Archive for the ‘Life science’ Category

Sizeism! Attack!

November 18, 2010

Wait until some of the fat-acceptance people find out about this.

Here was a typical response, back in 2007, to the New England Journal of Medicine paper by Nicholas Christakis and James Fowler, which applied network theory to the spread of obesity:

[The] media, in parroting the study’s claims to have documented the “social contagion” of obesity, are fueling the war on fat people by uncritically reporting that “obesity” is contagious. What can we expect next? Quarantine? Apartheid?


What the Christakis-Fowler research actually shows is the social contagion of fat hatred, especially in regard to the way it’s being disseminated and reported.


[We] see this study being used to justify more intrusive public health programs and actions. More fat children being removed from their homes to “save” them from their allegedly fattening parents…More shunning of fat kids and adults, more job and academic and social discrimination.


The first reports of this study indicating “obesity is contagious” (reports assuming, of course, that “obesity” is a terrible thing) brought chilling visions of quarantine, apartheid, and even lynching to some minds. Including mine.

Now there’s a new paper, co-written by Christakis and just published in PLoS Computational Biology, which develops a model for the spread of obesity on social networks. Towards the end the authors briefly discuss the likely usefulness of some hypothetical public-health interventions:

If the spatial correlations [between infected and susceptible individuals] were fixed to be a certain value (for example obese people cluster together due to selection bias in friendships or confounding factors), then this would actually serve to slow infection. Since we do not observe contagion of losing weight, it does not seem like it would be beneficial to have an intervention which broke up obese clusters…[We] can see that the fraction infected decreases with , the correlation of susceptible and infected people. If an intervention actively reduced this number, by isolating or clustering infected people, this could reduce the prevalence…Our results actually suggest that clusters of obese people serve to slow the spread of obesity by reducing social contagion to non-obese others outside of the clusters.


Nature publishes attack on inclusive fitness

August 30, 2010

Those of you reluctant to babysit your sister’s kids or play wingman for your twin brother may appreciate this criticism of the inclusive-fitness theory of eusociality. Favoured by the Oxford school of evolutionary biologists (J.B.S. Haldane, W.D. Hamilton, John Maynard Smith and Richard Dawkins), inclusive fitness and kin selection have since the 1960s been the popular explanations of brood care for offspring, foregone reproduction by some individuals, and other cooperative, self-sacrificing behaviour by ants, wasps, bees (and other social species including humans). Hamilton gives a crude explanation below.

More exactly, Hamilton’s inequality says that altruism is favoured when the coefficient of genetic relatedness exceeds the reproductive cost-benefit ratio (for donor and recipient together) of the cooperative act. Hence Haldane’s famous answer, when asked if he would sacrifice his life for that of his brother: “No, but I would to save two brothers or eight cousins”. (The high proportion of shared alleles among some insects explains, so the story goes, why a worker bee should sacrifice her reproductive potential for just 1.5 sisters.)

Nature and ScienceDaily have discussions of the new paper. Because one of the authors is E.O. Wilson, and the targets of criticism are confrères from the 1970s like Dawkins and Robert Trivers, some people are treating this as part of a late-career volte-face against orthodoxy and towards group selection. In truth, as Razib Khan shows, Wilson has been quietly at this since the Sociobiology days. Not surprisingly, few people – enemies or friends – noticed.

Jerry built

May 6, 2010

From the early edition of PNAS“Footprints of nonsentient design inside the human genome”:

Intelligent design (ID)—the latest incarnation of religious creationism—posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent. Yet, many complex biological traits are gratuitously complicated, function poorly, and debilitate their bearers. Furthermore, such dysfunctional traits abound not only in the phenotypes but inside the genomes of eukaryotic species. Here, I highlight several outlandish features of the human genome that defy notions of ID by a caring cognitive agent. These range from de novo mutational glitches that collectively kill or maim countless individuals (including embryos and fetuses) to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly baroque regulatory pathways) that are endogenous in every human genome. Gross imperfection at the molecular level presents a conundrum for the traditional paradigms of natural theology as well as for recent assertions of ID, but it is consistent with the notion of nonsentient contrivance by evolutionary forces. In this important philosophical sense, the science of evolutionary genetics should rightly be viewed as an ally (not an adversary) of mainstream religions because it helps the latter to escape the profound theological enigmas posed by notions of ID.

This last bit seems incoherent and unnecessary.

Complexity and self-organization as ideology

May 2, 2010

In a lecture from a few years ago, later published as Shaping Life: Genes, Embryos and Evolution, John Maynard Smith remarked that, in biology, ‘to believe in self-organization seems to be associated with left-wing or feminist views’, while for economists it was often found alongside right-wing political opinions.

So, in one field, people like Brian Goodwin and Richard Lewontin (see the video below) opposed a kind of ‘holism’ to what they saw as the dominant reductionism of molecular biology.

Elsewhere, of course, pro-market hostility to command, control and planned economies was more mainstream.

But with gene-culture evolution now a prominent research program, with supporters from L.L. Cavalli-Sforza to E.O. Wilson, I’m not sure this equation (or the related claim, often made, about levels of selection and political affiliation) still holds for biology.

As for economics, any relationship has always seemed non-obvious to me. Commodity exchange through markets isn’t the only way of organizing a complex division of labour. To suggest otherwise is a sneaky claim to generality.

Confusion arises because self-organization is often used more as a woolly descriptive slogan than a well-defined concept.

To suggest that a given system tends, over time, to increase in Kolmogorov complexity without structured external interference (which is one attempted definition) isn’t thereby to assert that it also climbs Mount Improbable (i.e. reaches fitness peaks).

So there’s a world of difference between recognizing that market exchange can spontaneously achieve well-defined average prices (which is true), claiming that these prices are first-best Pareto optima (which is unlikely), then taking this all as demonstrating the supremacy of market over non-market allocation.

Finally, there are other universal features of self-organizing closed systems.

Many-particle systems with random pairwise interactions (e.g. money transfer between participants in market exchange) that conserve some property (e.g. labour for classical economists, utility for neoclassicals) tend towards highly uneven income distributions, with Gini coefficients of roughly 0.5.

These distributions, where many people have low income but a few are very wealthy, are unlikely to be altered by tinkering with tax or welfare payments.

Climate change idiocy and the fate of scientists’ credibility

April 8, 2010

Recently I’ve been engaging with a lot of popular science, because I have time, and also because I enjoy feeling smart when I explain how plants employ quantum effects during photosynthesis at the swanky dinner parties I attend, you know, like…practically every night. While a lot of the material I encounter is in “fun fact” form, like the quantum photosynthesis thing, lately I have noticed that scientists and science reporters have been increasingly writing and lecturing on the dangers of climate change denial. Understandably, they seem more and more frustrated with the prevalence of mainstream denial of climate change in publications that have national and international distribution; indeed, Wilson Da Silva, editor of Cosmos Magazine, lambasts The Australian for giving editorial precedence to its political agenda at the expense of accurate and credible scientific reportage:

“Even worse than not covering science is to dismiss it when it doesn’t meet political prejudices. Sounds absurd, but that’s what The Australian appears to do, particularly on climate change. Many of its articles dismiss or underplay scientific concerns, undermine widely accepted scientific evidence and highlight minority opinions from scientists with little or no credibility among their peers. Its editorials are even more ludicrous: reading them, you could think man-made climate change is nothing but a conspiracy of left-wing scientists determined to de-industrialise society.” (Editorial, Cosmos 32, p. 5)

It’s not just scientists and science reporters who are fed up with irresponsible editorialising spouted by publications like The Australian. Jonathon Holmes (the guy on the ABC’s Media Watch) actually managed to get into a textual stoush with Daily Telegraph columnist Piers Akerman over his use of an unsubstantiated quote in an article attempting to ridicule climate change science. Holmes often condemns the pervasiveness of editorialised climate change denial in the mass media, and eloquently teases out the intricate tactics that allow dickheads who promulgate denial (under the guise of “healthy scepticism”) to get away with it. Furthermore, if you listen to a podcast of last week’s Science Show (ABC Radio National), you can hear a bunch of actual scientists from America (where climate change denial is virtually endemic) discussing the cultural implications of denial, and how it will impact the way we actually deal with the lived reality of climate change.

The climate change “debate” is so beyond a joke now that I worry for the future of scientists’ credibility in matters of even the most ubiquitous and mundane technological advances (male contraceptives? a new, organic substitute for nylon? the cataloguing of species inhabiting Tasmania’s waters?). For a while, I was convinced that scientists needed to overhaul their PR methods, that it was the pressure to publish new findings as soon as you can vaguely substantiate them, and corporate funding for research that was causing all the problems. These are still major issues for all research scientists, everywhere. But the ostensible decline of scientists’ credibility in the mainstream media has moved beyond the realms of PR. Media organisations need to be held accountable for the geyser of bullshit they’re spouting. It’s scientists, experts in the field of climate science, as well as all other scientific researchers who know that climate change denial is an irresponsible lie that has mass appeal, that need to know how mass media operates and challenge the very mechanisms that are undermining their own credibility! Damn it scientists, you can do better!

How thick is your cortex?

February 25, 2010

Support for the parieto-frontal integration theory of general intelligence in this open-access PNAS paper, Distributed neural system for general intelligence revealed by lesion mapping:

General intelligence (g) captures the performance variance shared across cognitive tasks and correlates with real-world success. Yet it remains debated whether g reflects the combined performance of brain systems involved in these tasks or draws on specialized systems mediating their interactions. Here we investigated the neural substrates of g in 241 patients with focal brain damage using voxel-based lesion–symptom mapping. A hierarchical factor analysis across multiple cognitive tasks was used to derive a robust measure of g. Statistically significant associations were found between g and damage to a remarkably circumscribed albeit distributed network in frontal and parietal cortex, critically including white matter association tracts and frontopolar cortex. We suggest that general intelligence draws on connections between regions that integrate verbal, visuospatial, working memory, and executive processes.

General intelligence (Spearman’s g) is just about the most controversial topic out there, from Gould’s Mismeasure of Man and The Bell Curve to more recent contributions (for and against). Positive correlation between test results across a range of cognitive tasks suggest something links verbal skills, spatial reasoning and memory (but not face recognition). So the debate is more or less about the status of factor analysis.

Dawn of the dead: timing Australia’s megafauna extinction

January 26, 2010

Dating and explaining the extinction of megafauna in Australia and North America is a controversial pursuit. Research assigning blame either to humans or glacial cycles is felt to have political implications, and is sometimes assessed on these grounds. Onlookers seem to find the former argument more or less congenial according to whether or not they think indigenous peoples were responsible ‘custodians’ of the land, who respected a harmonious ‘balance of nature’, an equilibrium later disrupted by the arrival of European pathogens, agriculture and industry.

There are two basic models whereby hunter-gatherers are said to have caused enough ecosystem disruption to wipe out large mammals. For North America and New Zealand, the proximal cause is said to be a ‘blitzkrieg’ of rapid human predation. In Australia, the ultimate driver is usually claimed to be human burning practices leading to vegetation change. Evidence for the latter is:

  • Many large herbivores became extinct, across a wide range of habitats and climates, around the time humans colonised Australia, about 55 to 45 ka (thousands of years) ago.
  • Megafauna survived longer where human arrival was later (Tasmania).
  • No unusual levels of aridity, or other climatic instability, around this time.
  • Sediment cores show an increase in microscopic charcoal.
  • Sudden changes in the diet of wombats and flightless birds, including the emu, suggest a corresponding change in vegetation. 
  • Specialised leaf-eating herbivores (browsers) were less successful than grazers, implying that undifferentiated scrub replaced a ‘habitat mosaic’ of trees and grasslands.  

The leading alternative view attributes the extinctions largely to climate change. Its case against a human-induced event goes like this:

  • Late survival of megafauna (notably at Cuddie Springs), with fossils dated to about 35 ka, refutes the notion of continent-wide extinction and indicates long-term coexistence between humans and large marsupials.
  • The late-Pleistocene population of Australia was neither dense nor sedentary enough for fire-stick farming to have more than a local effect, or to control the lightning regime. 
  • Beyond the glacial cycle, there was a long-term trend towards greater aridity from 300 ka, along with increased ENSO activity from 60 ka, which produced drying of bodies such as Lake Mungo, and changed fire regimes and consequently vegetation. Accessible water became too scarce for megafauna to survive.
  • Most megafauna were extinct by at least 80 ka, i.e. before human arrival. The extinctions occurring ca 46 ka were thus merely the tail of a staggered process.

Now Science has published a report showing that the Cuddie Springs deposits have been re-dated, and show no ‘late survival’ of megafauna. From the abstract:

Giant marsupials, reptiles, and flightless birds once inhabited Australia (see the first figure). But 23 of the 24 genera of these megafauna disappeared in the late Pleistocene (~125 to ~12 thousand years ago). Most Australian megafauna appear to have survived until 51 to 40 thousand years ago, with human impact by hunting or vegetation change proposed as the extinction drivers (14). Yet, one site has stood out as an anomaly: Cuddie Springs in interior New South Wales. Persistent claims have been made that this site contains megafauna fossils associated with stone tools in sediments deposited 40 to 30 thousand years ago (57), thus indicating prolonged overlap between people and megafauna. These claims have been challenged (2, 8) based on concerns about possible reworking of fossils from older deposits. To resolve this conundrum, Grün et al. (9) have now directly dated the fossils themselves. The results provide no evidence for the late survival of megafauna at the site.

More from ScienceDaily.

This has been received in some quarters as final proof that the theory of human-induced extinctions is correct. Findings are often reported this way. It’s certainly a strong result: there’s now no real evidence of megafauna persisting until the onset of higher aridity around 30 ka. It’s especially compelling when combined with the recent Tasmanian result, which shows that some megafauna did survive later (up to 41 ka, after their extinction on the mainland), until human arrival. Against the hypothesis of ‘staggered attenuation’, there’s not much fossil evidence for decreasing megafaunal diversity once sampling bias is taken into account. The worth of this new paper is that attention can now be devoted solely to the critical interval 50-40 ka, when the extinctions surely occurred. The exact mechanism, however, hasn’t been confirmed.

Darwin hijacked?

December 30, 2009

The latest issue of the  London Review of Books has a rambling piece by Steven Shapin about the ‘global festivities’ around Darwin Year.

Though much of the article is blandly unobjectionable, there’s a good deal of nitpicking, axe grinding and misrepresentation. Even where his targets are deserving, Shapin lets them off the hook with breezy, half-hearted argumentation.

Sample: if, as evolutionary psychology claims, our cognitive architecture is made up of special-purpose modules locally adapted for hunting and gathering in the Pleistocene, why are there postmodernists? If you’re neither witty nor Jerry Fodor, you can’t get away with this stuff.

But, for reasons I’ll outline below, the article deserves attention.

Shapin asks why past anniversaries of Galileo, Descartes, Newton and Einstein didn’t attract similar hoopla. None of them was afforded so many reverential publications and events, not to mention a feature film starring Paul Bettany and Jennifer Connelly (though, to be fair, Gauss got a banknote).

The reason, he surmises, is that ‘science is discovery and not invention’: while nobody would have written King Lear if Shakespeare hadn’t, someone besides Darwin would surely have uncovered natural selection.

If, then, ‘the individual doesn’t matter in the course of science’, why the special fuss over Darwin?

Well, says Shapin, it’s not the true, historical figure being celebrated, but a heroic image deployed for a personality cult. And behind official Darwin-ism lies a narrow interpretation of evolutionary biology, trying to pass itself off as the one true gospel.

So-called adaptationism (popularly associated with Richard Dawkins, Daniel Dennett and Steven Pinker) attributes changes in allele frequencies largely to positive selection of adaptive traits (rather than emphasizing random drift or spandrels). It also provides the foundation for  evolutionary psychology and sociobiology, disciplines which have been controversial, to say the least.

Now this politicized, tendentious stream of thought has hijacked Darwin Year, staging a coup for control of the academy by ‘laying claim’ to the ‘founding father.’

It’s a nice story, and has its convincing aspects.

But it’s a bit overblown, unless I’ve entirely misunderstood the prior theoretical positions of both Jennifer Connelly and the Cultural Studies department at Melbourne Uni. In short, it’s a just-so story, the kind ‘adaptationists’ are often accused of peddling: a neat explanation of the facts that leaves no room for accident or contingency.

For example, though it may suit a contemporary historian of science (Shapin is a professor at Harvard) to emphasize intra-disciplinary battles for power (‘a struggle among scientists for Darwin’s soul’), the truth is that this year’s Darwin fuss has occurred largely outside academia, in popular media and publishing.

How to account for this broad public appeal?

Shapin doesn’t mention it, but surely one contributing factor is that  unlike, say, classical mechanics, calculus, special relativity or almost every epochal scientific discovery – Darwin’s theory was initially given non-mathematical expression, and is still intuitively accessible to a broad audience through a simple, natural-language triplet: reproduction-mutation-selection.

It also seems clear that Darwin Year was lent contemporary relevance by religious hostility to evolution, and a corresponding desire to ‘promote public education about science’ as ‘our most reliable knowledge system’.  Yet this, Shapin argues, is ‘not quite what it seems’, for ‘ignorance of evolution is not an indication of hostility to science’ tout court.

Unfortunately his claim is left unsupported by any evidence. It scarcely seems credible: among people who believe that Darwin led to Hitler (or that anthropogenic climate change is a priori impossible, and the IPCC is in the pay of communists), you suspect that Occam’s razor is more-or-less an occult concept.

At any rate, Shapin suggests, Darwin’s conscription as an atheist figurehead is flawed, because science and religion are distinct issues.

Look:  ‘A survey published in Nature in 1997 found that 40 per cent of American scientists professed belief in an immortal soul and a prayer-answering God, a figure basically unchanged since 1916.’

This is misleading: in 1998 the same researchers, using improved sampling techniques, found that, among members of the National Academy of Sciences, belief in a personal god had fallen from 28 per cent in 1916 to 7 per cent in 1998; disbelief had risen from 53 per cent to 73 per cent. The same survey found belief in human immortality had fallen from 35 per cent to 8 per cent over the same period; disbelief climbed from 25 per cent to 77 per cent.

Ultimately, the only way Shapin can admit that the ‘centre of gravity of Darwin Year has been a celebration of secularism’ is to see atheism itself as a plot by the Dawkins/Dennett/Pinker/Wilson cabal, ‘an occasion for extending versions of scientific materialism and rationalism to ever new cultural domains’.

By now the reader is inclined to think ‘so what?’, and to judge Shapin more than a little paranoid.

His one extended description of the ‘adaptationist’ position could only charitably be described as a strawman. In the same passage he appears profoundly ignorant (of course he is not) of theoretical innovations in the behavioural sciences since the 1980s, areas likes niche construction and gene-culture coevolution.

So why did his publisher allow him to indulge at such length?

In soliciting his essay (and since it was also the venue for Fodor’s 2007 claim that ‘natural selection can no longer be taken for granted’), it appears that the LRB is trying to revive the famous Dawkins-Gould debate.

Then, leftist scientists such as Stephen Jay Gould and Richard Lewontin suggested that certain theorists’ emphasis on adaptive optima and positively selected traits appeared to justify social inequality as somehow natural or ‘genetically determined’. In polemics with Dawkins and others, both sides mostly contended over arcana like phyletic gradualism and the target of selection.

The LRB seems nonetheless to have marked Dawkins as some kind of reactionary, and latterly deemed progressive (and worthy of publication) any old hatchet job on him or his acolytes. To claim that Darwin believed in natural selection itself is now, apparently, grounds for attack.

Unfortunately, decades later, Gould is no longer around, and the political valences of the contending parties are not quite so clear.

In seeing everywhere the malign influence of so-called adaptationists  their manipulations explaining every aspect of the Darwin Year festivities  their opponents seem to have forgotten Gould’s great lesson.

History is contingent: sometimes it just turns out that way.

Dawkins as ethologist

December 22, 2009

If you happened to catch Andrew Denton’s interview with Richard Dawkins, shown last night on ABC1, here’s a nice antidote: a long, chapter-length piece by Dawkins himself describing his career and early life. Despite naming W.D. Hamilton his “intellectual hero”, and briefly mentioning the importance of “new theoretical ideas” from John Maynard Smith and Robert Trivers, as well as George C. Williams, Dawkins doesn’t attend much to the intellectual context in evolutionary biology, from which his “gene-centred” popularisations developed. Instead most of the detail is about his research in ethology in the sixties and seventies.

That’s okay: Dawkins has given most of these scholars their due elsewhere, and if you’re like me his account of the original ethological work will correct an imbalance in your knowledge.