Showing posts with label Anthropology. Show all posts
Showing posts with label Anthropology. Show all posts

11 February 2010

Analysing ancestry

Nature reports, today, the first "near complete" genome sequence of an "ancient human" from a lock of frozen hair. Ancient is a relative term, here, since the individual concerned dates from about four thousand years ago (8000HY, or 2000BCE) but it's far enough back to offer new insights into human history – indicators for a previously unevidenced migration from Siberia to Greenland in approximately 6500HY, for instance. A PNAS article last month indicated that biological diversity in much older human populations was greater than now, on a par with current great apes.

Divining the possible strands of our unwritten past is done, and has always been done, in many ways. I wrote, three years ago, about a statistical study of how the skull has evolved. Involvement in a combined aid/research project at a central African site, last summer, brought me the payoff of new insights emerging from dust and data analysis. But I find the new genetic searchlight on human prehistories particularly exciting. Perhaps I should get out more...


  • Rex Dalton, "Palaeogenetics: Icy resolve" in Nature, 2010. 463(7282): p.724.
  • C D Huff, et al, "Mobile elements reveal small population size in the ancient ancestors of Homo sapiens" in Proceedings of the National Academy of Sciences, 2010. 107(5): p. 2147.

24 June 2009

Surfer 9

It’s nearly seven years since I last reviewed Surfer, from Golden Software. Not from neglect, but because this is the first full digit version upgrade (from 8 to 9) which Golden have released in that time. Even seven years in, however, Surfer 8 was a finely tuned tool for its purpose; upgrade to 9 makes it even more so. [more...]

23 February 2009

Earth sciences, human impacts

As this appears in print, a new US president will be in his first weeks at the head of an administration informed by respected earth scientists including John Holdren, Jane Lubchenco, and Steven Chu. The words ‘earth science’ usually evoke those disciplines concerned with the lithosphere (particularly geology, seismology, and vulcanology), but public concern is rising about the effects of human interaction with the other three spheres as well – and all sectors of the earth sciences are intensive consumers of computing resources.

Computational science began with water. Societies dependent upon fertile flood plains surrounded by arid regions needed advance knowledge of when their rivers would ebb and flood; and from that arose everything from algebra to astronomy. Today, from acute surges in the Thames to chronic vulnerability in Bangladesh, from one-off disasters such as the 2004 tsunami to the global rise in sea level, flooding remains a primary concern. A tsunami is not only a hydrospheric phenomenon, it is also in the class of seismic events. Sea levels are rising due to many causes, but one significant influence is melting of old ice as a result of changing climate – which also affects the crust beneath it, and the flow of Coriolis currents. Scientific computing in these areas embraces collection, assembly, and analysis of huge, complex data sets. There are other data associated with the human impacts of earth science events: mortality, economic dislocation, rescue, recovery, and medical demand. [more...]

14 February 2009

Eating in a hungry world

Though an uncompromising nonbeliever myself, I'm not deaf to the wisdom of others who frame their ethics in faith terms. For that reason, I usually find the BBC's "Thought for the day" slot worth listening to. To quote the BBC:

"A unique reflection from a faith perspective on topical issues and news events. Speakers from across the world’s major faiths offer a spiritual insight rooted in the theology of their own tradition."

It doesn't always deliver, but an investment of three minutes is a small price to pay for the many times when it does.

Akhandadhi Das, in particular, is usually excellent value. So is Rabbi Lionel Blue, who also provides a bonus in the form of good jokes. Both of them, and others besides, enlarge my humanity.

Today's thought came from Canon Lucy Winkett (of St Paul's cathedral, in London. It was interesting throughout, starting from the calorific and locomotion requirements of Homo neanderthalensis , passing through reference to Valentine's Day excess, and finishing with the observation which caught me to spark this post: "eating is a moral issue in a hungry world".

When it becomes available, I'll add a link to the MP3 file download. Here, after a delay of a week because something happened at the BBC's site, is the player link.

Response to events like the Isra'eli assault on Gaza should not obscure the ongoing, everyday violence inflicted on a majority of our world ... of which hunger is both a significant component and an avoidable foundation.

21 September 2008

PRT responses to Dr C and Poor Pothecary (1)

For some time, I've been trying to redeem that IOU which I rashly left on the 12th (almost prehistory in blog time), promising to discuss prospect/refuge theory in response to Dr C's and JSBlog's comments.

Alas, it hasn't worked. All attempts to construct a thoughtful essay which gathered in and marshalled all my thoughts on the subject just built messier and messier versions of the same self indulgent ramble.

So... I've given up, and will attempt a series of short postcards, taking each thought one at a time.

Let's start with Dr C's assurance that "that we are not born with a fully developed Prospect-Refuge mentality". I fully accept that. He goes on to add that he is sure "the neural pathways that allow the adult to express this behavior are there in some kind of Ur-network way", which I also agree with one caveat which I'll come back to.

A preliminary disclaimer: although I'm not quite a lay person where developmental psychology is concerned by comparison with Dr C's professional background I might as well be. Anything I say is either empirical or tentative exploration of what may be true alongside anything Dr C has said (or will say), and not in opposition to it. For apparent contradictions I may seek resolution; from real ones, I back down and no contest.

The clear truth, I think, is that we are not born with a fully developed anything – certainly in the psychological sense. That's precisely why we are so evolutionarily successful. Like the PC on which I'm typing this, we come with a hard wired BIOS plus a basic toolkit of peripheral drivers and the rudiments of an operating system assembled for us by evolution to give us head start in the fundamentals of learning. The full form of the operating system, and the applications software layer on top of that, are bootstrapped from the foundation set by early experience of specific environment partially mediated through parental and social attentions.

(Dr C may well, by now, have decided that I'm talking complete rubbish ... but making a fool of myself rarely stops me from putting my foot in my mouth, so let's press on.)

Observation of both human and other "higher" mammals (I shall be talking about cats in due course) convinces me that they have a very firmly encoded set of basic software (to that, also, I'll return in another post). How far, and to what extent, it is used depends on environment ... but the ways in which the organism learns from the environment is shaped by that basic software – and remains available to new learning in new environments, later in life. Specifically, I am empirically persuaded that a fundamental prospect/refuge instruction set is present in every animal I've been able to observe.

That's enough to be going on with. Part 2 will chug along in due course ... though its form will probably depend upon responses (if any) to this one.

24 May 2007

Atlas dithered ... shrugged ... looked for common cause.

Nature or nurture ... an old debate, but never really laid to rest. Pretty much everyone agrees that we are a mixture of both, but no two people can quite agree on the composition of that mix.

Two friends have just exchanged differences of opinion on one aspect of this, prompted by an article here which suggests that we are neurologically "hard wired for empathy". It links with the digital free will thread weaving back and forth between here and Dr C's place; Dr C is far better qualified to comment than I, but I'll have quick layperson's poke at it anyway from a purely cybernetic viewpoint.

My two friends fall on either side of me in their responses: one optimistic, one pessimistic. On the one hand, human beings are wired for empathy and that's our hope for the future; on the other, we are a nasty brutish lot who act only in our own narrow self interest. Me, I think both can probably be true at once - and hope, like despair, lies exactly in the fuzziness of our programming.

It's obvious that we must have some level of hard wiring. At the most basic level, we must have the equivalent of a PC's BIOS - instructions which tell us how to get started, how to learn and how to stay alive long enough to do it. The work of Jaroslav Koch[1] showed (however morally uncertain I may be about his methods) that a human baby left largely to its own devices can learn an extraordinary amount in a very short time - like climbing ladders by age eight months, for example. In many aboriginal societies it is, or was, the habit to throw babes in arms into water - where they show an innate ability to swim, without any of the protracted learning which we need later in life.

It's also obvious from our extraordinary adaptability that we are very open to sophisticated responsive self programming through experience. Empirical observation suggests that we can, in some cases at least, even override the hard wiring where experiential programming gives a better result. We are also able to adapt our most fundamental sensory and motor apparatus to tasks far from the evolutionary inheritance which shaped them - such as reading the forces at play on a car and responding reflexively with control movements.

Given that flexibility and adaptability, it seems at one level not to matter what is hard wiring what is software. What matters is the final result of the mix.

Getting back to altruism and selfishness ... it seems likely to me that, for a social animal in a hostile environment, both would have been necessary to survival. A social animal which does not act to maximise the welfare of the group will reduce its own survival potential, since the group may be wiped out and leave the animal alone at the mercy of its enemies. Evolution would therefore select in favour of altruism. Only when the group had broken down to the point where it no longer offered mutual protection, or when resources were insufficient to sustain the whole group, would "every ape for itself" make survival sense - but, when that point came, evolution would select in favour of ruthless selfishness. The result, then, would have been a total control system which contained both imperatives in variable and conditional balance.

The real problem in today's world is that all of this relates to the group of which the individual organism feels itself to be part. Other groups are "them", and the survival advantages of altruism towards them would be far less clear - indeed, in competition for scarce resources, it would be a disadvantage. Individual selfishness, in time of group solidarity, would therefore transfer to the cause of group selfishness, the group being a single entity ("us") in the larger context of other groups ("them").

The group, in the aboriginal state, would have been extended sexual units. As populations rose, as social complexity increased, as agriculture and settlement and commerce developed, the group would grow and extend: tribe, nation, state. But the basic dynamic between groups would remain the same, as would the tension between selfishness and altruism within the expanded group itself.

If genetic selection for altruism (whether hard wired or programmed) is to operate in larger contexts, we will have to learn how to see larger groups of "them" as "us". That seems feasible, given time: in the definition of "us", humans are as flexible and adaptable as in everything else, and the expanding scope of communications between people blurs the us/them boundaries.

Looking around me, people have an astonishing plurality of "us" and "them" definitions, and an even greater capacity for defining the same person as both "us" and "them" in different circumstances. Generally speaking, clear external threat encourages bonding together of larger "us" groups, while general insecurity encourages fragmentation - which fits pretty well the idea of a social animal balancing two contrary survival imperatives between individual selfishness and group loyalty.

I seem to have wandered considerably off the point. Those who know me will tell you that this is nothing unusual. To try and salvage something from the tangled ball which I have created: I'm not sure it really matters whether or not we are hard wired for altruism; what matters is that we have the potential for altruism within our make up. To survive as a species (and, therefore, in a modern crowded, interconnected world, as individuals) we must both ensure that it is both triggered and encouraged. To do that we must act to ensure that self interest and altruism are, for as many people as possible, aligned.


1. Koch, J., Superbaby. 1976, London, Orbis. 0856134112 (pbk)

11 May 2007

Tunnels of the mind

Jim Putnam commented on, and extended, part of my Tube Tales post ("But the unknown is also potential opportunity") in ways that brought me back (tangentially, perhaps even tenuously) to Dr C's information thread.

For our ancestors, this tension between the twin responses of fear and curiosity was a daily knife edge of physical survival. I am starving; is this bright red berry food or toxin? If I take on this big animal I've not seen before, who will end up eating whom? Get it wrong and I die. Get it wrong in the direction of excessive caution and my whole group dies of starvation. Get it wrong too often in the direction of boldness and the group loses too many members to remain viable. For many, that remains real today: only those of us in the cosseted developed world can leave it to soldiers and explorers. My feelings at an unsigned side tunnel probably originated in the same dilemma: does this side path curving into unknown forest take me to a position of observational vantage, or past the eyes of a hidden predator? As Jim says, "without someone venturing into the unknown, much of our lives would be drastically restricted".

Jay Appleton's The Experience of Landscape is a fascinating exploration how such atavistic considerations shape the arts, and has a lot to say about wider responses. Jim extends them to the inner life: "It isn't merely venturing into the physical unknown ... ... ... Exploring the limits of our imagination can be frightening, but it can also be extremely rewarding."

One of my clichés (or, from a more charitable point of view, one of my articles of faith) is that "there is nowhere more exciting than the inside of my own head". So, I'm instantly in agreement with him (though without compromising my agreement with Dr C that the mind is absolutely dependent upon sensory data received from outside). "Head", here, is a shorthand placeholder, not a literal reference to a physical part of my anatomy.

I suppose what I really mean by "head", in this context, is partly that amorphous and wholly informational software construct which philosophers call "mind". Since I am wholly convinced by the theorem that mind is a function of body, and cannot exist apart from it, I am more comfortable with the word head. Nevertheless, mind clearly is no more the same thing as body than (say) Linux or Microsoft Windows is part of the PC on which it runs. As with a PC, though, it is impossible in practice to separate the pure idea of the program from the specifics of particular hardware: implementation is an amalgam of both.

Residing inside this head, probably straddling the hardware and software, are curiosity and caution. The balance between the two is, as I said above, a delicate one. It's my personal belief that what we derogatorily label "laziness" is one important subroutine of the caution architecture.

Curiosity makes me wonder about something ... that something is unknown, and so may be a threat or aid to survival. If the threat or benefit seems likely to be imminent, curiosity potential exceeds inertia and I investigate. On the other hand, investigating takes energy which I can't afford to waste - it may be needed at any moment for fight, flight or foraging. Or other curiosities compete with greater urgency, and I have to prioritise. Either way, if the strange something doesn't seem to be of immediate importance, I file the curiosity away in memory for possible future investigation and conserve energy.

Jim provides, in a later post, an example of how this translates to the unnatural ease of post industrial life. I have wondered since I was about eight or nine years old how "will not" became elided to "won't" ... but the curiosity never, over the decades, rose to a level which would have overcome the action threshold. Then Jim asked the question, which triggered a new state. Another member of my "tribe" had shown interest in the same object of curiosity. At one level, this emphasised its importance; it had become a tribal issue instead of an individual one. This particular curiosity suddenly exceeded the inertia which had previously restrained it - and I reached for the OED.

I was discussing this yesterday with two colleagues, a psychologist and a neurochemist, both of whom queried two aspects of the analogy which I am using here. First, they believe that by making a distinction between hardware and software, even for illustrative purposes, I am rendering my analogy worthless. There is only program: brain and body are integrally part of it, not platform and vehicle for it. At the same time, they also dispute the usefulness of analogies which encourage talk of a program, when both body and mind manifestations comprise an uncountably large community of quasi autonomous, competing, coëxisting, coöperating, interrelated, interconnected and nested programs.

Perhaps they are right; but I still retain a strong gut level faith in the power of story ... the phrase "gut level" being, quite possibly, more than figuratively true.


1. Appleton, J., The Experience of Landscape. Hull, 1986, Hull University Press. 0859584615.

09 March 2007

Modelling the ideal

(Declaration of debt: This one came to be written partly as a direct result of my conversations in here with Dr. C.)

Plato posited a cosmology in which the variability of what see we around us results from imperfect manifestation of ideal forms. So, for example, the large black horse and the small piebald horse you pass in a field are variant images of an ideal pattern of perfect horsehood. It’s not difficult to square this, at least intuitively, with modern ideas of micromutation and genetic blueprints. It is also a view of the universe mirrored in the idea of a theoretical model – the model being an idealised image of the varying reality (whatever reality may be, once you start looking at it closely). If all of this seems whimsical, consider the work of Dor Abrahamson[1] and others on how students learn statistics and probability concepts.

Statisticians have a very close, if ambivalent, relation to this business of models and ideals. Like sculptors working a block of marble in search of the form within, they seek to reveal the model which sits as a shining ideal behind the grubby uncertainties of real data – in fact, statistics could be defined as the quantification of deviance from the ideal. This Platonic vision is clearest in classical frequentist statistics with the attempt to place key population descriptors on one of a predefined list of approved mathematical distributions but it’s just as real, if less obvious, for Bayesian approaches. Even where models are not themselves statistical, do not themselves use statistical methods, and eschew any statistical connection, they are usually derived from origins in probabilistic investigation and their relation to reality is therefore a statistical concern.

IBM, for instance, is interested in building cerebral cortex biomimetics using confabulation theory. UCSD’s Robert Hecht-Nielsen, in a talk to IBM’s Almaden Institute on Cognitive Computing last year, emphasised that confabulation architecture contains ‘no algorithms, rules, Bayesian networks, etc’[2]. Confabulation, however, depends on maximisation of cogency, and cogency is defined by a probability statement of relation between assumed facts, so evaluation of outcomes as mimesis is a statistical exercise in biocomparison (Bayesian and otherwise). I hope to return to this in a future issue.

Less ambitious than modelling the functions of the cerebral cortex itself, though not necessarily less interesting, is statistical study of the braincase which contains it. This is the aim of a research study, still in the unfunded preapproval pilot phase, by a young African academic. Since the work is contentious for sociopolitical and religious reasons, and nascent careers fragile, I won’t identify the researcher or university more closely than that; my primary interest here is, in any case, not the study itself but the informational framework within which it is to be conducted. It asks whether there is an evolutionary ‘trajectory’ for evolutionary development of the cerebral cortex, indirectly inductable from analogous trajectories of three hundred descriptors for the physical forms of the cortex components and the container within which they sit. [...More]


[1] Abrahamson, D., Bottom-up stats: Toward an agent-based “unified” probability and statistics, in Small steps for agents… giant steps for students?: Learning with agent-based models. 2006 San Francisco, American Educational Research Association.

[2] Hecht-Nielsen, R., The Mechanism of Thought. 2006 San Diego, California, USA, IBM Almaden Institute on Cognitive Computing.

[3] Mithen, S.J., The singing Neanderthals: the origins of music, language, mind and body. 2005, London, Weidenfeld & Nicolson. 0297643177 (hard).

[4] Rao, C.R., Journal of the Royal Statistical Society, "The Utilization of Multiple Measurements in Problems of Biological Classification". 1948. 10(2): 45pp.

[5] van Vark, G.N., Statistica Neerlandica, "Some applications of multivariate statistics to physical anthropology". 2005. 59(3): 10pp.

[6] Thomson, A. and Randall-MacIver, R. Ancient Races of the Thebaid. 1905, Oxford, Oxford University Press