The past few months Technorati really stopped working for me. Hardly any new links back in, at least that they detected. They unveiled a new site recently, you can read about it at TechCrunch. I really hate it, though to be honest I’d stopped using Technorati for a while. It looks like they pruned a lot of blogs, and that might be why I stopped seeing new links. In any case, here’s an unrepresentative and personal reason why I really think it’s a step back:
The page for Gene Expression at ScienceBlogs (this domain).
The page for Gene Expression at gnxp.com, the original blog I started in the spring of 2002 and still contribute to. I’ve noticed for a while now that they were downgrading the relevance of this independent site, but they just decided to remove it from their index now.
Looks like Technorati’s long tail moment is over.
If you care, the two sites receive comparable traffic, with gnxp.com usually a little ahead over the long term. About half of the total readership of both blogs reads both blogs.

If you have more than a marginal interest in evolutionary biology you will no doubt have stumbled upon the conundrum of sex & sexes. Matt Ridley’s most prominent work, The Red Queen: Sex and the Evolution of Human Nature, covered both the theoretical framework and applied implications of the subject. Ridley leaned heavily upon William D. Hamilton’s scientific work, which extended upon Leigh Van Valen’s concept of the book’s titular Red Queen. The complex interplay between pathogens & multicelluar organisms across the eons is a topic of such breadth and depth that a substantial proportion of the territory in evolutionary biology is still devoted to it, and how sex may relate this dance. Hamilton spent the second half of his career focusing on just this question, outlined in Narrow Roads of Gene Land, volume 2 of his collected papers.*
The question of sex begins with a simple self-evident curiosity: why not cloning? Assume that you are a creature who can be expected in any given generation to have two offspring reach maturity. Imagine two populations, one clonal and purely female and another sexual with females and males. In the later case let us assume a 50:50 sex ratio (this does not always occur, but often does for a peculiar evolutionary genetic reason). All things equal the former population should be able to produce twice as many offspring for subsequent generations. Males are a waste of a body, a “vehicle” as Richard Dawkins would say. Instead of producing offspring the bodies of males serve as halfway houses for genes. Consider the circumscribed lives of drones among the hymenoptera. An answer may be that if men are a plague upon women, they may also offer women a salvation from plagues. The evolutionary psychologist Geoffrey Miller constructs a speculative illustration of this principle in The Mating Mind, while the behavioral ecologist Bobbi S. Low reports on more concrete cases in Why Sex Matters. Why patriarchy? One must always engage the pathogens which inevitability threaten to turn into the bane of a multicellular organism’s existence.
These are big questions, but fleshing out the details can only be done case by case. Though there are some ethnographic and biological anthropological research programs attempting to tease apart the nature of the relationship between disease load and sexual behavior, there are obvious limits to this sort of work. Humans are big slow breeding organisms constrained by ethical considerations. At the other extreme are those who play with parameters in silico (much of Hamilton’s later theorizing was in simulation and not analysis). To split the difference one might look to fast reproducing model organisms, attempting to draw general inferences from specific results.
That is what a letter to Nature attempts to do in relation to sex, or more accurately sex with self or non-self, Mutation load and rapid adaptation favour outcrossing over self-fertilization:

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I’m not a close follower of the news, but the past week I’ve checked The New York Times for David Rohde’s chronicle of his period of captivity and escape from the Taliban. All five articles are up now (and an epilogue).

I stumbled onto a fascinating working paper today (via the sagacious Andrew Gelman), All Together Now: Putting Congress, State Legislatures, and Individuals in a Common Ideological Space. It uses the NPAT survey of political opinions to construct an ideological scale (as opposed to self-reports). This is a wide ranging piece of proto-scholarship, with a lot of ideas and results, but one thing that struck me are the probability density distributions on page 13 & 14. The title says it all, but the charts are reproduced below….

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Or, perhaps they’re norming to their local context. In any case, Andrew Gelman pointed to Boris Shor’s site, who then linked to his research on ideology, which led me this working paper, All Together Now: Putting Congress, State Legislatures, and Individuals in a Common Ideological Space. Here’s what jumped out at me:

I have also found that the common space scores perform exceedingly well as a predictor of individual vote choice compared with even a non-naive three item composite ideology. The common space scores even do as well or better than party identi cation in predicting both presidential and congressional voting. In fact, conventional de nitions of ideology, predicated on self-reporting, show themselves to be completely inadequate.

The “common space scores” is derived from Project Vote Smart’s NPAT.

Pamela Ronald of Tommorow’s Table, author of Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food. Additionally, David Sloan Wilson, has moved his blog to ScienceBlogs. It’s called Evolution for Everyone, after the book of the same name. You can read my review of his book here.

Dr. Daniel MacArthur and Luke Jostins. Also see the #asgh2009 hash-tag.

Today I listened to a Planet Money podcast about Angola’s oil economy, which is an extreme manifestation of the typical dysfunctions which occur due to the presence of black gold. But it got me to thinking about a book I read recently, Africa: Altered States, Ordinary Miracles. Though the author is a journalist and not a scholar there is a good balance between historical and economic framing and the expected travelogue. Most of the chapters can be read a la carte, and are geographically or topically constrained. For instance, one of the last chapters is about the arrival of Chinese to Africa. Some estimates suggest that at any given time there are 5 million Chinese workers on the continent!

For me the most interesting chapter was on Angola. I would be interested in what a scholar of the history of this nation would say about the historical sketch presented. Like many Portuguese possessions Angola has a mixed-race population, mesticos. They are predominantly European in culture and outlook, and according to the author they generally played the role of middlemen minority in this region between Europeans and native Africans. For most of the colonial period the mesticos engaged in arbitrage activity involving human capital. They were slavers. The 20th century brought unexpected, and unwanted changes, for the mesticos. The Salazar dictatorship encouraged a mass migration of white Portuguese, particularly of working or lower classes, to Angola in an effort to relieve population pressures. The mesticos then found their indispensable role as middlemen irrelevant, and in fact the new immigrants received preference in a host of jobs which had traditionally been in the purview of the mesticos. While in other colonial possessions mixed-race minorities tended to identify with the mother country, the mesticos did not, because the mother country was destroying their niche within Angola.

From what I can tell the mesticos are only a few percent of the population. Angola, like most African nations, is ethnically diverse. According to the author of Africa: Altered States, Ordinary Miracles most of the nationalist movements were taking an Africanist position, and de facto aligned with particular ethnic groups. The mesticos lacked the numbers to be of importance within these ethnic coalitions. Additionally, they could not align themselves with the colonialist position because 20th century Portuguese colonialism was qualitatively different from what had come before and was leading to their dispossession.

There was one political grouping, which had a presence in Portugal, which was open to them. And that was the Communist party. The Communist party spoke in terms of class, and not nationalism or ethnic loyalties, and so mesticos were accepted within its apparatus. An argument therefore emerges that Angola’s Marxist-Leninist political movement was in fact a vehicle for the empowerment of a mercantile middleman minority! Though the bete noire of the Marxists, Jonas Savimbi, wore many ideological hats, his movement to a first approximation a reassertion of the indigenous African groups of the interior in opposition to the coastal mesticos and the arriviste Portuguese. By the 1990s Communism was spent as an international force, and the Popular Movement for the Liberation of Angola rapidly transformed into an officially socialist party, but its commitment to socialism is notional. Rather, Angola operates in a fashion similar to most one-party petro-states.

Note: The current President of Angola is not a mestico, but the child of immigrants from Sao Tome and Principe.

Dr. Daniel MacArthur and Luke Jostins. Also see the #asgh2009 hash-tag.

One of the banes of modern life is the stack of papers in one’s “to-read” list. I guess that goes to show how cushy modern life is, as what sort of complaint is that? In any case, I began to consider this after reading Joe Thornton’s magisterial response to Michael Behe’s giddy excitement over his most recent paper, An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Thornton dispatches Behe’s muddled misconceptions with economy and precision, but after reading the paper, as opposed to cogent summaries such as Carl Zimmer’s in The New York Times I’m even more at a loss as to how Behe arrived at the conclusions he did as to the paper’s significance (please read the paper, available on Thornton’s lab website, and then try and make sense of what Behe is asserting) . But at least Michael Behe prompted me to push the paper to the top of my stack.
To understand why this paper is important, one has to know a bit of the history of evolutionary theory (ironic in that this paper points to the importance of contingency, that is, historical sequence of events, in evolution). The arguments about whether evolutionary process is contingent or not go back a century. One can see glimmers of it in the debates between R. A. Fisher and Sewall Wright, the two preeminent figures of 20th century population genetics (Fisher arguably invented the field). Fisher and Wright are relevant to the discussion around this paper because of their views about the genetic architecture of evolutionary process. The former tended to elaborate a simple perspective whereby the focus was on genetic variants of independent and additive effect against an averaged genetic background. As an example, presumably the thousands of genes which effect normal variation in height, and are selected en mass when a shift in height away from the mean value results in higher reproductive fitness. In a Fisherian world the adaptive landscape is smooth and without discontinuity, with a simple symmetrical peak around which the species’ total population flows. The world may not be flat, but its geometry is elegant. In contrast, Sewall Wright conceived of the adaptive landscape as far more rugged, subject to the complex interlocking effects of epistasis as well as stochastic random walks, and fragmented into numerous populations with some barriers to gene flow. Wright’s ideas were not entirely coherent, as his biographer Will Provine lays out in Sewall Wright and Evolutionary Biology, but the metaphors and generally more empirical methodology left an imprint (while Fisher’s contributions tended to be theoretical, Wright was an experimental geneticist with a more intuitive feel for the shape of reality). Though Stephen Jay Gould gave a hearty nod to Sewall Wright as a primary influence (though he also argued that Wright watered-down his own theories to conform to Neo-Darwinian orthodoxy), Gould’s nemesis William D. Hamilton declared that Wright was the strongest influence upon his later work in his collection of papers. The combination of Wright’s extremely long career (he was 1 year older than Fisher, but outlasted him by 26 years) and his occasional tendency toward lack of clarity may go some way to explaining how and why such disparate intellectuals could look to him as an influence.
The tension between Fisher’s elegant formalism which led one toward an ahistorical sensibility, and Wright’s more sloppy empirically informed conjectures, has to a great extent echoed down the decades. In the 1960s Ernst Mayr attacked “beanbag genetics,” in other words, Fisher’s genetics. Fisher’s British colleague, J. B. S. Haldane, rose to the challenge (Fisher had died by this point), publishing A Defense of Beanbag Genetics. In more recent years Stephen Jay Gould laid out his vision of historical contingency in Structure of Evolutionary Theory. As the inevitable counterpoint Richard Dawkins took Simon Conway Morris’ side in The Ancestor’s Tale, arguing for the inevitability of particular morphological types due to the deterministic character of natural selection. And so it goes.
Thornton’s paper does not resolve this general argument, but it does illustrate starkly the constraints which natural selection faces in a universe of finite time:

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