Friday, January 29, 2016

What is selfish DNA?

Richard Dawkins’ The Selfish Gene was a landmark book in many ways: the first to lay out for a general audience the gene-centred view of evolution, but also one of the first to re-invigorate (arguably since the 1920s) science popularization as a part of the cultural conversation – and to show how beautifully written it should aspire to be. Dawkins might be divisive today for a variety of reasons, but science popularizers owe him a huge debt.

That’s why it is good and proper to have The Selfish Gene celebrated in Matt Ridley’s nice article in Nature. You can tell that I’m preparing to land a punch, can’t you?

Well, sort of. You see, I can’t help but be frustrated at how Matt turns one of the most problematic aspects of the book into a virtue. He suggests that Dawkins’ viewpoint was the inspiration for the discussions of selfish genes presented in Nature in 1980 by Orgel and Crick and by Doolittle and Sapienza. And it is true that The Selfish Gene is the first citation in both papers.

But both cite the book as one of the most recent discussions of the issue. As Orgel and Crick say, “The idea is not new. We have not attempted to trace it back to its root.” So it is not at all clear that, as Matt says, “a throwaway remark by Dawkins led to an entirely new theory in genomics”.

The problem is not simply one of quibbling about priority, however. Matt points out that this “throwaway remark” concerns the “apparently surplus DNA” – in the hugely problematic later coinage, junk DNA – that populates the genome, and which Dawkins suggested is merely parasitic. Yes indeed, and this is what those two later Nature papers discuss – as Orgel and Crick put it, DNA that “makes no specific contribution to the phenotype”.

But is this what The Selfish Gene is about? Absolutely not, and that’s why Dawkins’ remark was throwaway. His contention was that all genes should be regarded as “selfish”. Orgel, Crick, Doolittle and Sapienza are specifically talking about DNA that is produced and sustained by non-phenotypic selection. This, they say, is what we might regard as truly selfish DNA. Now, one can argue about the word “selfish” even in that context – it perhaps only makes sense if this DNA becomes detrimental to the survival of the organism. But the implication is that the phenotypic DNA is then not selfish, and that the term should be reserved for parasitic DNA. That makes good sense – and it is precisely these waters that Dawkins’ title muddied.

I can’t resist also asking what Matt means by saying that “genes that cause birds and bees to breed survive at the expense of other genes”. (“No other explanation makes sense…”) It seems to me more meaningful to say “genes that cause birds and bees to breed survive while helping other genes to survive.” I don’t exactly mean here to allude to the semantic selfish/cooperative debate (although there are good reasons to have it), but rather, it seems to me that Matt’s statement only makes sense if we replace “genes” with “alleles”. This is not pedantry. Genes do not, in general, compete with each other – at least, that is not the basis of the neodarwinian modern synthesis. Although one might find examples where specific genes do propagate at the expense of others, in general it is surely different variants of the same gene that compete with each other. And when a new allele proves to be more successful, other genes come along for the ride. To fail to make this distinction (which of course Matt recognizes) seems to me to propagate a very common misconception in evolutionary genetics, which is that genes are little pseudo-organisms all competing with one another. That isn’t a helpful or accurate way to present the picture.

Matt understands all this far better than I do. So I am quite prepared for him to tell me I have something wrong here.

Friday, January 15, 2016

More on the beauty question

Here’s my review of Frank Wilczek’s book A Beautiful Question: Finding Nature’s Deep Design, which appeared in Physics World last year.


There aren’t many books on which you will find admiring blurbs by both Lawrence Krauss and Deepak Chopra, but this is one. You can see why. Wilczek writes in a freewheeling, almost poetic way, while retaining a penetrating and rigorous vision of what he wants to say about physics, science and the world.

His opening question – “Is the world a work of art?” – sets the tone: at the same time lyrical and baffling. Wilczek’s answer, as you might guess from the title, is “Yes, and it’s a beautiful one.” He reaches this conclusion after surveying the central role that symmetry plays in modern physics, from the shapes of atomic orbitals to the structure of quantum chromodynamics. He makes one of the most compelling cases I have seen for why symmetry can be considered a guiding principle worth heeding in efforts to push back the frontiers of physical theory. The latest prospect of doing that – of expanding fundamental physics beyond the Standard Model, which Wilczek prefers to call the Core Theory – comes from the principle of supersymmetry, which promises to unify bosons (“force particles”, with integer spin) and fermions (“substance particles”, with half-integer spin). This idea looms large on the agenda of the Large Hadron Collider now that it has returned to operation after an upgrade. Thanks to Wilczek, I now have a better sense of why the theory not only might be true but ought to be.

All the same, if this were a regular popular science book then it would be considered something of a mess. Like poetry, Wilczek’s prose is often highly concentrated thought, and he doesn’t always bother to unravel it or even to define his terms. Even with the glossary, I’m not sure how much the uninitiated reader will get from statements such as “Color gluons are the avatars of gauge symmetry 3.0.” What seem to be more straightforward concepts, such as light perception by the eye, become reconfigured into shapes that, while fitting into Wilczek’s intellectual framework, take time to decrypt: “When we perceive a color, we see a symbol of change, not anything that changes.”

Wilczek’s suggestion that, when the going gets tough, we read the text like poetry rather than hoping to understand all it says, seems optimistic. But these challenges aren’t, I think, exactly defects of the book, because this is not a regular science book. Like Stephen Hawking's A Brief History of Time, it is instead the unique vision of a brilliant mind (with that added advantage that it doesn’t pretend otherwise). For every baffling passage there are other moments when Wilczek explains something in a way that no one else has, or perhaps could, so that you come away with a fresh perspective on something that you thought you understood already. Never again will I be frustrated by pop-science suggestions that Einstein simply decided to posit the constancy of the speed of light: of course he didn’t, and Wilczek cuts straight to the physics of the matter. Put simply, he sees things differently, and that’s the true and compelling reason to read the book.

For the fact is that this book is not a work of explanation but, like Plato’s Timaeus, an extended argument – indeed, what you might call a gentle polemic. It wants to steer us towards Wilczek’s own answer to his initial question. And so, quietly and soberly, he marshals facts that fit his case and soft-pedals ones that don’t. That’s fine – it is what polemics do – so long as we recognize what’s happening. For example, in his discussion of Pythagorean musical consonance he gives us a simple (albeit speculative) physical mechanism for why we prefer harmonies with simple frequency ratios while all but ignoring the fact that we plainly don’t: unless you’ve heard music played in tunings other than equal temperament, you’ll never have heard the interval of a Pythagorean fifth. And the discussion of Chinese yin and yang glosses over the fact that it not an aesthetic idea but a philosophical one: beauty is never, to my knowledge, mentioned by Chinese philosophers in this context.

Such goal-directed argument is most apparent in Wilczek’s discussion of beauty itself, for which the closest thing he gives to a definition is “symmetry and economy of means”. But neither of these features plays a key role either in most art or in most theories of aesthetics. Immanuel Kant, who made one of the most searching enquiries into the nature of beauty, argued that there is something repugnant in too much order and regularity. Even Francis Bacon asserted that “There is no excellent beauty that hath not some strangeness in the proportion”.

Kant’s careful distinction between real beauty and the intellectual satisfaction of perceiving an idea is precisely what physicists ignore when, like Lewis Carroll’s Humpty Dumpty, they make the word mean just what they want it to mean. Wilczek at least admits that not all types of beauty are included in his picture; but the physicists’ usual conception of beauty is Platonic in the extreme and barely if at all relevant to the arts. For Plato it was precisely art’s lack of symmetry (and thus intelligibility) that denied it access to real beauty: art was just too messy to be beautiful. It seems clear, and important, that many physicists do feel a kind of transcendent joy in the symmetries of nature’s laws. But if they really want to talk about it in terms of beauty, they should acknowledge that there is an intellectual heritage to that notion that they will have to confront.

Thursday, January 14, 2016

What's in a name?

Shawn Burdette’s blog post on element-naming has some nice things in it, but I wonder if he appreciates that the entire discussion around the names of the four new elements is itself largely a bit of fun? Sure, I can imagine that there are some people signing the petitions for lemmium and octarine thinking that the Japanese or Russian teams are going to say “Hey, several of those Brits want us to name this element after a heavy-rock musician we’ve never heard of/some magical colour in a series of books by a fantasy writer we’ve never heard of – well, that seems like a good idea to us.” Who knows, perhaps they are hoping one of the scientists will pipe up with “Oh yeah, I remember Silver Machine from my student days in Kyoto/St Petersburg. Let’s do it, freaks!” But really, do most of the signatories think this is anything but a fun way to celebrate a couple of recently deceased people whose work they liked?

The point is that most people aren’t suggesting names because they have the slightest hope, or even wish, that they’ll be taken seriously, or that the researchers need a bit of help. Rather, this is an unusually rich opportunity to both make a few funny/wistful/ridiculous suggestions and to have a considered discussion about how these names come about. If we aren’t allowed to do that unless we are “in the element discovery business”, it’s a sadder world. Certainly that’s why I said in my Nature piece that levium is a name I’d love to see, not one that I think ought to be adopted. It was a personal view (the clue was in the article category), not an absurd attempt to “impose my ideas for element names on the discoverers”. And if it is sanctimonious to wish for element names to be inclusive rather than proprietorial, so be it.

Which brings us to nationalism. Let me confess right away that I am not entirely consistent on this, because I can’t help feeling a soft spot for the Curies’ polonium. Poland had a pretty crap time of it in the 19th and early 20th century, and besides, Marie seemed to have regarded this as a kind of homage to a distant homeland rather than a boast. No, my case is not airtight. But as Shawn says, germanium and francium did seem more aggressively flag-waving (I’ve never got to the bottom of the accusations of egotism behind Lecoq’s gallium.)

And it surely doesn’t stop there: americium smells of the Cold War, although in fairness this doesn’t appear to refer solely to the United States. If berkelium, californium, dubnium, hassium and livermorium aren’t necessarily expressions of patriotism, they do seem to veer towards bragging. Shawn asks: well, why not? It is damned hard to do this work, why shouldn’t the teams get the credit, even if it seems a little vain? I’m not convinced. They definitely deserve credit, of course, but there are other avenues for that. My biggest concern, though, is that this triumphalism is a reflection of the competitiveness of the whole business, which seems unfortunate and tiresome. When there is a dispute over priority and then the “winner” goes and names the element after themselves (in effect), it is like sticking your tongue out at the “losers”: it’s us, not you. The disputatious nature of element-making during the Cold War years is notorious, and even if things are somewhat more collaborative now, there are still arguments.

It’s precisely because the work is so hard that priority can be so contentious: it is a matter of fine judgement whether a claim is convincing or not. The Russian team insists that their claim for having seen element 113 in 2003 should count as the first, and that the Japanese group came second the next year. Their complaint that the Japanese result isn’t going to be easily reproduced by anyone, and that in any case the leader of that team Kosuke Morita learnt his chops at Dubna in the first place, seems particularly ungracious. All the same, can we be so sure that the Russians don’t have a case? I trust the IUPAC experts, but it seems unlikely that there are completely cut-and-dry arguments. Imagine if the situation was reversed: if the Japanese had toiled hard to get a suggestive decay signature, their first shot at an element discovered in the Far East, only to be dismissed by IUPAC in favour of those Russians again, who go and slap “moscovium” on it. Would we feel that was a good name that enhanced the justice of the situation?

This, of course, is science as normal – different people arrive at much the same result at much the same time, and priority is a murky issue. But this is precisely why a winner-takes-all approach to naming adds to the distorted view of discovery that such emphasis on coming first produces. I fully understand that for some individual scientists, priority can matter hugely to career prospects, even though it damned well shouldn’t. But to big, substantially funded projects like this? I don’t think so. Even if element-naming wasn’t solipsistic, there would surely still be a strong desire to claim priority. But do we have to make it worse?

Does music really need a new philosophy?

I always enjoy Roger Scruton’s writing on music, even when I disagree with him vehemently. That holds true for his piece on the role of philosophy in music. We should ignore the habitual bluster about the melodic and harmonic paucity of popular music, which Scruton seems insistent on analysing in a social vacuum as though it is beholden to the same compositional and aesthetic rules as Mozart; indeed, most of what Scruton writes about music totally ignores the fact that it is a cultural activity with many functions, not just an artifact to appreciate over a glass of fine wine. (I have visions of him challenging the idea that Bowie was a great musical artist because his songs had poor voice-leading.) And Scruton’s perpetual denigration of today’s callow youth, passively consuming processed musical pap under their hoodies, makes you wish he’d get to bloody well know a few young people instead of sneering at them from afar. Most of the kids I know are learning an instrument – not that this is an essential aspect of active engagement with music, but it obviously helps.

I’m not sure that Scruton’s article is really concerned so much with philosophy at all (there is a large body of work on this that he doesn’t touch on, and which is not obsessing about modernist ideas, such as Stephen Davies’ excellent 2005 book Themes in the Philosophy of Music). His emphasis is rather on systems and rules of composition. Still, I agree with him that Schoenberg’s twelve-tone method is pretty arbitrary, that Adorno wrote with priestly dogmatism, and that serialism systematically undermined the accumulated wisdom about making melodies coherent. However, just as Schoenberg didn’t realise why this was so, so Scruton has only the vaguest sense of why Western tonal music does have this property of auditory coherence. It’s depressing to hear yet another appeal to the “naturalness” of the Western diatonic scale (under which system of intonation, one wonders? Have you heard how weird the Pythagorean scale sounds to our ears now?). Not only is there no good evidence that the harmonies it creates are innately consonant (with the exception of the octave and perhaps the fifth), but Scruton’s appeal to the harmonic series ignores the fact that Schoenberg appealed to the very same source of justification – he just wanted to “emancipate” the higher harmonics. If Scruton showed more awareness of musical cultures whose harmonic norms depart widely from Western tonality (say, Croatian ganga or Indonesian gamelan), I think he’d be less inclined to assert its naturalness.

The existence of a tonic and of a hierarchy of note usage is indeed a feature of how much musical melody becomes intelligible and perceptually grouped, and also contributes to its tense of tension and release. The circle of fifths, modulation and voice-leading aren’t by any means essential in rich and complex music, but they can certainly be put to good use for coherence, variation and nuance in Western tonal music, once they become part of the learnt musical language. So if all this is ditched, then Scruton is quite right to assert that other “binding” structures are needed if one wants music that has an easily apprehended cognitive structure. (I have written about this in some detail, with specific focus on serialism and modernism here.)

But there are ways to achieve cognitive coherence within serialism, and Berg in particular was masterful in using rhythm, pitch relationships and other techniques to do so. (I don’t fully understand how he does it, but I suspect it was intuitive.) Without such things, Scruton rightly asserts that no “normal ear” (which is to say, no mind employing the mental grouping mechanisms we acquire for navigating an auditory landscape) can hold the music together. Yet if he showed any interest in the cognition of music, he’d be less sure that the traditional rules of the Western tonal style were the only means of achieving this.

Yet does music have to hold together in that way? We’re back to Scruton’s insistence on listening to all music with an ear attuned to Mozart. True, if we’re not going to do that then we have to learn a new way of listening, which is not easy when you’ve been immersed in the Western tonal tradition from birth (as most Westerners have). But might it not be worth trying? Personally, I’ve found that it is. Ligeti, for example, offers musical experiences based on texture or a kind of pointillist sonic painting. OK, you won’t go away humming the tunes, but I would be sad if that were always held up as the test of fulfilling music.

Beyond all this, the notion that all contemporary classical (whatever that means) music today is in thrall to serialism is of course absurd. These remarks might have been more pertinent 50 years ago, but now the diversity of styles is exhilarating and dizzying. Pierre Boulez is dead, Roger, and we can do what we like! (I don’t mean to knock Pierre, who seemed to loosen up somewhat in old age, but really he was a bit of a serialist snob in his time.)

What is the “philosophy” that Scruton wants to see in place of that of Adorno and the other champions of modernism? One, apparently, in which “true artists are not the antagonists of tradition but their [sic] latest advocates”. There speaks a dyed-in-the-wool conservative, of course, but I have some sympathy with the idea that innovators extend and transform tradition rather than sticking the boot into it. Even the Sex Pistols arguably did that (if the “tradition” includes MC5, Iggy and the Stooges and garage rock generally). But I wouldn’t expect Scruton to approve of that example.

Thanks to Ángel Lamuño for bringing Scruton’s article to my attention.

Tuesday, January 12, 2016

The place of the periodic table

I can fully understand that Eric Scerri, who has done so much to explain, popularize and clarify the periodic table, would object to my suggestion in a Nature article that “chemists rarely need to refer to it” and that it “holds more interest and glamour for the public than it does for the working chemist”. These statements are too general; I should say “many” (most?) chemists. There are some who surely do use it, and a rather small group of others – Eric among them, of course – who expend a lot of time and thought on the right way to structure it. Those latter questions are interesting and valuable, and I regret that Eric seems to have been offended by an apparent implication (not intended) that they are not.

If I exaggerate, it’s to make a point, which is that it is not terribly good for chemistry if it is seen as being all about the periodic table – and that is the impression I think non-scientists often get. Not only does it obscure what most chemists do, but it leads to the idea that the quantum explanation of the periodic table means that chemistry is “just physics”, or that, now we know all the elements (except ones we make ourselves), “pure” chemistry is pretty much over as an academic discipline (if you don’t believe me, see here). And chemistry is not alone in the risks associated with giving too much emphasis to its organizational schemas, as I say. One could easily get the impression, from Higgs- and LHC-mania (which is fine in itself), that all physicists want to do is find new particles. Yet most physicists never need to consult the tabulation of the standard model, even mentally. Nor do most biologists need to know the genetic code (though of course they learn it anyway). This is not a question of whether these lists and tables and classifications are significant – of course they are. It is about guiding public perception away from the notion that this is what the respective disciplines are all about.

The periodic table is not a “mere list”. It is far richer than that. But chemistry as a whole is much, much richer still, because it is primarily about making things with, and not simply categorizing, its building blocks. I am not convinced that this is widely understood (Tom Lehrer’s song, for all that it’s fun, suggests as much), and I worry that at least some of the excitement about the new elements amounts to the perception that “hey, we’ve completed the list!” That’s the challenge that needs to be faced.

Sunday, January 10, 2016

The myth of the Enlightenment (again)

To cite Kant in defence of the “Enlightement values” of freedom of speech, democratic representation, universal equality and so forth, as Nick Cohen does here, is simply to invite the response that Kant rejected democracy and displayed the conventional misogyny, racism and class-based snobberies of his times. In other words, it is to incite an empty argument in which we hold Kant anachronistically to account for the prejudices that just about every other educated and privileged male European of his age shared.

Which is why it drives me up the bloody wall that folks like Cohen are still banging on about “Enlightenment values” – by which they generally mean some carefully selected values advanced by certain Enlightenment figures that we (some of us – me and Nick alike) would like to see upheld today, such as freedom to think for ourselves. The sad irony is that Kent seems to think this is a different category of statement than speaking of equally meaningless (because utterly polysemous) “Christian values”.

Cohen’s criticisms of the pope in his article are entirely justified. Trying to support them by appealing to some fictitious Enlightenment does him no favours at all. He calls “people who call themselves liberals” (that would be me, then) “thoughtless prigs” who probably don’t know what the Enlightenment was. Isn’t it odd, then, that folk who talk today about Enlightenment values are usually arguing in favour of a secular, classless, “rationalistic” democracy? Because, to state the bleedin’ obvious, there were no secular classless democracies in eighteenth century Europe.

And the heroes of the Enlightenment had no intention of introducing them. Take that other Enlightenment icon Voltaire. Like Kant, Voltaire had some attractive ideas about religious tolerance and separation of church and state. But he was representative of the philosophes in opposing any idea that reason should become a universal basis for thought. It was grand for the ruling classes, but far too dangerous to advocate for the lower orders, who needed to be kept in ignorance for the sake of the social order. Here’s what he said about that: “the rabble… are not worthy of being enlightened and are apt for every yoke”. Voltaire has been said to be a deist, which means that he believed in a God whose existence can be deduced by reason rather than revelation, and who made the world according to rational principles. But he insisted that ideas like this should be confined to the better classes. The message of the church should be kept simple for the lower orders, so that they didn’t get confused. Voltaire said that complex ideas such as deism are suited only “among the well-bred, among those who wish to think.”

The Enlightenment was not strongly secular in any case. Atheism was very rare, and condemned by almost all philosophers as a danger to social stability. Rousseau calls for religious tolerance – except for atheists, who should be banished from the state because their lack of fear of divine punishment meant that they couldn’t be trusted to obey the laws.

The idea that the Enlightenment was some great Age of Reason is now rejected by most historians. So why do intelligent people like Nick Cohen still invoke this trope today whenever they fear that irrational and dogmatic forces are threatening to undermine science and society? I suspect it has something to do with the allure of the Golden Age: things were all rosy once, but now the barbarians are dragging us back to that other mythical period in history, the “Dark Ages”. Sadly, history is never so simple.

Stand up for principles of tolerance, compassion, equality, reasoned decision-making, and free speech, by all means. But don’t try to conscript bad history to your cause. What people today call “Enlightenment values” are like universal human rights: we might like them and think they are worth defending (I do), but that doesn’t alter the fact that they are a modern invention.