Thursday, January 28, 2016

Nature, Nurture, and the Height of Racism

Or why biological differences between difference "races" are not necessarily anything to do with "race"

This post is not really about human height or race or nature versus nurture (though it concerns all these subjects) it is about the way in which we are so easily led astray when we think about such matters.

People from (say) the UK who go to (say) Japan (I haven’t as it happens) tend to note that the average Japanese person is shorter than the average person back home. This is certainly a recurring theme in the (sometimes borderline racist) film Lost in Translation[1] – though the visitors in that case were, of course, American.

What is the explanation for this difference? It is tempting to jump to the conclusion (as the Daily Telegraph’s questionable Short people have 'shortage' of genes - from where I stole the picture of the three women above - appears to) that it is all down to genes.

I suppose the reasoning goes something like this:

1) British people are taller (on average) than Japanese people (probably true).

2) Height is highly heritable (certainly true).

3) British people have different genes to Japanese people (sort of true).

ergo

The difference in the average height of British people and Japanese people is explained by their differing genetic make-ups (QI-style klaxon should go off).

Counter-intuitively (at least if your intuitions are the same as mine were before I knew anything about genetics) this reasoning is entirely fallacious[2]. NB: This is not to say the conclusion itself is necessarily wrong. I do not actually know how much, if any, of the average difference in height between British people and Japanese people is explained by genes and I am not sure anybody really does for certain. Moreover, I do not think this is a particularly interesting topic. The reason why the reasoning presented above is wrong is, however, rather interesting.

Let us take each of the premises in turn:

1) British people are taller (on average) than Japanese people

According to Society at a Glance 2009: OECD Social Indicators - OECD 2009, the average height of Japanese men was 1.72m (when measured in 2005) and that of UK men 1.77m (when measured in 2006). So there is an average difference, but only one of about 5cm.

2) Height is highly heritable

A few years ago there was a comedy film (which I confess I’ve never actually seen) starring Arnold Schwarzenegger and Danny DeVito masquerading as (presumably) dizygotic (non-identical) twins:

It is well established that tall parents tend to have tall children and small parents tend to have small children. Of course, we can all think of exceptions to this “rule” and if AS and DD really were twins they would constitute such an exception. In real life, we know that AS and DD are not really twins and I rather expect that AS had taller parents and DD had shorter ones. But I think we can safely assume that, even if they had been brought up in the same household and given the same diet and activities throughout life, AS would have still turned out much taller than DD. To put this into scientific terms: the variation[3] in human height across populations really is largely explained by genetics – approximately 80% of the variation according to Scientific American.

3) British people have different genes to Japanese people

What probably strikes most British people first about Japanese people is their epicanthic eye folds – though this trait is by no means exclusively found among Japanese and other East Asian people. The trait is also sometimes encountered in “white” people in places like Poland and Finland and in “black” people and in parts of Africa in places such as Namibia. The trait is nevertheless, even if not a necessary or sufficient condition of “Eastasianess”, clearly genetic. Japanese people (unlike Brits) also tend to be lactose intolerant. This is another clearly genetic trait - albeit a less visible one and one that is also found (somewhat surprisingly) in my very Teutonic looking German nephew and, as it happens, in most of the world’s population[4]. Height in humans is, to the extent it is determined by genes, determined by lots of different genes working together in complicated ways and it is entirely possible that “tallness genes” are less common among Japanese people[5]. But the fact that Japanese people have characteristic features or eschew the consumption of lactose-rich comestibles gives us no particular reason to jump to any conclusions on the presence or absence of other genes in that population[6].

But surely, the man on the Clapham Omnibus insists, consistent differences – with respect to highly heritable characteristics (like height) – between distinct populations must be largely due to nature rather than nurture?

As the song goes, “it ain’t necessarily so” …… and here’s an explanation of why:

Imagine that the aforementioned Arnold Schwarzenegger and Danny DeVito had both really been blessed with twin brothers - monozygotic (identical) twins. Let us call them Colin Schwarzenegger and Basil DeVito. Let us further imagine that the two sets of twins were cruelly separated at birth and each paired off with one of the other set of twins: Arnold and Basil banished at birth to the otherwise uninhabited “Short Island” (an Island where there were very meagre supplies of food); and the (more fortunate) Colin and Danny to “Long Island (where food was plentiful).

On Short Island, A and B both reach adulthood but their growth is stunted:

The luckier C and D on Long Island achieve their full potential (at least from a growth point of view):

(I don’t know how they came by their suits.)

So here we have a case where there is a significant average difference between the (admittedly small) populations of the two islands and where the difference relates to a highly heritable characteristic (to wit height). The variation in height (the difference between A and B on SI and the difference between C and D on LI) is (assuming they shared their rations on SI fairly) entirely due to genetics. Nonetheless, the difference between the two populations, in this thought-experiment, is entirely explained by the differences in the two environments.

This example is, of course, rather contrived. In real life, it is far more difficult to establish whether differences within and between populations have largely (or entirely) genetic or environmental bases. But what this example conclusively demonstrates is that argument presented at the start of this post is a non sequitur. Just because there are significant differences (with respect to highly heritable traits) between nations or races (or any other groups of individuals we care to demarcate) does not entitle us to conclude that those difference are explained by nature rather than nurture.

In other words, the mere fact that differences in height within the UK and within Japan are largely explained by genetics does not - in and of itself - entitle us to conclude that the difference between the UK and Japan explained by genetics. Armed only with that information, we cannot decide whether the difference between the two populations is largely (or entirely) explained by (say) diet rather than by genes. Neither conclusion is ruled out or established by the fact that height is highly heritable.

So next time you hear someone observing that “Jews are clever with money” or “Black people make good runners and have a good sense of rhythm” or “Asian people are highly intelligent” or “Hungarians are good at chess” or whatever, please bear in mind that, even if such claims are statistically true and even if being good at handling money, running, playing the drums, and playing chess are highly heritable, it doesn’t necessarily follow that Jewish, Black, Asian, or Hungarian genes have anything much to do with the observations made.

It should, perhaps, also be added that (let’s play safe here and take the most innocuous example) even if there are genes for being good at chess and these really are more common amongst Hungarians and this “fact” really does explain Hungary’s historical prowess in this field, the implications for social policy are very limited. After all, we know that men are better at running than women and that this fact is explained by biology (men are, after all, taller than women); but if you had a requirement for a fast runner and Paula Radcliffe and I applied for the job, I rather think it would be a mistake to be guided in your choice of candidate by your knowledge of general biology and gender.

In short, neither reason nor science do (or could) lend any support to racism (or sexism).









  1. A film – like the even more questionable Breakfast at Tiffany’s - I confess I rather enjoyed, despite my discomfort at the casual (though unconscious and unintentional) racism.
  2. Of course if the trait were 100% heritable (like blood grouping) such an inference would be valid.
  3. I wrote here about the different between explaining things like height by genetics and explaining the variation in things like height by genetics.
  4. A story for another day.
  5. The implication of the article I pinched my picture from.
  6. I explore the theme of race and genetic essentialism here.

Thursday, December 3, 2015

Why are there no unicorns …. or are there?

Charles Arthur (@charlesarthur), reacting to a question from a ten year old, posted the following tweet:

Which turns out, like many “silly questions” to be a rather profound one … and one which I certainly struggled to answer (if you have any more answers or object to any of my reasoning or claimed facts, please comment below).

The initial pedantic responses to the question from various geeks like me (and indeed – in one case - from me) pointed out that rhinos don’t have true horns (their “horns” comprise matted hairs) and that they do usually have two horns (one behind the other). But neither of these observations (relevant though they are) do anything to diminish the force of Charles’s question.

As Charles responded to one claim that rhinos don’t have horns: “let’s impale you on one and see how that goes”.

Lots of creatures have horns, antlers, tusks, swords etc, which I shall generalize to: Pointy Things Sticking Out Of Their Heads (PTSOOTHs). Swordfish, walruses, elephants, deer, narwhals, rhinoceroses, and many others spring to mind in this context.

Ptsooths may be composed of bone, cartilage, hair, skin, or tooth enamel. Ptsooths start out, in evolutionary terms, as small bumps that confer some tiny advantage, and evolve from there. They may serve (or have served in different phases of evolution) various purposes which include: protection from predation, hunting weapons, digging tools, and sexual signalling devices.

The term “sexual signalling devices” covers a multitude of sins here. Huge antlers may signal “don’t mess with me” to rival males (and may be used to actually fight rival males) and “please mess with me” to females. In this kind of situation, runaway sexual selection often occurs and – as with the peacock’s tail – we can end up with ptsooths that are far too big for the purpose for which they originally evolved and that may actually be an encumbrance for the ptsoothholder – at least in its non-sexual life.

But to get back to the real topic here, all vertebrates have basic bilateral symmetry[1]. The symmetry is not absolute. Most men have unsymmetrical testicles and while we usually have two lungs and two kidneys, humans only have one spleen, one penis/clitoris, and (timelords aside) one heart. Our single heart does not, however, offend the basic symmetry of the body as much as many imagine:

[2]

The spleen does:

[2]

But these are soft tissues. Vertebrate skeletons are far more symmetrical and (save for the backbone itself and a few other bits) contain two of everything. In particular, the skull (or at least areas of the skull from which ptsooths grow or could grow) develops (embryologically speaking) from two symmetrical sets of bones that fuse together.

[3]

You can see the join!

Jaws (mandibles), foreheads (frontal bones), crowns (parietal bones) are all made from two symmetrical halves with a join (suture) down the middle. Even “single” skull bones – like the occipital bone at the back of the skull – are formed (earlier on in embryo development) from two (or four) initial symmetrically arranged sites.

So to really come to the point (pun intended) animals with ptsooths generally have two or four or six – ie even numbers of ptsooths – because they grow ptsooths from bits of bone that come in pairs and not from the joints between them.

So this could be why there are no unicorns …… but (to go back to Charles’s initial question) what about rhinos? (Let’s just consider the long front horn or consider Asian rhinos which do only have one horn it seems[4]).

Well because the rhino “horn” is essentially a modified tuft of hair, it was free to start evolving wherever on the skull it wished to. After all, many of us have tufts of hair between our eyebrows or on our noses (which many of us pluck out in order not to further enhance our rhino resemblances). Both single or double ptsooths could be useful and the rhino went for a tandem (or single) arrangement because it could[5].

It should be noted that both rhinos and deer still have bilateral symmetry – if Damien Hirst sawed either in half down the middle he’d end up with two pieces that were essentially mirror images of each other. (By the way, I wonder what he did with the other half of his shark?)

”But what about narwhals (the ‘unicorns’ of the sea)?” I hear you all cry.

Well this is where it starts to get really interesting! (So I hope you’ve persevered this far.)

The narwhal[6] “horn” is in fact a tooth – a left canine tooth to be precise. It grows very long and in a helical fashion. The socket for the tusk has migrated very close to the line of symmetry of the narwhal and grows straight forward – providing the unicorn-like appearance:

[7]

– but narwhals are actually slightly asymmetrical:

[8]

Very occasionally, narwhals grow two tusks, but they never grow a single right tusk or reverse the handedness of the helical twist of either tusk.

Unicorns also have a twisted horns and it is often claimed that depictions of unicorn horns were based on observations of narwhal horns.

[9]

Unicorns, however, twist both ways:

[10]

There again, so does DNA – in its depictions! In real life, DNA[11] only goes one way – the opposite way to the narwhal horn.

The ancestors of modern deer also had tusks[12]. Later they evolved horns and their tusks withered away as their horns grew. I see no reason – in principle – why deer or antelope (or other ungulates) could not have evolved to grow (say) only their left horns and why that single horn could not (with a slight asymmetrical deformation in skull development) have moved over towards the centre of the head. Such a “unicorn” would not be quite symmetrical but, given that they have helical horns, unicorns aren’t really symmetrical either.

In fact, thinking about it, I don’t really see why – if the horn were composed of two fused halves (like the swordfish “bill”) – we couldn’t have had a “unicorn” with a single symmetrical untwisted horn.

Moreover, if the frontal and parietal bones of the skull withered away and the occipital bone filled in for them (stranger things have happened in skull evolution) why couldn’t a single horn develop from the middle of that bone in roughly the right place for a unicorn style horn? I know not.

In conclusion then, I have no idea why there are no unicorns …… perhaps there are!



Postscript: Since writing the stuff above, Rab Austen (‏@RabAusten) has reminded me that the triceratops also had a (front) horn on the midline of its skull. This was a "real" (bony) horn and would - as Paolo Viscardi (‏@PaoloViscardi who has forgotten more about bones than I shall ever learn about them) kindly confirmed - have been formed from the fusing of two symmetrical elements - like the swordfish bill. I'm not sure whether a horn formed like this could then grow with a helical twist (though as Paolo also points out, stranger things happen at sea) but Rab's insight certainly lends support to the claim that there is no reason - in principle - why a horse-like creature could not have evolved a bony horn in the middle of its forehead.


  1. Invertebrates often have bilateral symmetry too. Even starfish - which superficially have radial symmetry - have a complicated and interesting way of forming that involves bilateral symmetry. Other invertebrates - snails and sponges spring to mind - break the "rule" in other ways.
  2. http://keckmedicine.adam.com
  3. http://http://fineartamerica.com
  4. Thank you to Steve Jones (‏@TheEulerID) for this information
  5. http://news.bbcimg.co.uk
  6. Please note that evolution does not work in the way I talk about it (metaphorically) in this post. Evolution has no plan, intent, or purpose. It's all natural (or sexual) selection acting on random mutations, It is, however, often easier to describe what happens in evolution using teleological language - as long as we don't forget that it's just a metaphor! OK?
  7. I'm getting all my information about narwhals from Chris McManus's excellent Right Hand, Left Hand which I urge you all to read.
  8. https://cdn-images-1.medium.com
  9. http://www.mermaidsrock.net
  10. http://http://kristell-ink.com
  11. OK I'm talking B-DNA not Z-DNA ... pedant!
  12. Deer Antlers: Regeneration, Function and Evolution by By Richard J. Goss esp p72 et seq

Monday, August 4, 2014

The riddle of Ridley

This piece was inspired by Nick Cohen’s piece (which I urge you to read) in yesterday's Observer: Why do we still honour free-market intellectuals? (It's mystifying that the former chairman of Northern Rock is still garnering plaudits).

The author of our current misfortunes?

Matt Ridley (AKA The Right Hon Matthew, 5th Viscount Ridley) is famous (or perhaps infamous) for (let us put this as neutrally as possible) being “in charge” of Northern Rock when it went pear-shaped (to use a metaphor borrowed from biology) in 2007. This debacle was the first (at least the first that came to everyone’s attention) in a series of events that culminated in the virtual collapse of the UK banking system and the economic mess from which we are only just recovering (at least if the optimists are to be believed).

I, however, knew of Matt Ridley long before 2007, as the author as a series of books on evolutionary biology and genetics. While I should hesitate to recommend Dr Ridley’s financial advice to anyone (ditto his views on climate change – but that’s a story for another day), I should have no hesitation in recommending his excellent popular science books.

The only criticism I might make of those books is that Ridley is sometimes too ready to borrow metaphors from evolutionary biology and try and apply them in his thinking on how the economy works or (even more tendentiously) ought (in a moral sense) to work. You can often see this species of thinking lurking below his writing. Richard Dawkins (who writes in similar fields and has often worked alongside Ridley) is rather more keen to note (though I am paraphrasing Dawkins here) that just because nature is “red in tooth and claw” it does not follow that the best run economies are, or that (even if such economies were the most financially successful) they would be an ethical success.

But let us move on and look at some (evolutionary) science……..

First, some human psychology:

It is a puzzling fact about humans (revealed in a number of experiments) that when acting as an audience at (say) a random number guessing game, they will accord extra respect to those who guess the “correct” numbers (and less respect to those who guess the “incorrect” numbers) even though they know the game is entirely random. If popular films are an accurate portrayal of reality (I would not know as I have never entered a casino) winners at roulette accrue similarly inflated (and entirely undeserved) prestige.

Of course, winning at some gambling games – for example Black Jack – can be a sign of cleverness. If you can remember the sequence of cards and calculate the odds in your head as the game progresses you can stack the odds in your favour. But usually, gambling involves pure chance. It is often claimed that some people are “expert” poker players, but the last time I read something on this subject, the author was suggesting that the statistics on this are by no means unequivocal. It is entirely possible (he opined) that “top” poker players are simply “lucky” poker players.

So why do we admire people who happen to make the right (entirely serendipitous) guesses? One answer I have seen put forward is that we (for evolutionary reasons) prefer to ascribe what happens in the world to agency rather than to random chance: the movement in the bushes might be a random effect of the wind, but those who assumed it might be a stalking lion were more likely to live long enough to become our ancestors.

Secondly, some evolutionary theory:

It was at one time thought - even sometimes by Darwin himself (despite what we often read and despite the fact that the modern non-Lamarckian theory is styled “Darwinian”) - that a significant element in evolution is the inheritance, by offspring, of characteristics acquired in life by parents. The example usually given of this sort of phenomenon is the ancestors of the giraffe having to stretch their necks to reach the leaves of tall trees and then passing on their elongated necks to future generations who then did the same and became taller still.

Microbiologists were among the last scientists to disabuse themselves of Lamarckian notions. The example of giraffe gymnastics is clearly far-fetched but, for a long time, it really did seem as though populations of bacteria could be "trained" to survive increasing concentrations of antibiotics in their growth media – like heroin addicts learning to tolerate increasing doses of their chosen drug I suppose – and could pass this learned ability on to their daughter cells. What actually happens is that a few “lucky” mutant bacteria just happen to survive each round of antibiotic treatment and go on to produce new generations with a similar genetic make-up (plus a few new mutants).

In other words, the successful bacteria do not owe their survival to any of their own achievements in life.

Perhaps you can already see where I am going with this ………..

Bankers

Certainly until the events of the last few years, I suppose that people naturally (and as we have seen for good evolutionary reasons) tended to assume that successful bankers were successful because they were highly talented people who owed their success to their talents. Successful bankers were awarded prestige and honours and, even though some people wondered aloud whether bankers really deserved to be paid salaries and bonuses hundreds or thousands of times greater than what (say) a university researcher discovering a new antibiotic might expect, most people accepted that successful bankers deserved high salaries.

But there’s an entirely plausible alternative hypothesis for what the mechanism at work here is – made all the more plausible since the events of 2007. What if bankers make entirely random decisions? The financial environment in which they make those random decisions, selects some to survive and prosper, and some to go bust; but the bankers themselves have no more special foresight than bacteria growing on media contaminated with varying concentrations of antibiotic.

What, in short, if banking (and perhaps commerce in general in a market economy) is Darwinian rather than Larmarckian?

What if successful bankers do not deserve any more reward in life than successful bacteria?

Given Mark Ridley’s fondness for drawing parallels (at least implicitly) between evolutionary biology and the financial world, I am surprised he has never given serious consideration to this hypothesis. And, even more to the point, subscription to such a hypothesis would entirely absolve Matt Ridley of any culpability for the plight of millions who have been far less fortunate in life than the Viscount and who now find themselves at the (lack of) mercy of events which were certainly beyond their control.

(Also published at Bad Reason)

Sunday, October 27, 2013

Why Michael Gove's department is confused about genes and education; and why you probably are too.



In the Guardian on Saturday October 12 it was reported that Michael Gove's special adviser Dominic Cummings had "provoked outrage" by claiming that "up to seventy percent of a child's performance is related to his or her genes".

Now it seems that Mr Cummings has been mis-quoted here. I happen know this because he told me himself in a tweet. His twitter name is @odysseanproject – which I suppose will amuse fans of Diary of a Nobody. Mr Pooter’s favourite joke about his friends Gowing and Cummings was that Gowing was always coming and Cummings was always going.

But I digress.

What the Guardian ought to have said and (it seems) Dominic Cummings did say is that "up to seventy percent of the variation in children's performances is related to their genes".

So why is that different from saying "up to seventy percent of a child's performance is related to his or her genes"? To see why, we need only consider the following simple thought experiment:

Imagine you adopted two randomly chosen children born one the same day (Mary and Jane perhaps) and gave them exactly the same upbringing, environment, life experiences, and education. (Of course that would be impossible in practice, but this is only a thought experiment.) Now imagine that we tested them both (several times perhaps to make sure one of them was not having an off day) at eighteen years old and Mary got straight Bs and Jane got straight Cs.

The variation in the results of the two individuals must, I hope you see, be entirely due to their respective genetic makeups.

Now let us repeat the thought experiment but provide much better education. This time (we could imagine) Mary gets straight As and Jane gets straight Bs. The variation in the results of the two individuals must still be one hundred percent due to their respective genetic makeups. The improvement in results is, however, entirely due to the change in environment - specifically the improvement in education.

This observation illustrates why Dominic Cummings's statement (as mis-reported) is drivel. The seventy percent figure relates to the explanation for the variation in a population not to the performance of an individual.

Asking about the relative contributions of genetics and environment to a particular child’s performance is a bit like asking what whether the height or the length of a rectangle contributes most to its area. Such a question makes no sense.

Asking about the relative contributions of genetics and environment to variation, on the other hand, makes perfect sense.

Some things in a human population may be vary a lot – like personal income. Other things in a human population may vary much less – like height – you do not find people who are two million meters tall for example.

The degree of variation in a population can actually be quantified. (This is quite complicated, and there are different ways of doing it, but let us just stick with the basic idea.) Once we have quantified the amount of variation, we can talk about what factors contribute most to that variation.

If, in the case of school children and academic performance, we took away one of the contributions to variation (which we could do in theory) by breeding a cohort of school kids who were all genetic clones (which would take away the variation due to genetics) or by giving a cohort of school kids exactly the same education (which would take away the variation due to quality of education); in either case, the amount of variation in the population would be reduced. It would obviously be reduced more if you took away whatever was making the biggest contribution.

If we pretend for the moment, and for the sake of simplicity, that education and genes are the only factors (of course there are many others such as social class, but let us keep things simple) what may seem slightly paradoxical is that if we gave all children exactly the same education, though this would reduce the variation in the population, it would increase the relative contribution of genetic factors - it must do so because all variation in a population receiving exactly the same education must be down to the genes.

Of course, as I expect almost everyone agrees (regardless of their politics) the variation in academic achievement (and many other attributes) of the population depends on a complex mixture of factors. Teasing out the relative contributions of the various factors is far more tricky than you might think. Even if we take something like height - which is far easier to measure objectively than academic ability and is undisputedly highly heritable (tall parents tend to have tall kids and vice versa) - it is still far from clear to what extent the variation in human height around the world is down to genes or environment.

I have no idea what the correct figure is for the genetic contribution to the variation in academic achievement in the population at large, but (though I am very much on the political left) it wouldn't surprise me at all to learn that the true figure is even higher than seventy percent.

But, given the fact that nobody knows the facts for sure, people at either end of the political spectrum are wont to provide ideologically-driven rather than data-driven answers to the empirical question: How much is nature and how much is nurture? Hence the irate tone of much of the discussion on this topic in the media this week.

The left's commitment to egalitarian principles lead them to conclude that it must be mostly due to nurture. Only if we believe that, they suppose, can we imagine a future where social inequities are put right through progressive social intervention.

The right's commitment to in-egalitarian principles lead them to conclude that it must be mostly due to nature. Only if we believe that, they suppose, can we justify the claim that doing anything to improve the lot of the hoi polloi is a waste of time.

So why do I claim that both sides get the whole thing rather back to front?

Let us conduct another couple of thought experiments:

First let us first suppose that we have the most extreme case possible of the frequently encountered left-wing belief about the way the world is. Everyone in our imaginary society is a genetic clone with an exactly equal genetic endowment of academic potential and any differences in ultimate achievement will be entirely due to how we nurture the individuals concerned. How would we then structure our education system? We should have to choose individuals completely arbitrarily from the pool and train some of them up to be clever enough to be surgeons or rocket scientists or whatever; and - at the other end - some of them to be just clever enough to tie their own shoe-laces so that they could perform jobs requiring very little intelligence - like the job of Education Secretary I suppose.

But isn't this more or less what right-wing education policy has always been (and what the likes of Michael Gove and Dominic Cummings seem to want to go fully back to): a system where people are picked arbitrarily from the pool on the basis of social class (rather than innate ability) and given the training they require to fulfil their allotted stations in life?

Now, instead of a society of genetic clones, let us imagine a society where everyone is born with different potentials. No matter how well I had been nurtured, I could never have become a Premiere League football player; and the likes of Michael Gove could, no matter how well he had been nurtured, never have understood averages or become a professor of thermodynamics.

...a bit like the world Dominic Cummings and other right-wingers (probably largely correctly) believe we do inhabit.

In this world, it no longer makes sense to choose people arbitrarily from the pool and nurture (only) them. The only policy that makes sense is to nurture everybody so that each person achieves the best he or she is capable of and those who come out on top represent those who started out with the best genes rather than those who were fortunate enough to be given an education.

...rather like the sort of education system left-wingers tend to argue for in fact.

Okay, I've over-simplified here and rather caricatured the various political positions, but I hope I have also successfully made a serious point: the thinking about nature and nurture, on both left and right, is often terribly confused.





A version of this post was included in the @pod_delusion podcast of 2013-10-17.

Thursday, April 25, 2013

DNA double helix: 60 years of sexism in science

Picture 51

Rosalind Franklin 1920-1958

Sixty years ago today, on 25 April 1953, Francis Crick and James Watson published a paper in Nature describing the double helix structure of DNA.

There have been a flurry of excellent articles in the newspapers to commemorate this auspicious anniversary and, (especially) if you are at all unfamiliar with the history and significance of Crick and Watson's discovery, I wholeheartedly recommend Adam Rutherford's piece in today's Guardian.

Adam also relates some details of Rosalind Franklin's story and the way she was belittled by her male colleagues. Franklin's contribution to the unravelling of the structure of DNA was, to some extent, written out of history - a wrong which has only been righted in relatively recent times - and a number of commentators have sought to rescue her reputation (as they see it), set the record straight, and put Rosalind Franklin's name up there where it belongs alongside Watson's and Crick's. (see for example Anne Sayre and Lynne Osman Elkin)

This is not, however, quite the simple female-goody versus male-baddies tale that some modern accounts suggest. Real stories rarely fit tidy narratives.

Part of the reason Rosalind Franklin was "written out of history" is simply the fact that she died tragically young and Nobel Prizes are never awarded posthumously. Of course whether she would have received the Prize if she had lived is impossible to say, but even Jim Watson is on record as saying that she should have done. The famous Picture 51 (above) which played a crucial role in the DNA story is often credited to Franklin (see eg wikipedia) and is certainly testament to her skills in this field but it was actually taken[1] by her (male) student Raymond Gosling who (as Adam Rutherford also notes) has been written out of history to an even greater degree than his female supervisor. While Jim Watson is astonishingly patronizing in the pages of The Double Helix : A Personal Account of the Discovery of the Structure of DNA, Francis Crick (as is often noted) is far more generous to Franklin and fully acknowledges the significance of her contribution. He does, however, correctly point out that X-ray crystallography alone could never have revealed the detailed chemical structure of DNA and that the Crick/Watson approach to the problem and Franklin's approach were very much complementary strands (if you'll forgive the pun).

As I say, life is complicated.

But regardless of the complex twists and turns (sorry I can't help myself) of history and science, there is no doubt, however, that Rosalind Franklin was the victim of appalling sexism - and not just from Jim Watson.

Inspired by the various newspaper articles I read today, I dug out my copy of What Mad Pursuit (Crick's autobiographical account of the subject at hand) and reminded myself of one or two things he had to say:

People have discussed the handicap that Rosalind suffered in being both a scientist and a woman. Undoubtedly there were irritating [sic] restrictions - she was not allowed to have coffee in one of the faculty rooms reserved for men only - but these were mainly trivial, or so it seemed to me at the time. (op cit p 68)
Well yes, but though I'm a man, I can kind of imagine that a woman might find something like that a teensy bit more than "trivially irritating".

Crick goes on to say:

Feminists have sometimes tried to make out that Rosalind was an early martyr to their cause, but I do not believe the facts support this interpretation. [...] I don't think Rosalind saw herself as a crusader or a pioneer. I think she just wanted to be treated as a serious scientist. (ibid p 69)
Now perhaps I've got the wrong end of the chromosome here, but I always thought that a world where women can be treated as serious scientists is exactly the sort of thing those dreadful feminists have always been arguing for.

As a younger man, Crick and Watson's work inspired me to go to university and study genetics. It's hard to imagine they inspired many women to do the same. Let us hope that one legacy of the Rosalind Franklin story is that the next sixty years see many more young women entering science and being taken seriously when they do.



[1] The only reason I know this is again down to the aforementioned Adam Rutherford.

Monday, August 27, 2012

RNA, the True Secret of Life?





In THE DOUBLE HELIX A Personal Account of the Discovery of the Structure of DNA, James Watson narrates the famous story of Francis Crick bursting into the Eagle Pub to tell everyone within earshot that he had found the secret of life.

Certainly, DNA is one secret of life and (leaving aside a few viruses – which aren’t really alive) is a common (and rather vital) denominator of all terrestrial life. But life has many secrets. Since Crick and Watson (building on the often neglected contributions of Rosalind Franklin) elucidated the structure of DNA, life has revealed more and more of those secrets. But one important secret remains almost as well kept as ever: the secret of just how life emerged in the first place.

There are several rival theories as to how life may have originated on earth (or some other space-rock) but the question of just how we got from a non-living “Primordial Soup” to DNA-based life presents a particular puzzle.

What struck Crick and Watson immediately as they surveyed the model double helix they had constructed were the implications of that structure for DNA replication. Each strand of the DNA double helix comprises a series of nucleotides and (as was later found) these nucleotides constitute the individual “letters” of the DNA code. The two strands of the DNA helix are complementary and the sequence of one strand can be inferred from the sequence of the other. If two strands are separated and furnished with a supply of fresh nucleotides, each strand can serve as the template for the assembly of a new copy of the original double helix.

But if all DNA could do were to serve as a template for making more copies of itself, it would be pretty boring stuff. What makes DNA interesting is that it also serves as a template for making proteins.

It is important to realize here that while proteins are often structural molecules – like muscle proteins – they may also be enzymes – like the enzymes often included in modern detergents. Enzymes are tightly folded proteins that “catalyse” (ie speed-up without getting directly involved themselves) other reactions. Enzymes have specific shapes which allow them to bind to other molecules and thereby encourage those other molecules to react with one another. Enzymes are crucially important for regulating what goes on inside living things.

The way in which proteins (including enzymes) are produced from DNA is quite complex. The first stage involves the creation of multiple RNA copies of the “master” DNA template. RNA is a very similar molecule to DNA – consisting of long chains of nucleotides – but it is normally single-stranded. The second stage involves the creation (from the RNA templates) of long chains of amino acids (which is what proteins are).

But here’s the thing ....

In order to make proteins from DNA, and even to replicate DNA, you need to have proteins (enzymes) that make everything work properly. And where do these enzymes come from? They are coded for by the DNA.

While this system works perfectly well once it is all in place, it is difficult to imagine how the system ever got going in the first place. The solution to this conundrum is that the DNA/protein system is probably not what originally got going. It is almost certainly a refinement of a far simpler system.

It is a feature of the aforementioned single stranded RNA molecule that (as well as serving as a DNA analogue – at least for one strand of DNA) it can also adopt tightly folded configurations which double-stranded DNA could never imitate. This means that, in certain respects, RNA molecules are rather like protein molecules and, it was discovered, can act like primitive enzymes that catalyse other reactions.

Once you have RNA molecules (formed entirely randomly as the primordial soup dribbled down hot rocks) that just happen to be able to catalyse (however poorly) reactions that result in RNA copying, you’re away! The “chicken and egg” problem presented by the DNA/protein system is circumvented. A self-catalysing RNA system will, given a supply of nucleotides, keep on replicating until the cows come home – which, given that replicating systems constantly mutate and the best mutations are chosen by natural selection (and later on in the process by human breeders) is exactly what happened in the end.

Nobody knows for certain how terrestrial life began, but the RNA hypothesis is a strong contender. We may never know exactly what did happen but there is a plethora of exciting research going on with RNA (and similar nucleotide polymers) that is confirming the plausibility of some theories as to what might have happened.

So next time you are enjoying a pint in a university-town, watch out for someone bursting in and announcing that the real secret of life has just been found.

Sunday, April 8, 2012

What is a gene?

Alongside their usual “UNICORNS CAUSE CANCER” style headlines, the tabloid press are also quite fond of “BOFFINS DISCOVER THE GENE FOR BELIEVING IN UNICORNS” style headlines. I think it kind of goes without saying that most of those who write such headlines have only the vaguest idea of what a gene is. To be fair, the more we discover, the vaguer the scientific notion of what a gene is has become, but the basics are very well established.

So what is a gene?

There are all sorts of useful analogies, similes, and metaphors we can use here. I think my favourite is the story of the pilgrim who asked for an audience with the Dalai Lama.
He was told he must first spend five years in contemplation. After the five years, he was ushered into the Dalai Lama's presence, who said, 'Well, my son, what do you wish to know?' So the pilgrim said, 'I wish to know the meaning of life, father.' And the Dalai Lama smiled and said, 'Well my son, life is like a beanstalk, isn't it?' “In Held 'twas In I” by Procol Harum
But I’m going to try here to describe what a gene (the real secret of life) really is instead of what it is a bit like.

Now we’ve all heard of the “chromosome”. Say this word to most people (and indeed Google images) and it probably conjures up an image like this:


Now there’s a good reason why the word “chromosome” conjures up an image like this. Basically, it’s when chromosomes look like this that we can see them under normal microscopes. But chromosomes only look like this (all bunched up and double) when they are getting ready to divide. Most of the time, and in most organisms, chromosomes look nothing like this.

Most people (even journalists) who’ve heard of chromosomes have also heard of “DNA” and are aware that it comes in the form of a double helix:


This is basically what you are looking at (ignoring all sorts of caveats that we can sweep under the lab bench for now) when you look at a length of chromosome (or at one of the strands of the chromosome in the doubled up chromosome in the chromosome picture).

So there you have it, chromosomes are (caveats aside) basically long strands of DNA.

But we haven’t mentioned “genes” yet I hear you cry.

Well a gene is a short(ish) bit of chromosome (or DNA strand if you prefer). Now (returning to analogies) “genes” are often compared here to beads on a string. But, since there isn’t really any “string” (just molecules and links between them) popper beads maybe provide a better analogy …. except that there aren’t really any beads either.

Let’s look at the DNA molecule in more detail:

DNA is made from Nucleotides – which is what the “N” stands for in “DNA”. There are just four different nucleotides involved Adenine, Cytosine, Guanine, and Thymine - which are often denoted by their initial letters: A, C, G and T.

If we un-twist the DNA and look at a short bit of it, it looks a bit like this:


But that’s already a bit complicated, so let’s simplify things still further:


(For any pedants reading, each box here represents a nucleotide together with a phosphate deoxyribose; but let's keep things simple.)

Now the more astute among you will have noticed that these two strands are complementary – the sequence of Gs, Cs,As and Ts in the strand at the bottom can be inferred from the sequence of Gs, Cs,As and Ts in the strand at the top (and vice versa).

As this implies, we only really need one strand and, indeed, we are only really interested in one stand today: the” sense” strand. The complementary strand is “anti-sense” and we can ignore it until we come to DNA duplication – which we’re not going to come to in this post.
Going back to analogies again for a second, it’s a bit like every time Guardian journalist Ben Goldacre (@BenGoldacre / http://www.badscience.net) writes a sensible sentence in his blog, Daily Mail journalist Melanie Phillips (@MelanieLatest / http://melaniephillips.com) writes a completely irrational and nonsensical sentence in her blog, and the two kind of cancel each other out.
Anyway, this leaves us with:


These are a bit like popper beads I suppose, but they are nucleotides not genes. There may be, not billions and billions and squillions (said in a Lancashire accent), but certainly hundreds or thousands of these in one gene.

So what use is that?

Well these for nucleotides form a kind of code – a code comprising only four “letters”, but a very powerful code for all that.

But if a chromosome is just a long series of nucleotides and a gene is a simply a part of that series, how do we know where one gene ends and the next one begins?

Well I suppose (and here I’m going to resort to a serious(ish) analogy) it’s a bit like the old style telegrams where you were restricted to twenty-six capital letters and that was it. You had to write stuff like ….
LEAVE THE CAR STOP JACK WILL PICK YOU UP FROM THE STATION STOP BILL WILL BE THERE TOO STOP LATE ON FRIDAY NIGHT WELL MAKE OUR WAY UP TO KATES STOP BUM A LIFT IN THE MORNING TO CHARLIES STOP AUNT DORIS WILL ALSO STOP STOP
…. in order to avoid misreading (try it without the STOPs).

It’s like that with the genetic code. There’s no punctuation, it’s all in the sequence of “letters”, but, as has been noted, we don’t even have twenty-six, we only have four. These make up three letter “words” called “DNA triplets” and each triplet codes for one amino acid.

Just as a DNA strand is a string of nucleotides, a protein is a sequence of amino acids and each gene coded for the string of amino acids that make up a particular protein. Like this:


So the sequence of nucleotides CTA codes for the amino acid “aspartic acid”, AAA codes for the amino acid “phenylalanine” and ATG codes for “stop making protein”.

Since this “protein” only has two amino acids in it, I’m not sure you can really call it a “protein”. It would more usually be called a “dipeptide”. But you’ve almost certainly eaten some of this (give or take a methyl group); it is the artificial sweetener called “aspartame” or “Nutrasweet”. I doubt that there are actually any real genes out in the wild for making aspartame, but I suppose there could be, and it’s a nice simple example of what a very short gene could do.

Conclusion


So now you understand what a gene is. It’s a sequence of nucleotides that codes for a protein (or at least part of a protein – some proteins are made from more than one amino acid chain).

I suppose, armed only with the understanding presented above, you could (naively) begin to imagine that if you have lots of genes for (say) muscle protein (or genes that produce extra good quality muscle protein) you might be more likely to make it as athlete, but how does it all get so complicated and how can you have a gene for believing in unicorns?

Well part of the answer (the full answers really are complicated) is that proteins, as well as being structural like muscle proteins, can be regulatory, like enzymes – which control all sorts of things that go on in our bodies.

Once you consider that the products of some genes can control what other genes do (in all sorts of complicated direct and indirect ways that we don’t need to go into here) you begin to realize that genetics is very sophisticated and subtle and complex.

Your computer is not really built from the kind of transistors you used to get in transistor radios any more (and still less from valves) but the principle is the same. A transistor is a switch that turns another switch on and off. Once you start putting a few transistors together, you rapidly start to get quite complex behaviour. Put shedloads together and you get something that can do stuff like decide to stall my Ford Galaxy just before I want to set off from a junction (while producing a fault-code which my garage insists doesn’t exist).

Anyway I digress. My point is that even simple feedback mechanisms (and the feedback mechanisms in genetics are far from simple) can produce really really complex behaviour.

Some species of bird are genetically programmed to build very sophisticated nests to lie in. My cats are genetically programmed to catch birds (fortunately for the birds they’re both rather crap at it) but are not genetically programmed (and not bright enough) to even move a twig out of the way before lying down on an otherwise perfectly comfortable and sunny patch of grass in the garden.

These complex behaviours require lots of genes (and maybe lots of so called “junk” DNA) working in harmony. On the other hand, the colours of my cats (one is black and the other is tortoiseshell) arise from the actions of just one or two genes (though even here – especially in the case of the tortoiseshell – things are a bit more complicated than you might imagine).

So while you probably can’t really have a gene for believing in unicorns, you probably can (for example) have a genetic makeup that makes you more susceptible to superstition and irrational views.

At heart, however, a gene is simply a code for making a protein.