I went through the GSS and looked at a host of variables. Some of them might not be surprising to you (WORDSUM score), and some of them more so (# of sex partners since 18). The point was to collect a lot of disparate data, spanning explicit and implicit cultural markers. I tried excluding any question where N was smaller than 100 for any category, though some of the questions have N's bigger than 1,000. On some characters New Englanders cluster together against McCain Belt Whites. On other characters Yankees and McCain Belt Whites custer together against White Ethnics. Finally, there are cases where White Ethnic cluster with McCain Belt whites against Yankees. In many (most it seems to me) cases the pattern seems to be McCain Belt Whites at one end, Yankees at the other, and White Ethnics in the middle, and more often than not, closer to Yankees than McCain Belt Whites.
The cases where the White Ethnics are outgroups can I think be chalked up to aspects of Roman Catholicism and the immigrant culture which make them unique vis-a-vis the other two groups, who are old line Protestant stock. Sometimes, as in abortion on demand, I suspect that the White Ethnics are more conservative than Yankees because of their Catholicism, but they still remain more liberal than McCain Belt conservatives. On the balance, I would say that FSE is plausible and supported by these data, even though Yankees did not turn White Ethnics into Catholic Yankees, they did change their outlook or standard reference point a considerable amount (i.e., they may be socially conservative and emphasize education to a lower extent than Yankees, but they are far more liberal and more educated than McCain Belters. In some cases it seems likely that White Ethnics and Yankees evolved together over time as one regional culture, so I don't know if one can say that similarities are always due to FSE as such, though I would argue that contingency means that the original Yankee culture loaded the die in turns of future developmental paths.
A little history is warranted at this point. Around 30,000 whites settlers arrived in New England during the 17th century, but 75% arrived in the period between 1630-1640. Most of the derives from this decade and entered into a period of population growth unrivaled in the New World. The next major wave of immigrants were of course the Catholic Irish. Italians and Quebecois are also significant segments of the White Ethnic population. In sharp contrast to the Puritans, who were screened for education and skills to produce the world's first universal literacy middle class society, the white ethnics came from contexts where they were much lower on the social ladder. The Irish and Italians were classical European peasant populations who lacked the bourgeois sensibilities of the Puritans.
In the McCain Belt the dominant ethnicity is Scots-Irish, broadly construed. They generally arrived in the 18th century into the port of Philadelphia and expanded through the Southern Uplands, driving all the way to the Gulf of Mexico by the early 19th century. A secondary element consisted of migrants from the Southern lowlands, from the Tidewater down to the Carolinas. From these groups the small planter minority emerged. But demographically the former are more important, and represent the heart of the McCain Belt white culture.
Collecting these data was tedious. I expect comments to not be tedious.
Clicking on any of the phrases below will result in an image of the chart below
Abortion On Demand, Affirmative Action, Aged Should Live With Children, Drinks Alcohol, Allow Anti-Religion Book in Library, Allow Anti-Religionist To Speak, Allow Communist To Speak, Allow Doctors To Assist Death, Allow Racist Books In Library, Allow Racists To Speak, Amount Of Sex Within Last Year, Attendance (Religion), Ban Prayer In School, Beaten As Child Or Adult, Belief In Life After Death, Concern About Racial Issues, Confidence In Education, Confidence In Existence Of God, Confidence In Financial Institutions, Confidence In Military, Confidence In Organized Religion, Confidence In Science, Courts Dealing With Criminals, # Of Children, Disparate Racial Outcomes Inborn, Divorced, Educational Level, Ever Smoked, Extramarital Sex, Favor Law Against Interracial Marriage, Federal Income Tax Rate, Gun Permits, Had Affair While Married, Homosexuality Wrong, Hours Watching TV, How Fundamentalist, How Often Read Newspaper, How Often Spend Evenings With Relatives, How Often Spend Time With Neighbors, How Often You Pray, Human Evolution, Hunt?, Ideal Number Of Children, Life Exciting?, Liking For England, Liking For Israel, Birth Control For Teens, Make Divorce Laws Easier, Males Who Have Paid For Sex, Marijuana Legal, Marital Status, Marriage Happy, Money Spent On Blacks, Money Spent On Education, Money Spent On , Money Spent On Environment, Money Spent On Mass Transit, Money Spent On Military, Money Spent On National Parks, Money Spent On Roads, Money Spent On Space Program, Money Spent On , Mother Working Doesn't Hurt Children, Own Or Rent, Owns Gun, People Can Be Trusted, People Are Selfish, Political Views, Vocab Score (rough proxy for intelligence), Seen Porn In Past Year, Sex Partners Since 18 Female, Sex Partners Since 18 Male, Spanking Appropriate, Threatened Within Gun Or Shot At, Warm Feelings Toward Jews, World Is Evil, Wrong To Cheat On Taxes, Years In Armed Forces
Wednesday, November 19, 2008
Two studies published today demonstrate what was immediately evident from genome-wide association studies of many common diseases: the genetic variants identified account for only a small fraction of risk.
In these cases, the authors try to predict whether an individual will get type II diabetes from a number of clinical variables, as well as recently identified genetic risk factors. The genetic factors only marginally improve the prediction of diabetes, likely to a clinically insignificant extent.
This was obvious, of course, from the initial studies themselves--you can't expect variants responsible for a meager fraction of overall disease risk to function as effective predictors of the disease. But somewhat notable nonetheless.
Tuesday, November 18, 2008
Previously I looked at changing fashions in academic theories and their associated buzzwords, using the articles archived in JSTOR as a sample: see part 1, part 2, and part 3. What about the thing that arts & humanities academics are supposed to study -- the text itself? I mean, the vulgar consuming public may flit from one "it" author to the next, but surely academics are above such fickleness?
Most of them are happy to admit that they don't make grand claims about Truth -- that's only what us evil science people do. But they don't freely admit to being driven mostly by a blind adherence to fashion -- whatever they're showing in Paris this season -- and it's time to strike back at them for this, after that knuckle-rapping they tried to give us in the '90s. Again, I've already showed how fashion works in their theories -- now it's time to show that their consumption patterns (i.e., which authors or artists they read and analyze) are also driven by fashion.
Here is a graph using only English-language articles and reviews from the "Language and Literature" category of journals in JSTOR:
The search terms were the authors' surnames, except for Jane Austen, whose full name I searched. This presents no problem for Proust and Kafka, although Joyce is a bit more common as a surname. We don't have to worry about Joyce Carol Oates, as she became popular when James Joyce was declining in popularity. Still, it's clear that the order-of-magnitude increase in "Joyce" is due to James Joyce, as no one else with that name was so popular among professors.
The graph starts at 1915 because 1914 is, according to an arts-major legend, the year that Modernism was born. I included Jane Austen for comparison. Even a traditional author like she shows ups and downs, although her popularity does not oscillate nearly as wildly as it does for the Modernists. She is clearly less popular than they are, though.
From the mid-1920s to the mid-1940s, Joyce and Proust are neck and neck, but in the post-WWII period, Joyce has always been more popular -- for christ's sake, fully 10% of all Lang & Lit articles refer to him during 1970 - 1990. Even scientists were savvy enough to know that he was the guy you named something after just to prove how clever and initiated you were.
Kafka is only slightly less popular than Proust -- which I find surprising, since Proust would seem to have much greater snob appeal, Kafka being the emo band whose posters you plastered your walls with in high school, but who you loudly deny ever having liked once you're a grown-up. Unfortunately I can't easily tell where these articles are coming from -- are the upper crust of arts departments writing mostly about Proust and Joyce, while the reject departments with no friends write mostly about Kafka and Salinger? I have no intuition here, so arts people, feel free to weigh in.
At any rate, we see that, just as with their theoretical badges, academics make their consumption a fashion symbol too. Between 1935 and 1945, the three Modernists begin to soar in popularity, but somewhere between 1955 and 1965 they hit diminishing returns, peak around 1975, and get tossed out after that. Note that this is not due to the rise of Postmodernism -- that only got started in the mid-1970s and was big in the 1980s and '90s. Already by 1965, Modernist authors saw their growth slow down. Besides, Postmodernism was attacking the assumptions of another group of academics, rather than attacking a group of authors, painters, or musicians.
The data only go up through 2001. Just eyeballing it, it's conceivable that by 2025, these three Modernists won't be given more respect than established authors like Jane Austen, and of course some may see their popularity plummet further to zero. This is a separate question from their artistic merit, obviously. For example, here's some insight into the popularity of Shakespeare in Samuel Pepys' London:
[A]nd then to the King's Theatre, where we saw "Midsummer's Night's Dream," which I had never seen before, nor shall ever again, for it is the most insipid ridiculous play that ever I saw in my life. I saw, I confess, some good dancing and some handsome women, which was all my pleasure.
A devil's advocate would say that academics gradually stopped writing about these authors because they'd exhausted what there is to say about them. But that's not true: the trajectories are too similar. They just happened to decide "we've gotten all we can" from all three authors at more or less the same time? That sounds, instead, like they just grew bored of the Modernists in general and only wore them out to formal events where they're de rigueur, rather than show them off to every stranger they chatted up at a cocktail party, academic conference, or public restroom.
I noticed today that Heather Mac Donald has just engaged in another dialog with Michael Novak about God over at Beliefnet. As an unabashed vocal unbeliever Heather is exceptional on the American Right (compare to George F. Will's relative diffidence about his agnosticism). Simultaneously, there has been some concern that the youth vote swung so decisively toward the Democrats this election. Since it is also known that the young people are more secular than past generations, I wonder if some of the shift might not simply be due to the stronger association between American conservatism and a specific religious tradition (conservative Protestantism). Below the fold are tables which I generated using the GSS. I combined ages and political ideologies to simplify the categories (e.g., adding extremely and slightly liberal together with liberal into one category). Also, I filtered the sample so that all respondents were white.
I am struck by the decline in self-identified conservatives who are not 100% sure that God exists. Below is a chart showing the change in the proportion of more secular sectors. I simply added all the categories except for the two most religious ones.
With the economy the way it is I assume some readers will shift from wine to beer, so if you haven't, check out A Better Brew (no need to click if you're into Budweiser obviously).
Monday, November 17, 2008
I really don't have much to add that's original, I've long tired of the "definition wars." Early this year Steve wrote a column rebutting some criticisms that Malik makes of his definition of race in Strange Fruit: Why Both Sides are Wrong in the Race Debate. The book is out in the United States now...I'm halfway through it, and there's nothing new to anyone who reads this weblog. The fundamental problem is that it is too easy to use the statistical inferences which are generated by human population genetics as a launching point for a thousand verbal shell games. Like the species concept debate I think pragmatists are well advised to be instrumentalists.
Here is what L. L. Cavalli-Sforza said 2 years ago after I asked him about Lewontin's Fallacy:
Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.
In other words, between group differences may be both small and important. Whether this is so is an empirical matter.
Labels: human biodiversity
That's what the The Audacious Epigone concludes (based in part on a post of mine). This is a hobby-horse of Half Sigma's. He's not the only one who has observed the alliance between Whiter People and minorities; roughly the highest and lowest socioeconomic strata. Historically and internationally this is not too surprising a coalition, though from what I recall during the French revolution the nobility and religious peasantry of the Vendee were allied on reactionary grounds against the radical bourgeoisie in the middle. Perhaps a better analog might be the relationship between the anti-clerical intelligentsia and proletariat against the traditionalist middle class in some European countries. Also, pooling the whole white population without regard to geography, the intelligence difference is not large, if it exists, when it comes to political ideology.
Sunday, November 16, 2008
Cultural Regions of the United States came out in the 1970s, so it is a little dated in terms of "contemporary" observations. For example, the author obviously didn't internalize the long-term impact of Quebec's Quiet Revolution, as he posited that because of fertility rate differences between traditionalist Quebec and progressive New England the latter region would eventually be inundated by immigrants from the former. Despite the large numbers of French (Quebecois) Americans along the northern periphery of New England the ethnic flood never occurred because of the convergence of cultural mores and birthrates between the two regions. But the data and interpretation of 19th century America in the book remain valuable.
One of the obvious inferences that can be made from the data is that New Englanders shaped the culture and polities of many regions of the United States where they were a minority. Boston was self-consciously the Athens of America. Not only does this region have many elite universities, but the more prominent state institutions such as the Universities of Michigan and Wisconsin were started in part by Yankees who valued these sorts of public investments. The role of New Englanders in primary education throughout the United States is well known, Puritan America may have been the world's first universally literate society, and they were intent on spreading this trait across every group into the United States.
Though New Englanders were often outnumbered by later waves of immigration from the Upland South (e.g., Scots-Irish), as in the Pacific Northwest's Willamette Valley or Northern California, they were overrepresented among the intelligentsia and captains of industry. In the western Upper Midwest Yankees were absorbed by a sea of Northern European immigration, but for several generations they retained a hold on the cultural and capital classes. One might contend that many of the complaints about the "brainwashing" which occurs at elite universities of bright but impressionable young men and women is simply the latest manifestation of the conflict between numerically superior Middle America and the elitist New England outlook (even outside of New England, see Leland Stanford's biography).
Here's a table from page 209:
There's an important note to this table, a disproportionate number of those from the "Middle Atlantic" are from areas of upstate New York which were settled from New England, so the proportions for New England are large underestimates. You can see that even in 1850 the general cultural outline of many states was established. In Wisconsin and Minnesota the original Yankee stock paled in comparison to the numbers of Scandinavians and Germans. Far less of this would occur in Michigan, and some immigrant groups such as the Dutch in southwest portion of the state had folkways very similar to those of the Yankees from New England. Some states, such as Illinois and Ohio, were bisected between a northern and southern half where migrants from different areas of the United States settled. In contrast, Indiana was settled mostly from neighboring regions of the South.
Here's a map of female white life expectancy:
Source: 8 Americas
One of the "fun facts" of American demographics is that the largest ancestry group consists not of Anglo-Saxon stock, but of Germans. So Wikipedia says, "They currently form the largest self-reported ancestry group in the United States, accounting for 49 million people, or 17% of the U.S. population." Considering that Germans were a numerous, if not dominant, group numerically as far back as the 18th century (majorities across large portions of southeast Pennsylvania), and then the significant 19th century migration this isn't totally implausible. On the other hand in the 2000 Census 8.7% of Americans claimed English ancestry. Many people find this very implausible, that is, far too low a figure. You can inspect the Census data and see what's going on, but I figured I'd bring some of the information in one post so that Wikipedia entries will no longer have a "citation needed" note when people make the claim for the low numbers of English Americans being an artifact.
And with proportions....
The proportions above use the white population in the Census as the baseline.
It seems pretty clear here: the "American" group is sucking up many people of British Isles origin. Additionally, I haven't posted it, but there are weird changes in people claiming single or multiple ancestries. This is probably a result of the way in which the question was worded and results tabulated, the balance between single and multiple ancestries shifted a lot among many groups in favor of the former. This obviously doesn't make sense, these are European groups who aren't subject to a great deal of immigration, and have been intermarrying more & more each generation.
Next there is some interesting data from page 38 Ethnic Options:
As you can see, British Isles groups tend to be very inconsistent year-by-year in their ethnic affinity. I believe this suggests very weak distinctive self-identification. In part this is probably due to the fact that the immigrant experience is so far back for people whose forebears arrived in North America in the 1600s and 1700s, but, I also believe that it is due to the fact that Anglo-Saxon culture is to some extant the default culture of the United States. The fact that Anglo-Saxon identity is so malleable and shallow in explicit (if not implicit background) terms also suggests one hypothesis for the relatively robusticity of a group like German Americans vs. English Americans over the past 30 years: German ancestry is more memorable, distinctive and "ethnic" than English ancestry. So if someone is 1/4 German and 3/4 "American," one might naturally give "German" as the response when queried about ethnicity because the "American" element is not coded as ethnicity at all. Checking through the Census data it also seems that "American" is tabulated only if no other ethnic groups are given by respondent. This suggests to me that there are many of the people bracketed into German, Irish, etc., probably listed "American" as one of their ethnicities, which itself is probably a proxy for Anglo-Saxon background.
Relying on self-reports is obviously problematic for ethnicity in a nation where a large majority are likely compounds. How can we get a real sense of the distribution of American European ethnicities? Here's an idea: a social scientist could simply go back several generations in the genealogy of 10,000 random white Americans in the family Family Search database. Individual could be more appropriately coded ethnically.
Saturday, November 15, 2008
This article, Some See Big Problem in Wisconsin Drinking, speaks to some of John Emerson's comments below. This made me laugh:
Most people in Wisconsin say the beer-drinking traditions reflect the customs of German immigrants, passed down generations. More than 40 percent of Wisconsin residents can trace their ancestry to Germany. Some experts, though, are skeptical of the ethnic explanation. It has been a very long time, after all, since German was spoken in the beer halls of Wisconsin.
Look, these people might not speak German, but they still eat raw meat (not that there's anything wrong with that!). And Norwegian Americans might not speak Norwegian, but they still eat Lutefisk. It is notable that the piece does not quote by name any of those "experts." I wonder if the author just didn't want to make an ethnic generalization in relation to the origins of drunkenness, and so just inserted the stock "don't generalize!" admonition in there....
As a supplement of some of my posts, I've stitched together some maps from American Ethnic Geography. It should make everything clearer (the Midland region might some incoherent to you, but most of the Scots-Irish disembarked around Philadelphia and pushed inland and then expanded throughout the Upland South)....
Sydney Brenner has some things to say about fat people, and did so in an impolitic manner. James Watson did pretty much the same thing 8 years go. Really, when you have old scientists who have made their name, you have to be really careful about giving them face time without handlers....
Thursday, November 13, 2008
A few friends have emailed me some objections to the four culture model of american history. In short, though New England Puritans, Highland South Scotch-Irish and Lowland South Cavaliers are reasonable cultural entities which are easy to put a finger on, the Mid-Atlantic is a hodge-podge which to a great extent is simply thrown in a bin together for simplicity. In 1750 Pennsylvania was the first American colony where people of British descent became a minority. This sort of diversity makes it rather peculiar to speak of a Mid-Atlantic cultural folkway in which Germans, Dutch, Quakers, Roman Catholics, Swedes and Long Island Yankees can be thrown together into one pot. It's somewhat like assigning the term "environmental" to all the components of variance in quantitative genetics of a phenotype which can not be attributed to genetics. You know what it isn't, but what is it?
But that's just an aside. You might infer from the image above that the point of this post is not to explore what the term "Mid-Atlantic" can tell us in any model of social history. Instead, I want to focus on one aspect of American coalitional politics which might be of interest in the next 4 years: Mormon America is a representative of the New England Puritan cultural tradition in "Red America." A map is going to be more informative here than words.
When I say Mormons are "Puritan," I'm not saying this as a figure of speech; Mormon America is to a great extent both a direct cultural and genetic descendant of New England Puritanism! The proportion of "English" ancestry in Mormon America is somewhat exaggerated by the fact that missions were sent to England and so you had direct migrants from Europe to Utah. But this can't explain the whole of the phenomenon, American Mormonism began as a religion of Greater New England. First in upstate New York, and later in northern Ohio. Its relocation to the Midwest was problematic for a host of reasons, but the fact that they were often neighbors of people whose origins were in the South and they were quite clearly Yankees probably exacerbated tensions.
Mormonism is a very communitarian religion, not unexpected from a faith with Puritan origins. Mormon settlements in Utah were laid out like New England towns, as opposed to isolated yeoman farmsteads. Brigham Young socialized water usage to optimally allocate resources for irrigation. A tendency toward campaigns for temperance and high fertility were features of New England society. Mormons are famously fertile (relatively) and do not drink. In Wisconsin administrators preferred Yankee settlers because they were more likely to be willing to raise money for pubic goods such as schools than migrants from the South. Mormons may be low-tax Republicans, but those in good standing tithe a very large proportion of their income obligately in their private life (10% from what I recall), while the church runs itself like a corporation which has economies of scale.
Unlike evangelical Christians in the South, Mormons do not acceptwith resignation that many youth may "raise hell" before settling down. Mormons do not accept the Protestant contention that salvation is through faith alone. Behavior matters. Social pathologies and the personal disorder which has been a feature of Southern cultural life since its inception are not features of Mormon America, which reflects Puritan fixation on public order as a check on private liberty.
Over the past generation Mormons and Southern Protestants have entered into a de facto alliance because of their social traditionalism. The recent controversy over Proposition 8 in California will likely result in even more esteem for the Mormon church from structurally suspicious evangelicals (they do not believe Mormons are Christian, and resent that they claim that they are Christian). In other ways Mormons have come to identify themselves with conservative Protestant America, which to a great extent means Southern America. There are data which show that while 70% of Brigham Young University students rejected Creationism in 1930, 70% now accept it. I believe this is due to cultural influence from evangelical Protestantism, with whom Mormons are now politically allied.
But I believe that the differences between Puritan Mormon America and Southern evangelical America need to be kept in mind. Some of Mitt Romney's supporters were irritated that some conservative kingmakers (e.g., Richard Land) were leaning to Fred Thompson because of cultural affinities. Culture matters. Mormons may be aligned with the South, but the alliance will always play out in the framework of differences in cultural priors. Mitt Romney is a social conservative, and likely was before he had to lie to become governor of Massachusetts. But he is not a Southern social conservative, and that matters, and when he pretended to be he seemed phony.
Addendum: One can encapsulate what I'm trying to get at by considering an even more extreme case: Jews & black Americans. These two groups are most Left-leaning and Democratic demographics in American society, but, they obviously aren't equivalent and there are qualitative differences in their liberalism. This doesn't mean that the position of both these groups on the American Left is in question, but there will always be a tension within the alliance.
...is the title of an interesting essay by Ian Deary in this week's Nature. The article is short and quite accessible, and well worth a read.
Tuesday, November 11, 2008
You can watch Beyond Belief: Candles in the Dark online. Unfortunately the neat Flash interface means you can't just load an audio file into your ipod....
Monday, November 10, 2008
That's the result from a new experimental study of 1,000 people attending truck driving school. The authors tested all of them with Raven's Progressive Matrices, a real IQ test. They then put pairs of them through a prisoner's dilemma game, and found:
[M]easures of cognitive skill [CS] predict social awareness and choices in a sequential Prisoner's Dilemma game. Subjects with higher CS's more accurately forecast others' behavior....[S]ubjects with higher CS's also cooperate more as first movers.This set of genuine experiments improves on this older paper, which found that students at high-SAT schools cooperated more in prisoner's dilemmas than students at low-SAT schools. Now we know it's not just because posh, high-SAT schools facilitate a "culture of cooperation" or something like that. Smart individuals just figure it out on their own.....
Bottom line: More evidence that smarter groups are more likely to think win-win.
In a recent post, Agnostic dismissed Jean Twenge's thesis that narcissism has increased over the last couple of decades. Twenge has been on my reading list for a while, so this intrigued me. Not feeling knowledgeable enough to play devil's advocate against agnostic, I sent Professor Twenge an email inviting her to join the thread. She does a pretty good job of defending her thesis against agnostic's criticisms, in my opinion. I invite anyone who's interested to check out the thread, read the studies, and share their own two cents.
Do you have some marginal time today? Well, now you really don't, play around with the HGDP browser. If you click and find yourself a bit bewildered, read Do It Yourself: searching for evolution's signature in 53 human populations over at Genetic Future.
Related: So you want to be a population geneticist.
Labels: Population genetics
Sunday, November 09, 2008
It is good news that the social scientists are finally starting to think seriously about genetic variation and social behavior. This latest Science paper by UCSD political scientists James Fowler and Darren Schreiber is a case in point. A key argument they make in the paper is that political scientists cannot ignore behavior genetics because genetic variation is so ubiquitous also in political "phenotypes". (Of course, it was Alford, Funk and Hibbing who got the ball rolling, though Nick Martin had reported pretty much the same findings some twenty years earlier, but not in a political science journal). The paper then goes on to argue that an evolutionarily and biologically informed political science is the way of the future.
Sympathetic though I am to the behavior (and molecular) genetic work currently being undertaken by political scientists, I still think that it is unfortunate that it has no serious critics within the political science community. Evan Charney at Duke University has made some attempts to fill the void with a pretty standard attack on twin studies, but let us be charitable and say that he has not been particularly successful. The best argument against heritability estimates is not that they are wrong, but that they are not as structurally informative as is sometimes supposed. This is an argument that needs to be taken seriously. We can quibble about functional form and independence assumptions, the equal environment assumption, and the blatantly false assumption that all gene action is additive. In the end, it will not alter the fact that there is moderate genetic variation in virtually every trait you study.
The deeper question is this: what does it mean that a complex trait such as voting, the strength of partisanship, or attittudes toward abortion, say, are heritable, beyond the obvious but important implication that we can't interpret parent-child associations in environmental terms? It seems like a stretch to expect that there are genes with a proximal relationship to voting behavior, though of course the indirect effects of the genome can be developed through genome-level influences on intelligence and personality which in turn, ultimately, affect voting. But what are these mechanisms? Unless we know what they are, can heritability estimates be used to discipline any of the political science models?
These are all fascinating questions and Fowler and colleagues are only beginning to uncover the answers. I anticipate that Fowler and his partners in crime will continue to leave a trail of evidence from which we can build an even stronger case for a political science which does not make assumptions that are at odds with stylized facts from behavior genetics. Or, for that matter, at odds with facts derived from any of the other scientific disciplines from which the "genopolitics" crowd draw inspiration.
Part 1 of this note dealt with Sewall Wright's Shifting Balance theory of evolution (the SBT) in its original form, as propounded between 1929 and 1931. This final part deals with subsequent developments in the theory. These include refinements and elaborations, some changes of emphasis, one major addition, and one major change of substance. In particular I will cover:http://www.blogger.com/post-edit.g?blogID=10083047&postID=4815748383060203879
Blogger: Gene Expression - Edit Post "Notes on Sewall Wright: The Shifting Balance Theo..."
1. The role of new mutations
2. The concept of selective peaks
3. The effect of changes in environment
4. The adaptiveness of evolution
5. The process of intergroup selection
6. The three phases of the shifting balance.
I will throw in a few remarks about Fisher and Haldane as well.
NB: all page references are to Evolution: Selected Papers unless otherwise stated. Spelling and punctuation of quotations are as printed (some use American and some use British spelling). Square brackets indicate comments of my own.
1. The role of new mutations
First, a few words are necessary about the meaning of 'mutation'. In the 1930s very little was known about the physical and chemical nature of genes and therefore about the nature of changes to genes, in other words 'mutations'. In 1939 Wright gave a useful statement of current assumptions at that time: 'Presumably any particular gene can arise at a single step from only certain of the others and in turn mutate only to certain ones but the latter may be capable of producing mutations which could not have arisen from the former at one step and so on through a branching network of potentially unlimited extent' (306). This implies a 'step-by-step' evolution of genes themselves. Each gene may be said to have a first appearance in time, though recurrence of the same gene at different times is not excluded. The occurrence of mutations depends on the prior existence of the genes of which they are variants, so a particular type of mutation itself has an origin in time. The opportunity for mutations of a particular type will also depend on the frequency of the relevant genes in the population. If a gene is changing in frequency, the opportunity for new mutations of that gene will also be changing. We may therefore expect the rate of specific mutations to increase or decrease over time. This may explain some otherwise obscure comments in Fisher's Genetical Theory of Natural Selection (GTNS). In several places Fisher assumes that any new mutation will initially have a low rate of occurrence, but that this rate will increase over time (see especially GTNS p.78). This assumption makes sense if Fisher held the same view as Wright on the nature of mutations.
Wright's original formulation of the SBT said little about the role of beneficial new mutations in evolution. In 'Evolution in Mendelian populations' (EMP) (1931) Wright said only that in very large populations 'there is little scope for evolution. There would be complete equilibrium under uniform conditions if the number of allelomorphs at each locus were limited. With an unlimited chain of possible gene transformations, new favorable mutations should arise from time to time and gradually displace the hitherto more favored genes but with the most extreme slowness even in terms of geologic time' (150). This negative assessment of the prospects for evolution in large undivided populations conflicted with that of Fisher in GTNS, which appeared in 1930 after Wright's 'Evolution in Mendelian populations' (EMP) (1931) had been sent for printing. (A few short notes were added to take account of Fisher's work, but major changes were not possible.) Whereas Wright had concluded that large freely interbreeding populations were unfavourable to progressive evolution, Fisher believed that large populations (without strong barriers to gene flow) were favourable to evolution because of the greater scope they offered to new mutations. Fisher reinforced this in his published review of EMP, saying that 'even under static conditions, unless it is postulated that the organism is as well adapted as it could possibly be (in which case, obviously, evolutionary improvement is impossible), the equilibrium will be broken by the occurrence of any favourable mutation, of which a steady stream will doubtless occur in one or other of the very numerous individuals produced in each generation. The advantage of the large populations in picking up mutations of excessively low mutation rate seems to be overlooked [by Wright]... ' (Natural Selection, Heredity and Eugenics, p.288). Here, then, we find one of the major differences in the evolutionary theories of Wright and Fisher.
Wright elaborated and defended his position on this issue on several occasions, beginning with his own review of Fisher's GTNS in 1930. He notes that Fisher's 'scheme appears to depend on an inexhaustible flow of new favorable mutations. Dr. Fisher does not go into this matter of inexhaustibility but presumably it may be obtained by supposing that each locus is capable of an indefinitely extended series of multiple allelomorphs, each new gene becoming a potential source of genes which could not have appeared previously. The greatest difficulty seems to be in the posited favorable character of the mutations. Dr. Fisher, elsewhere presents cogent reasons as to why the great majority of all mutations should be deleterious. He shows that all mutations affecting a metrical character 'unless they possess countervailing advantages in other respects will be initially disadvantageous' [see Note 1]. He shows that in any case the greater the effect, the less the chance of being adaptive. [See Note 2] Add to this the point that mutations as a rule probably have multiple effects, and that the sign of the net selection pressure is determined by the greater effects, and it will be seen that the chances of occurrence of new mutations advantageous from the first are small indeed' (85).
There is a risk of ambiguity in this conclusion. If Wright means to say that only a small proportion of new mutations will be initially advantageous, his arguments are plausible, though not conclusive. If on the other hand he means to say that the 'chances of occurrence' of any such mutations, even in a large population, are small, the arguments are quite insufficient. It would be like confusing the probability that John Smith will die tomorrow, which is small, with the probability that someone will die tomorrow, which in a large population is virtually certain. Suppose that in a population of one billion, one in 100,000 individuals in each generation show some new mutation or other. There would then be 10,000 such new mutations in the population in each generation. Evidently, even if only a very small proportion of these mutations are advantageous, there might still be (in Fisher's terms) a 'steady stream' of them. Whether or not this is the case is an empirical matter.
Wright made similarly negative comments about new mutations on various occasions when defending the SBT:
1932: [under constant conditions] 'further evolution can only occur by the appearance of wholly new (instead of recurrent) mutations, and ones which happen to be favorable from the first. [Comment: this is valid only if 'new' means 'new under the same conditions'. Evolution might also occur through recurrence of mutations previously unfavourable but now favourable under new conditions.] Such mutations would change the character of the field [the 'adaptive landscape'] itself, increasing the elevation of the peak occupied by the species. Evolutionary progress through this mechanism is excessively slow since the chance of occurrence of such mutations is very small [comment: note the same ambiguity as in Wright's review of GTNS] and, after occurrence, the time required for attainment of sufficient frequency to be subject to selection to an appreciable extent is enormous' 165). [The last remark is puzzling. Any favourable new mutation is subject to selection from the outset, but it is at risk of being lost by random drift before it becomes safely established. It is not 'safe' until it has recurred a few hundred times. But in a large population, even with very low mutation rates this should only take a few hundred generations, which is not long in evolutionary time. This is one of Fisher's main arguments for the evolutionary advantage of large population size: see GTNS p.78. Once a mutation has reached a level of a hundred or so copies - say, a frequency of 1 in 10,000,000 in a population of a billion - the rate of advance will depend on the selective advantage of the gene. If the selective advantage is such as to double its frequency in 1,000 generations - equivalent to an advantage of rather less than 1 in 1,000 - the gene will go from first appearance to fixation (or equilibrium against back-mutation) in less than 30,000 generations. [See Note 3] This is not very long in geological time, though it would be imperceptibly slow to human observers, and until the later stages the gene would still be rare.]
1939: 'there is very little chance of occurrence of wholly new alleles in a large freely interbreeding population. There is also very little chance that any new mutation will be favorable at its first occurrence and even if favorable very little chance that it will attain sufficient frequency to be subject to selection to an appreciable extent' (321) [The italics for 'large' are Wright's own. The implicit assumption seems to be that in a large population every good mutation will already have been found. But note my previous comment that the advantageousness of a mutation is relative to conditions.]
1948: 'Presumably all mutations that are likely to arise at one or two steps from the more abundant genes present in the population have been tried by natural selection and found wanting, and thus are found at negligibly low frequencies if at all. There may be very valuable mutations which could only arise through a succession of unfavourable ones but these will have very little chance of occurring' (535) [see the previous comments]
1959: 'A genetic system can take the step from one selective peak to another one only by some non-selective process. A novel mutation may do this by creating a new peak, but this must be an excessively rare event' (Tax, p.451)
Wright maintained his opposition to the importance of new mutations to the end of his career. But his arguments are always brief and unquantified. There is a recurring ambiguity, as noted above, between the probability that a given new mutation will be advantageous, and the probability that any advantageous new mutation will occur. Fisher's view (GTNS p.78), was that in large populations, of the order of a billion (which includes most plant and invertebrate animal species), such mutations would occur often enough to be important in evolution. Wright opposed this conclusion, but it is difficult to avoid the feeling that in doing so he was trying to shore up a position which he had adopted without first considering mutation. It should at once be said that Fisher was equally stubborn (and more intemperate) in defending his own positions.
2. The concept of selective peaks
As noted in my post on Wright and the adaptive landscape, in 1932 Wright introduced the metaphor of a multidimensional field of gene combinations. I have discussed Wright's adaptive landscapes at length (see also here), so I will not repeat those discussions now. The point I wish to emphasize here is that the concept of selective peaks, valleys, etc, as introduced in 1932 was not just a new metaphor adopted for purposes of exposition, but an important addition of substance to the SBT.
From 1932 onwards it is a fundamental part of the SBT that there is a multiplicity of selective peaks in the field of possibilities available to a population. Many of these peaks are of different height (fitness). Under the influence of selection alone, and under constant conditions, a population cannot move from one peak to another. Under selection a population will tend to move towards one of the peaks, but usually the closest, which will seldom be the highest. It is therefore very likely that a population will be 'trapped' on an inferior peak, from which it cannot move purely by selection under constant conditions.
This aspect of the SBT is so important, and so familiar from Wright's later writings, that it is tempting to assume that in substance it was already there in the original version of the theory, even if the analogy of 'peaks' and 'valleys' was missing. In purely genetic terms, the meaning of a 'peak' in the landscape is that there is some set of gene frequencies such that any small departure from that set is opposed by selection. If there is more than one such set, there are multiple peaks. But the terminology of 'peaks', etc, is inessential. The substance of the theory could be stated quite well without it. It is therefore natural to expect some such equivalent statement in EMP, but I have not found one. It is true that, when discussing evolution in large populations in his 1929 summary, Wright does say that 'changed conditions cause a usually slight and reversible shift of the gene frequencies to new equilibrium points' (78), but in the context of his discussion in EMP (150) it appears that Wright was thinking only of a shift in the equilibrium between selection and mutation. His repeated claims that such shifts are essentially reversible would be difficult to reconcile with the concept of multiple peaks, and indeed, once Wright had clearly formulated that concept, he abandoned the claim of irreversibility.
The concept of multiple selective peaks is closely related to Wright's emphasis on epistatic fitness interactions, but this familiar feature of Wright's philosophy of evolution is also lacking from EMP. The beginnings of a new emphasis on epistasis can be found in 'Statistical theory of evolution' (1931), written after EMP but published slightly earlier. In discussing populations of intermediate size, Wright points out that 'it is the organism as a whole that is selected, not the individual genes, and a gene favored in one combination may be unfavorable in another' (95). And in subdivided populations 'exceptionally favorable combinations of genes may come to predominate in some of the subgroups' (95). But there is still, as far as I can see, no indication that even large populations may have alternative stable states, as proposed by Wright in 1932.
It is natural to wonder how Wright arrived at his 1932 conception of multiple selective peaks. It is possible that his reading of the section on 'Simple metrical characters' in GTNS had planted the seed. We know from Wright's correspondence that he was encouraged by receiving an offprint from Haldane in which the latter outlined similar ideas (Provine 275). It is also possible that Wright had privately reached his conception (without the geometrical analogy) much earlier, as Provine seems to think (Provine 275). But if Wright did indeed have the concept in mind when writing the paper which became EMP it is odd that he did not incorporate it in that work. I can only leave this as an unsolved puzzle.
3. The effect of changes in environment
As I have mentioned in previous posts (and as is also pointed out by Provine), until 1931 Wright considered that the evolutionary effects of temporary changes in environment would 'usually' or 'essentially' be reversible (78, 85, 150). But in 1932, with his paper on 'The roles of mutation, inbreeding, crossbreeding and selection in evolution', he took a new position. After introducing his concept of the multidimensional field of gene combinations, and the associated diagrams, he notes that 'the environment, living and non-living, of any species is actually in continual change. In terms of our diagram this means that certain of the high places are gradually being depressed and certain of the low places are becoming higher... Here we undoubtedly have an important evolutionary process and one which has been generally recognised. It consists largely of change without advance in adaptation. The mechanism is, however, one which shuffles the species around in the general field. Since the species will be shuffled out of low peaks more easily than high ones, it should gradually find its way to the higher general regions of the field as a whole' (167). This formulation is repeated, usually in similar words, in most of Wright's subsequent general surveys of evolutionary theory, e.g. 323, 374, 535, and 562.
It is perhaps not immediately clear (and Wright does not explain) why 'the species will be shuffled out of low peaks more easily than high ones'. Presumably it is partly because higher peaks may have stronger selection coefficients, and will therefore resist drift more strongly, but mainly because, other things being equal, higher peaks will have wider zones of attraction. A population may therefore drift further from the peak but still be pulled back towards it by selection. In geometrical terms, if two solid figures have the same shape, the taller figure will have the larger base. In genetic terms, the higher the fitness of a genotype relative to the average fitness of the population, the wider will be the range of gene frequencies within which the genes making up that genotype will be positively selected. But this is not an absolute rule. If a peak of fitness depends on very specific epistatic interactions of several genes, the peak may be high but narrow, like a spike. In this case a population may be easily jolted out of a high peak by environmental change, and never return to it. Changing environments may therefore be expected to promote mainly genes that are advantageous in a wide range of genetic combinations.
We are bound to ask why Wright changed his mind about the effects of environmental change. Wright himself gives no help on this point, because he never (I think) admitted that he had changed his mind. The change in 1932 goes together with Wright's formulation of the adaptive landscape concept, and in one sense goes very naturally with it. If we accept that there are multiple peaks of fitness in the landscape, and that it is largely a matter of chance which peak is most accessible to a population, then any factor which causes populations to move in a quasi-random way around the landscape could have the effect of 'shuffling' the population from one zone of attraction to another. But in another sense there is a tension between the landscape concept and environmental change, since the effect of environmental change is not so much to move the population around a fixed underlying landscape as to modify the landscape itself. As several commentators have suggested, in a changing environment the proper analogy is not so much with a solid landscape as with a choppy sea.
It is quite possible that Wright's change of mind in 1932 resulted simply from his own reflection on the issues. But he may also have been influenced by the positions already taken by Fisher and Haldane. As I mentioned in my post on Fisher and epistasis, in the section on 'Simple metrical characters' in GTNS Fisher had pointed out that metrical traits under stabilising selection could lead to multiple stable equilibrium gene frequencies, and that changes in selection coefficients due to environmental change could produce a lasting shift from one equilibrium to another. Wright had certainly read this section of GTNS, since he quotes from it in his review of the book. At that time (1930) he still thought that the effects of environmental change would usually be reversible, but he qualifies that position, saying: 'It may be granted that an irregular sequence of environmental conditions would result occasionally in irreversible changes (because of epistatic relationships), thus giving a real, if very slow, evolutionary process... ' (85). Over the next year Wright may have come to reconsider whether the process would only be 'occasional'. Haldane's The Causes of Evolution (1932, p.56) also contains a highly relevant passage: 'the change from one stable equilibrium to another may take place as the result of the isolation of a small unrepresentative group of the population, a temporary change in the environment which alters the relative viability of different types, or in several other ways...'. Unfortunately I do not know the exact dates of publication of Haldane's book and Wright's article of the same year, so it is not clear whether Wright could have seen it before writing his article. Wright had certainly read an article by Haldane of 1931 on 'Metastable Populations', which also discusses the theory of multiple equilibria, but this article refers only to chance fluctuations in the composition of populations, and not to environmental change, as possible reasons for a switch between alternative equilibria.
Whatever the reasons for Wright's new position on environmental fluctuation, he cannot be accused of playing down its importance. Several times he emphasised it: 'here we undoubtedly have an evolutionary process of major importance' (322), 'it can hardly be doubted that this has been one of the most important causes of evolution' (374), and 'there can be no doubt that a large part, perhaps the major portion, of evolutionary change, is of this character' (562). Nevertheless, it has often escaped the notice of later biologists, who assume that Wright continued to see genetic drift as the only way out of evolutionary stagnation.
Despite Wright's acceptance of, and even emphasis on, environmental change as a possible cause of 'peak shift', in some respects the implications of this new position were not fully assimilated into Wright's evolutionary philosophy. First, Wright might have been expected to rethink his position on the importance of population size and structure. On the face of it, a population of any size - large, small, or medium - may equally be affected by environmental change, and equally likely to shift from one peak to another. If this is so, Wright's belief in the ineffectiveness of evolution in large populations would need to be reconsidered. I am not aware that Wright did so. Second, if environmental change is capable of upsetting the equilibrium, perhaps other factors might also do so. One such factor is migration. If different gene frequencies are able to evolve in subpopulations, through genetic drift or local selective pressures, then migration between subpopulations may upset the equilibrium in some or all of them. Wright's SBT does allow for one particular effect of migration: if one subpopulation happens to have reached a higher selective peak than others, migration from that subpopulation may shift others towards the higher peak. But my point is that any migration between subpopulations with different gene frequencies may break up the existing equilibria and give the opportunity for new, and often higher, equilibria to be attained. It therefore seems that even if new favourable mutations are too rare, and mutation pressure is too weak, shifts between equilibria might occur in three ways: genetic drift in small subpopulations, environmental changes (biotic or nonbiotic) which might in principle affect populations of any size, and migration between subpopulations of any size.
4. The adaptiveness of evolution
I can deal more briefly with this topic because it has been dealt with thoroughly by Provine, who traces the change in emphasis from nonadaptive evolution, even at the level of differences between species, in Wright's early work, to a much stronger emphasis on adaptation in the post-war writings.
The only point I would add is that even in his later writings Wright saw adaptation as occurring mainly through intergroup selection. Selection within a single population, large or small, is in Wright's view ineffective in producing continuing adaptation because any single population will soon become stuck on a suboptimal selective peak. Evolution within subpopulations leads to divergence between them, either through genetic drift or fluctuating environmental factors. Neither of these is adaptive with respect to long term trends. This is obvious in the case of genetic drift, but even selection under fluctuating environment may be regarded as a quasi-random factor. It contributes to long-term adaptation only by providing the variation between subpopulations on which intergroup selection can work: 'In this theory [the SBT], the joint effects of random drift and intrademic selection merely supply raw material for interdemic selection' (618). Some subpopulations will, by chance, have combinations of genes which have the potential to increase fitness in the species as a whole, and these are spread by intergroup (interdemic) selection. The processes which generate diversity between subpopulations may be seen as analogous to mutation in the conventional neo-Darwinian framework: each mutation may have some underlying cause, and is not strictly random in the sense that mutations in all directions are equally probable, but it is random with respect to the long-term adaptiveness of the species as a whole.
It should be evident by now that Wright's SBT is a radical departure from the neo-Darwinism of Fisher, Haldane, and most other theorists of the 'evolutionary synthesis', and it should not be surprising that it has found admirers among such rebels against the synthesis as the punctuationists and the group selectionists of the last few decades.
5. The process of intergroup selection
Despite its importance in the SBT, Wright says little about the process of intergroup (or interdemic) selection. In principle one can envisage three different ways in which groups with higher average fitness could influence the properties of the wider population:
a) one group may become extinct, and a fitter group may then expand into the unoccupied territory
b) one group may move into the territory occupied by another group and displace it without interbreeding
c) members of one group may migrate into the territory of another, and influence its gene pool by interbreeding.
I do not think that Wright ever mentions process (a). In various places he seems to favour either process (b) or (c). In 1931 he says that 'exceptionally favorable combinations of genes may come to predominate in some of the sub-groups. These may be expected to expand their range while others dwindle' (95, see also 152). Since there is no mention of interbreeding, this seems to be closest to process (b). In 1932, on the other hand, he says that successful local races 'will expand in numbers and by crossbreeding will pull the whole species toward the new position' (168). This is closer to process (c). In 1939 he combines both (b) and (c), saying successful races 'by cross breeding with other races, as well as by actual displacement of these, will pull the species as a whole toward the new position' (324). In 1940 he says that successful local races may 'tend to displace all other local strains by intergroup selection (excess migration)' (351). The word 'displace' tends to suggest process (b). Also in 1940 he refers to some groups 'supplying more than [their] share of migrants to other regions, thus grading them up to the same type' (375, see also 423). The reference to 'grading up' may seem to imply a mingling of populations and interbreeding (process (c)). There is of course no reason why both processes should not play a part, as explicitly suggested in 1939. But both face some obvious difficulties. With process (b) it is necessary to explain why there is no interbreeding between the different types. This would be surprising unless some degree of reproductive isolation - i.e. speciation - had already evolved. With process (c) the problem is to explain why interbreeding does not break up the advantageous gene combinations on which the superiority of one group is supposed to rest. The problem is expecially severe if the successful group is initially small in relation to the whole population, as assumed at least in the original version of the SBT, with its reliance on genetic drift. This issue has been studied in several recent assessments of the SBT, the general conclusion being that the process is possible but, like the SBT as a whole, requires rather a lot of quantitative conditions to be met if it is to succeed.
As I mentioned in Part 1 of this note, 'intergroup selection' as envisaged by Wright has little to do with 'group selection' as envisaged by most of its recent advocates. Wright does not suggest that successful groups have evolved adaptations for group living, or that their members behave 'altruistically' towards each other. His claim is rather that the subdivided population structure allows some groups, by chance, to form combinations of genes that are advantageous to individual fitness. The higher mean fitness of the groups is the resultant of these individual fitness advantages.
However, in some of his later writings Wright does mention the possibility of the evolution of altruistic social traits through intergroup selection, for example: 'characters may be fixed [through random drift in small subpopulations] that are favourable to the group as a whole even though disadvantageous in individual competition' (536, see also Tax p.466). The problem, of course, is that this requires migration from other groups to be near zero if the 'altruistic' groups are to survive for more than a brief period without being undermined by freeloaders.
6. The three phases of the shifting balance
Finally, in his later writings on the SBT Wright often refers to three 'phases' of the shifting balance. Like the term 'shifting balance' itself, the 3-phase formulation seems to have been first used in the article of 1970 on 'Random drift and the shifting balance theory of evolution'. The phases are described as the 'phase of random drift', in which gene frequencies in each deme drift around the current selective peak; the 'phase of mass selection', in which a deme has drifted into the zone of attraction of a new selective peak, and moves rapidly towards it under the influence of selection; and the 'phase of interdemic selection'.
The explicit distinction between three phases seems to be new in 1970, but it is essentially a clarification of the process which had been implicit in various writings at least since 1932. I won't comment further on the substance of the three phases, which have already been discussed under various headings.
The purpose of this Note has been mainly to analyse the various aspects of the SBT in their chronological development, and not to assess its credibility. A few years ago I drew attention to some recent controversy, mainly in the journal 'Evolution', by biologists pro and con the SBT. These discussions still seem to be relevant, but I note that some aspects of the SBT (or of Wright's philosophy of evolution more generally) have not been sufficiently recognised. One is the important change in 1932 when Wright recognised that environmental fluctuations, as well as genetic drift, could have lasting effects on the genetic equilibrium of a population. Despite Wright repeating this point on several occasions, it has been widely overlooked (Dobzhansky being a notable exception, and Provine a more recent one). There is some excuse for this if, as I have argued, the implications of the change were never sufficiently absorbed by Wright himself. The second point is that Wright was consistently negative towards the prospects for new favourable mutations. I have suggested that his comments involve an ambiguity between the rarity of new favourable mutations among all mutations, which is not disputed, and the rarity of occurrence of any such mutations, even in a large population and over a timescale of many generations. Wright's negative conclusions are only valid if such mutations are rare in both senses. His position implies that the differences between populations, whether closely related species or subpopulations of the same species, will arise mainly by different epistatic combinations of existing genes, rather than by the selection of new variants. This is in principle testable.
This is the last of my planned notes on Sewall Wright, and it is a relief to get to the end of the journey. I will not attempt any overall assessment at this stage, but I will probably prepare a post giving links to all the notes in the series, as well as to related notes on Fisher and Haldane.
Note 1. See GTNS p.107, but note that according to Fisher, if the effect of the mutation is small (say, no more than 1 percent of the standard deviation of the trait), even mutation rates as low as one in a million may be sufficient to overcome the initial selective disadvantage and eventually push the mutation into a frequency where it is favoured by selection.
Note 2. The reference is evidently to the section in GTNS on 'The nature of adaptation'. What Fisher shows, given his assumptions, is that:
a) other things being equal, a smaller mutation is always more likely to be advantageous than a larger one. (As Kimura pointed out much later, this is partially offset by the consideration that the size of any advantage is likely to be greater for a larger mutation, and this affects the probability that it will survive in the population. Overall, mutations with effects somewhat above the minimum size have the highest probability of survival.)
b) for any given size of mutation, the probability of being advantageous is lower the more aspects of fitness are affected by it.
Using a very schematic geometrical model, Fisher quantifies the probability that mutations of a given size will be advantageous. It is assumed in the model that the present position of the organism is at some distance from a local optimum. The probability that a mutation will be advantageous is inversely related both to the size of the mutation and to the square root of the number of dimensions of fitness affected. For very small mutations the probability is close to 1/2, declining to zero for mutations with an effect more than twice the distance between the starting point and the local optimum (this zero probability being an assumption built into the model, rather than proved by it). But note that the probabilities are not always very small, even for mutations with an effect quite substantial relative to the present distance between the organism and the optimum. Also, since the probability declines in proportion only to the square root of the number of dimensions of fitness affected, not to that number itself, the decline is not as rapid as might be feared. Contrary to some popularisations, Fisher does not claim that mutations with very large or complex effects are impossible, or even highly improbable, only that they are less likely to be advantageous than those with smaller and/or simpler effects.
Note 3: Some readers may wonder how this can be reconciled with Haldane's rule of thumb that up to one mutation can go to fixation, on average, in every 300 generations - see my post on Haldane's Dilemma. I think the explanation has two parts. First, Haldane's '300 generations' estimate assumes that a gene under selection starts from a position of balance between adverse selection and mutation pressure, and then becomes favourable due to a change in environment. On this assumption the gene will already have a small but not negligible frequency in the population. Second, the '300 generations' figure does not mean that a single gene under selection goes from rarity to fixation in 300 generations, but rather that, on average, one gene could be fixed in every 300 generations. There is a difference between these two claims. Under typical selection intensities of 1 in 1000, or even 1 in 100, the process of fixation for a single initially rare gene would obviously take longer than 300 generations. Haldane's model assumes that there are a number of genes undergoing selection simultaneously or overlapping with each other. If we imagine, say, 100 genes starting the process of selection at the same time, and all taking 30,000 generations to reach fixation, the average number of genes fixed per generation over the period of 30,000 generations would be 100/30,000 = 1/300, but these would all reach fixation in a bunch at the end of the period. More realistically, if the periods of selection are overlapping in a more-or-less random way, and selection has been in progress for long enough, we would expect any period of, say, a thousand generations to see a few genes reaching fixation, with an average of about 1 per 300 generations.
R. A. Fisher, The Genetical Theory of Natural Selection, 1931, variorum edition ed. J. H. Bennett, 1999.
R. A. Fisher: Natural Selection, Heredity and Eugenics: Including selected correspondence of R. A. Fisher with Leonard Darwin and others, edited by J. H. Bennett (1983).
J. B. S. Haldane, 'Metastable populations', Proceedings of the Cambridge Philosophical Society, 27, 1931, 137-142.
J. B. S. Haldane, The Causes of Evolution, 1932 (reprint ed. E. Leigh, 1990)
William B. Provine, Sewall Wright and Evolutionary Biology, 1986.
Sewall Wright: 'Physiological genetics, ecology of populations, and natural selection', in Evolution After Darwin, vol. 1, ed. Sol Tax, 1960 (Tax). (Article first published in 1959.)
Sewall Wright: Evolution: Selected Papers (ESP), ed. William B.Provine, 1986.
Sewall Wright: 'Random drift and the shifting balance theory of evolution', in Mathematical Topics in Population Genetics, ed. Kojima, 1970.
Thursday, November 06, 2008
The McCain Belt:
So, why did McCain do best, relative to George W. Bush in 2004, in states like #1. Tennessee, #3. Arkansas, #5 Oklahoma, #7 West Virginia, #9 Kentucky, and #10 Alabama?
Until recently I'll be honest and admit that I had very little interest in American history beyond what I learned in high school (in contrast to my interest in the Classical period or China, etc.). It seemed rather boring because we live in America, the history is all around us, and I could watch documentaries, etc. At least that was my logic, and it's not totally faulty. The problem is that our knowledge of American history which we obtain through direct experience as Americans is implicit, and we tend to lack clarity which would allow us to discern predictable dynamics. My ignorance combined with a lack of formal paradigm meant I simply wouldn't have noted the reemergence of familiar dynamics several times within the past few years.
David Hackett Fisher's Four Folkways aren't perfect, there's a lot you can quarrel with. But it adds a lot of value as a framework which you can use to understand the flows and patterns of American history; dynamics which we ourselves are seeing as a snapshot currently. Since most pundits are ignorant of course they'll miss the big picture. I don't know enough myself to really hazard much which would add value to anyone's understanding aside from what they might get from reading Albion's Seed or The Age of Lincoln. But...though I'm not being original, I think it is important to emphasize that much of the arc of American political history can be conceived of as a set of cyclical dynamics which are the product of alliances across the Four Folkways (the demographic weights of the Four Folkways in American society at a given time are obviously crucial). As an example, during the 1930s and in the early 19th century New England stood alone against the dominant American political configuration, steadfastly adhering to a minority party. In contrast, the 1850s and the current period seem to be witnessing a more equitable division as the two northern and southern folkways align with each other in a "50:50" nation.
I also think that it is important to emphasize that much of popular history which focuses on individuals and wars might not help you generate a good model of the past which has any utility for comprehending the present. The framework above would be implicit within a narrative, humans are embedded in a sociocultural matrix, but you might fail to discern any systematic pattern if you're focusing on the personalities. This is I think a problem with a lot of "pop history" in documentary form; "boring" cultural and economic parameters take a back seat (or are mentioned in passing) to interesting, but structurally trivial, personal epiphenoma (e.g., Thomas Jefferson and John Adams died on the 4th of July).
Note: An important issue to emphasize about the Four Folkways is that they may evolve so that the way in which they relate to each other changes over time. In 1800 New England was arguably the most socially conservative and evangelical Protestant part of the United States, while the lowland South was at the other end of the spectrum. It was no surprise at the time that the architects of American church-state separation were low country Virginia planters, while explicit state support and preference for a particular church lasted longest in New England. Obviously things have changed, but the point is that New England and the lowland South evolved as roughly discrete units over time due to local dynamics as well as parameters which effected the United States broadly. Even though the distribution of "New England" and the "South" in parameter space has changed as a function of time, they are still discernable discrete distributions.
A new theory of MHC evolution: beyond selection on the immune genes:
The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a 'sheltered load' nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.
Wednesday, November 05, 2008
Nature this week has published articles describing the genomes sequences of two individuals--one Nigerian and one Chinese. Both were sequenced using Illumina's short read technology, and the brute force approach of deep sequencing seems to have worked fairly well--they estimate their SNP calling error rate is on the order of 0.6%. Recall that SNPs called from the Venter genome had an order of magnitude more errors.
Dan MacArthur at Genetic Future has more.
I have some posts on my other weblog about the way regionalism played out in this election. The electoral college map flip; drift?, Where Obama overperformed & underperformed and The Great White Sort. Steve points out the relevance of Affordable Family Formation and the Dirt Gap. It seems likely that we're entering into a very ideologically polarized and sectional period; likely narrow flips back and forth. Looking at state level exit polls can only say so much. I would be willing to bet that a survey of white voters in the Tampa area, where Midwestern retirees congregate, would show Obama gains, while northern Florida whites would resemble those in the rest of the South. This is why I think Florida turned out to be a wash in the white vote.
P.S. If you haven't read Albion's Seed, and these sorts of patterns interest you, you need to read it. It adds a lot of insight. It is handy to know what the "Western Reserve" was, and why it matters today. Or why there is a Portland, OR, and Portland, ME, and a Salem, OR, and Salem, MA.
Monday, November 03, 2008
They say a picture is worth a thousand words, and here is the proof. (There is also a report in the UK Times, which is where I first saw it - honest - but the Times article didn't come up on Google.)
Sunday, November 02, 2008
Jim Manzi writes that it's plausible that epistatic interactions are central to complex mental phenotypes, and that they might therefore prevent genome-wide association studies from achieving much success. In the comments to a response post by Razib, Jason Malloy does a pretty good job of showing that traits like IQ are primarily additive and that epistasis therefore won't prevent successful GWA with good sample sizes. [UPDATE 06-25-2009: I've read more behavior genetics, and I'm not quite sure that Jason's view is correct. I think it's still an open question, actually.]
With all that in mind, some epistasis does exist, and it is worth uncovering. It will not be uncovered directly by genome-wide searches, though, because of multiple testing issues. Even a two-dimensional search overwhelms foreseeable sample sizes. However, a multi-step approach could work by breaking down the multiple dimensions into individual searches. Say that gene-A and gene-B only have an effect when they appear together. Thus, a GWA should pickup an effect from either gene-A or gene-B (whichever has a higher minor allele frequency, presumably), even if that effect is smaller than the overall effect of having both of them. Now, suppose we identify via GWA that gene-A is contributing to the phenotype. We could then do a second scan for interactions and identify gene-B.
Of course, scientists are not limited solely to association searches. They can also harness biological evidence of epistasis to help identify candidates. Because traits like IQ are primarily additive, epistasis is not the overwhelming bogeyman that it might first appear, and it should be possible to tackle in the years to come.
Hirschhorn, J. N., & Daly, M. J. (2005). Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics, 6, 95-108.