A Chemist in Theory

Climate denial's next top model

2011-10-09T17:19:00.005+01:00

I've noticed an insidious and increasingly widespread meme in the climate-change denial community. Having summarily failed to establish actual misconduct on the part of climate science research, or undermine the validity of their models and methods, climate change denialists have taken to denying the very idea of using a model to test a hypothesis (for an example, look at comment #29 here, or this).

I can hardly think of a more anti-scientific attitude, and the people making these statements have either never set foot in science or didn't know what they were doing when they got there.

Models are the bones of science. Forget any theory-of-everything mumbo-jumbo you might've heard from physicists, heady from decades of happy marriage to the gorgeous standard model of particle physics, bombshell thought it may be. We cannot simply take our best set of approximations and extrapolate up to whatever we want to test in the large-scale world. It doesn't work, for various reasons (not least of which is complexity, in lower-case and capital-C forms). Equally, we cannot test most things from a purely empirical standpoint, a benchtop experiment or scientific intervention with a simple yes-or-no outcome. Some behaviour doesn't appear at these scales, or presents itself quite paradoxically.

So we're left with empirical or theoretical models. Approximations. Good approximations. No more clearly can this be seen than in chemistry, halfway between the empirical fleshiness of biology and the theoretical purity of physics. Chemistry is a menagerie of models. Organic chemists operate at a level of approximation that would make any quantum physicist faint in horror; inorganic chemists engage molecular orbitals which are little more than convenient fictions of correct symmetry. These are grounded approximations, proven in experiment and traced to their roots in theory (electronegativity is a wonderful example), but approximations none the less. Powerful intellectual ideas, cutting to the heart of chemical behaviour, and allowing us to create and communicate ideas.

Models are deeply important in other fields of science. The recent discovery of a probably-diamond stellar remnant in orbit around another star was established by the proper modelling of various possible remants, to see what matched. Biochemistry uses carefully constructed patterns of reaction to represent living creatures. And climate science uses awesomely powerful computer modelling to figure out what's driving our atmosphere.

Deal with it.

One of my favourite chemists, R. T. Sanderson, has written on the use of real, physical models in teaching chemistry. I really like ball and stick models. Therefore you can imagine my delight at this video of augmented reality ligand binding:

How the Syrian opposition charges its batteries?

2011-06-03T09:04:00.003+01:00

This morning's NPR World Story of the Day discusses the attempts to organise Syria's opposition movement. The activist groups face ongoing challenges ranging from military attacks to power cuts. How can you organise resistance when you can't charge your phone?

"For example, Blackberry. We have a glass of water and two Duracell battery. We put it for one hour in this glass, then we use the USB and we put it just in the water. And it's... that gives us two hours or three hours charge to talk."

Original here.

Obviously I have no idea how this is supposed to work, and it's quite possible that it's just a language issue. If people really are promulgating this as a way to recharge their phones, interested in finding out whether this is a popular meme in Syria, or in activist groups in general. (It does not appear to be.)

Regarding the Pfizer Sandwich closure

2011-03-01T22:08:00.004Z

Pfizer is to close its historic research facility in Sandwich, Kent. It would be difficult to overstate the scale of this closure, and the magnitude of its impact on the pharmaceutical research community in the UK. I've been to the Sandwich labs. They are a sprawl of buildings with the population the size of a small town. They have their own (subsidised) Starbucks.

I'm not really qualified to talk at any great length about the state of the pharmaceutical industry - I will defer to whatever Derek Lowe has to say on the subject - but I've had a thought I'd like to share. Pulling a successful drug from the chemical space has never been easy, with success rates in the just-double-figures or lower. Never the less, the drug business built a reasonably efficient and quite profitable machine to tease out these leads.

The pharma system is built on blockbusters, big money makers that have to support a handful of complete failures or niche drugs, and in the glory days of the 1980s and 1990s it appears that quite enough were arriving for the whole operation to come out in the black. More recent history, however, is littered with high-profile failures. It's not so much that the well of molecular possibility has gone dry - it was never gushing - but that it's gone from recalcitrant to downright surly.

Against this background it seems one approach to success might be to cut down the failures. To get to my idea, it seems that university and government biotech spin-off companies, having performed much of the preliminary study and trimmed down the possibilities under the umbrella of pure science, have a better chance of then bringing a commercially and clinically successful molecule to market than the pharmaceutical business, which traditionally starts from a broader search.

Given the ongoing economic crisis and the longstanding pressure from on universities to balance their books, might we be on the brink of a sea-change in the way medicines are created? I am probably overstating something that's comically obvious, but there you go.

Fearless woman's life in science

2010-12-21T08:57:00.003Z

Science Friday had a segment last week on Prof. Daniel Tranel's research with a woman known as "SM" who experiences no fear because of lesions to her amygdala. She has experienced this condition from birth and began working with the group for two decades. She is quite accustomed to participating, to the extent that she will call the lab and ask if there are any projects coming along if she has not heard from them in a while. What a fascinating relationship with science she must have.

On Futurism

2010-11-30T08:39:00.004Z

It strikes me that the problem with futurism (see: Kurzweil) is that genuine progress does not depend upon the technologies available, but the combinations and interfaces between them. This makes the problem space much larger than any world-gazing generalist can hope to engage with successfully.

While it would have been trivial to suppose in the 1950s that space travel, radio, chemistry and computing would become significant in the future, the futurists of the period largely extrapolated those trends in isolation. It was the unanticipated combinations that changed the world. It took the communications satellite (space + radio), microprocessors (chemistry + computing) and mobile phones (radio + microprocessors) to get us to the smart phone, that novella-sized glowing slice of sci-fi tech which lets us order pizza or view the streets of the world with equal impunity.

Knowing all of the elements does not grant one a total understanding of chemistry.

(See also this thought experiment.)

Evan Harris on Royal Free and Lancet culpability in Wakefield case

2010-05-31T16:09:00.010+01:00

"After Wakefield: the real questions that need addressing" from Evan Harris (famously pro-science Lib Dem) at the BMJ. Harris discusses the lapses in oversight that allowed Wakefield's unethical research to be performed and published. I've discussed this previously in the context of Jay Gordon's defense of Mr. Wakefield. I wrote that Mr. Wakefield's actions were possible because medical research is performed with the assumption of some basic level of ethical behavior on the part of the researchers, a trust which Mr. Wakefield readily exploited. I argued that the ultimate consequence of Mr. Wakefield's actions would be much-increased oversight of medical research, as a necessary evil to prevent others from slipping ethics breaches through.

With, in retrospect, massive hyperbole and a staggering lack of relevant experience, I imagined a world in which scientists must prove beyond a reasonable doubt that their work was performed ethically, with no concealed interests or misrepresented methods, and laid the blame for this at Mr. Wakefield's feet.

Harris' efficient article makes the case that the oversight under which the research took place and was published and was subsequently investigated was not merely liberal but downright cursory. And while I believe that Mr. Wakefield is ultimately responsible for his own deceptions, it appears that had he not existed, some other unethical researcher would have come along and taken advantage of this lax environment for his/her own benefit. In other words, there were lapses that allowed Mr. Wakefield to do his dirty work, they are a concern all of their own, and they may eclipse "MMR-gate" entirely.

Coming soon!

2010-05-03T15:52:00.001+01:00

Sorry for the absence of updates recently. In the mean time I've punted the "Free Radicals" posts over to a twitter feed @alexacit.

Free Radicals Feb 2010

2010-03-04T00:30:00.001Z

The best of the past month in my RSS feed:

Chemistry

"Very Cool Chemistry" at ACS Chemical & Engineering news: ultra-low temperature chemical reactions dominated by quantum mechanics.

A gorgeous article on "Crystals in Light" at Accounts of Chemical Research.

Mismatched DNA base pairs may have a detectable magnetic signature, at JCP. I wonder, do any of the cell's DNA repair systems operate on this principle, or is it electronic?

A nifty molecular syringe for metal ions.

A fairly pure solution of left-handed molecules is jumbled into a mix of left and right mechanically using ultrasound, rather than chemistry.

Maintaining spins for memory for a quantum computer, and maintaining alignment of molecules with laser pulses.

A silicon analogue of a substituted benzene with some kind of aromaticity. And it's green!

Watching guanine structures swap back and forth under an electron microscope.

Not one but two papers on how the water networks surrounding molecules control reactivity.

Collapsing bubbles create incredible temperatures and unique reaction conditions.

Paper titles don't get much more descriptive than "Water Freezes Differently on Positively and Negatively Charged Surfaces of Pyroelectric Materials".

Make Magazine has some neat links in its story on microfluidics using thread; the article itself is here. It turns out that hairspray is useful in making micro-electrodes, too.

Imagine hydrogen peroxide, but instead of hydrogen, you've got fluorine. That's dioxygen difluoride, which is about as insane as it sounds.

A new paper on non-thermal chemical effects from microwaves, a few months after it seemed pretty much settled that they didn't exist. (Original paper.)

The formation of large crystals involves an intermediate step in which nano-crystals aggregate and order over surprisingly long distances in solution.

A copper complex goes for a bumpy ride over a hot surface, providing some insights into how the hot surface controls chemistry on the way.

Biology

New Scientist goes for the pop-culture jugular with "The real Avatar: ocean bacteria act as 'superorganism'", also at C&EN and the original paper at Nature. Undersea bacteria use electron transfer to share energy around their colony.

Childhood stress may echo long into adulthood, according to a mouse study in the Journal of Neuroscience

Wonky address labels may have a role to play in the degenerative effects of prions, thanks to Nature for making sense of this one. Over in Science it turns out that prions may evolve by a darwinian mechanism.

SCIAM discuss recent research proposing that arsenic's tumour-causing ability is due to meddling with the ubiquitous hedgehog gene.

Here's an RNA that binds to a protein that normally acts on DNA, to inhibit its activity.

Aetiology's guest blogger Zainab Khan on the "hygiene hypothesis" that hyper-cleanliness may lead to allergies and other conditions. Also, a treatment for peanut allergies might be on the cards.

Individuals in the same plant species diversify to partition up the environment and use resources .

Earthworms cheese it when a mole's on the loose (video).

Physics

I was surprised to discover that there's a nuclear exchange interaction, which can be neglected using a Hartree product wavefunction in a similar way to neglecting the exchange interaction in electrons.

Nature asks: does the LHC have serious inherent engineering flaws?

Active galaxies perhaps aren't as important in the production of high-energy cosmic rays as was previously thought.

The effects of general relativity tested with a wonderfully elegant tabletop experiment.

Computing

Philip Ball presents the "Wisdom of the fool's choice", on automatic recommendation systems such as Last.fm and Amazon.

How could scientists cope without Google? Nature addresses this in the context of China and Google's recent spat.

Roger Ebert is getting a synthetic version of his own voice thanks to an Edinburgh-based company. I didn't realise until after I'd heard the results that I've never actually heard his voice before. The Roger Ebert I know is entirely prose. CereProc has some interviews on its own site, and for context there's Esquire's recent piece on Ebert and his own thoughts.

Teaching

"'Dubious' university research should be scrapped" and "Claims of 'dubious research' could deter vital academic investment" from the Scotsman. A St. Andrews philosophy professor's worry that teaching quality has taken a back seat to staff's pet projects triggers a debate on the direction of post-crunch university funding. I'm attending a keynote on the research-teaching relationship this month, so expect a full post.

"Textbooks That Professors Can Rewrite Digitally" at the New York Times. Macmillan proposes lecturer-editable electronic textbooks.

Politics and society

"Concessions over science advice principles" at Nature: government drops proposed requirement that scientific advisors must meet them in the middle on politically-sensitive issues.

Turkey's GMO-control rules, which Nature dub "An absurd law", may fail to accommodate research.

An attempt to study avalance effects with tranquillised pigs is abandoned after public outcry.

A model Mars mission falls down as participants fail to read their own manuals. I'll be having fun digging through the logs here.

A simple model partitions the United States into regions controlled by different fast-food joints. Note how different the map is when McDonalds's rivals are treated as seperate, competing entities, and when they're treated as an anti-McD coalition. McDonalds may be everywhere, but alternatives are easy to find.

Peter Atkins on textbooks, eBooks, and interactivity.

2010-02-17T13:25:00.011Z

Nature recently published an interview with Peter Atkins (probably subscribers only) on textbook writing. Atkins' Physical Chemistry and Molecular Quantum Mechanics are deserved classics in their field, and I greatly enjoyed his Four Laws that Drive the Universe, a slim text which discussed thermodynamics from first principles, although I sometimes find his explanations a little opaque.

I was especially interested by his frank comments on the writing cycle, where major textbooks are rewritten into a new edition every three or four years. Atkins implies that this arises from second hand book sales, which completely overwhelm sales of new books around the three year mark. This is presumably as undergraduates finish up and ditch their old texts. If a new edition of the book is released, it is adopted by lecturers, page and chapter references change, there's a disincentive to buy the used texts, and sales go back up. This could be viewed quite cynically. Atkins points out that he insists on completely overhauling his books with each new edition, which is certainly true from my own experience with his work, but perhaps not all authors are so dilligent.

Atkins proposes the following:

If the second-hand market could be eliminated, books would last longer than 3 years and could be cheaper. There is a way — to produce electronic books [e-books] and kill them after a year.

Atkins is proposing one-year "book rentals", but he needn't go that far. eBooks simply cannot be sold second hand at the moment, so let's set rentals aside for the moment and look at the general case in which books can't be resold. These comments are remarkably similar to those made in the fiction and videogame publishing over the past few years. They're all markets with strong second hand sales, and correspondingly there's a great pressure on publishers to make as much money as possible during the brief window in which the item is popular, either by making a massive commercial blockbuster or charging a lot per copy. By eliminating second-hand sales, the product will sell more, can stay on sale longer, and thus each copy can be cheaper.^[1]

Non-transferrability raises subtle issues. If I can purchase Physical Chemistry for £50, and resell it at £20 in a few years' time, then the book has only cost me £30. Similarly an undergraduate can purchase a relatively specialised text which they may only need for a semester or a year, on the understanding that they can sell it on if it's no longer needed. Losing the right of resale should act to push down the price students are willing to pay for the electronic versions of textbooks.

For very specialist texts, and other scenarios in which an outright purchase of a textbook isn't financially justifiable, students fall back on university libraries. Atkins' textbook rental idea could have a niche here as a middle-ground between outright ownership of the textbook and the inconvenience of borrowing. The libraries themselves are soon to get an alternative. Springer is trialling a service in which PDF text books can be downloaded for free using an institution's site licence, much as scientific journal articles already are. With essentially infinite copies of books available to check out, and no shelf space limitation, catalogues could be larger and students have easier access, again much like scientific journals.

It's unlikely that many publishers will embrace these ideas as strongly as Springer has. Libraries are as much a threat to textbook sales as the second hand market, but that's mitigated by inconvenience (the limited number of books and copies they can carry, time limits, etc.), such that there's an equilibrium between book sales and book borrowing. If the convenience is increased markedly, that equilibrium shifts markedly. An "infinite library" from which anyone could check out any book at any time, although attractive in principle, would make electronic or hardcopy textbook purchases a less attractive, driving down sales, so the site licence fee would be large to compensate. Compromises will be necessary, such as limiting the licence to works which are no longer selling well or are out of print.^[2]

Returning to the article, Atkins is clearly considering the potential in interactive texts, such as those headed for the iPad:

To produce an e-book you have to be more of an impresario than an author. You have the pictures, the unfolding of different depths of information. It's an extraordinarily demanding task.

I've got to say that, for all my conjecture above, I'm ambivalent about the idea of multimedia or electronic textbooks. They seem an obvious step forward. Chemistry is visual, structural, and three dimensional so visual aids one can toy around with are a boon. I've got a fifth edition of McMurry's Organic Chemistry here which packs a plethora of paired 3D structure images and stereoscope. My model kit is never far away. I use generate intricate visualisations of data. I prefer to discuss my results by talking around charts.

However, in practice I just don't like using computer resources to learn. I've used wholly-hypertext learning materials before, incorporating java applets, videos, and so on, and I can't say the interactivity was worth the cost in concentration from eye-strain after looking at the computer screen for an hour. Most of the CD-ROM and online suppliments that came with my textbooks have never been used. Perhaps it's just the inconvenient bulk of computer, or the display, and the tablet computer and e-paper and reflective LCDs will clear all this up, but I'm going to take some convincing.

Lastly I'd like to engage in a little futurism. Atkins suggests that an electronic textbook could stay on sale longer than three years per edition due to a change in the market. If it were to remain on sale for ten years, say, it would require updates, which could easily be pushed through electronically. Perhaps we can expect an application- or OS-like system where major updates (i.e. new editions) must be paid for while minor corrections and expansions are free. Extrapolating, if the book were to stay on sale indefinitely, we would require that lecturers have a DOI or URL-like identifier to allow for permanent references to content that had moved significantly around the book with major updates. Outright purchase a textbook seems nonsensical in such a scenario, and my mind boggles at how one would integrate a hardcopy version of the textbook.

^[1]Electronic distribution has its own advantages in prolonging sales which I won't get into here.
^[2]Out in the non-academic world, Sony's Daily Reader allows the owner to check out books from a local library. However the library must first licence a number of virtual copies of the book, to check out one at a time from nonexistent bookshelves. A simple, obvious, and rather dubious solution.

HuffPo: blame Lancet, not Wakefield, for paper deceptions

2010-02-03T15:12:00.015Z

So, Andrew Wakefield has finally had his comeuppance, with the GMC taking him to task for hiding conflicts of interest, lying about the study itself, performing research on children without approval or competence, and other staggering violations of basic ethics. The Lancet has, correspondingly, retracted the infamous paper, as "the claims in the original paper that children were 'consecutively referred' and that investigations were 'approved' by the local ethics committee have been proven to be false". Jay Gordon, MD^[1] ("Nationally renowned pediatrician on the faculty of UCLA School of Medicine. Soccer Player.") at the Huffington Post chimes in:

This prestigious journal is now forced to cover their own embarrassment at having done virtually no rigorous due diligence of Dr. Wakefield's methodology, data gathering and conclusions before they published the paper in 1998.

Whether or not you believe that Andrew Wakefield is a savior, a misguided researcher with "his heart in the right place" or an attention-mongering, unethical "biostitute" the real blame must be shared by the world's most-respected medical journal, The Lancet, for allowing the flaws and potential conflicts of interest to go unnoticed. The self-righteous attitude they now assume serves no one, least of all families affected by autism.

I have to wonder how Jay Gordon, MD expected the Lancet to find "flaws and [...] conflicts of interest" which Wakefield actively concealed. Likewise it's hard to use "rigorous due dilligence" in assessing how someone performed a study when their description is not the experiment which was actually performed.

It's true that the Lancet did not dig into Wakefield's supposed ethical approval, which might have revealed his deceptions. However there is nothing unusual about this. Medical research is published under the assumption that the researchers will act with their patients' and test subjects' best interests in mind, and furthermore that any breaches will be the result of error and not malice. To operate under the opposite assumption, that all research is unethical and flawed until conclusively proven otherwise, would be practically fascistic. In exploiting the trust placed in him by the medical community for his own ends, Wakefield has taken us on a step down that horrid path.

Gordon continues:

A large leap was made in assigning any sort of "proof" from the small Lancet study. I'm not certain that Dr. Wakefield, himself, feels that anything was proven.

This statement boggles the mind. Wakefield is not one of the many innocent scientists probing the edge of knowledge, whose found their work blown out of proportion by a hungry press. He is unrelenting in his defense of his research, long after it has been discredited by further study, and actively promoted the vaccination-autism link in every available venue. Even if his research were performed ethically and honestly - and it's now clear that it was not - he has continued to promote his hypothesis to the media in spite of a staggering volume of evidence to the contrary. It's pure, Frankenstein-grade hubris.

As I wrote this post, Jim Carrey and Jenny McCarthy published this conspiracy theory in defense of Wakefield's research, likening it to Fleischmann and Pons's cold fusion publication. (One wonders whether Carrey and McCarthy will be funding cold fusion research, considering the obvious value the place in it.) It's clear that this single study and its lead author, found technically and ethically lacking, are too important to the vaccine-autism movement for them to be discredited. (More on that here.)

^[1]Actually, Carrey and McCarthy's son's physician. It'll be interesting to see whether his stance on the proof level of Wakefield's study changes now that his clients have issued a statement.

Update: A follow-up post is available here.

Entropy and time, revisited

2010-01-12T11:03:00.003Z

Scientific American has printed an interesting interview with Sean Carroll on his book From Eternity to Here, discussing the origin of time from a cosmological perspective. (I think I have a copy of the linked-to 2008 article floating around here, too.)

(Previously)

Dealing with variables that depend on each other.

2009-11-16T11:14:00.021Z

This article attempts to follow the effect of the recession on the games industry using a graph. It seems that industry growth has been in decline since a peak in Sept 07, and that since March sales have been shrinking dramatically. I think it's actually an interesting example of how particular graphing tools are only useful in particular situations.

The graph plots year-on-year change in sales figures. Year-on-year figures are useful, because they allow you to normalise for the variation across the year. Suppose you're running a games company. Games traditionally sell very poorly in the summer and rocket off the shelves around Christmas. If you plot a simple graph of sales figures over the year, it really doesn't tell you much about how your business have been doing, because the variation you see is almost entirely down to the expected seasonal peaks and troughs. By comparing this year's figures to last year's figures, however, you can see whether your company had better summer.

My issue with the graph is that it plots these figuers over several years, and therefore the data points for different years are actually dependent upon each other. If you have an unusually good month this year, the same month next year will look bad by comparison. The chart tells us that Sept 07 was an incredible 80% better than Sept 06. In turn, Sept 08 looks pretty bad, because of the huge sales the year before. In fact, Sept 08 could've been a pretty good month.

A more informative way to represent this data would be as a series of individual year-on-year graphs, and highlight that the areas above the zero line are periods of growth. With a bit of cropping, I get this:

Sales were actually up fairly consistently for the year Sept 07 to Sept 08. Contrary to the downward slope, this was a growth period, it's just that growth in the summer wasn't quite as impressive as the growth in the summer, and January was more or less static. Here's some colour, and with the scale for decline extended to match the scale for growth:

Now we have to look seperately at Sept 08 to Sept 09, and remember that we're comparing it to the year before. It's telling us that sales in the winter of 2008 were even better than they were in the winter 2007, but summer sales have dropped by comparison.

The trouble with sticking these two charts next to each other was that a single graph was presenting two different sets of figures as though they related to the same thing. Each of the two charts above uses the previous year as its baseline, so you can't really do that. Presenting them as seperate charts, and applying colour coding to indicate the importance of positive and negative values and not just the movement of the line, clarifies this.

To really grasp what's going on over the whole period, we have to remove the dependence between the two charts, and give them the same baseline. To do this I'll take Sept 06 to Sept 07 as our starting year and plot the change compared to that year throughout.

For most of the year, sales in Sept 08 to Sept 09 were actually better than those in Sept 06 to Sept 07. The growth in the summer of 2008 concealed this in the original graph, implying that sales this year had fallen far below 2007 levels. Unwittingly building in this dependence between the different parts of the line made a big difference to how the results were presented.

Given that the years 2006 and 2007 were both huge success stories, selling at that rate is objectively impressive. It's been pointed out to me that my sales analysis is rather naive, though. Games publishers have investors, and they expect to see the publisher sell games at an ever faster rate with each passing year as an indication that the company is growing. Even if the company's still selling well, that growth has to be there. Correspondingly a year-on-year shrink isn't good news, even if it's a shrink to sales volumes which were once unprecedented.

UK Government sends message to its advisors: You Don't Matter

2009-10-30T17:26:00.005Z

The UK Government has just sacked the head of its drugs advisory body, for claiming that his organisation's work had been "devalued" in favour of the government's existing policies. It's a claim that's hard to argue against, given that the government soundly ignored this body's advice in the past whenever it conflicted with their pre-established policy stance (e.g. this and this). By simply using science as a way to promote its existing agenda, and not as a way of making actual decisions, the government had been sending a clear message to its advisors. "Your decisions and expertise do not actually matter. You are here to service us." This firing merely underlines that truth.

Given that this is the government behind the "dodgy dossier", such evidence- and reality-averse approaches to running the country are hardly surprising. However I have little reason to conclude that any of the other parties would act any differently. Is there a party out there willing to act on what the cold, hard facts tell it, or must I resign myself to living in a country where decisions are made on the basis of preconception, supposition, instinct, hysteria, and the opinions of whoever can best whisper in the MPs' ears?

Update: The article has since been expanded. I find this quote especially telling:

I cannot have public confusion between scientific advice and policy and have therefore lost confidence in your ability to advise me as Chair of the ACMD. I would therefore ask you to step down from the Council with immediate effect.

The letter asking for him to step down:

It is important that the government's messages on drugs are clear and as an advisor you do nothing to undermine the public understanding of them.

Clearly, if there's a mismatch between policy and the evidence, it should be kept out of public sight. So much for the ACMD's independence.

Here's to you, helpful bookseller

2009-08-07T21:15:00.003+01:00

I actually found this anecdote on "Not Always Right" kind of charming. Chemistry gets a bad reputation because of the connotations of "chemical", and they not only managed to explain what chemistry is in a simple way, but they convinced someone who was deeply opposed to the idea! So here's to you, whoever you are. I've stuck a printout of that page up above my desk.

The man at the reins of the caveman at the reins of the Soil Association

2009-08-01T12:42:00.008+01:00

I've been following the response to the recent systematic review of the health benefits and nutritional content of organic food with some interest. It's left me with an odd sense of despair which I'm trying to figure out. It's not so much the Soil Association's piss-poor retort¹, but the sense that neither statement has any bearing on the public's feelings on the issue, or policy.

The Soil Association's willful misrepresentation of a powerful scientific tool (systematic review) is odious, but I don't think that it's going to adversely affect the public's understanding of systematic review. Anyone who blithely swallows their implied argument of "cherry picking" does so because it's a pleasing rationalisation of their existing bias, not because it makes any logical sense, so I doubt they will form some general conclusion that systematic reviews are a poor tool. Likewise, I doubt many who accept the report's findings will do so because of an understanding of its methodological rigour. This is an example of "confirmation bias", the tendency for us to favour findings which match our preconceived notions, and to dismiss those that contradict them.

I've recently finished reading Dan Gardner's "Risk" ², which draws extensively on evolutionary psychology and the structure of the mind to discuss how we rationally and irrationally interact with risks. At the heart of the book is the notion that our brains run on two "systems", essentially the instinctive and the rational. The animal-like and instinctive "system 1", crafted by evolution, calls its shots using various hard-coded and unconscious "heuristics". The rational "system 2", the conscious human, applies flexible logic, imagination, reason, and emotion.

Unfortunately for the human, the caveman brain gets to call the shots by default. Speed is the issue. If the sleek modern mind scratches its chin as we're approached by a tiger, heedless of the caveman's instinctive cry to flee, we're hosed. So the caveman gets first dibs, and it's up to the modern mind to attempt to interpret correct that response if it gets the time. Often, its override doesn't work very well, especially if the caveman's in an imposing emotional state. The caveman's decision can stand unopposed, with the modern man only stepping in to provide a post-hoc rationalisation. This is bad enough when I've elected to buy Legends Springer, but it's a serious concern when the caveman winds up making public policy decisions.

The depressing - and hopefully inaccurate - conclusion is that our rational minds are cludgy patches to a piece of software that is meant to roam the savanna, a piece of software as cold and remorseless as any nightmarish android.³ I've concluded that this idea was floating around in my mind after I finished Gardner's book, and that what bothers me about the Soil Association's reaction, and everyone else's for that matter, is that it's such a stunning reminder of what irrational beings we actually are. If we're really just puny minds at the reigns of mighty cave men, what hope is there? What power exists that could "change our minds" for more than a lifespan?

I'm finishing this blog entry a few days after I started it, so my emotional state isn't quite the same. That last question is no longer rhetorical. To what extent can our modern mind over-rule the ancient one? What can we, as individuals or communities, do to take a more rational approach? Can politics move beyond using science as another rhetorical club when it's in its favour and discrediting it when it's not? I have no reason to believe so, but I hope that our rational minds are up to the job.

¹Goldacre's links once again providing a fun counterpoint to his article titles.
²Amazon link.
³In the extreme case, we have this result, which suggets the conscious mind's freedom is an illusion, and the unconscious brain has already made our decisions for us! However the decision in question - pressing a button when the time seems "right" - is probably instinctive anyway.

This is going to make my job so much easier

2009-07-13T19:46:00.001+01:00

Dubious research says little about videogames

2009-01-28T18:05:00.006Z

"Video game conditioning spills over into real life", New Scientist says. I can't say I'm convinced.

My main objection is that the conditioning they're talking about had nothing to do with the virtual environment in question. In the experiment (abstract here*), subjects were hooked up to a bicycling video game. Apparently they were informed that it was to test a new sports drink delivery system, so I would imagine the scenario is one involving exercise bikes which control the speed at which the player travels. (Details would be appreciated if anyone can read the article.)

Whenever their own team passed by, the players were given a mouthful of sweet drink via the hose; whenever the opponents overtook them, they were given a mouthful of salty tea. Both teams had easily distinguishable logos on the back of their shirts. The researchers then called the participants back in for an fMRI session, and looked at how they responded to the presence of the opposing team's logo. It turns out, they didn't like sitting near it (on a towel) in the waiting room. The response to the logo was correlated with activity in some brain regions on the fMRI.

They conclude that "stimulus in the virtual environment can acquire motivational properties that persist and modify behavior in the real world". Well, I call bullshit. The main stimulus here wasn't in the virtual environment. They were being fed unpleasant drinks whenever the opposing logo was on screen, and pleasant drinks whenever their own team's logo appeared. That's more than enough to condition the subjects against the opposing logo.

Imagine a "Clockwork Orange" scenario where you were tied to a chair watching "Jaws" and I pinched you in the neck every time Roy Schneider spoke, and gave you delicious cake whenever the shark killed someone. Would I be able to reasonably conclude that the movie had conditioned you to hate Schneider's voice and love seeing people get mauled?

Let's speculate. What if they gave the players a positive taste when they were overtaken by opponents, and a negative one when they were overtaken by their own team? Without altering the "virtual world", I'd be willing to bet they'd get entirely the opposite response to logos. This would quite easily invalidate the idea that "stimulus in the virtual environment" was responsible. This test, while obvious, was not performed.

Furthermore, they could've just as easily sat the subjects down in front of the game, sans straws, and performed the same experiment. Failure in a game is often accompanied by a negative visual and audio stimulus, however even this is probably not necessary for conditioning, as being passed by the "other team" is supposed to illicit a negative response in itself (you are losing). This would be much closer to an actual video game experience**, and any conditioning shown would purely be the "video game conditioning" the New Scientist article speaks of.

The act of conditioning their subjects with drinks is so unnecessary to the experiment's goals, and puts such a massive hole in the research, that I have to wonder what the hell they were thinking.

They find an interesting correlation between the subject's self-perceived immersion in the game and their susceptibility to the conditioning, which is much more valid a conclusion in my opinion. I'm curious as to whether one's involvement in a virtual world makes one necessarily vulnerable to being conditioned, in comparison to a neutral situation, or watching TV, or reading a book. Perhaps one's degree of involvement in any fiction- or non-fiction media increases susceptiblity to conditioning. However that research simply has not been done here.

A better title for the study would be "real-life conditioning spills into real life". Sadly, that's not nearly as headline-grabbing.

*New Scientist provide the article's DOI but I couldn't find a way to actually use it on the journal website, which was irritating. It's The Journal of Neuroscience, January 28, 2009, 29(4):1046-1051.

**I don't know about you, but I don't chug salt every time Mario pops his clogs

Rookie footballer to be turned into one-man "clone" of greatest living footballers

2009-01-03T16:41:00.004Z

So, I'm reading the Daily Record in the barber shop, and I come across this (which admittedly loses some of its impact with the omission of the print version's diagrams). Arton Baleci is being (self-)trained in the techniques of eleven elite footballers, given state-of-the-art visual acuity training, and subjected to a regime of neuro-linguistic programming (that's a whole other rant), to create a "clone" combining the capabilities of the greatest football players of our time. Does that sound familiar to anyone? What dark powers could be bankrolling his training?

("The Beautiful Aim", the website for Baleci's project. My advice is that if anybody offers him anything involving nanomachines, he should decline politely.)

Time's arrow

2008-12-31T18:08:00.004Z

As we prepare to lurch into 2009, Roger Ebert has posted a review of The Curious Case of Benjamin Button which makes some interesting comments (with his usual wit) about the importance of the "arrow of time" in a film narrative, and how logically perverse and alien Button's life becomes as a result.

From physics, it seems that the only aspect of the universe which is asymmetric (and in fact antisymmetric) with respect to time is the entropy of a closed system (such as the universe): it must always increase during any process. I half-remember something from "A Brief History of Time" on that subject (I read it about half a decade ago). The key point is that very concept of time is an artefact of our existence as chemical beings, driven inexorably by thermodynamics. Ebert's review doesn't go into these sorts of technicalities, but it makes me wonder about the psychology of life (would we even call it life?) without a sense of time. It would be as staggeringly alien as the planet at the centre of Stanislaw Lem's "Solaris", I suspect.

Stop the communis!

2008-11-05T15:27:00.015Z

Via one of Switched's interminable parade of "top X" gallery articles, the Sydney Morning Herald reported back in September that the "ratio communis, a key region of the brain, was malfunctioning" during mobile phone texting or GPS usage. Oh no! This has been somewhat credulously re-reported by Switched (with the the embellishment that "UK" researchers made the finding), and God knows how many other blogs, with the usual concerns about what radio is doing to our brains. Scary stuff, for as the article says, the ratio communis keels over completely: "Instead of fluorescing on brain scans, it flickered, grey and dull." Indeed, there have been "fatalities when this key decision-making part of the brain failed". This amazing research led the American College of Emergency Physicians (ACEP) to issue warnings against texting while rollerblading, driving, and so on.

Not to spoil all the fun, but it's nonsense, and either someone pranked the SMH, or the SMH have pranked us. Switched was sceptical on principle, but didn't spend the ten minutes required to confirm their suspicion. "Ratio communis", which the article thinks means "common sense" in latin, actually means ~~"common scheme" in most of the instances I can unearth~~ something closer to "common meaning". It does not appear to refer to any part of the brain, even as a neologism, for it does not appear anywhere on the entirety of PubMed, the go-to archive of medical research (the words appear, separated, in 95 articles). On the intertrons, it only appears in the appropriate neurological context in blogs parroting the SMH story. The ACEP press release is conspicuous by its absence from their website - the warnings the SMH article refers to are from a seperate media release which went out back in August.

I can't help but wonder about the "scientific literature" that crossed the desk at the Sydney Morning Herald and which prompted their article. Either the literature, or the article itself, is a finely-crafted satire at our complete stupidity when a blinking semiconductor box is placed in front of us. (I've contacted the paper to try and discern which.) The reference to fMRI, suggesting that scientists can watch our "common sense centre" shut down as we tap away at our gadgets, was just the icing on the take which, alas, gave it a sheen of veracity and led to a fair few people taking it seriously. Inadvertently, it's satirised our tendency to take anything shown by "science" at face value. I'm glad that it drew less attention than George Carlo's epic fail of a press release about how wi-fi causes autism, at least.

Review: Bad Science by Ben Goldacre

2008-10-31T23:52:00.010Z

Ben Goldacre's Bad Science column in The Guardian, and the namesake blog, are rigorous in scholarship, precise in analysis, and refreshingly reluctant to demonise. An oasis of genuine optimism, Goldacre engages with fad, misconception, and systematic bias in medical and scientific research, and offers up thoughtful solutions to the deep problems in medicine, both mainstream and alternative. Eager to teach, Goldacre peppers his writing with clear explainations of how things work and why some things just ain't so, carefully avoiding away from the oh-so-tempting, mind-closing "you don't know what you're talking about, here's why" approach to sceptical discourse. Instead, he supposes that we could all understand and engage with the science and medicine headlines, if we were armed with the right tools and relieved of a few popular misconceptions. So I had high hopes for his book, also named Bad Science. (I was lucky enough to get a signed copy. Thanks Michael!)

Bad Science reminds me of Darrel Huff's classic How to Lie with Statistics, which was a humourous primer for spotting statistical cons in advertising and the media, and also Stephen Poole's Unspeak, which repurposed close reading as a bullshit-detection system. Increasingly subtle or technical slip-ups are used as worked examples against which increasingly subtle or technical mental tools are deployed. Armed with these tools, we can recognise deception or error in our day to day lives, and we can understand stories in the media in more depth. Goldacre opens with "detox footbath Barbie", introducing the idea of a controlled experiment, and leads us on a brisk but clear tour though the scientific method and medical statistics. Even sophisticated topics like meta-analysis are dealt with honestly and unpatronisingly.

Never accepting a simple answer, Bad Science also takes some time out to elaborate on some of the surprising revelations along the way. The need for experimental controls in medicine (in the context of homeopathy, a subject which Goldacre appreciates has been done to death) is underlined by the amazing power of the placebo effect, and Goldacre takes a brief detour to discuss the potential for this controversial therapy. His discussion of the "antioxidant paradox", that antioxidant suppliments seem to be actively harmful while high blood antioxidant levels are protective, is much more than a simple debunking. Instead he takes the time to discuss the larger implications of this find for our understanding of how the human body works. (This is reminiscent of the writing in Bad Medicine, Wanjek's thoughtfully scattershot romp through medical misconception).

Goldacre also lets rip about some of his pet hates, but is careful to lay the blame with systems and cultures rather than individuals. The idea of science as an intimidating and arbitrary authority figure is prevalent in the media, and is a projection of journalists' own fears, he argues. By depicting science as an ivory tower sending down pronouncements, the media does its best to discourage us from thinking about the stories. On the other hand world-changing studies and daring pioneers make for easy headlines, and the media are all too willing to loft figures like Andrew Wakefield or Deepak Chopra up as new authorities. The real tragedy, he argues, is that the media shakes off any blame when the wind changes, hanging the former heroes out to dry as quacks or shrugging their shoulders about those crazy scientists, always changing their minds.

Mainstream medicine arguably takes even more heat then "alternative", a step up from "bumbling" to "dangerous", and Goldacre goes as far as to describe pharmaceutical industry behavior as "evil". Mercifully few authorities take homeopathy seriously, for example. However catastrophic failures or misuses of science and statistics deceive doctors and policy-makers on the effectiveness of drugs and treatments, while the publication system fails to properly combat these errors. It's here that the book gets most technical, far removed from the sort of material most readers are likely to encounter, and this part of the book offers striking lesson that perhaps shooting down waffle about distance healing isn't the best use of a sceptic's time.

Personal empowerment is a recurring theme of the book. Science need not be an intimidating authority figure, because we could all potentially understand the process. Likewise some problems can only be dealt with at a personal level, not with a magical sciencey-sounding pill or exercise program. When it keeps these goals in mind, Bad Science is a great success. Later chapters quickly turn into stand-alone case studies in an effor to impress on us the importance of understanding science and medicine - we've all got an interest in staying healthy, after all - and come across as more fragmented. It's here that the book's origins in a succession of blog posts and columns begin to shine through. Even so, it's always wittily, clearly, and precisely written. Bad Science is a superb guide to understanding and engaging with the science and medicine in our everyday lives, and I wholeheartedly recommend it.

(Book links help support Cooking Fiasco.)

More from my .log files

2008-09-19T19:46:00.001+01:00

The Gaussian03 fortunes continue to amuse:

"THE ACADEMIC HIERARCHY"

THE PRESIDENT:
LEAPS TALL BUILDINGS IN A SINGLE BOUND,
IS MORE POWERFUL THAN A LOCOMOTIVE,
IS FASTER THAN A SPEEDING BULLET,
WALKS ON WATER,
GIVES POLICY TO GOD.

THE VICE PRESIDENT FOR ACADEMIC AFFAIRS:
LEAPS SHORT BUILDINGS IN A SINGLE BOUND,
IS MORE POWERFUL THAN A SWITCH ENGINE,
IS JUST AS FAST AS A SPEEDING BULLET,
WALKS ON WATER IF SEA IS CALM,
TALKS WITH GOD.

PROFESSOR:
LEAPS SHORT BUILDINGS WITH A RUNNING START AND FAVORABLE WINDS,
IS ALMOST AS POWERFUL AS A SWITCH ENGINE,
CAN FIRE A SPEEDING BULLET,
WALKS ON WATER IN AN INDOOR SWIMMING POOL,
TALKS WITH GOD IF SPECIAL REQUEST IS APPROVED.

ASSOCIATE PROFESSOR:
BARELY CLEARS A QUONSET HUT,
LOSES TUG OF WAR WITH LOCOMOTIVE,
MISFIRES FREQUENTLY,
SWIMS WELL,
IS OCCASIONALLY ADDRESSED BY GOD.

ASSISTANT PROFESSOR:
MAKES HIGH MARKS ON WALLS WHEN TRYING TO LEAP TALL BUILDINGS,
IS RUN OVER BY LOCOMOTIVES,
CAN SOMETIMES HANDLE A GUN WITHOUT INFLICTING SELF INJURY,
DOG PADDLES,
TALKS TO ANIMALS.

GRADUATE STUDENT:
RUNS INTO BUILDINGS,
RECOGNIZES LOCOMOTIVES TWO OUT OF THREE TIMES,
IS NOT ISSUED AMMUNITION,
CAN STAY AFLOAT WITH A LIFE JACKET,
TALKS TO WALLS.

UNDERGRADUATE AND WORK STUDY STUDENT:
FALLS OVER DOORSTEP WHEN TRYING TO ENTER BUILDINGS,
SAYS, "LOOK AT THE CHOO-CHOO,"
WETS HIMSELF WITH A WATER PISTOL,
PLAYS IN MUD PUDDLES,
MUMBLES TO HIMSELF.

DEPARTMENT SECRETARY:
LIFTS TALL BUILDINGS AND WALKS UNDER THEM,
KICKS LOCOMOTIVES OFF THE TRACKS,
CATCHES SPEEDING BULLETS IN HER TEETH AND EATS THEM,
FREEZES WATER WITH A SINGLE GLANCE,
IS GOD.

Alex's Law^H^H^H Guess of Phone Run Times

2008-09-15T07:15:00.000+01:00

If we assume that the listed talk time for a phone is the amount of time taken to drain the battery completely by making one continuous phone call, and the listed standby time for a phone is the amount of time taken to drain the battery completely with the phone powered on and with radio active, but otherwise idle, we can conclude that:

If you use the phone for half the rated talk time, you will have half the rated standby time available.

e.g. if my phone is rated for 400h (2 weeks) on standby, and 4h of talk time, in practice I can use the phone for a week if I make 2 hours of calls.

This is a useful rule of thumb for sizing up phone manufacturers' ratings, which use preposterously unlikely fringe cases. To remove the deception factor, just cut the rated standby and talk times in half. I'm sure I'm not the first to realise this, but it seemed worth writing down. Of course, it assumes the phone is not used for other functions. If surfing the web or sending text messages strains the phone as much as calling, then those can just be lumped into the talk time pile. If they drain it less or more, then there's some cludge factor involved.

LIGOland

2008-09-15T05:04:00.007+01:00

As promised, a report on my trip to LIGO Hanford Observatory (1:30pm, second Saturday of the month, entry free, approx. 2.5 hours). Our tour opened with an explanatory movie, the gist of which I'll relate for clarity. LIGO (Laser Interferometer Gravitational Observatory) is an experiment to detect gravity waves, the shadowy warpings of space and time given out when massive bodies interact. The textbook example is that of binary neutron stars, pairs of absurdly massive dead stars which circle each other, losing energy by emitting gravity waves until they collide in a final burst of energy. They hope that by measuring the gravity waves from sorts of events, in combination with conventional electromagnetic (light, radio, x-ray) signals, they can get a better understanding of how gravity works on a large scale. The oh-so-topical Large Hadron Collider is chasing gravity too, from the opposite end (the tiny subatomic interactions which give rise to gravity in the first place).

Each of LIGO's observatories consists of a pair of 4km arms, meeting at one end to form a right angle. These form a gigantic Michelson interferometer. A single laser beam is generated at the intersection, split, and sent out along the arms. The lasers reflect off mirrors, and return to the intersection, then are recombined and sent to a detector. If the arms are of equal length, then the recombined beams interfere to zero. If the arms are different lengths, then they fail to interfere properly and there's an appreciable signal. A passing gravity wave distorts space-time so that the arms are of different lengths (or equivalently, time passes at different rates) and thus there's a measurable signal. (CalTech's own info page.)

These are impressively sensitive instruments. After the film, our tour guide demonstrated an interferometer maybe a foot across, tugging on the metal frame with a string. The minute warping of the apparatus caused the laser pointer to fade in and out, while more delicate motions, such as nearby footsteps, were made plain by connecting up a light sensor in the laser's path to a loudspeaker. By scaling up the instrument, even more minute changes can be picked up, an elegant bit of "big science". In principle, LIGO is sensitive down to less than the radius of a proton.

Like the footsteps of our guide, any number of mundane things can change the lengths of the arms, or just wiggle the mirrors around, and our tour seemed to revolve around their efforts to wipe out this unwanted noise. First and foremost, there are two LIGO observatories, one in Hanford in Washington state, the northwest of the United States, and one in Livingston, Louisiana in the southeast of the United States. Therefore any signal detected at one and missed at the other can be assumed to be background noise. (Another upshot is that the two detectors are in slightly different planes in space, so the relative strengths of the two signals can be used to triangulate the source of a gravity wave, at least in principle.)

Secondly, and perhaps most obviously from my perspective as a visitor, they built one of the observatories at Hanford. As my earlier post relates, Hanford lent itself to the atomic weapons program due to its utter isolation (and water supply, of course). It took us about twenty unnerving minutes of driving in the nuclear reservation to get out there. This helps to cut out traffic noise. Presumably out of necessity rather than anything else, the Louisiana counterpart detector is surrounded by logging, and unlike the Washington sands, the local ground carries vibrations of just the right frequencies to mess with the mirrors' fancier stabilising equipment.

That's where things get less elegant, more ingenious. The movie related that the mirrors hang from wires, which attach to vibration-isolated platforms, and sets of teeny electromagnets can prod the mirrors back and forth to counterbalance any unwanted wiggles. The control systems are designed to anticipate certain kinds of wobbles and damp them out. Another example of the device's sensitivity: the atoms in the suspension wires jiggle around because of their own heat, making the wires vibrate at their resonant frequencies like violin strings. On the opposite end of the scale, they brought in a freshman to write an application which would automatically account for the one-foot tidal warping of the Earth's surface as the sun and moon circle overhead.

This opening preamble was probably a little long for my taste, although it was a great chance to quiz a member of the LIGO staff. Now we got a wander across the site to the intersection of the beams themselves. Did I mention that we're in the desert? And the arms are 4km long? As much as I would've liked to see the mirrors up close, that's a hell of a hike, and the drop-in tour doesn't go there. Our tour guide was happy to relate anecdotes and field even more questions, in spite of the weather. Honestly, we were suffering a little by the end. Come in the winter, if you insist on the afternoon drop-in like we did.

Our tour concluded in the control room, an appealingly dim-lit NORAD-esque chamber, ablink with readouts and spectra from LIGO. There aren't any genuine signals yet. At its current 25 million-light-year range (bigger than the entire local group of galaxies), they're only expecting to see colliding neutron stars every ten years, give or take, but upgrades set for the next couple of decades should expand its range tenfold, raising the frequency of detections a thousand times (the volume covered goes up with the cube of range), so that certain events should be detected daily. To be honest, I think LIGO isn't an operation instrument yet, and it's in a prolonged setup phase until these upgrades are complete. Until then, they've certainly built the world's most sensitive seismometers, as we got to watch individual trucks popping up as blips on the control room readouts.

Where next? The obvious way to escape all those rumbles is to put the detectors in space. That's the idea behind LISA, whose arms will be links between satellites in orbit of the sun. This will allow them to study gravitational waves of frequencies which are inescapably concealed by noise on the Earth. I wish them all the best of luck. As for the tour, it was perhaps a little too limited in terms of what we got to see on the site, and there was much repetition between the tour and the video, but if you're keen to ask questions (or one of the other visitors is), there's a lot to learn. (The tour guide, if anything, was too keen to talk, apparently ignorant of the blasting heat.) And it's not every day you get to clamber around on top of a scientific tool. (My fiance was disappointed when it turned out there was not actually any lego, though.)

Geographic nominative determinism?

2008-09-07T08:24:00.003+01:00

I have to wonder if there's any cosmic significance to a new orgasmic response study coming out of Paisley of all places.