Wednesday, May 25, 2016

Still selfish after all these years?

The 40th anniversary of the publication of Richard Dawkins’ The Selfish Gene is a cause for celebration, as I’ve said.

This anniversary has also reawakened the debate about the book’s title. Do we still think genes are “selfish”? Siddhartha Mukherjee's The Gene makes no mention of the idea, while talking about pretty much everything else. It’s no surprise that Dawkins sticks to his guns, of course. He justifies it in this fashion:

"If you ask what is this adaptation good for, why does the animal do this – have a red crest, or whatever it is - the answer is always, for the good of the genes that made it. That is the central message of The Selfish Gene and that remains true, and reinforced."

This is a statement crafted to brook no dissent. It says nothing about selfishness of genes. It says that adaptations are, well, adaptive, in that they help the organism survive and pass on its genes. But for a gene to be metaphorically selfish, it must surely promote its survival at the expense of other genes.

I’m not going to rehearse again the argument that the “selfish gene” promotes the misconception – which I suspect is now very common – that different genes, not different alleles of the same gene, compete with one another. (In the comment to my blog post above, Matt Ridley points out that there can be exceptions, but at such a stretch as to prove the rule. Still, as Matt says, we're basically on the same page.) The fact is that genes can only propagate with the help of other genes. John Maynard Smith recognized this in the 1970s, and so did Dawkins. He chose the wrong title, and the wrong metaphor, and wrote a superb book about them.

I find it curious that there’s such strong opposition to that fact. For example, I’m struck by how, when the selfish-gene trope is questioned, defenders will often point to rare circumstances in which genes really do seem to be “selfish” – which is to say, where propagation of a gene might be deleterious to the success of an organism (and thus to its other genes). It is hard to overstate how bizarre this argument is. It justifies a metaphor designed to explain the genetic basis of evolutionary adaptation by pointing to a situation in which genetic selection is non-adaptive. You might equally then say that, when genes are truly selfish, natural selection doesn’t “work”.

What is meant to be implied in such arguments is that this selfishness is always there lurking in the character of genes, but that it is usually masked and only bursts free in exceptional circumstances. That, of course, underlines the peril of such an anthropomorphic metaphor in the first place. The notion that genes have any “true” character is absurd. Genetic evolution is a hugely complex process – far more complex than Dawkins could have known in 1976. And complex processes are rarely served well by simple, reductionistic metaphors.

Think of it this way. There are situations in which Darwinian natural selection favours the emergence of sub-optimal fitness (for example, here). This is no big surprise, and certainly doesn’t throw into doubt the fundamental truth of Darwin’s idea. However, we could then, in the spirit of the above, argue that the real character of natural selection is to favour the less-than-fittest, but this is usually masked by the emergence of optimal fitness.

There is an old guard of evolutionary theorists, battle-scarred from bouts with creationism and intelligent design, who are never going to accept this, and who will never see why the selfish gene has become a hindrance to understanding. They can be recognized from the emotive hysteria of their responses to any such suggestion – you will find them clearly identified in David Dobbs’ excellent response to criticisms of his Aeon article on the subject. It is a shame that they have fallen into such a polarized attitude. As the other responses to David’s piece attest, the argument has moved on.

Monday, May 09, 2016

SATs are harder than you think

How’s your classical mechanics? Mine’s a bit crap. That’s why I’m having trouble working out the following question.

You have a cylinder that rotates around a horizontal axis, like the sort used to pull up buckets from wells. Around the cylinder is wrapped a rope attached to a weight. As the weight falls and the rope unwinds, you measure the time it takes to descend a certain distance.

Now you increase the mass of the cylinder – say, it’s made from iron, not wood (but of the same size). Does the weight fall more slowly? At risk of embarrassment, I’ll say that I think it does. The torque on the cylinder is the same in both cases, but what changes is the cylinder’s moment of inertia, and thereby (via torque = moment of inertia times angular acceleration) the angular acceleration. So the weight takes longer to descend the same distance when attached to the iron cylinder because the angular acceleration is less.

Also, the greater mass of the cylinder means, via Amonton’s Law, that the friction with the axis is greater in the latter case.

Am I right? Or do I need (it is quite possible) to go back to my A-level mechanics?

The reason I ask is that I am trying to understand a question in the SATs science test (now dropped, by the way) for Year 6, i.e. 11-year-olds.

You might wonder why 11-year-olds are having to grapple with torques and so forth. So am I. But they come up in this question:





Now, I suspect that the answer the pupils are expected to give is that the bigger piece of card incurs more air resistance. That is true. But it is not the only influence at play, since the card obviously adds to the rotor’s mass. So this is a rather complicated question in mechanics.

You might think I’m overthinking the problem. But I can’t see how it is ever a good idea to choose a question for which a little more knowledge makes the problem harder. Or am I just wrong here about the answer?

Elsewhere in the SATs papers you find difficulties that seem to be the result purely of bad questioning. Take this one, from an English Reading and Comprehension test. Pupils have to read the following passage:



Then they are asked



My (10-year-old) daughter was puzzled by this reference to “burning of rocks in space”. What does it mean to burn rocks in space? For one thing, you can’t do it. I mean sure, meteorites will get hot and oxidized as they fall through the atmosphere but not in space. And the frictional heating is not really about burning. “Burning up” is something of a euphemism here, and it does not mean the same thing as “burning”. The intended answer is trivial, of course: “in a flash” just means that the “burning up” happens quickly. But this question is worded in such a way that prevents it from quite making sense.

Is anyone checking this stuff, before it is unleashed on unsuspecting and highly stressed pupils and teachers?

Wednesday, April 27, 2016

Where's the soul?

I worry much more than I should about whether embryos have souls. That’s to say, I worry about how those folks who believe that at some stage humans are granted a soul by the grace of God make sense of this question.

But as I discovered while reviewing Henry Greely’s book The End of Sex, Father Tadeusz Pacholcyzk – who has a doctorate in neuroscience from Yale and writes for the National Catholic Bioethics Center in Philadelphia – has at least cleared up one thing for me. Whether or not embryos have a soul should, he says, have no bearing on our judgement about the rights and wrongs of using human embryo tissue for research into stem cells, or presumably for research into anything else. He clarifies that Catholic tradition has no unanimous verdict or tradition on the precise moment of ensoulment. However, Saint Augustine, rarely consulted for his knowledge of embryology, “seemed to shift his opinion back and forth during his lifetime between immediate and delayed ensoulment”. No wonder; it’s a tough question. Much, much tougher, indeed, than Augustine could ever have imagined, because of course we can’t expect him to have known that only about 12% of fertilized eggs in vivo will develop beyond three months of pregnancy. We had best assume, then, that ensoulment is delayed until some time after that, for otherwise heaven will be overwhelmingly filled with souls of embryos less than three months old. I don’t think any of the Christian Fathers ever imagined that heaven should be as odd a place as that.

The point, Pacholcyzk says, is irrelevant in any case, because a human embryo at any stage is destined for a soul “and should not be cannibalized for stem cell extraction”. (The use of “cannibalize” to denote dismemberment for spare parts applies, by the way, only to machines. For living organisms, it refers to the eating of one’s own species. But heck, it sounds bad, doesn’t it?) We must assume that the creation of embryos for any other purpose than procreation is also prohibited by Catholic teaching. In fact, Pacholcyzk says, it is even more immoral to destroy an embryo that had not received an immortal soul (although we don’t, remember, know if anyone actually does this, because we don’t know when ensoulment happens) than to destroy an ensouled embryo – worse than murder! – “because the immortal soul is the principle by which that person could come to an eternal destiny with God in heaven”. That person? Yes, an embryo is always a person – or rather, “the privileged sanctuary of one meant to develop as a human person.”

But evidently, the majority of human embryos are not, as Pacholcyzk insists, “meant [by God, one assumes] to develop as a human person” – they don’t get beyond three months. Or has God really made such a hash of human procreation, so that all these embryos destined for personhood keep failing to attain it?

The corollary to all this must be that the Catholic Church disapproves of IVF too, since that generally involves the creation of embryos that are not given the opportunity to grow to personhood. And as the Catholic World Report reminded us in 2012, it does indeed:

Catholic teaching prohibits in vitro fertilization, maintaining that a child has the right to be conceived in the marital embrace of his parents. Human sexuality has two components, the unitive and procreative; IVF separates these components and makes the procreative its only goal. Pope Paul VI said that there is an “inseparable connection, willed by God, and unable to be broken by man on his own initiative, between the two meanings of the conjugal act: the unitive meaning and the procreative meaning.

There are other issues involved. IVF makes the child a commodity produced in a laboratory, and makes doctors, technicians, and even business people part of the conception process. The sperm used is usually obtained by masturbation, which the Church teaches is immoral. The sperm or eggs used may not come from the couple desiring the child; because one of the spouses may be infertile, it may be necessary to use the sperm or eggs from an outsider.

That phrase, making a child conceived through IVF “a commodity produced in a laboratory”, is one of the most obscene I have ever heard from the church in modern times. God’s love is infinite – but you, Louise Brown (and four million others), are just a commodity produced in a laboratory.

Of course, Catholic countries don’t tend to feel they can be quite this hardline with their citizens, and so they cook up some crude compromise, such as Italy insisting that all embryos created in IVF (a maximum of three) must be implanted. This flouts Catholic teaching, and also flouts the right of people using IVF to the best chance of making it work. Everyone loses.

Actually, there is a form of IVF that the Catholic church will sanction. It is called gamete intra-Fallopian transfer, or (cutely) GIFT. Here’s how I described it in my book Unnatural. The woman’s eggs are collected as in IVF and mixed with sperm in vitro. This mixture is then immediately transferred back to the woman’s Fallopian tubes, so that fertilization can occur inside the body. One claimed benefit of GIFT is that the embryo can begin its earliest development in ‘natural surroundings’ rather than in an ‘artificial environment’. It’s not clear that a developing embryo cares in the slightest about this distinction, and indeed GIFT both is more invasive than standard IVF and makes it impossible to select the embryo of best apparent quality from several prepared in vitro. But it’s OK with the church, provided that the sperm is collected using a condom (a perforated, leaky one, mind) in sexual intercourse and not by masturbation – because everything then seems to be happening in its ‘natural’ place, with just a momentary sleight-of-hand involving a Petri dish. This obsession with the ‘proper’ mechanics, notwithstanding the lengths that are necessary here to achieve it, speaks of a deeply strange attitude towards the relation between sex and procreation, not to mention the bizarre and, I should have thought, highly disrespectful notion of a God who watches as if with clipboard in hand (but ready to avert his eyes at the crucial point) to tick off each step when it happens as it ‘ought’.

Generally I want to find ways to respect what people believe. But the Catholic position on IVF is on a par, in its inhumanity, with its position on condom use. If I sound sarcastic about it, please don’t read that as flippancy. It is fury. If these folks could content themselves with expressing their prejudices as blind faith and dogma, I would find it more palatable than if they tried to justify them with idiotic attempts at rational argument. I’m told that “Father Tad... studied in Rome, where he did advanced studies in theology and in bioethics.” I don’t find a shred of ethical reasoning in his comments on embryo research. It is unreason of the most retrograde kind.

Wednesday, March 23, 2016

On the attack

One of the easiest ways to bring humour to music is with timbre. It’s cheap (literally) but still funny to play Led Zeppelin’s “Whole Lotta Love” or Richard Strauss’s “Also Sprach Zarathustra” on kazoo, as the Temple City Kazoo Orchestra did in the 1970s. Most things played on kazoo are funny. It just has a comical timbre.

Such performances inadvertently make a serious point about timbre, which is that it can matter more than the notes. This is overlooked when music is considered as notes on paper. Yet musicologists have largely neglected it, for the simple reason that we don’t really know what it is. One definition amounts to a negative: if two sound signals differ while being identical in pitch and loudness, the difference is down to timbre.

One feature of timbre is the spectrum of pitches in a note: the amplitudes of the various overtones. These are quite different, for example, for a trumpet and a violin both the same note. But our sense of timbre depends also on how this spectrum, and the overall volume, changes over time, particularly in the initial “attack” period of the first few fractions of a second. These are acoustic properties, though, and it might be more relevant to ask what are the perceptual qualities by which we distinguish timbre. Some music psychologists claim that these are things like “brightness” and attack, others argue that we interpret timbre in terms of the physical processes we imagine causing the sound: blowing, plucking, striking and so on. It’s significant too that we often talk of the “colour” of the sound.

Arnold Schoenberg thought it should be possible to write music based on changes of timbre rather than pitch. It’s because we don’t know enough about how the brain organizes timbre that this notion didn’t really work. All the same, Schoenberg and his pupils created a style called Klangfarbenmelodie (sound colour melody) in which melodies were parceled out between instruments of different timbre, producing a mesmeric, shimmering effect. Anton Webern’s arrangement of a part of Bach “The Musical Offering” is the most renowned example.

There’s one thing for sure: timbre is central to our appreciation of music, and if we relegate it below more readily definable qualities like pitch and rhythm then we miss out on a huge part of what conditions our emotional response. It would be fair to say that critical opinion on the music of heavy-metal band Motörhead, led by the late bass guitarist Lemmy Kilmister, was divided. But if ever there was a music defined by timbre, this was it.

Thursday, March 17, 2016

The Roman melting pot

Here's my column for the March issue of Nature Materials.

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Recycling of materials is generally good for the planet, but it makes life hard for archaeologists. Analysis of ancient materials, for example by studying element or isotope compositions, can provide clues about the provenance of the raw materials and thus about the trade routes and economies of past cultures. But that business becomes complex, even indecipherable, if materials were reused and perhaps reprocessed in piecemeal fashion.

This, however, does seem to have been the way of the world. Extracting metals from ores and minerals from quarries and mines, and making glass and ceramics, were labour-intensive and often costly affairs, so that a great deal of the materials inventory was repurposed. Besides, the knowledge was sometimes lacking to make a particular material from scratch in situ. The glorious cobalt-blue glass in the windows of medieval French churches and cathedrals is often rich in sodium, characteristic of glass from the Mediterranean region. It was probably made from shards imported from the south using techniques that the northern Europeans didn’t possess, and perhaps dating back to Roman or Byzantine times. The twelfth-century monk Theophilus records that the French collected such glass and remelted it to make their windows [1].

In that instance, composition does say something about provenance. But if glass was recycled en masse, the chemical signature of its origin may get scrambled. It’s not surprising that such reuse was very common, for making glass from scratch was hugely burdensome: by one estimate, 100 kg of wood was needed to produce the ash for making 2 kg of glass, and collecting it took a whole day [2].

Just how extensively glass was recycled in large batches in Roman times is made clear in a new study by Jackson and Paynter [3]. Their analysis of glass fragments from a Roman site in York, England, shows that a lot of it came out of “a great big melting pot”: a jumble of recycled items melted together. The fragments can be broadly divided into classes differentiated by their antimony and manganese compositions. Both of these metals were typically added purposely during the Roman glass-making process because they could remove the colour (typically a blue-green tint) imparted by the impurities, such as iron, in the sand or ash [4]. Manganese was known in medieval Europe as “glassmaker’s soap”.

It’s the difficulty of making it that meant colourless glass was highly prized – and so particularly likely to be recycled. The results of Jackson and Paynter confirm how common this was. The largest category of glass samples that they analysed – around 40 percent of the total – contained high levels of both Sb and Mn, implying that glass rendered colourless by either additive would be separated from the rest and then recycled by melting.

But most of those samples aren’t colourless. That’s because remelting tends to incorporate other impurities, such as aluminium, titanium and iron, from the crucibles, furnaces or blowing irons. The recycled glass may then end up as tinted and undistinguished as that made with only low amounts of Mn. As a result, while it is derived from once highly prized, colourless glass reserved for fine tableware, this high Sb-Mn glass becomes devalued and used for mundane, material-intensive items such as windows and bottles. Eventually it just disappears into the melting pot.

1. Theophilus, On Divers Arts, transl. Hawthorne, J. G. & Smith, C. S. (Dover, New York, 1979).
2. Smedley, J. W., Jackson, C. M. & Booth, C. A., in Ceramics and Civilisation Vol. 8, eds McCray, P. & Kingery, W. D. (American Ceramic Society, 1998).
3. Jackson, C. M. & Paynter, S., Archaeometry 58, 68-95 (2016). [here]
4. Jackson, C. M., Archaeometry 47, 763-780 (2005).

Tuesday, March 01, 2016

Many worlds or many words?

I’ve been rereading Max Tegmark’s 1997 paper on the Many Worlds Interpretation of quantum mechanics, written in response to an informal poll taken that year at a quantum workshop. There, the MWI was the second most popular interpretation adduced by the attendees, after the Copenhagen Interpretation (which is here undefined). What, Tegmark asks, can account for the robust, even increasing, popularity of the MWI even after it has been so heavily criticized?

He gives various possible reasons, among them the idea that the emerging understanding of decoherence in the 1970s and 1980s removed the apparently serious objection “why don’t we perceive superpositions then?” Perhaps that’s true. Tegmark also says that enough experimental evidence had accumulated by then that quantum mechanics really is weird (quantum nonlocality, molecular superpositions etc) that maybe experimentalists (apparently a more skeptical bunch than theorists) were concluding, “hell, why not?” Again, perhaps so. Perhaps they really did think that “weirdness” here justified weirdness “there”. Perhaps they had become more ready to embrace quantum explanations of homeopathy and telepathy too.

But honestly, some of the stuff here. It’s delightful to see Tegmark actually write down for once the wave vector for an observer, since I’ve always wondered what that looked like. This particular observer makes a measurement on the spin state of a silver atom, and is happy with an up result but unhappy with a down result. In the former case, her state looks like this: |☺>. The latter case? Oh, you got there before me: |☹>. These two states are then combined as tensor products with the corresponding spin states. These equations are identified by numbers, rather as you do when you’re doing science.

Well, but what then of the objection that the very notion of probability is problematic when one is dealing with the MWI, given that everything that can happen does happen with certainty? This issue has been much debated, and certainly it is subtle. Subtler, I think, than the resolution Tegmark proposes. Let’s suppose, he says, that the observer is sleeping in bed when the spin measurement is made, and is placed in one or other of two identical rooms depending on the outcome. Yes, I can see you asking in what sense she is then an observer, and invoking Wigner’s friend and so on, but stay with me. You could at least imagine some apparatus designed to do this, right? So then she wakes up and wonders which room she is in. And she can then meaningfully calculate the probabilities – 50% for each. And, says Tegmark, these probabilities “could have been computed in advance of the experiment, used as gambling odds, etc., before the orthodox linguist would allow us to call them probabilities.”

Did you spot the flaw? She went to sleep – perhaps having realized that she’d have a 50% chance of waking up in either room – and then when she woke up she could find out which. But hang on – she? The “she” who went to sleep is not the “she” who woke up in one of the rooms. According to this view of the MWI, that first she is a superposition of the two shes who woke up. All that first she can say is that with 100% certainty, two future shes will occupy both rooms. At that point, the “probability” that “she” will wake up in room A or room B is a meaningless concept. “She”, or some other observer, could still place a bet on it, though, right, knowing that there will be one outcome or the other? Not really – rational betters would know that it makes no difference, if the MWI holds true. They’ll win and lose either way, with certainty. I wonder if Max, who I think truly does believe the MWI, would place a bet?

The point, I think, is that a linguist would be less bothered by the definition of “probability” here than by the definition of the observer. Posing the issue this way involves the usual refusal to admit that we lack any coherent way to relate the experiences of an individual before a quantum event (on which their life history is contingent) to the whole notion of that “same” individual afterwards. Still, we have the maths: |☺> + |☹> (pardon me for not normalizing) becomes |☺> and |☹> afterwards. And in Tegmark’s universe, it’s the maths that counts.

Oh, and I didn’t even ask what happens when the probability of the spin measurements is not 50:50 but 70:30. Another day, perhaps.

Friday, February 19, 2016

Manipulated by music

Here's my music psychology column from the latest issue of Sapere magazine.

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Does Alex, the ultra-violent delinquent in Anthony Burgess’ novel A Clockwork Orange, find something in Beethoven that matches his psychopathic tendencies? Does Beethoven perhaps even incite them? We’re left to guess. It seems more than mere coincidence however, that 16 years after Stanley Kubrick’s notorious movie of the novel, musicologist Susan McClary argued that Beethoven’s Ninth Symphony, one of Alex’s favourites, articulates a rapist’s rage.

That suggestion drew much criticism, even derision. But behind it seems to lie the suspicion that music can influence behaviour, for better or worse. It’s an ancient idea. Aristotle felt that the wrong kind of music can lead a person astray, while the right kind cultivates good citizenship. Such convictions meant that music was strictly regulated in Athens and Sparta. The Greeks organized their music in terms of modes – a little like our major and minor scales – and Plato insists that the Dorian mode is the one to induce bravery and resolve. Armies have long marched to war to the sounds of martial music, whether it’s the skirling of a Scottish bagpipe or Wagner’s “Ride of the Valkyries” blasting from the attack helicopters in Apocalypse Now.

That’s just one arena in which music is thought to manipulate mood. Ever since efficiency became the mantra of the modern workplace, employers have hoped that music will boost workers’ productivity. There’s a great deal of wishful thinking and shoddy science in this field, but some serious study too. The stereotype is of factories piping music to workers engaged in robotic routines, but in fact much of the interest is in using music to boost creativity. One study in 2012 found that workers in a computer software company solved problems faster and had better ideas when allowed to listen to music of their choice: a sign that positive mood makes for better work, rather than an indication of specific links between the type of music and productivity. The effects were small, though, and almost non-existent for expert workers.

Retailers have a strong interest in this stuff. Can music make people buy more? I’m afraid so. It’s been shown that certain musical genres enhance our receptiveness to – and what we’ll pay for – certain products. We’ll pay more for mundane products like toothbrushes and light bulbs when we hear country music, and more for products connected to “social identity” (jewellery, pin badges) when listening to classical music. But sellers beware: get the musical choice wrong, and it’s worse than no music at all.