Gene Expression

Hold everything equal and offer no insight

2009-07-03T16:40:00.000-07:00

I was listening to Marketplace the other day and Kevin Hassett delivered a commentary combining economics with a revisionist evaluation of the American Revolution. Hassett's argument seems to be that the Revolution, which was notionally predicated on taxation without representation, will in the long run be a historical blip of no consequence as the United States converges upon the same tax and spend structure as the United Kingdom. From this convergence of tax and expenditure structures Hassett infers an eventual closing of the $10,000 GDP per capita gap between the United States and the United Kingdom. What therefore was the point of breaking away if 200 years later the USA is going to be so similar to the United Kingdom?

There are many ways to critique this sort of analysis, but there are two major issues that I jumped out for me. First, 200 years is not a trivial interval of time, especially when taking into account the large numbers of Americans who lived between then and now. To view economic history as convergence toward equilibria as a few parameters are modulated at some point in the future seems worthless, just as pointing out that the Sun will go nova, or that the universe may be doomed to heat death. There is a big difference between asserting that the GDP per capita gap will close within 10 years, and within 100 years. Tractable and elegant macroeconomic models may be mostly junk over the short term, but I'm pretty sure that they're total junk over the long term. Inferences from stylized facts may provoke, but spare me the assumption that that the error bars of projections aren't so huge as to make them useless even for government work. Second, it isn't as if the only things that separate the United States and the United Kingdom are institutional frameworks. Even within the United States there is quite a bit of regional variation in culture. Perhaps Hassett would say that specific variation in the instantiation of human capital is totally irrelevant, but most people wouldn't assume that as a given. Secondarily there is a sense here that historical contingency doesn't exist, that there is no path dependence in economic development. So the 200 year interval whereby the American Revolution served as an exogenous shock which tore the thirteen colonies out of the British Empire had no significant effect by shifting initial parameters in a manner which might "lock in" a bias toward some developmental paths as opposed to others. But evaluated over a long enough interval all historical events can be marginalized as futile acts against the trendline, whatever it is.

Instead of using an abstract framework riddled with assumptions that many people would find laughable, why not go the route of pointing to the nature of the British settler colonies which did not revolt, but eventually became independent? Obviously Australia, Canada and New Zealand are different in myriad ways from the United States, but are the comparisons more strained than the model that Hassett posits?

Gladwell at it again

2009-07-02T13:22:00.000-07:00

In the new issue of The New Yorker, Malcolm Gladwell reviews some book about using the appeal of FREE to grow your business. This is supposed to apply most strongly to information, so that as more and more of a firm's product / service consists of information, the more it can use the appeal of FREE to earn money.

What both Gladwell and the reviewed book's author, Chris Anderson, don't seem to realize is that the appeal of FREE creates pathological behavior.

Gladwell even cites a revealing behavioral economics experiment by Dan Ariely:

Ariely offered a group of subjects a choice between two kinds of chocolate -- Hershey's Kisses, for one cent, and Lindt truffles, for fifteen cents. Three-quarters of the subjects chose the truffles. Then he redid the experiment, reducing the price of both chocolates by one cent. The Kisses were now free. What happened? The order of preference was reversed. Sixty-nine per cent of the subjects chose the Kisses. The price difference between the two chocolates was exactly the same, but that magic word "free" has the power to create a consumer stampede.

In other words, FREE caused people to choose an inferior product more than they would have if the prices were both positive. Thus, in a world where there is more FREE stuff, the quality of stuff will decline. It's hard to believe that this needs to be pointed out. And again, this is not the same as prices declining because technology has become more efficient -- prices are still above 0 in that case. FREE lives in a world of its own.

If you're only trying to get people to buy your target product by packaging it with a FREE trinket, then that's fine. You're still selling something, but just drawing the customer in with FREE stuff. This jibes with another behavioral economics finding -- that when two items A and B are similar to each other but very different from item C, all lying on the same utility curve, people ignore C because it's hard to compare it to the altneratives. They end up hyper-comparing A and B since their features are so similar, and whichever one is marginally better wins.

So if you have three more or less equally useful products, A B and C, where B is essentially what A is, just with something FREE thrown in, people find it a no-brainer to choose B.

An exception to the rule of "FREE leads to lower quality" might be the products that result from dick-swinging competitions, where the producer will churn out lots of FREE stuff just to show how great they are at what they do. They're concerned more with reputation than getting by. Academic work could be an example -- lots of nerds post and critique scientific work at arXiv, PLoS, as well as the more quantitatively oriented blogs.

But in general, you can imagine the quality level you'd enjoy from a free car or an all-volunteer police force. Even sticking with just information, per Chris Anderson, look at what movies you can download without cost on a peer-to-peer site or whatever -- they mostly all suck, being limited to the library of DVDs that geeks own. Sign up for NetFlix or a similar service, and you have access to a superior library of movies, and it hardly costs you anything -- it's just not FREE. Ditto for music files you can download cost-free from a P2P site vs. iTunes, or even buying the actual CD used from Amazon or eBay.

Admittedly I don't know much about computer security, but just by extending the analogy of a voluntary police force, I'd wager that security software that costs anything is better than FREE or open source security software.

To summarize, though, Gladwell's discussion about FREE misses the most important part -- it tends to lower quality. I don't want to live in a word of lower quality of items that aren't of major consequence, and (hopefully) the people in charge of high-consequence items like the police and my workplace's computer security will never be persuaded to go for FREE crap in the first place. This aspect alone answers the question he poses in the sub-headline, "Is free the future?" However, wrapping your brain around the idea that FREE tends to lower quality is discordant with a Progressive worldview, which explains why Gladwell just doesn't get it.

The war against basa

2009-07-02T08:57:00.001-07:00

Catfish plan risks trade war:

It looks like catfish, it tastes like catfish, and it acts like catfish.
But to U.S. catfish farmers, the whiskered, bottom-feeding fish from Vietnam is something else: a cheap variety that's usurping the humble catfish's place on Americans' tables and threatening their livelihoods.

So after years of arguing that the Vietnamese fish isn't catfish - and winning a federal law saying as much - the U.S. farmers are now trying to have it both ways. Under their latest lobbying strategy, they want the Vietnamese imports considered catfish so that they will be covered by a new inspections regime that they pushed through Congress last year.

The move - an example of how influential industries work their will in Congress - could block Vietnamese imports for years and risks a broader trade war.

It doesn't taste like catfish.

It's hard out there being a non-Indo-European speaker in Europe

2009-07-01T14:33:00.000-07:00

Matt Yglesias points out that in terms of suicide rates Finland is a Scandinavian outlier, and clusters with Japan and Korea. But interestingly, there's another European nation which is even more suicidal than Finland. Hungary. Below the fold are the data for the OECD nations....

Shameless Plug

2009-07-01T08:44:00.000-07:00

I'm still working on a post about Darwin's theories of heredity, but I need to re-read the 900 pages of Variation of Animals and Plants Under Domestication first, so it may take me some time.

Meanwhile, and irrelevant to anything, I see that one of my favourite artists, Imogen Heap, has a new album coming out soon(ish). Here is a video trailer. Also check out Imogen's delightful video blogs, all available on YouTube.

Genetics of Cape Coloureds

2009-06-30T08:36:00.000-07:00

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.

My new blog about health, nutrition, and diet

2009-06-30T00:02:00.000-07:00

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.

From genome-wide association studies to molecular biology

2009-06-28T17:10:00.000-07:00

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.

Science of Bubbles

2009-06-28T12:20:00.000-07:00

Long article in Scientific American, The Science of Economic Bubbles and Busts. H/T Calculated Risk.

Basa beats catfish

2009-06-25T21:28:00.000-07:00

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.

Lamarckism: Lessons from History

2009-06-25T03:20:00.000-07:00

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'.

CHARLES-EDOUARD BROWN-SEQUARD

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.

PAUL KAMMERER

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.

JOHN HESLOP-HARRISON

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. ]

WILLIAM McDOUGALL

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.

TROFIM LYSENKO

No need to comment.

EDWARD STEELE

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.

Monopoly allows innovation to flourish

2009-06-25T00:28:00.000-07:00

Updated

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.

Duffy and malaria in baboons?

2009-06-24T19:33:00.000-07:00

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.

Fat and tuberculosis

2009-06-23T18:21:00.000-07:00

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.

But these days, obesity is thought to be harmful, leading to chronic inflammation and metabolic disorders that set the stage for heart disease. So what went awry? When did excess fat stop being a protective mechanism that assured survival and instead become a liability?

A provocative new hypothesis suggests that in some people, fat not only stores energy but also revs up the body's immune system. This subgroup may have enjoyed a survival advantage in the 1800s, when people were plagued by a disease that decimated Europe: tuberculosis.

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.

Class and opposition to teenage sex: A life history perspective

2009-06-23T02:51:00.000-07:00

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? [1] 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."

[1] 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.

Evolution

2009-06-23T02:11:00.000-07:00

It's hard out there being a reproductively fit couple

Why are most genetic associations found through candidate gene studies wrong?

2009-06-21T15:47:00.000-07:00

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 [1][2]. 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 [3].

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.

[1] 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.

[2] http://jnci.oxfordjournals.org/cgi/content/full/96/6/434#FD1

[3] 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.

Religious people are breeding, producing more religion....(?)

2009-06-21T14:12:00.000-07:00

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).

What Darwin Said - Part 2: Mechanisms of Evolution

2009-06-20T04:00:00.000-07:00

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.

A. SELECTION

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:

Heredity
Speciation
Gradualism
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.

Height changes in Germany

2009-06-19T19:33:00.000-07:00

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.

A blast from the eugenic past

2009-06-17T21:53:00.000-07:00

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.

TFR by class and nation

2009-06-17T12:02:00.000-07:00

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.

	Poorest Fifth	Middle Fifth	Richest Fifth
Armenia	2.5	1.4	1.6
Bangladesh	4.6	3.3	2.2
Benin	7.2	6.5	3.5
Bolivia	7.4	4.4	2.1
Brazil	4.8	2.1	0.7
Burkina Faso	7.2	6.8	4.5
Cambodia	4.7	3.9	2.2
Cameroon	5.9	5	3.6
Central African Republic	5.1	4.8	4.9
Chad	7.1	6.2	6.2
Colombia	4.4	2.4	1.8
Comoros	6.4	4.5	3
Cote d'Ivoire	6.4	5.7	3.7
Domican Republic	5.1	3.3	2.1
Egypt	4	3.3	2.9
Eritrea	8	6.4	3.7
Ethiopia	6.3	5.9	3.6
Gabon	6.3	4.1	3
Ghana	6.3	5	2.4
Guatemala	7.6	5.1	2.9
Guinea	5.8	6.3	4
Haiti	6.8	5	2.7
India	3.4	2.6	1.8
Indonesia	3.3	2.6	2
Jordan	5.2	4.3	3.1
Kazakhstan	3.4	2.1	1.2
Kenya	6.5	4.7	3
Kyrgyzstan	4.6	3.6	2
Madagascar	8.1	6.8	3.4
Malawi	7.1	6.4	4.8
Mali	7.3	7.3	5.3
Mauritania	5.4	4.9	3.5
Morocco	6.7	4.2	2.3
Mozambique	5.2	5.4	4.4
Namibia	6	4.6	2.7
Nepal	5.3	4.7	2.3
Nicaragua	5.6	3.1	2.1
Niger	8.4	7.8	5.7
Peru	5.5	2.6	1.6
Philippines	6.5	3.6	2.1
Rwanda	6	5.9	5.4
Senegal	7.4	6.2	3.6
South Africa	4.8	2.7	1.9
Tanzania	7.8	6.1	3.4
Togo	7.8	6	2.9
Turkey	3.9	2.7	1.7
Turkmenistan	3.4	3	2.1
Uganda	8.5	7.5	4.1
Uzbekistan	4.4	3.2	2.2
Vietnam	2.2	1.8	1.4
Yemen	7.3	7.3	4.7
Zambia	7.3	6.8	3.6
Zimbabwe	4.9	4.5	2.5

NYT article on depression genetics

2009-06-17T07:37:00.000-07:00

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.

g in a monkey?

2009-06-17T01:28:00.000-07:00

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.

Differences in fertility by class internationally

2009-06-17T01:11:00.000-07:00

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....

Date below.

% Who have 3 or more children by class (WVS 5)

	Upper middle	Lower middle	Working	Lower
Italy	12.2	13.2	13.7	26.7
Spain	14.4	14.2	26	53.9
Canada	26.2	27.3	33	26.1
Japan	22	23.1	21.7	25.6
South Africa	23.2	26.3	29.3	34.9
Australia	28.8	35.5	35.6	51.6
Sweden	22.6	19.6	23.1	19.2
Argentina	15.2	24.6	35.4	49.7
Finland	24.1	26.2	24.3	23.2
South Korea	13.3	21.8	31.8	28.3
Poland	11	21.2	23.9	31.7
Chile	28	33.3	46.4	47.3
India	40.6	44.2	45.3	59.3
Bulgaria	6.9	4.7	7	22.8
Romania	11.4	15.3	21.6	36.4
China	17.3	22.4	26.7	30.9
Taiwan	24.3	28	43.2	64.5
Turkey	22.5	32	31.4	54.6
Ukraine	3.2	7.8	8	9.6
Peru	29.9	28.7	37.3	53.2
Ghana	21.9	28.1	30.5	41.5
Moldova	12.2	15	26.4	26.5
Georgia	10.9	16.7	24.8	26
Indonesia	29.7	31.1	32.8	43.4
Vietnam	32.9	31.9	34.5	38.4
Serbia	10.3	8.1	10.5	14.5
Egypt	43.9	52.4	57.7	61.8
Morocco	22.7	40.3	44.8	48
Jordan	68.8	71.9	63.5	61.8
Iraq	48.8	45.8	53.2	52.5
Trinidad	24.7	30.2	32	48
Malaysia	29.8	34.1	28.1	41.4
Burkina Faso	27.9	33.4	39.9	44.7
Ethiopia	16.7	10.7	18.7	17.8
Mali	50.3	45.7	57.7	62.5
Rwanda	31.8	42.7	43	44.3
Zambia	18.3	26.5	22.9	39.7
Germany	15.6	19.1	22.6	21.7

WVS 3 & 4
Finland	23.2	24.1	16.8	26.7
Norway	23.6	23.9	25	27.3
Sweden	20.3	19	23.3	24.7

Mean number of children by class

WVS 5	Upper middle	Lower middle	Working	Lower
Sweden	1.58	1.55	1.62	1.56
Finland	1.76	1.64	1.6	1.53
Italy	1.12	1.3	1.25	1.69
Spain	1.23	1.27	1.89	2.57
Canada	1.7	1.74	2.07	1.88
Japan	1.55	1.72	1.59	1.05
South Korea	1.35	1.72	1.85	1.86
Argentina	1.23	1.61	2.24	2.61

WVS 3 & 4	Upper middle	Lower middle	Working	Lower
Finland	1.44	2.45	1.72	1.79
Norway	1.64	1.66	1.73	1.65
Sweden	1.47	1.42	1.67	1.63
Spain	1.31	1.48	1.73	2.15
Argentina	1.29	1.81	2.35	2.77
Canada	1.66	2.01	1.97	1.87
Japan	1.41	1.69	1.59	1.59
United States	1.76	1.6	1.77	N < 50, omitted

Mean # of children USA from GSS, whites age 50 and over (year 2000 and after)
Graduate degre	Bachelor	Junior College	High School	Less than High School
1.95	2.12	2.41	2.48	3.07

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.