Click on the cover to link to OUP's e-catalogue then turn to the biology section.

Interview Podcast with George Miller

Interview Podcast with George Miller
Click on the pic to link to the NOT A CHIMP podcast on Blackwell's Website

Preface to "Not A Chimp: The Hunt For The Genes That Make Us Human"

In many ways, this book is born out of frustration for a professional career in popular science television where ideas about comparative primate cognition, and the similarities and differences between us and our primate relatives, have continually circled me but constantly evaded my grasp in terms of the opportunity to transform them into science documentary. On the plus side, keeping a watching brief for over a quarter of a century on subjects like comparative animal cognition and evolution allows you to watch a great deal of water flow under the bridge. Fashions come and fashions go - specifically, perspectives on the similarity - or otherwise - of human and ape minds.

I remember the first Horizon science documentary about the chimpanzee Washoe, the great ape communicator, using American Sign Language to bridge the species barrier. And, later, Kanzi the bonobo jabbing his lexicon. These were the apes, as Sue Savage-Rumbaugh has put it, that were "on the brink of the human mind".

I remember when the pre-print of Machiavellian Intelligence, by Andrew Whiten and Dick Byrne, plopped onto the doormat of the BBC Antenna science series office in 1988. Suddenly primatology had become a great deal more exciting. Could primates, and especially higher primates like chimpanzees, really be as full of guile, as dastardly, as cunning, and as manipulative as the eponymous Florentine politician? Could they really reach deep into the minds of other individuals to see what they believed and what they wanted, and turn that information into deception?

I remember discussing primate cognition with a young Danny Povinelli, as we sat finger-feeding ourselves shrimp gumbo and new potatoes out of plastic Tupperware containers in a Lafayette restaurant surrounded by an alligator-infested moat, before returning to his kingdom - the New Iberia Research Centre - where the University of Louisiana had lured him back to his native deep South by turning a chimpanzee breeding centre for medical laboratory fodder into a primate cognition laboratory with one of the largest groups of captive chimpanzees in the country. He looked like a kid who had just been thrown the keys to the tuck shop.

In those days Povinelli shared the zeitgeist - spread by Whiten's and Byrne's work, and started by Nick Humphrey and Alison Jolly before them - that, since the most exacting and potentially treacherous environment faced by chimpanzees and other primates was not physical, but the social environment of their peers, they had evolved a form of social cognition very much like our own, in order to deal with it. This was further elaborated into a full-blown "social brain" hypothesis by Robin Dunbar, who related brain neocortex size to social group size throughout the primates and up to man. Povinelli's early work reflects this optimism for the mental life of apes, but both ape-language and ape-cognition research was subjected to a cold douche of searching criticism during the 1990s, and misgivings set in regarding the effectiveness of the experiments that had been constructed to guage ape cognition. Now the worm has turned again, with a number of research groups emerging with bolder and bolder claims for the Machiavellian machinations of primate minds, only to be powerfully countered by the curmudgeonly skepticism, chiefly by Povinelli, that these researchers are merely projecting their mental life onto that of their subjects; that, rather in the frustrating manner of Zeno's arrow that could never quite reach its target because it continually halved its distance to it, no experiment constructed thus far can actually get inside the mind of a chimp and show us exactly what it does and doesn't know, or how much, about the minds of others or the way the physical world works. One influential part of the world of comparative animal cognition talks of a continuum between ape and human minds and shrinks the cognitive distance between us and chimps to almost negligible proportions, while another returns us to the unfashionable idea that human cognition is unique, among the primates, after all.

When I began writing this book the working title was "The 1.6% that makes us human". My aim had always been to scrutinize the impression put about in the popular science media that humans and chimps differ by a mere 1.6% in our genetic code - or even less - and that it therefore makes complete sense that this minuscule genetic difference translates into equally small differences in cognition and behaviour between apes and man. However, contemporary genome science and technology, over the last few years, have dramatically advanced the power and resolution with which scientists can investigate genomes, eclipsing the earlier days of genomic investigation that gave rise to the "1.6% mantra".

As with comparative cognitive studies, conclusions on chimp-human similarity and difference in genome research depend crucially on perspective. To look at the complete set of human chromosomes, side by side with chimpanzee chromosomes, at the level of resolution of a powerful light microscope, for instance, is to be overwhelmed by the similarity between them. Overwhelmed with a sense of how close our kinship is with the other great apes. True, our chromosome 2 is a combination of two chimp chromosomes - giving humans a complement of 23 chromosome pairs to 24 in chimps, gorillas and orang-utans - but even here you can see exactly where the two chimp chromosomes have fused to produce one. The banding patterns you visualize by staining the chromosomes match up with astonishing similarity - and that banding similarity extends to many of the other chromosomes in the two genomes. However, look at a recent map of the chromosomes of chimps and humans, aligned side by side, produced by researchers who have mapped all inversions - end-on-end flips of large chunks of DNA - and the chromosomes are all but blotted out by a blizzard of red lines denoting inverted sequence. Now you become overwhelmed by how much structural change has occurred between the two genomes in just 6 million years. True, not all inversions result in changes in the working of genes - but many do - and inversions might even have been responsible for the initial divergence of chimp ancestor from human ancestor.

The extent to which you estimate the difference between chimp and human genomes depends entirely on where you look and how deeply. Modern genomics technology has led us deep into the mine that is the genome and has uncovered an extraordinary range of genetic mechanisms, many of which have one thing in common. They operate to promote variability - they amplify differences between individuals in one species. We now know, for instance, that each human is less genetically identical to anyone else than we thought only three years ago. When we compare human genomes to chimpanzee genomes these mechanisms magnify genetic distance still further. I have tried, in this book, to follow in the footsteps of these genome scientists as they dig deeper and deeper into the "Aladdin's Cave" of the genome. At times the going gets difficult. Scientists, like any explorers, are prone to taking wrong turnings, getting trapped in thickets, and covering hard ground, before breaking through into new insights. I hope that those of you who recoil from genetics with all the visceral horror with which many regard the sport of pot-holing will steel yourselves and follow me as far as I have dared to go into Aladdin's Cave. For only then will you see the riches within and begin to appreciate, as I have, just how limited popular accounts of human-chimpanzee genetic difference really are. Let me try and persuade you that this is a journey, if a little arduous at times, that is well worth taking.

There are a number of scientists around the world who have the breadth and the vision to have begun the task of rolling genetics, comparative animal cognition, and neuroscience into a comprehensive new approach to the study of human nature and this is part, at least, of their story. They strive to describe the nature of humans in terms of the extent to which we are genuinely different to chimpanzees and the other great apes. Somehow, over 6 million years, we humans evolved from something that probably resembled a chimpanzee (though we cannot yet be entirely sure) and the answer to our evolution has to lie in a growing number of structural changes in our genome, versus that of the chimpanzee, that have led to the evolution of a large number of genes that have, effectively, re-designed our brains and led to our advanced and peculiar human cognition.

If you don't believe me, hand this book to your nearest friendly chimpanzee and see what he makes of it!

Thursday, 14 January 2010

Massive Differences Found Between Chimp And Human Y Chromosomes

I'm publishing Lizzie Buchen's very clear Nature report in entirety. David Page's group have been fascinated by the evolution of the sex chromosomes and their painstaking sequencing has paid off in this revelation as to just how different the Y chromosome is between chimps and humans. This seems to be another case of how species "churn" their genomes differently. The Y chromosome has suffered from relative gene loss in the chimp and gene gain in the human. The majority of the genome evolution seems to have occurred in a section of so-called palindromic sequences which appear to have been duplicated many times. Rapid duplication of genes, or DNA sequence including genes, has historically been very difficult to pick up by standard sequencing techniques. Because the duplication has occurred relatively recently - within approx. 6 million years, the dupes are all very similar and so the sequencer cannot tell them apart as dupes. However more painstaking, and modern, sequencing techniques have revealed the extent of this duplication. The advantage of dupes to genome evolution is that natural selection can act differentially on any dupe, perhaps creating new genes with a different function. In the case of the Y chromosome this has certainly to do with sperm production and particularly "sperm wars" between males in species where the female multiply mates, creating competition in her reproductive tract between the sperm of a number of males. Sperm competition is far more pronounced in chimpanzees than humans.

The fickle Y chromosome

Chimp genome reveals rapid rate of change.

Lizzie Buchen

The male sex chromosome, long dismissed as the underachieving runt of the genome, has now been fully sequenced in a common chimpanzee. And comparison with its human counterpart — the only other Y chromosome to have been sequenced in such detail — reveals a rate of change that puts the rest of the genome to shame.

The common chimp (Pan troglodytes) and human Y chromosomes are "horrendously different from each other", says David Page of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who led the work. "It looks like there's been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages."

Sex chromosomes evolved some 200 million–300 million years ago, but the chimpanzee and human lineages diverged only 6 million–7 million years ago. Comparisons of the chimp and human genomes suggested that not much has changed between the species since1.

But those analyses excluded the Y chromosome, much of the genetic sequence of which is made up of palindromes and elaborate mirrored sets of bases that elude standard whole-genome sequencing techniques. Portions of the chimp Y chromosome were sequenced a few years ago2,3, but the full landscape is only now available, after Page and his team precisely sequenced large segments of the chromosome, then stitched them together. They report their findings in a paper published online in Nature on 13 January4.

As the earlier studies had suggested, many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human. Page's team found that the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans. The remainder of the chimp and human genomes are thought to differ in gene number by less than 1%.

Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa, whereas this is true for less than 2% of the remainder of the genome.

Even the portions that do line up have undergone erratic relocation. In the only other chromosome to have been sequenced to the same degree of completeness in both species, chromosome 21, the authors found much less rearrangement.

"If you're marching along the human chromosome 21, you might as well be marching along the chimp chromosome 21. It's like an unbroken piece of glass," says Page. "But the relationship between the human and chimp Y chromosomes has been blown to pieces."

The rapid evolution of the Y chromosome is not a total surprise, because the Y chromosome has no partner during cell division and so largely avoids the exchange of DNA that occurs between partnered chromosomes and keeps modifications in check. "It's expected that they are going to be more different than the rest of the genome, but the extent of it is pretty amazing," says geneticist Christine Disteche at the University of Washington in Seattle.

The Y chromosome is also prone to change because most of its characterized genes are involved in producing sperm, which are at the frontline of reproductive fitness, particularly in chimps; receptive females will often mate with many males in one session, so the male with the most virile sperm has the highest likelihood of success.

"The Y is full of surprises," Page says. "When we sequenced the chimp genome people thought we'd understand why we have language and write poetry. But one of the most dramatic differences turns out to be sperm production."


1. The Chimpanzee Sequencing and Analysis Consortium . Nature 437, 69-87 (2005).
2. Hughes, J. F. et al. Nature 437, 100-103 (2005).
3. Kuroki, Y. et al. Nature Genet. 38, 158-167 (2006).
4. Hughes, J. F. et al. Nature doi:10.1038/nature08700 (2010).

Source: Nature

Monday, 11 January 2010

Gene-Culture And The Setoronin Transporter Gene

In the penultimate chapter of NOT A CHIMP I try to lay some foundations for a proper bio-social approach to the study of the evolution of human social behaviour through the evolution of several prominent neuro-transmitters. In particular, I reported that the "short" allele of the serotonin transporter gene had been implicated in creative dance in the context of proto-religious collective human mystical experience. I also reported the finding that variability in short, long and extra-long repeat versions of this gene were more prevalent in more demonic societies typified by long-range geographical distribution - like rhesus macaques and humans. Further research has also implicated the short allele of this gene in anxious, depressive and occasionally violent personality traits.

In this interesting open paper in Proceedings of the Royal Society B, Joan Chiao and Katherine Blizinsky fill in another aspect of this growing picture by associating the short allele of the serotonin transporter with gene-culture evolution of collectivistic traits in human society.

As the authors say: "A fundamental way in which culture shapes human behaviour is through self-construal style, or in how people define themselves and their relation to others in their environment. In particular, cultural psychologists have identified two primary styles of self-construal across cultures: individualism and collectivism. Individualistic cultures encourage thinking of people as independent of each other. By contrast, collectivistic cultures endorse thinking of people as highly interconnected to one another. Individualistic cultures emphasize self-expression and pursuit of individuality over group goals, whereas collectivistic cultures favour maintenance of social harmony over assertion of individuality. Self-construal style affects a wide range of human behaviour, including how people feel, think, perceive and reason about people and objects in their environment, and their underlying neural substrates."

However, there is one other important ingredient in the mix - disease. Previous work, they report, has shown that the S allele is selected for in those cultures with great history and contemporary prevalence of disease-causing pathogens like malaria, typhus and leprosy. The S allele appears to be linked with collectivism and the authors posit that a cultural norm of collectivism could help to protect against the run of disease by enhancing conformity and parochialism. It would seem that this would leave many cultures open to affective disorders but in highly collectivized societies, for instance in Asia, this seems not to be the case. Their answer? " Here we propose that by favouring social harmony over individuality, collectivistic cultural norms may have evolved to also serve an adaptive, ‘anti-psychopathology’ function, creating an environmental niche that reduces the risk of exposure to environmental pathogens, such as chronic life stress, for group members. Consistent with a gene-by-environment (GxE) theory of affective disorders, reduced exposure to chronic life stress for individuals living in collectivistic relative to individualistic cultures would then cause reduced prevalence of affective disorders among genetically susceptible individuals. Hence, culture variation in the epidemiological prevalence of anxiety and depression is likely due to geographical variation in the cultural adoption of collectivistic social norms." So, collectivism helps fight disease and protects against the downside of the S allele - affective disorder.