sawyl: (A self portrait)
I took Dean Burnett's test and came out with equal A's and B's with an E to split the difference. Which, according to my interpretation, pegs me a physical chemist. Talk about spookily accurate...
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As a determined stander, I'm pleased to learn that my preference is endorsed by science. Maybe it'll be enough to persuade my grandmother...
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Via SciAm, I've discovered what might just be the greatest science quote ever. When asked why the US government should spend money on a particle accelerator without any strategic value Robert R. Wilson replied:

It has only to do with the respect with which we regard one another, the dignity of man, our love of culture. It has to do with: Are we good painters, good sculptors, great poets? I mean all the things we really venerate in our country and are patriotic about. It has nothing to do directly with defending our country except to make it worth defending.

Amen.

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Good meeting/seminar this afternoon on the new UM IO server, a feature that ought to massively improve the performance of STASH for model configurations with high CPU counts. The implementation details were fascinating. I particularly liked the idea of being able to dynamically balance the IO load across the servers — something that Unicos/MK never managed to do! I also thought it was interesting that using asynchronous sends to pass metadata requests to the IO servers didn't improve performance, but instead caused some collective operations to hang waiting on locks.

Fascinating stuff.
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According to the Guardian, the government are cutting funding for four major science projects, including two near-neighbours:

[The projects] include a national supercomputing service for developing drugs and modelling climate change; an international computer science centre at the Daresbury research and innovation campus in Cheshire; redevelopment of the Institute for Animal Health; and upgrades to facilities at the Rothera research station in Antarctica.

Which sounds to me like they're withdrawing funding from the Son of HECToR project. And as if that wasn't bad enough for climate research, it sounds as though NERC are going to be short of money too:

The Natural Environment Research Council, a major funder of environmental research, has ringfenced money for three major projects: the Halley Antarctic base, a replacement for the research ship, Discovery, and building work at its Keyworth site. "Aside from these projects, it will be very difficult to support new capital projects in the coming years unless additional funds can be secured," a spokeswoman said.

Doubleplusungood.

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I've mentioned it once already, but here are some more thoughts on Cordelia Fine's pithy, funny, fascinating Delusions of Gender. The book examines many of the common claims made about the differences between the sexes and and surveys the evidence to see if they claims are scientifically justifiable. Which, it transpires, they generally aren't.

Musing after the jump... )

Delusions of Gender a delightful and necessary reminder both of the continued need for better gender equality and of the the dangers of making bold social claims on the grounds of weak science. Fine's evidence-heavy approach gives the book a solid grounding and believability, while her snarky sense of humour — "...researchers don't actually know for sure whether what they are measuring correlates well, or even at all with the level of testosterone acting on the foetal brain. We won't let this hold us back. (After all, we're only trying to find the biological roots to gender inequality, so why be fussy, right?" ibid. 109 — keeps things moving and prevents the sort of dryness and chaffing that all too often results from heavy fact exposure.

Highly recommended.

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According to a short piece in New Scientist people who don't favour a particular hand "...are more easily persuaded to feel a certain way than consistent right-handers." The science bit says that this could be do with the increased number of connections between the part of the left brain that generates a consist world view and the part of the right brain that notices when the world view needs to be updated:

"Increased access to the part of the brain involved in noticing things that don't fit might make you more likely to change your mind," [Ruth] Propper [of Montclair State University, NJ] says.

Intriguing.

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I've finally found the time to sit down and watch Paul Nurse's excellent exploration of public hostility towards science in general and climate science, AIDS and HIV, and GM crops in particular. Nurse is a fantastic presenter: enthusiastic, sympathetic, but still willing to challenge and criticise where necessary. The most impressive moments come in an interview with a climate sceptic, who Sir Paul reduces to incoherence spluttering by suggesting that the man's attitude to the concensus view of climate change is exactly like that of a cancer patient who decides to ignore the established medical opinion about his treatment in favour of treating himself with a homebrew remedy.

I'm not entirely sure I agree with some of the statements in the program, particularly those that suggest that science stands completely separate from politics. Maybe, in an ideal world, it does, but we need to accept that scientists are people and people are political — as Berlin says somewhere, politics is what happens whenever two people's views cannot be completely reconciled with each other. I definitely agree with Nurse's point that scientists need to promote their work more widely and engage with the public understanding, but I was surprised that, apart from a brief throwaway remark, he didn't argue that science should be more heavily promoted and taught in schools.

Minor quibbles aside, it was a quite superb bit of programming — a sign that there's life in the old Horizon yet. As Tim Dowling said of it in the Guardian, it's a pity it's one show and not a four year degree course.
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Over at the Guardian, Martin Robbins has a note perfect parody of a light-weight piece of pointless science journalism, followed by a series of deadpan pastiches of CiF comments:

In this paragraph I will state the main claim that the research makes, making appropriate use of "scare quotes" to ensure that it's clear that I have no opinion about this research whatsoever.

In this paragraph I will briefly (because no paragraph should be more than one line) state which existing scientific ideas this new research "challenges".

But Robbins' spoof echoes some of the serious points made by Ed Yong in a post that argues that while journalists may not have an obligation to a particular scientist or theory, they do have an obligation to truth:

A veteran science journalist recently wrote: "Reporters are messengers – their job is to tell, as accurately as they can, what has been said, with the benefit of such insight as their experience allows them to bring, not to second guess whether what is said is right". That’s rubbish. If you are not actually providing any analysis, if you’re not effectively “taking a side”, then you are just a messenger, a middleman, a megaphone with ears. If that’s your idea of journalism, then my RSS reader is a journalist.

Exactly.

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According to today's Bad Science, The Sun, irony of ironies, is having conniptions over the NHS's provision of pornography in fertility clinics. After dealing with the complaint in short order — the average spend is twenty quid per trust per year — Dr Ben investigates the more interesting question of whether there might be valid scientific reasons for provided, um, performance enhancers:

But it gets more interesting. There is already evidence from animal research that males increase the amount of sperm in their ejaculate when there is more competition around. In 2005, Kilgallon and Simmons conducted an experiment to see whether human males viewing “images depicting sperm competition” also had a higher percentage of motile sperm in their ejaculates.

God knows what the right wing press would make out of the grant proposal for this bit of research...

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My favourite recent science quote comes from this NYT piece on bedbugs:

[Stephen A. Kells] feeds his bugs expired blood-bank blood through parafilm, which he describes as “waxy Saran Wrap.”

Coby Schal of North Carolina State said he formerly used condoms filled with rabbit blood, but switched to parafilm because his condom budget raised eyebrows with university auditors.

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I'm currently reading Giles Foden's Turbulence, which features a thinly fictionalised version of L.F. Richardson and which is narrated by a young Met Office scientist. My problem is that, so far at least, most of the science seems distinctly ropey giving the impression that someone, either Foden or the narrator, really doesn't understand the basics. Here, for example, is the narrator musing on the geophysics of the Great Rift Valley:

[Edward Bullard] showed that gravity is lower than it ought to be in some of these Rift lakes. This negative gravity means there is material down there that's lighter than its surroundings, material that's longing to rise — and would do so in an instant were it not fore side-pressing rocks holding it down like a pair of pliers. Bullard's anomalies mean some of the Rift is not just foundered valleys, the consequences of all fall. Some of it must have been pushed down. If there is a shift of plate tectonics, that material will come flying up.

Negative gravity? And rocks having to be restrained from flying up? Really?

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I eventually managed to fix my UM compilation problem. When I checked the batch job used to drive the compile, I noticed that it included a LoadLeveler directive which explicitly set the shell to /bin/ksh. This overrode my normal shell, bash, and prevented my normal startup scripts, with their code to set up FCM, from being picked up. Once I knew this, I was quickly able to fix the problem by creating a .profile script which included a sensible basic path and enough of an environment to drive the build system.

But despite fixing this problem the model still failed to run correctly, crashing almost immediately after the start of the atmosphere model. Checking the output I found a whole load of errors from a script that appeared to be setting up the OASIS coupler — these might, for all I know, be perfectly normal — followed by a fatal error complaining of an atmosphere basis time mismatch. I'm not quite sure why this happened — I think the error indicates that the start dump does not match the model start time — because I simply copied the job from a colleague. It was at this point that the obvious occurred to me: I should simply get in contact with my colleague and get him to run the job. Far easier.
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Today's highlight: a bootleg copy of one of [livejournal.com profile] doctor_squale's academic papers from Numerical Linear Algebra with Applications. It was fantastically erudite. Which is to say I only understood about a tenth of it.
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Never send a philosopher to do a physicist's job. Here's John Gray in Saturday's Guardian discussing Jeremy Rifkin's The Empathic Civilization:

The essence of any catch-22 is that there is no way out, but Rifkin shrinks from this cruel logic, with the result that his argument verges on incoherence. How could human empathy possibly defeat the force of entropy, an irreversible physical process? Does Rifkin believe an increase in altruism can lead to the repeal of the second law of thermodynamics?

Yes, the second law of thermodynamics — coincidentally, C.P. Snow's scientific shibboleth — states that the entropy of an isolated system always increases. Yet it is still possible for the entropy of part of a system to decrease, provided this is offset by an increase in the overall entropy of the system. Thus it is perfectly practical to decrease the local entropy on, say, Earth, by exploiting an increase in entropy elsewhere in the universe, say, I don't know, the Sun.

Perhaps I do Professor Gray a disservice, but I don't really feel that he really understands the concept of entropy. Which makes the claim that Rifkin's argument is incoherent, or nearly so, impossible to assess and rather calls into question the point of the review...

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Via Ken MacLeod, the shocking revelation that Professor Phil Jones has an untidy office. Amazing. An academic with an untidy office. Hardly atypical of the breed.

My father's office was always in a state of utter chaos: papers piled feet deep, stacks of books in four or five different languages, old coffee machines, bags of dirty sports gear, broken radios, mugs and crockery, even a cruet set on his coffee table. I'm glad he never got raided by the Thought Police. Not that they'd have found anything. Not with all the rubbish piled everywhere...
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Yesterdays edition of Night Waves featured an interesting interview with David King. King generally acquitted himself rather well, although at times he seemed frustrated with the quality of some of the questions and on a number of occasions suggested to his interviewer, Anne McElvoy, that she didn't really under the basics of science because if she did she wouldn't be asking what she'd just asked...
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I've mentioned this a few time, but my recent journeys to and from work have been greatly enhanced by The Oxford Book of Modern Science Writing edited by Richard Dawkins, who proves himself to be a thorough and knowledgeable guide full of boundless enthusiasm and with supreme literary sensibilities.

Having set himself the challenge to pick out the best that twentieth century scientific writing has to offer, Dawkins divides his prizes into four broad categories: what scientists study; who scientists are; what scientists think; and what scientists delight in. As might be expected the anthology shows a bias towards the biological, especially in the first section, but the range and quality of the writing on display more that justifies the selection. The second section, on scientists as people, featured a range of essays, some more amusing than others, on what it means to be a scientist and the sorts of scrapes scientists get themselves in. Although most of the pieces were good, I particularly liked Oliver Sacks' brilliant Uncle Tungsten and Steven J. Gould's Worm for a Century, and All Seasons.

The third section, on scientific ways of thinking, shifted away from the biological and the personal to the mathematical and cosmological. There were classic essays from Shannon and Turing, some excellent pop maths columns on Conway's Life game and Zeno's paradox, and, as a finale, a handful of pieces on relativity, non-euclidian geometry and string theory. The book finished off with a consideration, again more mathematical than biological, of what it is that makes a theory beautiful or elegant; what sort of puzzles and ideas tend to capture the scientific mind; and what the complexity of life or convolutions of the carbon cycle or the wonders of astronomy teach us about life.

As an anthology of scientific writing, I can't recommend this highly enough. Although I might not have liked every essay in the book, almost everything was though provoking and a large proportion were extremely beautifully pieces of writing and I definitely felt better for knowing of their existence; while the essays I loved left me wanting to chase down the original sources to see where they might take me.
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In what was probably the best science programme of recent years, The Secret Life of Chaos found Jim Al-Khalili exploring the impact of chaos theory on modern science and mathematics.

Starting with Turing's computational morphology studies, which showed how complexity could emerge from simple systems described by a handful of equations, it moved on to Boris Belousov's fascinating discovery of a chemical oscillator which, when run in a petri dish, showed the sorts of patterns predicted by Turing's theoretical work. This, along with work by Edward Lorenz and Benoît Mandelbrot, was seen as ushering a shift from the classical, clockwork universe of Newton to a chaotic system where patterns an complexity emerge from small perturbations in simple mathematical sets of equations that involve iterative feedback.

In a final tour de force, the programme then fed back into itself, returning to the question of biological complexity with a discussion of evolution as a chaotic system. By expressing evolution as a concentrator for minor differences with natural selection acting as the feedback mechanism, it became possible to understand how the vast complexities of life could emerge from a relatively simple system. This point was backed up with NaturalMotion's work using genetic algorithms to teach bio-mechanical computer simulations to walk and interact with the features of a virtual environment.

This view of nature chimes rather nicely a piece of recent reading: Ernst Mayr's rejection of Platonism, described in The Growth of Biological Thought (anthologised in The Oxford Book of Modern Scientific Writing). Mayr rather neatly describes how Plato's ideas of the world naturally grows out of his background as a geometrist, predisposing him to see the world as a series of distorted versions of perfect geometric shapes (essences), whereas the world is actually more complex, more fractal, with apparently similar patterns repeated with minor changes between individual instances. Thus, I suspect, the rejection of the clockwork view of the universe isn't so much a rejection of Newton as the rejection of the pervasive influence Platonism in post-enlightenment scientific thought.

The programme was pure class from start to finish and I thought the way it pulled together a number of apparently separate elements into a coherent whole was a particular strength. It was a brilliant reminder of the sort of the BBC can do if it really tries...
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I very much liked Stephen J. Gould's reaction to Darwin's late work, original published in Hen's Teeth and Horse's Toes but also anthologised in The Oxford Book of Modern Scientific Writing:

Darwin was not a conscious philosopher. He did not, like Huxley and Lyell, write explicit treaties on methodology. Yet I do not think he was unaware of what he was doing, as he cleverly composed a series of books tat two levels, thus expressing his love for nature in the small and his ardent desire to establish both evolution and the principles of historical sciences. I was musing on this issue as I completed the worm book two weeks ago. Was Darwin really conscious of what he had done as he wrote his last professional lines, or did he proceed intuitively, as men of his genius sometimes do? Then I can to the very last paragraph, and I shook with the joy of insight. Clever old man; he knew full well. In his last words, he looked back to his beginning, compared those worms with his first corals, and completed his life's work in both the large and the small...

It's a brilliant evocation of one of those moments of visceral intellectual excitement where, when reading a great piece of scientific or philosophical writing, everything clicks into place and the scope of the thing being examined suddenly increases as you comprehend the sheer audacity author's underlying intentions. It's a rare thing, but Gould really seems to capture it.

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