Thursday, December 20, 2007

Skeptics' Circle #76 (and Encephalon too)

The 76th edition of the Skeptics' Circle has been released, it's being hosted over at Aardvarchaeology. My favorite entries are: Coffee House Poetry's fun atheistic rant and Whiskey Before Breakfast's entry on how the 20th century certainly wasn't the bloodiest in history (on a per capita basis at least).

Oh... I almost forgot about the latest edition of Encephalon.

Thursday, December 13, 2007

Open access

I recently moved between universities: from the University of Cape Town to the University of Kwa-Zulu Natal. Unfortunately, my new university is a bit under resourced and doesn't have institutional access to quite a few journals. (Including fairly prominent ones). It was then (and particularly when I started blogging) that I realized just how frustrating, annoying and counter-productive the barriers to accessing knowledge really is. I suspect many people who access the web mainly from their well-financed institutions also fail to realize just what an issue this can be.

The bottom line with respect to open access is this: scholars do research, peer review it and even edit the journals, all without expecting to be paid. (Researchers get paid by their institutions, of course, and part of their job description is usually producing academic papers - the point is scholars don't expect to be paid by journals for their work). The publishing houses, however, charge exorbitant prices for access to their scholarly journals and the result is a high financial barrier. There was a time the arrangement between the scholarly community and publishers made sense: before the internet was created, when journals had to be printed in order to be distributed. Since it's now possible to distribute journal articles digitally at extremely low cost, this relationship has become outdated and unnecessary. As the Budapest Open Access Initiate put it, the internet makes possible :

world-wide electronic distribution of the peer-reviewed journal literature and completely free and unrestricted access to it by all scientists, scholars, teachers, students, and other curious minds. Removing access barriers to this literature will accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge.

Open access is good for everyone except those companies with a vested interest in the status quo. We should not let a special interest group stand in the way of a great public good being realized.

What to do? If you are an author, self-archive and consider publishing in open access journals. (Opening access, by the way, seems to increase an article's readership and impact). Everybody else, spread the word (e.g.: join my group on Facebook: "Support Open Access"), support open access journals (read them, cite them) and sign the Budapest Open Access Initiative if you haven't done so already.

P.s. Yes, I realize I'm late on the bandwagon.

Wednesday, December 12, 2007

My second BMJ rapid response gets published

BMJ have published my reply to the authors' rapid response to my criticisms, it can be found here. There are a few fairly minor differences between my blog and my rapid response but the gist is the same. I tried hard to be conciliatory. I suspect I failed miserably.

Rapid human evolution

It is commonly accepted among evolutionary psychologists (at least in the Santa Barbara school*) that "our modern skulls house a stone age mind". As Tooby & Cosmides put it,
natural selection... takes a long time to design a circuit of any complexity. The time it takes to build circuits that are suited to a given environment is so slow it is hard to even imagine -- it's like a stone being sculpted by wind-blown sand. Even relatively simple changes can take tens of thousands of years. The environment that humans -- and, therefore, human minds -- evolved in was very different from our modern environment. Our ancestors spent well over 99% of our species' evolutionary history living in hunter-gatherer societies. That means that our forebearers lived in small, nomadic bands of a few dozen individuals who got all of their food each day by gathering plants or by hunting animals.
Similarly, Edward Hudgens explains,
Evolutionary psychologists downplay the possibility of significant cognitive evolution in the 10,000 or so years since the advent of agriculture (a period of time known as the Holocene) for reasons of both science and political correctness. Scientifically, 10,000 years (500 generations) is not much time for natural selection to act, and it certainly is not enough time to evolve new, complex adaptations—sophisticated mechanisms coded for by numerous genes.
New research just released in PNAS has the potential to undermine these claims fatally. John Hawks and his colleagues argue that human evolution accelerated very rapidly in the last 40,000 years. The abstract:
Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9M HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (1) site heterozygosity at least tenfold lower than is observed in humans, (2) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (3) an implausibly high number of adaptive substit utions between humans and chimpanzees, and(4) nearly 100 times the observed number of high-frequency LD blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.
(See also: John Hawks's two blog entries on his study, and Reuters' report)

*The Santa Barbara school of evolutionary psychology is the best known type of EP, its foremost exponents are Leda Cosmides, John Tooby, Donald Symons, David M. Buss, Steven Pinker, Margo Wilson and Martin Daly. (It's so called because Symons, Tooby & Cosmides are at UC Santa Barbara).

Tuesday, December 11, 2007

Active parents raise active children: the authors reply

Recently, I wrote a rather scathing blog entry (see also my follow-up post) and a more measured "rapid response" to a BMJ (British Medical Journal) article that argued parents socialize their children into being physically either more active or more sedentary. Now the authors have replied to my criticism with a rapid response of their own. (Actually, the response was published almost a week ago - oh the dangers of going on holiday!). Suffice it to say I don't think Mattocks et. al. have neither met my criticism or understood it fully, so I'm going to respond to them both here and at the BMJ website. (Submissions to BMJ's rapid response system aren't peer-reviewed but are approved by an editor, so there's no guarantee my response will in fact be published. I'll link to my response if it does get published).

A quick recap of the study: the authors (Mattocks et. al., 2007) wanted to determine which early life variables (before age 5) affected the physical activity of children at ages 11-12 (which was objectively measured with accelerometers). They found that (among other things) "children are slightly more active if their parents are active early in the child's life and suggest "helping parents to increase their physical activity... may promote children's activity." It's clear from the quotations (and the rest of the study) that the authors were thinking solely in terms of socialization. As I pointed out in my critical blog entry (which I recommend you read if you haven't done so), there's an obvious possible confound here: genetics. Since (1) all behavioral traits are heritable (Turkheimer, 2000) and (2) children inherit 50% of their genes from each parent, "genetic factors are always possible confounds when relating parenting style (or other parental behavior) to outcomes in children". Consequently, because genetic factors were not controlled for, Mattock's et. al.'s study does not distinguish between the relevant possible causal hypotheses and therefore fails to add very much to our knowledge.

The authors' reply to my criticism, I think, amounts to the following: 'controlling for genetic factors is really hard' (first paragraph), and (2) 'not all the hypotheses we tested are confounded by genetic factors' (most of the second paragraph). Let's take these replies in turn. The literature about the determinants of physical activity is certainly not one of my specialities so I don't have an opinion about whether or not it's possible to control for genetics at the present time. Let's grant, for argument's sake, that Mattocks et. al. are correct: that it's not possible to control for genetic factors. What follows? Does assuming this proposition at all support the truth of their finding concerning the link between active parents and active children? Clearly not - the fact that we cannot control for a confound manifestly (and unfortunately) does not make it causally inert. Because genetics is a possible confound (something Mattocks et. al. do not dispute in their reply), we simply can't draw a conclusion one way or another because, to repeat, their data fails to distinguish between the relevant alternative causal hypotheses. I note furthermore that Mattocks et. al. seem to have been intellectually careless - they don't seem to have considered genetic factors as possible confounds when designing the study at all. Firstly, electronic text-searches confirm my impression from reading their paper: they fail even to mention genetics. Secondly and damningly, their paper does contain a section entitled "Possible confounders" but it does not list genetics as a possible instance.

Mattocks et. al. are correct in saying that not all the variables they considered are possibly confounded by genetics. I focused on a subset of their variables and findings because I found the study through this ScienceDaily article (title: "Active Parents Raise Active Children") and because the authors themselves emphasize the correlation (what they regard as causation) between maternal physical activity during pregnancy and early life and children's physical activity later in life (see the conclusion of the abstract). Furthermore, it seems a majority of the study's positive findings are at least possibly confounded by genetics, even if in some cases a particularly plausible causal mechanism is absent. (The sum total of the positive findings were that activity at 11-12 was 'modestly associated with': "mother's body mass index before pregnancy, parents' smoking status during pregnancy, mother's age at birth of the child, mother's physical activity, parity, and season of birth.")

In short, genetics is a possible confound (a fact that remains unaltered whether or not it's possible to control for it), but, despite this, the authors didn't even try to control for it and happily drew causal conclusions in the absence of controls. My criticisms stand.


Mattocks, C., Ness, A., Deere, K., Tilling, K., Leary, S., Blair, S.N., Riddoch, C. (2007). Early life determinants of physical activity in 11 to 12 year olds: cohort study. BMJ (British Medical Journal). DOI: 10.1136/bmj.39385.443565.BE

Turkheimer, E. (2000) "Three Laws of Behavior Genetics and What They Mean," Current Directions in Psychological Science, 9(5): 160-164.

Monday, December 10, 2007

Race and IQ

A brouhaha is raging at the moment about race and IQ. James Watson started it off when he was quoted as saying he was "inherently gloomy about the prospect of Africa" because "all our social policies are based on the fact that their intelligence is the same as ours - whereas all the testing says not really". Then William Saletan over at Slate added fuel to the fire when he argued in a series of posts that Watson was supported by the scientific evidence. Saletan's claims were soon debunked by several people - most notably by Cosma Shalizi, Stephen Metcalf, and Richard Nisbett. (Saletan issued a semi-mea culpa about not realizing just how biased one of the journals he relied upon really was).

Now, the always fantastic and worth-reading Malcolm Gladwell has entered the debate with the release of his latest New Yorker article. The article is highly recommended - if you don't have the time or the patience to read all the articles I link to above, simply read Gladwell's contribution. It's a fine gloss.

Friday, December 7, 2007

75th Meeting of the Skeptics' Circle

The 75th Skeptics' Circle blog carnival is out; and it includes one of my entries. (Which marks the loss of my blog carnival virginity...)

By the way, I'm on holiday at the moment and my access to the internet is pretty limited. I doubt I'll blog much in the next week.

Tuesday, December 4, 2007

Encephalon #37

The latest edition of the psychology/AI/neuroscience/cog sci blog carnival, Encephalon, was just published. This time round it's being hosted over at A Blog Around the Clock. There are quite a few entries well worth checking out; my favorite was The Phineas Gage Fan Club report on a recent study on the influence of snap facial judgments on voting behavior.

Video: Evo-Devo in 60 seconds

Scientific American recently launched an interesting new vodcast, Instant Egghead, to accompany their 60 Second Science stable of podcasts. As you might have guessed, Instant Egghead explains various scientific concepts, theories or ideas in 60 seconds (tagline: "Explain Big Ideas. Fast.") . The two previous episodes covered Dark Matter and Moore's law, respectively; Episode 3 (embedded below, or click here to go to the SciAm site) is on Evo-Devo:

What I blog

In my very first entry, "Welcome", I said my blog:
will consist almost entirely of my irregular musing and reflections on recent (and sometimes not so recent) published academic papers in evolutionary and social psychology. Occasionally I might indulge myself by venturing further afield, probably mainly into political science. I may even sometimes fail to take myself seriously and blog about something other than a specific academic paper.
I now realize, however, that I underestimated just how powerless I am in the face of my very wide interests. So I've given up - I'm no longer even going to try restraining myself from blogging about issues that interest me. Basically, this means I won't try keeping to evolutionary and social psychology anymore. (Not that I have been anyway). Although the majority of the content here will be related to psychology, the scope of the blog is now (officially, instead of de facto) broader. I'll have occasional entries on biology, neuroscience, scientific skepticism, medicine, cognitive science and whatever else strikes my fancy really. Don't fear however: this will remain (a) a science blog (i.e. I won't start ranting about politics or discuss metaphysics) , (b) an academic blog (i.e. I won't start telling you what I ate for breakfast) and (c) a blog mainly about human behavior (i.e. I'll blog about other topics to the extent to which it impacts on our understanding of human behavior).

I hope you'll keep reading! (You few...)

Monday, December 3, 2007

News flash!

Updated: more links, embedded video.

Apparently, hormone fluctuations may be responsible for many mood disturbances in women! And, in other news, oceans contain water! Mountains are made of rock! Species evolve over time! I haven't actually read the articles this press release is based on (not my field), but I'm assuming they had more interesting findings. Hopefully...

More seriously, a new study in Current Biology has found that young chimpanzees have a better numerical working memory than adult humans beings. The abstract:
Chimpanzee memory has been extensively studied. The general assumption is that, as with many other cognitive functions, it is inferior to that of humans; some data, however, suggest that, in some circumstances, chimpanzee memory may indeed be superior to human memory. Here we report that young chimpanzees have an extraordinary working memory capability for numerical recollection — better even than that of human adults tested in the same apparatus following the same procedure.
New Scientist magazine has a great little video on the study, it's embedded below (or click here to go directly to the video at YouTube):

(See also the ScienceDaily press release, the Nature News writeup, the New Scientist article and Kyoto University's extensive collection of videos from the study).