Tuesday, 21 December 2010

Fearless woman's life in science

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.

Tuesday, 30 November 2010

On Futurism

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.)

Monday, 31 May 2010

Evan Harris on Royal Free and Lancet culpability in Wakefield case

"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.

Monday, 3 May 2010

Coming soon!

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

Thursday, 4 March 2010

Free Radicals Feb 2010

The best of the past month in my RSS feed:


"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.


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).


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.


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.


"'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.

Wednesday, 17 February 2010

Peter Atkins on textbooks, eBooks, and interactivity.

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.

Wednesday, 3 February 2010

HuffPo: blame Lancet, not Wakefield, for paper deceptions

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.

Tuesday, 12 January 2010

Entropy and time, revisited

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.)