Tuesday, June 30, 2009
A few weeks ago I noticed that the Wikipedia entry for Cape Coloureds has little fleshed out information on their genetics. As a mixed population it seems that people would be interested, but has always been hard to find anything from Google Scholar on this topic. But the recent Tishkoff paper, The Genetic Structure and History of Africans and African Americans, has some data. You can find a full post at my other weblog, but it seems that not only are the Cape Coloureds substantially European, Khoisan and Bantu, but likely they're also substantially Indian, and there is a definite East Asian element, no doubt from slaves brought from Maritime Southeast Asia by the VOC. There's also a lot of variance in this particular sample of Cape Coloureds. Assuming this is representative I would offer that the main reason is that the Coloured population has historically had many people entering it from other groups, and, many leaving to other groups.
Some readers here may already follow the food-related stuff I write about at my personal blog. Well, to allow myself to write more about diet, nutrition, and food in general, I've started a new blog called Low Carb Art and Science. Lord knows there are already lots of blogs that deal with the topic, but this one will have lots more data and a stronger emphasis on evolution. But there will be plenty of less serious stuff and easy recipes too. Plus I'll take an occasional interdisciplinary approach, as with an earlier post I wrote about the late Medieval shift away from carbs and toward meat.
The first post up is about the changing American diet and poorer health -- except that the graphs show that the changing American diet has been one that's rigidly adhered to what the health experts tell us to eat. The data weren't hard to find, analyze, and present, but I've never seen them before, let alone in a clear-to-see visual format. If you doubted whether the anti-meat, pro-grain message was being followed or not, and if so, whether it was making us healthier -- this will be a real eye-opener. Take-home lesson: eat more saturated fat and cholesterol, and less carbohydrates.
Comments closed here; comment over at Low Carb Art and Science.
Sunday, June 28, 2009
One of the rationales advanced for the identification of common alleles that confer modest risk to a disease via genome-wide association studies is that these associations will lead to biological insight into the disease. Two papers published today represent an important first step towards this goal for a variant associated with colorectal cancer.
Like many polymorphisms associated with complex diseases, the one investigated in these studies does not fall within a gene--this particular variant falls hundreds of thousands of bases away from the nearest gene. It does, however, fall within a non-coding element that is conserved across millions of years of evolution, suggesting that it is functional. These studies show that, indeed, the SNP falls in a binding site for a transcription factor, and that the two alleles have different binding affinities for that factor. Additionally, one of the studies shows that the genomic region containing the SNP loops over and makes physical contact with the nearest gene (MYC, a known oncogene), supporting the hypothesis that the SNP affects its regulation.
These studies raise more questions than they answer, of course. None of the studies find an association between the SNP itself and steady-state MYC expression in cell lines. My guess is that, like many transcriptional enhancers, developmental-time-point-specific manner. An important direction now is to determine when that important time point is.
Long article in Scientific American, The Science of Economic Bubbles and Busts. H/T Calculated Risk.
Thursday, June 25, 2009
In False Economy: A Surprising Economic History of the World* there's a chapter which covers "The Catfish War" between Vietnam and the United States in the early 2000s. Basically Vietnamese catfish were cheaper than American catfish, so American farmers got the government to force the Vietnamese to not label the fish catfish (it's a different species from the American variant). So Vietnamese catfish are now termed "basa" in the United States. Interestingly this might have backfired, the author of False Economy claims that many American consumers ended up thinking basa were an exotic premium import. But here's another reality: in blind taste tests people prefer Vietnamese catfish to American catfish.
I only mention this because I've been getting basa for a few weeks now. Today the supermarket was out of basa, but did have American catfish (where there used to be basa). So I got American catfish because I figured catfish is catfish. Well...American catfish kind of sucks compared to basa. I don't find catfish meat repellent or anything, but basa has a much nicer flavor and smell than American catfish. It's also easier to cook. And I don't have a subtle palette; I use a lot of hot sauce, so I can tolerate a large range in flavor. There just isn't any comparison. Perhaps it was a bad batch of catfish, but I've actually had catfish sandwiches and the like in New Orleans and Houston, and I think this was typical American catfish thinking back to that. Wikipedia said that people prefer basa to American catfish 3:1, but I would have expected 10:1.
* It's a well written work which illustrates general economic principles with concrete contemporary examples, but is far inferior to Rondo Cameron's A Concise Economic History of the World in terms of factual density.
In my recent post on Darwin's mechanisms of evolution I was rather dismissive about the Inheritance of Acquired Characteristics (IAC), commonly known as 'Lamarckism'. Darwin himself believed in the existence of IAC but gave it a relatively minor role in evolution. In comments on my post it was pointed out that there has recently been some revival of interest in IAC in the form of 'transgenerational epigenetics'. For a recent review see here. [Note added: as originally posted I somehow inserted the wrong link. Hope this one is now correct.]
Even if all of these reports are true, they don't (yet) amount to more than a small tweaking of evolutionary theory. The main examples seem more like congenital syphilis than 'Lamarckism' in the traditional sense: an animal is exposed to a substance that happens to affect the germ cells as well as the rest of the body. No big deal. But I think biologists should be cautious about accepting such reports without clear independent replication, for two reasons. First, because 'extraordinary claims need extraordinary evidence'. Second, because there is a long and dreary history of unsubstantiated, unreliable, and downright fraudulent claims about IAC. As much of this history is now generally forgotten, it may be useful to recall some of the 'highlights'.
Brown-Sequard was a distinguished if eccentric French physiologist. He achieved scientific fame for the discovery of what are now known as hormones, and notoriety when he claimed that life could be rejuvenated by the injection of crushed animals' testicles. At least he was willing to try it on himself. But the present point of interest is in his neurological experiments. For many years he experimented on thousands of guinea pigs, mainly by severing various nerves. He claimed that the untreated offspring of the experimental subjects showed certain symptoms, such as a liability to epileptic fits, which resembled those of the parents. Charles Darwin accepted the evidence as proving that IAC was at least possible. Darwin's younger friend George Romanes, a supporter of IAC, spent years trying to replicate the experiments, and claimed some slight success, but admitted that on the whole the results were negative. Brown-Sequard's results have never been conclusively explained, but unexplained results are not unusual in science. The Germans have the useful term 'Dreckeffekt' for this kind of thing.
W. L. TOWER
[Apology: I first gave the name as 'William Edward Tower', but on checking my source again I find the initials are 'W. L.'. Apologies if anyone has wasted time following up the incorrect name.]
Tower was an American entomologist who claimed in the early 1900s to have produced inheritable mutations in beetles by changes in temperature and humidity. The pioneer geneticist William Bateson questioned Tower's results and became increasingly critical, hinting at fraud. Tower admitted that there were errors in his reports, and claimed that his original records had been destroyed by a fire in his greenhouse. Hmm.
Kammerer's experiments on the Midwife Toad, made famous in a sympathetic book by Arthur Koestler, led to tragedy when it was discovered that the specimens had been artificially tampered with, and Kammerer committed suicide. There was certainly skullduggery by someone, though whether by Kammerer himself remains controversial.
Heslop-Harrison was an English botanist and entomologist who claimed to have induced heritable melanism in insects by chemical treatments. His claims were questioned by Haldane, Fisher and others. There must be suspicion of fraud, as Heslop-Harrison later became notorious for the unconnected allegation that he (literally) planted evidence on the Scottish island of Rhum to support his botanical theories. [NB Heslop-Harrison must not be confused with his still living son of the same name, also a botanist. ]
McDougall was a leading psychologist in the first half of the 20th century. He carried out a long series of experiments on rats which seemed to show that successive generations became better and better at learning mazes. I don't think anyone has suggested fraud, but subsequent attempts at replication pointed out a major defect in his methodology: the absence of a control group. When a control group was used, whose ancestors had not been trained, they showed much the same patterns of improvement - or non-improvement - as the experimental subjects themselves (see here.) The improvement therefore seems to have been due to some other factor or factors, such as better laboratory or cage conditions, and not to IAC.
No need to comment.
Edward Steele is an Australian immunologist who claimed in the 1970s to have produced inheritable immunological responses in mice. This led to a predictable spate of 'Darwin was wrong' and 'Back to Lamarck' news reports. Less publicity was given to at least three independent replication attempts with negative results.
The moral is - oh, draw your own.
This may be old hat for some readers, but it's worth reviewing and providing some good new data for. The motivation is the idea that monopoly-haters have that when some company comes to dominate the market, they will have no incentive to change things -- after all, they've already captured most of the audience. The response is that industries where invention is part of the companies' raison d'etre attract dynamic people, including the executives.
And such people do not rest on their laurels once they're free from competition -- on the contrary, they exclaim, "FINALLY, we can breathe free and get around to all those weird projects we'd thought of, and not have to pander to the lowest common denominator just to stay afloat!" Of course, only some of those high-risk projects will become the next big thing, but a large number of trials is required to find highly improbable things. When companies are fighting each other tooth-and-nail, a single bad decision could sink them for good, which makes companies in highly competitive situations much more risk-averse. Conversely, when you control the market, you can make all sorts of investments that go nowhere and still survive -- and it is this large number of attempts that boosts the expected number of successes.
With that said, let's review just a little bit of history impressionistically, and then turn to a new dataset that confirms the qualitative picture.
Taking only a whirlwind tour through the pre-Information Age time period, we'll just note that most major inventions could not have been born if the inventor had not been protected from competitive market forces -- usually from protection by a monopolistic and rich political entity. Royal patronage is one example. And before the education bubble, there weren't very many large research universitities in your country where you could carry out research -- for example, Oxford, Cambridge, and... well, that's about it, stretching back 900 years. They don't call it "the Ivory Tower" for nothing.
Looking a bit more at recent history, which is most relevant to any present debate we may have about the pros and cons of monopolies, just check out the Wikipedia article on Bell Labs, the research giant of AT&T that many considered the true Ivory Tower during its hey-day from roughly the 1940s through the early 1980s. From theoretical milestones such as the invention of information theory and cryptography, to concrete things like transistors, lasers, and cell phones, they invented the bulk of all the really cool shit since WWII. They were sued for antitrust violations in 1974, lost in 1982, and were broken up by 1984 or '85. Notice that since then, not much has come out -- not just from Bell Labs, but at all.
The same holds true for the Department of Defense, which invented the modern airliner and the internet, although they made large theoretical contributions too. For instance, the groundwork for information criteria -- one of the biggest ideas to arise in modern statistics, which tries to measure the discrepancy between our scientific models and reality -- was laid by two mathematicians working for the National Security Agency (Kullback and Leibler). And despite all the crowing you hear about the Military-Industrial Complex, only a pathetic amount actually goes to defense (which includes R&D) -- most goes to human resources, AKA bureaucracy. Moreover, this trend goes back at least to the late 1960s. Here is a graph of how much of the defense outlays go to defense vs. human resources (from here, Table 3.1; 2008 and beyond are estimates):
There are artificial peaks during WWII and the Korean War, although it doesn't decay very much during the 1950s and '60s, the height of the Cold War and Vietnam War. Since roughly 1968, though, the chunk going to actual defense has plummeted pretty steadily. This downsizing of the state began long before Thatcher and Reagan were elected -- apparently, they were jumping on a bandwagon that had already gained plenty of momentum. The key point is that the state began to give up its quasi-monopolistic role in doling out R&D dollars.
Update: I forgot! There is a finer-grained category called "General science, space, and technology," which is probably the R&D that we care most about for the present purposes. Here is a graph of the percent of all Defense outlays that went to this category:
This picture is even clearer than that of overall defense spending. There's a surge from the late 1950s up to 1966, a sharp drop until 1975, and a fairly steady level from then until now. This doesn't alter the picture much, but removes some of the non-science-related noise from the signal. [End of update]
Putting together these two major sources of innovation -- Bell Labs and the U.S. Defense Department -- if our hypothesis is right, we should expect lots of major inventions during the 1950s and '60s, even a decent amount during the 1940s and the 1970s, but virtually squat from the mid-1980s to the present. This reflects the time periods when they were more monopolistic vs. heavily downsized. What data can we use to test this?
Popular Mechanics just released a neat little book called Big Ideas: 100 Modern Inventions That Have Changed Our World. They include roughly 10 items in each of 10 categories: computers, leisure, communication, biology, convenience, medicine, transportation, building / manufacturing, household, and scientific research. They were arrived at by a group of around 20 people working at museums and universities. You can always quibble with these lists, but the really obvious entries are unlikely to get left out. There is no larger commentary in the book -- just a narrow description of how each invention came to be -- so it was not conceived with any particular hypothesis about invention in mind. They begin with the transistor in 1947 and go up to the present.
Pooling inventions across all categories, here is a graph of when these 100 big ideas were invented (using 5-year intervals):
What do you know? It's exactly what we'd expected. The only outliers are the late-1990s data-points. But most of these seemed to be to reflect the authors' grasping at straws to find anything in the past quarter-century worth mentioning. For example, they already included Sony's Walkman (1979), but they also included the MP3 player (late 1990s) -- leaving out Sony's Discman (1984), an earlier portable player of digitally stored music. And remember, each category only gets about 10 entries to cover 60 years. Also, portable e-mail gets an entry, even though they already include "regular" e-mail. And I don't know what Prozac (1995) is doing in the list of breakthroughs in medicine. Plus they included the hybrid electric car (1997) -- it's not even fully electric!
Still, some of the recent ones are deserved, such as cloning a sheep and sequencing the human genome. Overall, though, the pattern is pretty clear -- we haven't invented jackshit for the past 30 years. With the two main monopolistic Ivory Towers torn down -- one private and one public -- it's no surprise to see innovation at a historic low. Indeed, the last entries in the building / manufacturing and household categories date back to 1969 and 1974, respectively.
On the plus side, Microsoft and Google are pretty monopolistic, and they've been delivering cool new stuff at low cost (often for free -- and good free, not "home brew" free). But they're nowhere near as large as Bell Labs or the DoD was back in the good ol' days. I'm sure that once our elected leaders reflect on the reality of invention, they'll do the right thing and pump more funds into ballooning the state, as well as encouraging Microsoft, Google, and Verizon to merge into the next incarnation of monopoly-era AT&T.
Maybe then we'll get those fly-to-the-moon cars that we've been expecting for so long. I mean goddamn, it's almost 2015 and we still don't have a hoverboard.
Wednesday, June 24, 2009
So after my wingeing about the quality of genetic associations found through candidate gene studies, it's only appropriate that I point to a fun candidate gene association study published this week in Nature.
The interesting point here is that the organism isn't humans, but rather baboons, and the phenotype is susceptibility to malaria. Briefly, the authors find that a SNP in the promoter of the Duffy locus (recall that a mutation that abolishes the expression of Duffy in humans leads to protection from Plasmodium vivax and is one of the best characterized instances of recent positive selection in our species) appears to lead to protection from a malaria-like disease in baboons. The authors seem to really, really want this polymorphism to also be under selection in baboons (to complete the parallel story to humans), but they can't bring themselves to say the evidence is anything more that "suggestive" (and to be honest, even that may be wishful thinking).
So is the association true? The study suffers from the same problem of candidate gene studies mentioned before, in that it's small and the evidence for an association is fairly weak. If I had to bet, I'd guess no, the association isn't real. But collecting and genotyping a large sample of baboons is simply not feasible at this point (if it ever will be), so this is what's possible, and it's a kind of fun, suggestive study that would be really cool if it ends up being true.
Tuesday, June 23, 2009
Obesity May Have Offered Edge Over TB:
Over the course of human evolution, people with excess stores of fat have been more likely to survive famines, many scientists believe, living on to pass their genes to the next generation.
The original paper is here. I'm skeptical, but I'd like people who know more about the history and distribution of tuberculosis to weigh in. My working assumption is that excess fat was helpful in most pre-modern contexts (i.e., female fertility) and obesity wasn't common and simply a modern overshoot.
Labels: Origin of obesity
The GSS asks people about the morality of premarital sex between post-pubescent minors (TEENSEX):
What if [a male and female] are in their early teens, say 14 to 16 years old? In that case, do you think sex relations before marriage are always wrong, almost always wrong, wrong only sometimes, or not wrong at all?
Most people say "always wrong," so I'll just look at those responses; the other responses have little room to vary since all must add up to 100%. How does opposition vary across demographic groups?  As for social class, the elites say they're more ethical than the rabble, but on the other hand, they're big supporters of "sex is natural and therefore can't be harmful." So which is it?
Let's see what the data say:
Clearly, those with more prestigious jobs (SEI) are less opposed. Perhaps this is because the prestigious can get away with more shocking or outside-the-mainstream views. But that's not what the three other measures of social class suggest.
As for real income (REALINC, in $5000 intervals), opposition increases from poor to lower-middle income people ($40K), and then declines somewhat steadily among middle and upper income people. My guess here is that middle and upper income people don't think the teenage years count -- as long as their kids get advanced degrees, make a lot of money, and don't marry scumbags, they could care less if they fool around a little in high school.
Poor people, though, see their kids as living shorter lives -- they enter Adult World sooner, so it matters what they do right after puberty. If you live in the same town you grew up in and plan to get married in your early 20s, having a reputation as a slut in high school will harm your prospects a lot more than if you move across the country five times before marrying, and even then only 10 years after graduating.
Education (EDUC) and intelligence (WORDSUM) show a similar pattern to job prestige and real income, as all are indicators of social class. Opposition increases up through 6th grade graduates, but declines pretty steadily among those who made it through middle school and beyond. For intelligence, like the other class variables, there's an increase among the below-average, and then a steady decline among the above-average.
So, judging by these four ways of measuring social class, there seems to be a real difference between the upper, middle, and lower groups in how fast or slow they expect their children to grow up and do adult things. In biology jargon, this is a difference in life history strategies. There's a parallel here between parents who invest more in their sons or their daughters, according to the Trivers-Willard Hypothesis: richer families favor their sons, while poorer families favor their daughters. One study found support for this idea by looking at how Gypsy vs. Hungarian families in Hungary invested in their children (free PDF here). Since lower class families care more about their daughters, they'll freak out more if they engaged in premarital sex while still young and thus when reputations matter most. Upper class families will be thinking of their sons, though, and conclude, "Meh, let them sow their wild oats, as long as they settle down when the time comes."
 It seems like younger people would be least opposed, since 14 to 16 is awfully close to their own age. They might think the police will come after them next. Sure enough, age is a very strong predictor here -- indeed, the only demographic group I could find among whom a majority doesn't consider it "always wrong" is 18 year-olds.
It's hard out there being a reproductively fit couple
Sunday, June 21, 2009
In a recent post, I made a blanket statement that the vast majority of candidate gene association studies published in psychiatric genetics (actually, in nearly all fields of genetics) are wrong. I'm not just being offhandedly dismissive--below, I outline the statistical argument behind that claim. This discussion is cribbed almost verbatim from a discussion of the issue by statisticians at the Welcome Trust.
Let's assume that there are a finite number of loci in genome, and we test some number of those (in a genome-wide association study, this is on the order of 500K-1M; in a candidate gene study it's more likely in the tens. But the actual marker density is irrelevant for what follows) for association with some phenotype of interest. In general, the criterion used to decide if one has discovered a true association is the p-value, or the probability of seeing the data that you have given that there is no association. But that's not really the quantity you're interested in. The real quantity of interest is the probability that there's a true association given the data you see--the inverse of what's being reported.
By Bayes' Law, this probability depends on the prior probability of an association at that marker, the p-value threshold you've chosen to call a finding "significant", and crucially, the power you had to detect the association . Thus, the interpretation of a given p-value depends on the power to detect an association, such that the lower your power, the lower the probability that a "significant" association is true .
That's where recent evidence from large genome-wide association studies comes into play. For nearly all diseases, reproducible associations have small effect size and are only detectable when one has sample sizes in the thousands or tens of thousands (for many psychiatric phenotypes, even studies with these sample sizes don't seem to find much). The vast majority of candidate gene association studies had sample sizes in the low hundreds, and thus had essentially zero power to detect the true associations. By the argument above, in this situation the probability that a "significant" association is real approaches zero. The problem with candidate gene association studies is not that they were only targeting candidate genes, per se, but rather that they tended to have small sample sizes and were woefully underpowered to detect true associations.
 Let D be the data, T be the event that an association is true, t, be the event that an association is not true, and P(T) be the prior probability that an association is true.
P(T|D) = P(D|T)P(T) / [ P(D|T) P(T) + P(D|t) (1-P(T) ]
P(D|T) is the power, and P(D|t) is the p-value. Clearly, both are relevant here.
 As the authors note,
A key point from both perspectives is that interpreting the strength of evidence in an association study depends on the likely number of true associations, and the power to detect them which, in turn, depends on effect sizes and sample size. In a less-well-powered study it would be necessary to adopt more stringent thresholds to control the false-positive rate. Thus, when comparing two studies for a particular disease, with a hit with the same MAF and P value for association, the likelihood that this is a true positive will in general be greater for the study that is better powered, typically the larger study. In practice, smaller studies often employ less stringent P-value thresholds, which is precisely the opposite of what should occur.
I've pointed to the World Values Survey before. It comes in 5 waves spaced out over 2 decades, and has substantial, if not total, coverage. Additionally, for many non-developed countries the educational data to me suggest some high SES skew in terms of representativeness (though spot checking the American data that looks very representative, as there have been other national surveys you can cross-reference it with). On some of my blogs a few commenters have started to follow up posts and use the WVS to answer questions, instead of offering of speculations. It's not as complicated of an interface as the GSS, but it isn't as flexible either. Nevertheless, there are some obvious questions one might ask.
For example in general within societies the religious have more offspring than the non-religious. Even controlling for variables there is often a significant effect. That implies that over time if religiosity is heritable (whether biologically or culturally) societies should become more religious. So a priori assertions such as Mark Steyn's that Turkish secularism is doomed because the rural religious have outbred the citified secularists seem plausible. The WVS can help us answer this sort of question.
For example, if the religious are outbreeding the non-religious and religion is substantially heritable so as to counteract any rate of defection than younger age cohorts should be noticeably more religious, right? Are they in Turkey? I use Turkey as an example to illustrate how useful the WVS can be.
So first go to http://www.worldvaluessurvey.org/
I've circled some areas red to click through.
Click the area where I've circled read. You need to jump through some hoops (it uses POST to go from page to page).
I've broken down the importance of religion as a function of age. There is no trend toward greater religiosity among the young.
I've now broken down by both and age & sex. As in most societies secularism is more pronounced with youth among males.
I went back and looked at another question in regards to the influence of religious leaders on voting. There is no trend of younger people being more supportive of this. There are plenty of other religion & government related questions you can ask. When Steyn made that assertion I made sure to remember to poke around Turkey's WVS results, and they don't seem to support it. The theory is coherent, but the facts do that match. I hope this is a lesson for readers. Theory provides free information. But since there are tools to check inferences one makes from assumptions one should do so before taking theory as a given (all the above took me 3 minutes, excluding screen capture & Photoshop).
Saturday, June 20, 2009
This series of posts attempts to identify the key propositions of 'Darwinism', and assess their current standing. Part 1 dealt with 'The Pattern of Evolution'. Part 2 considers the 'Mechanisms of Evolution'. Darwin always regarded natural selection as the most important mechanism, but not to the exclusion of all other factors. The post has turned out longer than I intended, but I have not split it up, as I think it is desirable to consider all of Darwin's 'mechanisms' together.
THE MECHANISMS OF EVOLUTION
The Origin of Species has no single neat section listing the 'mechanisms of evolution', so it is necessary to extract them from various chapters of the Origin, supplemented by reference to Darwin's other main evolutionary works, the Variation of Animals and Plants under Domestication (1868), the Descent of Man (1871), and The Expression of the Emotions in Man and Animals (1872). Unless otherwise stated, all page references are to Charles Darwin: The Origin of Species: a Variorum Text, edited by Morse Peckham, 1959, reprinted 2006.
In the following analysis I will classify Darwin's mechanisms of evolution into three groups: (A) those that depend on selection; (B) those that depend on the inheritance of acquired characteristics; and (C) other factors.
1. NATURAL SELECTION
I assume that anyone reading this will have a good general understanding of natural selection, but one point may be worth mentioning. Darwin considered that the 'struggle for existence', and therefore the outcome of natural selection, should be interpreted as including 'success in leaving progeny' (146). In various places he recognised that natural selection can operate through differential fertility and not just differential survival. Unfortunately he did not emphasise this strongly or often enough, and it was common for post-Darwinian writers to interpret natural selection as literally a matter of life or death, with the corollary that if a trait did not affect survival as such, it could not have evolved by natural selection. Darwin himself occasionally slipped into this over-simplification.
2. ARTIFICIAL SELECTION
Darwin believed that the characteristics of domesticated animals and plants, and their differences from their wild ancestors, were mainly due to artificial selection; that is, selective breeding by man. He distinguished two forms of artificial selection: 'methodical', where breeders deliberately attempted to change the traits of their stock, and 'unconscious', where there is no intention to alter the stock, but selective breeding is a by-product of other actions (109). For example, a gardener may weed out and discard poor quality plants, or a dairy farmer may slaughter cows that do not produce enough milk.
The influence of artificial selection on domesticated animals and plants now seems self-evident. There is a tendency to assume that the principle of artificial selection was already widely accepted before Darwin, who was therefore able to take it as an uncontroversial basis for comparison with natural selection. From my own reading of pre-Darwinian biology I doubt this. On a minor point, Darwin seems to be the first author to use the term 'artificial selection' itself (though he only uses it occasionally, preferring 'selection by man'). I have searched the pre-1859 texts on Google Books for the phrase 'artificial selection', and not found it used in the Darwinian sense. More important, the concept of artificial selection was not widely accepted in mainstream biology before Darwin. It can be found among some writers on animal husbandry, such as Sir John Sebright, and occasionally among other writers, such as the anthropologist James Cowles Prichard, but seldom among general biologists. [See Note 1] Most biologists assumed that domesticated varieties were 'unnatural' and not relevant to general biology, so they said little about them . When they did discuss domesticated varieties, they did not put much emphasis on selective breeding, but assumed that the varieties had been distorted from the 'natural' form by unspecified factors of environment and nurture. The general neglect of selective breeding by biologists helps explain why Darwin dealt with the subject at such length, first in the opening chapter of the Origin, and then in his longest single work, Variation of Animals and Plants under Domestication.
3. SEXUAL SELECTION
The concept of sexual selection is introduced by Darwin briefly in the Origin (173-5), and at much greater length in the Descent of Man. He distinguished two forms of sexual selection: one based on combat between males, and one based on female preferences (or more rarely, on male preferences.) Post-Darwinian biologists were generally willing to accept the principle of selection by combat, but unwilling to accept female preference. One weakness of Darwin's account is that he did not explain how females come to have such preferences. He does however say 'The females are most excited by, or prefer pairing with, the more ornamented males, or those which are the best songsters, or play the best antics; but it is obviously probable, as has been actually observed in some cases, that they would at the same time prefer the more vigorous and lively males'. (Descent of Man, 1871, vol.1, p.262) Here Darwin comes close to the modern idea that the secondary sexual characteristics of the male act as 'honest indicators' of general health. Modern biologists generally accept the importance of female choice, but there remain theoretical questions about the possible factors behind it, such as Fisher's 'runaway' process, Zahavi's 'Handicap' principle, and Hamilton's theory of the role of parasites.
Darwin describes sexual selection as an alternative to natural selection, rather than a variant form of it. The distinction is largely a matter of convenience. In population genetics it is usually convenient to lump both forms of selection together, but in general biology it is more useful to distinguish between them. Sexual selection has two important special features: it can explain otherwise puzzling differences between the sexes, and it can explain traits such as the peacock's tail which appear disadvantageous to general fitness.
4. ECONOMY OF GROWTH
Darwin devotes a section of the Origin (295-7) to the principle of 'Economy of growth', by which he means 'that natural selection is continually trying to economise in every part of the organisation'. This can help explain the reduction and eventual loss of body parts that are no longer used: 'if under changed conditions of life a structure before useful becomes less useful, any diminution, however slight, in its development, will be seized on by natural selection, for it will profit the individual not to have its nutriment wasted in building up an useless structure'. As is clear from these passages, economy of growth is seen by Darwin as a special case of natural selection rather than a distinct mechanism.
B. INHERITANCE OF ACQUIRED CHARACTERISTICS
Darwin died in 1882. Like most biologists before 1883, when August Weismann first questioned the inheritance of acquired characteristics (IAC), Darwin believed that characteristics acquired by an organism during its lifetime were sometimes inherited by its offspring. The principle of IAC is now often known as 'Lamarckism', because it plays a major part in the evolutionary theory of Lamarck, but it was not invented by Lamarck, and it was seldom questioned before Weismann. Darwin gave IAC a significant but subordinate part in his theory of evolution in a number of ways, as follows.
5. USE AND DISUSE
It is a matter of everyday observation that muscles tend to increase in size if they are heavily used, while those that are not used tend to atrophy. Use and disuse can even affect hard parts like bones, which adapt to imposed strains. Provided it is accepted that acquired characteristics can be inherited, it is logical to infer that the increased use or disuse of body parts can lead to evolutionary change. Darwin discusses this in various places in the Origin (especially 280-6), and he makes it the main explanatory mechanism for the reduction of disused organs such as the wings of flightless birds. He always however regards it as subordinate to natural selection, and concludes 'On the whole, I think we may conclude that habit, use and disuse, have, in some cases, played a considerable part in the modification of the constitution, and of the structure of various organs; but that the effects of use and disuse have often been largely combined with, and sometimes overmastered by, the natural selection of innate differences' (289).
6. INHERITED HABIT
Just as the use of organs leads to their growth, the habitual repetition of actions increases their ease of performance. If the principle of IAC is accepted, it is plausible that habits may also be inherited. Darwin makes this one of the sources of the actions described as 'instinctive': 'If we suppose any habitual action to become inherited - and I think it can be shown that this does sometimes happen - then the resemblance between what originally was a habit and an instinct becomes so close as not to be distinguished' (382). Darwin however also points out that some of the most remarkable instincts - those of social insects - cannot be explained in this way, because the worker insects do not breed.
7. DIRECT EFFECT OF THE ENVIRONMENT
Environmental circumstances sometimes produce an effect on the individual. For example, human skin darkens in response to sunlight, and animals' fur is said to grow thicker in cold weather. If the principle of IAC applies to such changes, they may be inherited. Darwin discusses the direct effect of the environment at Origin pp. 276-80 and Descent vol. 1, pp.113-6 , but regards it as a relatively minor factor.
Assessment of IAC: It is now generally accepted that, with a few special exceptions such as the protective spines of water-fleas, culture, and syphilis, characteristics acquired by individuals in their lifetime are not transmitted to their offspring. (This is not true of the reproduction of cells within an organism, where genetically identical cells are environmentally differentiated into different cell-types which then usually transmit their acquired state to their 'descendants'.) IAC in genetic reproduction at the level of individuals is not logically impossible, but an analysis by John Maynard Smith suggested that it would only be beneficial to fitness in some rather special circumstances. A general system of IAC is therefore unlikely to evolve. From time to time someone (like Edward Steele in the 1980s) claims that IAC is important after all, but such claims have not yet stood up. Unless there is a major new discovery, it therefore seems that Darwin was wrong in attributing a significant role to IAC in evolution. We may still ask:
- was it reasonable, given the available evidence at the time, for Darwin to believe in IAC? and
- did Darwin change his views on the importance of IAC?
Was it reasonable for Darwin to believe in IAC?
I have pointed out that few biologists before Weismann's challenge of 1883 questioned the existence of IAC. Among the many attacks on Darwin's theories in his lifetime, his acceptance of IAC was seldom criticised. If it is reasonable to accept prevailing beliefs of the time, then it was reasonable for Darwin to accept IAC. Compared to some other evolutionists, such as Herbert Spencer and Ernst Haeckel, Darwin gave IAC a relatively minor role in evolution. But this does not entirely let him off the hook. The evidence for IAC was largely anecdotal, and Darwin could have been more critical of it. In Darwin's own lifetime, in the 1870s, Francis Galton anticipated Weismann in questioning IAC, but Darwin paid little attention to Galton's arguments. In Darwin's favour, however, it may at least be said that he recognised the difficulty of finding a mechanism by which IAC could work, and he attempted to do so in his 'provisional hypothesis of pangenesis', which I will discuss in a later post.
Did Darwin change his views on the importance of IAC?
There is a traditional view, for example in Sir Gavin de Beer's old biography of Darwin, that Darwin greatly increased the emphasis on IAC as time went on. My own assessment is that the changes in his position on IAC were minor. Some of the evidence usually given for a major change is inconclusive or irrelevant. For example, it is pointed out that in his last major evolutionary work, The Expression of the Emotions (1872) Darwin puts more emphasis on 'inherited habit' than on natural selection in explaining the inheritance of expressive behaviour. But this does not prove any change in his position, because he had not written previously on the subject of expression. We cannot know how much emphasis he would have given to 'inherited habit' if he had written a book on expression in, say, 1860. In order to fairly assess his position, we need to compare like with like, which can best be done by comparing successive editions of the same work: the two editions of Variation (1868 and 1875); the two editions of Descent (1871 and 1874); and of course the six editions of the Origin (1859 to 1872). In making these comparisons I find only a few amendments that increase the importance given to IAC. For example, where in the first edition of the Origin he had said 'In both varieties and species, use and disuse seem to have produced some effect', in the 5th edition he changes 'some effect' to 'a considerable effect' (738), and where in the first edition he said 'Habit no doubt sometimes comes into play in modifying instincts', in the 6th edition he changes 'sometimes' to 'often' (740). These are significant changes, but not a radical demotion of natural selection. Possibly as a result of Herbert Spencer's writings, which placed a much stronger emphasis than Darwin himself on IAC, Darwin increasingly recognised that IAC (if it occurs) and natural selection tend to work in the same direction, so that it is difficult to decide on their relative importance. In the 6th edition he includes a passage: 'We should keep in mind, as I have before insisted, that the inherited effects of the increased use of parts, and perhaps of their disuse, will be strengthened by natural selection. For all spontaneous variations in the right direction will thus be preserved; as will those individuals who inherit in the highest degree the effects of the increased and beneficial use of any part. How much to attribute in each particular case to the effects of use, and how much to natural selection, it seems impossible to decide' (253). In the Descent he writes: 'We may feel assured that the inherited effects of the long-continued use or disuse of parts will have done much in the same direction with natural selection' (vol. 2, p.387; see also vol.1, pp.121 and 143). Given the fundamental assumption that IAC is possible, these comments are entirely reasonable, and indeed the puzzle is not why Darwin increased the importance he gave to IAC, but why in 1859 he gave it so little.
C. OTHER FACTORS
8. CORRELATION OF GROWTH
Darwin always attached much importance to 'correlation of growth', saying 'the whole organisation is so tied together during its growth and development, that when slight variations in any one part occur, and are accumulated through natural selection, other parts become modified. This is a most important subject, most imperfectly understood' (290, see also Descent vol.1, p.130-1). For example, changes in the front legs may affect the hind legs, and changes in hard parts may affect the adjoining soft parts. Other examples are more surprising, such as the fact that white cats are often deaf. Darwin does not seem to have changed his views on the subject much, but in later editions of the Origin he does point out that it is difficult to be sure whether correlated variation represents a true functional connection or merely an accidental result of inheritance from a common ancestor.The importance of 'correlation of growth' in Darwin's system is that it can help explain traits that do not appear adaptive in themselves, but are correlated in development with adaptive traits. Darwin refers to correlated variation in combination with natural selection (or artificial selection in the case of domesticated varieties), but presumably in principle they could be correlated with traits produced by sexual selection or IAC as well.
Assessment: The idea that genetic changes can have multiple effects is familiar under the name of 'pleiotropy', and is a standard part of modern evolutionary theory. A trait that is not adaptive in itself, but is an unavoidable by-product of an adaptive change, was termed a 'spandrel' in Lewontin and Gould's well-known critique of 'adaptationism'. There remains controversy over the importance of 'spandrels', but they are clearly not 'anti-Darwinian', if by 'Darwinian' we mean what Darwin himself believed.
9. FLUCTUATING VARIABILITY
In the first edition of the Origin Darwin says that 'Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic' (164). In the 5th edition Darwin extends the sentence to say '... left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions'. This is the closest that Darwin comes to the modern idea of 'genetic drift', but it is not quite the same. A closer analogy would be with the idea of 'mutation pressure', where mutations towards a certain state occur more often than those away from it, and ultimately lead to fixation. Darwin assumes that every change has some cause, and that the continued operation of the same causes could eventually change the traits of a species in the absence of selection. I do not think he ever quite saw the possibility that an adaptively neutral trait might be lost (or fixed) in a population purely by chance. The importance of this factor depends on the frequency of traits that are 'neither useful nor injurious'. In the 6th edition of the Origin Darwin discussed objections by Bronn, Broca, and Nageli to his reliance on natural selection, and conceded that they had some force. He concludes 'In the earlier editions of this work I underrated, as it now seems probable, the frequency and importance of variations due to spontaneous variability' (232). In the Descent he says similarly 'in the earlier editions of my 'Origin of Species' I probably attributed too much to the action of natural selection or the survival of the fittest. I have altered the fifth edition of the Origin so as to confine my remarks to adaptive changes of structure. I had not formerly sufficiently considered the existence of many structures which appear to be, as far as we can judge, neither beneficial nor injurious, and this I believe to be one of the greatest oversights yet detected in my work' (vol. 1, p.152). He goes on to discuss his two aims in the Origin, of showing that 'species had not been separately created', and that natural selection had been the 'chief agent of change... Nevertheless I was not able to annul the influence of my former belief, then widely prevalent, that each species had been purposely created; and this led to my tacitly assuming that every detail of structure, except rudiments, was of some special, though unrecognised, service. Any one with this assumption in his mind would naturally extend the action of natural selection, either during past or present times, too far'. But even this was not Darwin's last word. In the second edition of Descent (1874), he amended the statement 'I probably attributed too much to the action of natural selection' by substituting 'perhaps' for 'probably', and inserted a statement that 'I am convinced, from the light gained even during the last few years, that many structures which now appear to us useless, will hereafter be proved to be useful, and will therefore come within the range of natural selection'. [Note 2] These changes seem to show some shift of emphasis back to the importance of natural selection.
Overall assessment: there is no doubt that Darwin reduced his emphasis on natural selection in the years between 1859 and his death in 1882. He somewhat increased the emphasis on the inheritance of acquired characteristics, and considerably increased the emphasis on 'non-adaptive' characters resulting from 'fluctuating variability'. But none of the changes are dramatic, and they leave natural selection as the main factor in most cases. Darwin himself fairly indicated the significance of the changes in the final sentence of the Introduction of the Origin. In the first to fourth editions this reads 'I am convinced that Natural Selection has been the main but not exclusive means of modification'. In the fifth and sixth editions this is modified to 'I am convinced that Natural Selection has been the most important, but not the exclusive, means of modification' (73). The shift is therefore from 'main' to 'most important'. From a modern point of view it is usually regretted that he shifted his ground at all, and especially that he gave any role to IAC, which is now generally rejected. On the other hand, there remains considerable doubt about the extent to which all traits are adaptive, or correlated with adaptive traits. Modern biologists would attribute non-adaptive change mainly to genetic drift, which Darwin was unaware of.
There remains a question which I have not considered: are there any important factors in evolution (other than genetic drift) which Darwin was not aware of, or considered but rejected? In Darwin's own day the main objection to his theories was that his proposed mechanisms were inadequate, and that there must be additional factors such as inherent tendencies to perfection or complexity. Such objections were usually, overtly or covertly, motivated by a belief in what is now called Intelligent Design. I will not discuss such objections here. The whole of the Origin is 'one long argument' against them.
I intend the remaining posts to cover:
Levels of Selection
Note 1: To check my own impressions of the literature, I have consulted the book Artificial Selection and the Development of Evolutionary Theory, edited by Carl Jay Bajema. Bajema includes a dozen or so pre-Darwinian texts referring to artificial selection, but none of these are by mainstream biologists, and most do not go beyond the vague principle that varieties can be 'improved' by selective breeding. Interestingly, there is a discussion of the effects of domestication by Charles Lyell in his Principles of Geology, which (to me) is notable for not mentioning the effect of selection at all. The only pre-Darwinian authors in Bajema's collection who seem to have clearly recognised selective breeding as the main origin of domesticated varieties are James Cowles Prichard and the 18th century French philosopher Maupertuis.
Note 2: these passages are towards the end of the chapter on 'Manner of Development' which is chapter 2 in the 2nd edition (chapter 4 in the first edition). The extensive changes in the 2nd edition have not yet been much studied by Darwin scholars, and there is no variorum text, so it is difficult to detect changes without a line-by-line comparison, which I have not attempted.
Friday, June 19, 2009
Growth and Puberty in German Children: Is There Still a Positive Secular Trend?:
In Germany, as elsewhere in northern Europe, the upward secular trend in height is slowing (ca. 2 cm/decade up to the mid-20th century, currently less than 1 cm/decade), and the age at menarche has stabilized at just under 13 years. It remains an open question whether the observed slowing will merely be temporary, or whether it indeed represents the near-attainment of an endpoint owing to relatively stable environmental conditions.
Wednesday, June 17, 2009
You can browse free PDFs of the Statistical Abstract of the United States online going back over 100 years (under "Earlier Editions"). It is filled with data on population, commerce, education, and so on. Excellent for doing quantitative history -- and not just boring things like how population size has changed over time. During the heyday of eugenics, from 1925 to about 1943 / '44, there was an entire chapter entitled "Defectives, Delinquents, and Dependents"-- they didn't mince words back then! I haven't gone through and collected a bunch of data from it yet, but there's all sorts of fun shit like this in the Statistical Abstract. Did railroads become safer or more dangerous over time? If you've got a little free time, you can figure it out.
So far I'm the only blogger who's done a lot with it, probably because no one else wants to waste the time to sort through all the PDFs and numbers from scanned PDFs into Excel. The more recent editions at least have digital PDFs that allow you to copy & paste, and the most recent ones have Excel spreadsheets all ready to download. Play around with it -- there's a lot to discover.
A reader pointed me to the Population Reference Bureau which has total fertility rates for women broken down by economic fifths. Unfortunately these data are limited to developing countries, but reader might be interested in any case. In no case do the women of the richest fifth have a higher fertility than the women in the poorest fifth.
Related: Differences in fertility by class internationally.
A family member just sent me this New York Times article on the recent failure to replicate a serotonin gene associated with depression in a meta-analysis by Risch and Merikangas. It gives a pretty good overview, but I think the article might be misleading in two ways:
First, beginning with the title "Report on Gene for Depression Is Now Faulted" will confuse people into thinking that the genetics behind depression will be simple, when in fact the reigning theory is that large numbers of genetic (and environmental) variants influence such complex mental traits.
Second, the critics of depression genetics make misleading points:
By contrast, she said, a major stressful event, like divorce, in itself raised the risk of depression by 40 percent.Stressful life events are themselves quite heritable.
Readers might be interested in a new paper in PLoS ONE, General Intelligence in Another Primate: Individual Differences across Cognitive Task Performance in a New World Monkey (Saguinus oedipus):
Individual differences in cognitive abilities within at least one other primate species can be characterized by a general intelligence factor, supporting the hypothesis that important aspects of human cognitive function most likely evolved from ancient neural substrates.
Update: See below....
The World Values Survey has a lot of data broken down by subjective social class. One of these asks how many children an individual has. So I thought it might be of interested to inspect WVS 5, generally taken around 2005, and compare differences by class in term of children. Of course there might be differences in the age breakdowns of the different classes, so that controlling for age there might be greater differences than evident. But as a coarse I thought it would be of interest. Because the data is in proportions I added up the percentage with 3 or more children in class (above replacement). For a few selected nations I calculated the mean for each class (I used WVS 3 and 4 to supplement).*
I didn't go into this with any particular hypothesis or expectation, but I'm going to explore particular questions in future posts....
Readers with insights about a specific nation (because you actually know something, not rank speculation) are welcome to clarify. I was struck by the differences between Scandinavia and southern Europe. Interestingly, both Chile and Argentina exhibit the southern European pattern.
Update: Mean fertility by subjective class isn't too hard to calculate. But the formatting is kind of crappy, so I put the table here. All from WVS 5. Remember that the N's for "Upper Class" are almost always very small, so I'd ignore those. I'm pretty sure that the survey sample for many Third World countries are of higher SES than the population median, so don't get too trusting of the specific numbers, but rather how the rank orders relate to each other up and down the social ladder.
Note: CSV file.
* I should have calculated the mean for each nation, but it's rather tedious.
Labels: World Values Survey
Tuesday, June 16, 2009
In 2003, Avshalom Caspi and colleagues published an influential article (Google Scholar lists it as having almost 2000 citations in 6 years) claiming that genetic variation in the seratonin transposter gene influences how people respond to traumatic events--the particular, in terms of risk of depression. For years, this has been the poster-child example of gene-environment interactions (for whatever reason, finding significant interaction terms like this is the Holy Grail of human genetics for some). Like the more recent dubious breastfeeding-IQ-genetics story (led by the same group, it should be noted), the authors identified a phenotype they wished to study (depression), an environmental factor that plays a role in the phenotype (traumatic events), genotyped a couple markers in a gene they thought might reasonably be expected to play a role in that phenotype (seratonin), and found a "statistically significant" interaction. Voila.
The 2003 article, as I noted, received quite a bit of attention. This led to attempts to replicate it, and this week, a comprehensive meta-analysis was published of those studies. The result: nothing. There is no evidence for an interaction between genotype at the seratonin receptor and trauma on risk of depression. And in retrospect, why should there be? The probability of happening on the proper combination of genotype and environmental exposure when sampling one environmental exposure (out of an infinite number) and a few gene markers (out of millions) is miniscule--the statistical burden of proof should be much higher than a simple p-value cutoff of 0.05.
These sorts of candidate gene association studies were/are used in all fields, but in my mind are lent the most credence in psychiatric genetics (the place where they should probably be given the least credence, IMO). This is just an additional cautionary tale: the vast majority of associations found through small candidate gene studies, even ones with functional work, plausibility, and the status of publication in a high-profile journal--MAOA and social problems, FADS and IQ (actually, any study published to date on IQ), NPY and stress--are likely wrong.
Saturday, June 13, 2009
PLoS Genetics has a nice paper identifying copy-number polymorphism in the transcription factor SOX5 as the causal mutation leading to the pea-comb phenotype (the bottom panels on the right) in chickens. The mutation leads to more widespread expression of the gene at a particular developmental time point, which presumably represses comb formation.
Thursday, June 11, 2009
The World Values Survey Wave 5 has several questions about how much people trust others. In particular, one question asks about religion and another nationality. There are four responses:
-Trust a little
-Not trust very much
-Not trust at all
In the WVS there are proportions for each class for many nations. I took each proportion, and multiplied them by a number where:
-Trust completely = 3
-Trust a little = 2
-Not trust very much = 1
-Not trust at all = 0
So that if 100% did not trust at all the number would add to 0, and if 100% trusted complete it would add to 4. Naturally most nations fell in between with a range. I assumed that there would be a strong correlation between the two values. It was very strong, as evidenced by the charts below.
OK, so how does religious trust related to how important people think is in their own lives? Again, there are four categories, from very important to not important at all. Again weighting the proportions so that 4 = very important and 0 = not important at all. So how about religious trust vs. religion important?
No need to label, there's just no relationship. Weird. I also drilled down for selected nations to see if there was a relationship within the nations in regards to trust (both kinds here) and how important religion was. Not really. In fact, in many nations the least religious trusted those of other religions the least, so it might be expressing a general anti-religious sentiment. As an anecdote I friend whose husband was French one commented how secular French have a distrust of religion in general, and view non-traditional religions with particular distaste, viewing them as cults (non-traditional as in evangelical Protestantism, Hare Krishna, etc.).
The raw data....
Labels: World Values Survey
Wednesday, June 10, 2009
Slate has a good explanation for why stores might be cutting back on plus sizes despite the fact that Americans are getting fatter. In part it has to the do with the fact that the distribution of weights is skewed to the right. The costs of production result in a focus toward the modal body size, not the mean or median. The lower limit is bounded in a way the upper is not....
When Young Men Are Scarce, They're More Likely To Play The Field Than To Propose:
In places where young women outnumber young men, research shows the hemlines rise but the marriage rates don't because the young men feel less pressure to settle down as more women compete for their affections.
The original paper is here.
Labels: Evolutionary Psychology
Tuesday, June 09, 2009
A study from Wicherts et al published online in the journal Intelligence today:
On the basis of several reviews of the literature, Lynn... concluded that the average IQ of the Black population of sub-Saharan Africa lies below 70. In this paper, the authors systematically review published empirical data on the performance of Africans on the following IQ tests: Draw-A-Man (DAM) test, Kaufman-Assessment Battery for Children (K-ABC), the Wechsler scales (WAIS & WISC), and several other IQ tests (but not the Raven's tests)... Results show that average IQ of Africans on these tests is approximately 82 when compared to UK norms.
UPDATE: Tables and Figures below the fold
Table 4. Results by subsets of samples.
Table 5. Estimates of mean IQs per country on the basis of studies in Table 2 and studies from the Raven's study.
Fig. 1. Scatterplot of data from study by Lynn (2006) and Lynn and Vanhanen (2006).
Fig. 2. Scatterplot of data from study by Rindermann (2007).
Fig. 3. Scatterplot of data from study by Lynn and Mikk (2007).
Fig. 4. Scatterplot of data from study by Lynn et al. (2007).
Fig. 5. Mean of samples that meet our inclusion criteria against the inverse of the standard error.
Fig. 6. Mean of samples from studies published prior to 2006 against the inverse of the standard error.
Monday, June 08, 2009
Cool new paper about ancient DNA, Mobile DNA Elements In Woolly Mammoth Genome Give New Clues To Mammalian Evolution:
The woolly mammoth died out several thousand years ago, but the genetic material they left behind is yielding new clues about the evolution of mammals. In a study published online in Genome Research, scientists have analyzed the mammoth genome looking for mobile DNA elements, revealing new insights into how some of these elements arose in mammals and shaped the genome of an animal headed for extinction.
The paper isn't online yet, but it will be here. Kind of mind-blowing that we might know so much about the genomics of an extinct organism. We've come a long way since E. B. Ford.
Genetic Architecture of Tameness in a Rat Model of Animal Domestication:
A common feature of domestic animals is tameness-i.e., they tolerate and are unafraid of human presence and handling. To gain insight into the genetic basis of tameness and aggression, we studied an intercross between two lines of rats (Rattus norvegicus) selected over >60 generations for increased tameness and increased aggression against humans, respectively. We measured 45 traits, including tameness and aggression, anxiety-related traits, organ weights, and levels of serum components in >700 rats from an intercross population. Using 201 genetic markers, we identified two significant quantitative trait loci (QTL) for tameness. These loci overlap with QTL for adrenal gland weight and for anxiety-related traits and are part of a five-locus epistatic network influencing tameness. An additional QTL influences the occurrence of white coat spots, but shows no significant effect on tameness. The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general.
Also see ScienceDaily.
Sunday, June 07, 2009
TGGP has a post up where he looks at attitudes toward polygyny in predominantly Muslim nations. The question is:
To what extent do you agree or disagree with men having more than one wife? Do you strongly agree, agree, disagree, or strongly disagree?
I decided to break-down by religion in those nations which had a large non-Muslim population. Results below.
Update: Above I only posted those Muslim nations with large enough religious minorities for there to be comparisons. Here are the frequencies who "strongly agree" + "agree" with men having more than one wife for all the nations:
Algeria - 43
Bangladesh - 5.5
Indonesia - 18.7
Iran - 11.5
Iraq - 47.1
Jordan - 18.7
Morocco - 37.5
Nigeria - 39.4
Pakistan - 1.1
Saudi Arabia - 42.1
Turkey - 15.6
Egypt - 10.3
Saturday, June 06, 2009
In this Darwin year many popular accounts of 'Darwinism' have appeared, but these seldom make a clear distinction among the different components of Darwin's theory of evolution. Many popularisations are simplified to the point of caricature, and presented in an absurdly uncritical way. I yield to few in my admiration for Darwin, but I do not think his memory is best served by oversimplifying his ideas or pretending that he was always right.
So I will attempt to identify the key propositions of 'Darwinism', with an assessment of their current standing. This will probably run to five or six posts, with propositions grouped under the headings:
The Pattern of Evolution
The Mechanisms of Evolution
Levels of Selection
THE PATTERN OF EVOLUTION
[Note: unless otherwise stated, all page references are to Charles Darwin: The Origin of Species: a Variorum Text, edited by Morse Peckham, 1959, reprinted 2006.]
1. DESCENT WITH MODIFICATION
The single most important proposition of Darwinism is that present-day organisms have descended, by natural processes of reproduction, from organisms that were substantially different. In Darwin's own preferred terminology, they are the product of 'descent with modification'.
Assessment: This is now accepted by all scientists. It is a proposition common to all theories of evolution. Of course Charles Darwin was not the first person to advocate it, and in the first edition of the Origin he took it for granted that any educated reader would be aware of this. For example, he refers to the evolutionist best-seller Vestiges of the Natural History of Creation (1844) on the assumption that it would be familiar to his readers. Darwin was however the first to secure the general acceptance of evolution by the scientific community. This occurred remarkably quickly in the 1860s. Even scientists like Richard Owen, who disagreed strongly with Darwin on other points, quickly accepted the fact of 'descent with modification'. Only a few holdouts like Louis Agassiz continued to defend 'special creation'. Quite why the basic fact of evolution was so quickly accepted is rather a puzzle in itself, on which I will make a few suggestions in due course.
2. EVOLUTION IS INTERMITTANT
In Darwin's theory there is no inevitability about evolution: organisms only change if there is a selective advantage in doing so. In stable habitats some species may stay virtually unchanged almost indefinitely, like the brachiopod Lingula. (522) Lack of evolutionary change is especially common among very simple organisms. Even complex organisms may go for long periods without change if they are well-adapted to an ecological niche (222-6: mostly added in the 3rd edition.) Few organisms are changing much at any given point in time, and for any species the periods of change may be short in comparison with the periods of non-change. The clearest statement of this point is made in the 4th and later editions: 'the periods during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they have retained the same form' (727), but there are comparable statements in the first edition, e.g. 'we have reason to believe that only a few species are undergoing change at any one period' (724, see also 202).
Assessment: The existence of evolutionary 'stasis' is now generally accepted, though there would be argument about its prevalence and the reasons for it; for example, S J. Gould's vague notions about 'developmental constraints'. In Darwin's time it was an important innovation in evolutionary theory, as previous evolutionists such as Lamarck and Robert Chambers (author of the Vestiges ) had assumed either that evolutionary change was continuous, or that organisms inevitably changed from time to time according to an inbuilt 'program'. Similar ideas were still prevalent in post-Darwinian biology, with many believing in inbuilt tendencies to progress or increased complexity.
3. THE EVOLUTIONARY TREE
According to Darwin, the general pattern of evolution resembles a branching tree, in which successful species give rise to more than one new species, diversifying to exploit different ecological opportunities. Once species have diverged, they do not merge again, which would produce the pattern of a network rather a tree. Tracing the branching pattern backwards from existing species, we usually find that they are more or less similar to each other depending on how far back we find their last common ancestor. This results in a hierarchical classification, traditionally represented by phyla, classes, orders, etc, in which the offshoots of each 'branch' are grouped together. (210-20, 648-60) The simplicity with which the 'branching tree' concept explained the traditional patterns of classification and comparative anatomy helps to explain the rapid acceptance of the general doctrine of evolution after 1859. Darwin adopted the 'tree' concept in his unpublished writings from the 1830s onwards. In 1855 Alfred Russel Wallace published a similar concept of a branching classification, but without an overtly evolutionary explanation. (At this point Wallace was already a covert evolutionist, but had not yet thought of the principle of natural selection.) Pre-Darwinian evolutionists had not generally seen evolution as 'tree-like'. Lamarck, for example, believed that new organisms of the simplest kind were continuously arising by spontaneous generation, and then evolved along a few main pathways from simple to complex (though Lamarck does allow for a limited amount of 'branching'). In the Lamarckian conception, similar species are not necessarily related to each other by common ancestry at all; for example, organisms of the type we call 'vertebrates' do not necessarily have common ancestors, because they may have separately evolved from different ancestors to the vertebrate stage of complexity. In Darwin's theory this is not possible. From the 3rd edition onwards Darwin did recognise the possibility of 'convergence of character', when species of different ancestry live under similar conditions (267-70), but thought it very unlikely ('incredible') that species from widely different ancestry could ever converge so far as to be indistinguishable in all respects.
Assessment: The branching concept of classification is generally accepted. It is most rigorously expressed in cladistic taxonomy. The main qualification to be made to the 'tree' concept in the light of modern knowledge is that 'branches' do sometimes join together. This can happen by symbiosis, as is thought to have happened in the origins of the eukaryotic cell; by hybridism between species (especially among plants); and by 'lateral genetic transfer' of genes by means of viruses, etc. These processes mean that there is an element of 'network' as well as 'branching' in evolution. This was the basis for a New Scientist cover story a few months ago with the sensationalist headline 'Darwin was wrong'. Most biologists regard it as a minor complication rather than a major upset to the conventional Darwinian account.
According to Darwin, the great majority of past species have become extinct without descendants: 'the manner in which all organic beings are grouped, shows that the greater number of species of each genus, and all the species of many genera, have left no descendants, but have become utterly extinct' (758).
Assessment: This is now taken for granted, to the extent that its importance is often overlooked. By the time of the Origin of Species, most biologists accepted that widespread extinction had taken place throughout geological history, but this had not been adequately incorporated into evolutionary theories. Previous evolutionists such as Lamarck, Etienne Geoffroy Saint-Hilaire, and Robert Chambers were very reluctant to accept extinction, and preferred to believe that species usually evolved into something else. Extinction is a natural corollary of an evolutionary theory based on natural selection and competition, whereas more optimistic theories, based on inherent tendencies to progress, etc, have difficulty explaining or accepting it.
5. ONE OR A FEW ORIGINAL FORMS
A branching pattern of evolution implies that existing species descend from a smaller number of ancestors, but it does not strictly imply that the number was originally very small. Based on comparative anatomy and other evidence, Darwin concludes that 'the theory of descent with modification embraces all the members of the same class' (by which he means a major group such as vertebrates or arthropods) (752). He continues, 'I believe that animals have descended from at most only four or five progenitors, and plants from an equal or lesser number. Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype.' After discussing his reasons for this, such as the chemical similarities between plants and animals, he concludes: 'Therefore I should infer from analogy that probably all the organic beings which have ever lived on the earth have descended from some one primordial form, into which life was first breathed' (753). G. H. Lewes later pointed out that this was too strong a conclusion, and in the 5th edition Darwin qualified it to say 'No doubt it is possible, as Mr G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants' (753).
Assessment: Darwin's conclusions have been vindicated by modern findings, and especially the fact that all organisms have essentially the same genetic code. There is however still a great deal of uncertainty about the origins and relationships of the metazoan phyla (Darwin's 'great classes'.) If anything, the problem has become more difficult since Darwin's time, when it was generally believed (e.g. by Haeckel) that there were only six or seven distinct phyla. Now over thirty phyla are generally recognised, and the relationships between them (e.g. between vertebrates and echinoderms), are far from clear.
6. THE ORIGIN OF LIFE
The Origin of Species provides no explanation of the origin of life itself. Natural selection presupposes the existence of reproducing organisms, and therefore cannot explain their first emergence. In the first edition of the Origin Darwin referred to a 'primordial form, into which life was first breathed'. In the second and later editions he added the words 'by the Creator'. He later regretted 'truckling to public opinion' in using such terminology, and said in a letter of 1863 'I really meant "appeared" by some wholly unknown process. It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter' (Life and Letters of Charles Darwin, ed. Francis Darwin, vol.3, p.18) He later privately speculated about the circumstances in which life might have emerged (in his famous 'warm little pond' letter of 1871), but I don't think he ever published any comments on the subject. In the 3rd edition of the Origin he did say 'Science in her present state does not countenance the belief that living creatures are now ever produced from inorganic matter' (223). In fact, this was more controversial than he recognised. In 1859 the French scientist Francois Pouchet claimed to have produced spontaneous generation under controlled conditions, and Charles Bastian later made similar claims in England. These claims were welcomed by some evolutionists, including A. R. Wallace and Ernst Haeckel, but Darwin was deeply sceptical - rightly, as it turned out, when the experiments of Pouchet and Bastian were convincingly discredited by Pasteur and John Tyndall.
Assessment: We still don't understand the origin of life. Vastly more is known about the chemical building blocks of life than in Darwin's time, so the subject is now open to serious scientific research, but we are probably still a long way from a solution. But such predictions are hazardous, and for all I know someone may already be cooking up the answer. Recent results on 'RNA world' are promising.
To summarise on the Pattern of evolution, and disregarding all questions of the mechanisms or causes of evolution, Darwin was largely successful in his conclusions. This was partly because he had sound judgement, but also to a large extent because he was able to draw on fifty years or so of progress in comparative anatomy, embryology, and taxonomy by such masters as Cuvier, Von Baer, Agassiz, Owen, and Milne-Edwards. This gave him a huge advantage over earlier evolutionists like Lamarck and his own grandfather Erasmus Darwin.
My next post, when I get round to it, will deal with the Darwinian mechanisms of evolution - natural selection, and about half a dozen others.
Friday, June 05, 2009
Iceland has long been of some interest because of its peculiar demographic history and their genetic consequences. So a new paper in PLoS Genetics is of interest, The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland:
The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.
Figure 3 is a PCA map which shows how individuals from different regions of Iceland sort out. The Scottish and Norwegian populations are there two, and they don't vary much along the components of variation which Icelanders sort out along, the conclusion being that the Iceland variation isn't due to different ancestral proportions. They further calculate that if the ancestral Iceland populations were like the modern Scottish and Norwegian ones, Icelanders are ~35% Scottish and ~65% Norwegian. Most of the differences between Icelanders and continental Europeans is no doubt due to drift because of their very small population size, no migration due to their isolation and the a few specific bottleneck events. But a section on natural selection in Icelanders is interesting:
We found eight SNPs, representing two chromosomal regions, for which the evidence of unusual population differentiation was genomewide-significant...Six of the SNPs lie in or near the TLR (toll-like receptor) genes TLR10 and TLR1, while the other two lie inside the NADSYN1 (NAD synthesase 1) gene....
Toll-like receptors were pinpointed in a recent paper as likely possibilities for localized adaptation.
Thursday, June 04, 2009
Dan MacArthur reviews 50 Genetics Ideas You Really Need to Know. Gives it "3.5 nucleotides out of 4."
Wednesday, June 03, 2009
A few years ago the Inductivist found that Protestant & Orthodox countries favored abortion to a greater degree than Roman Catholic ones. He did add though that many of the nations in the former category were nominally in the category (e.g., Sweden) I have always been curious about if Catholicism has any effect on attitudes toward abortion within nations. It is known in the USA that there isn't much of a difference between Catholics and non-Catholics on this topic, rather, it is conservative Protestants stand out. The World Values Survey has a question which asks if abortion is ever justifiable. I thought it would be interesting to break these data down between Catholics and non-Catholics in various countries.
I look at nations which had large Catholic and non-Catholic populations. Not just non-religious (like France), but with religious identified non-Catholics. For example, the Netherlands has large historical Catholic and Protestant populations. I used WVS waves 3 & 4 and aggregated them together. I looked at WVS 5 separately. So some nations are entered twice. Where there were no Protestants, such as in Bosnia, I used Orthodox Christians. In a few Latin American nations Protestants were distinct from Evangelicals. The former usually includes members of historic immigrant communities with culturally Protestant traditions. Their numbers were small in any case, so I simply substituted Evangelical, which usually refers to relatively recent converts to Pentecostalism.
As you can see, most of the variation is between nations, not within them. In many cases Protestants are more pro-life than Catholics. In nations such as Chile most Protestants are relatively conservative evangelicals, disproportionately from the lower socioeconomic strata. In the Netherlands I suspect it has to do with the conservative Protestant Bible Belt, while most liberal Dutch Reformed have simply become "Nones."
Tuesday, June 02, 2009
Asymmetric fMRI adaptation reveals no evidence for mirror neurons in humans:
Neurons in macaque ventral premotor cortex and inferior parietal lobe discharge during both the observation and the execution of motor acts. It has been claimed that these so-called mirror neurons form the basis of action understanding by matching the visual input with the corresponding motor program (direct matching). Functional magnetic resonance imaging (fMRI) adaptation can be used to test the direct matching account of action recognition by determining whether putative mirror neurons show adaptation for repeated motor acts independently of whether they are observed or executed. An unambiguous test of the hypothesis requires that the motor acts be meaningless to ensure that any adaptation effect is directly because of movement recognition/motor execution and not contextually determined inferences. We found adaptation for motor acts that were repeatedly observed or repeatedly executed. We also found adaptation for motor acts that were first observed and then executed, as would be expected if a previously seen act primed the subsequent execution of that act. Crucially, we found no signs of adaptation for motor acts that were first executed and then observed. Failure to find cross-modal adaptation for executed and observed motor acts is not compatible with the core assumption of mirror neuron theory, which holds that action recognition and understanding are based on motor simulation.
Many great claims have been made for mirror neurons. V.S. Ramachandran said on Edge MIRROR NEURONS and imitation learning as the driving force behind "the great leap forward" in human evolution.
Click the tab below the body of this post to read previous entries in the series about how previous generations were more depraved. One way to look at how civilized we are is to see how we behave in situations where our conduct can mean the difference between life and death for those around us -- for example, when we drive our car. Traffic deaths, of course, reflect properties of the car as much as the people involved, but teasing the two apart turns out to be pretty simple in this case.
In my brief review of Daniel Gardner's book The Science of Fear, I gave a few examples of how media coverage of some threat was outta-whack with the underlying risk, namely homicide and rape. Gardner spends a few pages talking about the epidemic of "road rage" that was allegedly sweeping across the country not too long ago, so why don't we have a look at what the data really say about when road rage may have been greater than usual.
First, here's a quick view of media coverage of "road rage," which begins in 1996:
What about actual traffic deaths, though? The data come from the National Safety Council, as recorded across several versions of the Statistical Abstract of the United States -- which, btw, is much cooler than the General Social Survey or the World Values Survey if you want to waste some time crunching numbers. I tracked the data back as far as they exist in the Stat Ab, and they include four ways of measuring traffic death rates. Here are the graphs:
The first is the most instructive -- it measures the number of deaths compared to the number of vehicles on the road and how long they're on the road. The other three measure deaths compared to some population size -- of vehicles, of drivers, or of the whole country -- but even if population size is constant, we expect more deaths if people drive a lot more. The distinction isn't so crucial here since the graphs look the same, but I'll refer to the first one because what it measures is more informative.
From 1950 to 2008, there's a simple exponential decline in traffic deaths (r^2 = 0.97). As roads are made safer, as all sorts of car parts are made to boost safety, and as people become more familiar with traffic, we expect deaths to decline, and that's just what we see. I looked at earlier versions of the Stat Ab, and there is a similar exponential decline in railroad-related deaths from 1920 to 1959 -- again, probably due to improving the technology of railroads, trains, and so on.
However, aside from the steady decline that we expect from safer machinery, there is a clear bulge away from the trend during the years 1961 - 1973. Although I haven't researched it, it seems impossible for roads to have went to shit during that time but not during the other times, or that cars made then were even less safe than the ones made before or after. The obvious answer is that people were just more reckless and/or hostile toward their fellow man in that period.
There's no other huge departure from the trend, so if any time period has been characterized by "road rage," it was The Sixties (which lasted until 1973 or '74). Consider the age group whose brains are most hijacked by hormones, and maybe by drugs and alcohol too -- say, 15 to 21 year-olds. The oldest members of this group who were driving during the road rage peak were born in 1940, while the youngest ones were born in 1958. Hmmm, born from 1940 to 1958 -- Baby Boomers. (Those born after 1957 - 8, and before 1964, are not cultural Boomers.) And this doesn't seem to be an effect of lots more teenagers on the road than at other times -- there have been echo booms afterward and yet no big swings away from the trend.
When the media and everyone hooked in to the media began talking about road rage 10 to 15 years ago, there was nothing new in the traffic death story -- indeed, the rate was continuing its decades-long decline. If you just want to know what is going on right now, the media may not be so bad at giving you that info. But this serves as yet another lesson to not believe anything they say, or imply, about trends unless there is a clear graph backing them up (or, in a pinch, a handful of data-points sprinkled throughout the prose).
I located, collected, analyzed, and wrote up all of the relevant data -- stretching back nearly 60 years -- in less than one day, and only using the internet and Excel. This shows us again that journalists are either too clueless, too lazy, or too stupid to figure anything out.
In light of p-ter's post on KITLG and cancer risk, I stumbled onto this today, Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type?:
One single-nucleotide polymorphism (SNP), 538G>A (Gly180Arg), in the ABCC11 gene determines the type of earwax. The G/G and G/A genotypes correspond to the wet type of earwax, whereas A/A corresponds to the dry type. Wide ethnic differences exist in the frequencies of those alleles, reflecting global migratory waves of the ancestors of humankind. We herein provide the evidence that this genetic polymorphism has an effect on the N-linked glycosylation of ABCC11, intracellular sorting, and proteasomal degradation of the variant protein. Immunohistochemical studies with cerumen gland-containing tissue specimens revealed that the ABCC11 WT protein was localized in intracellular granules and large vacuoles, as well as at the luminal membrane of secretory cells in the cerumen gland, whereas granular or vacuolar localization was not detected for the SNP (Arg180) variant. This SNP variant lacking N-linked glycosylation is recognized as a misfolded protein in the endoplasmic reticulum and readily undergoes ubiquitination and proteasomal degradation, which determines the dry type of earwax as a mendelian trait with a recessive phenotype. For rapid genetic diagnosis of axillary osmidrosis and potential risk of breast cancer, we developed specific primers for the SmartAmp method that enabled us to clinically genotype the ABCC11 gene within 30 min
I blogged a paper on this SNP relating it to earwax form a few years ago. Also see ScienceDaily. The variation in earwax seems to conform pretty closely to that of EDAR.
Monday, June 01, 2009
The World Values Survey has a question of the form:
Some people believe that individuals can decide their own destiny, while others think that it is impossible to escape a predetermined fate. Please tell me which comes closest to your view on this scale on which 1 means "everything in life is determined by fate," and 10 means that "people shape their fate themselves."
Below the fold are the percentages in selected nations which picked "10," which is basically the least fatalistic position.
Labels: World Values Survey
Microsoft's new search engine, Bing, is live. And yeah, I think it's kind of a Google clone. Where's the differentiation? Then again, Microsoft did have a history of coming out with crappy clones and slowly perfecting and overtaking. WordPerfect, Lotus and Netscape. But the is not always prediction, and Microsoft had some advantages against those companies which it does not in the "Web 2.0" domain.