tag:blogger.com,1999:blog-70076922190292835242023-06-15T12:17:10.889+01:00A Chemist in TheoryUnknownnoreply@blogger.comBlogger58125tag:blogger.com,1999:blog-7007692219029283524.post-21583342106382882522019-08-14T21:01:00.003+01:002019-08-14T21:04:23.386+01:00Exhibition: Food: Bigger than the PlateFood is an essential thread in human society, touching on everything from culture and design to politics and science. The V&A's current "<a href="https://www.vam.ac.uk/exhibitions/food-bigger-than-the-plate">Food: Bigger than the Plate</a>" exhibition looks to the history and products of design to draw our attention to these connections, and in particular to question the ones we take for granted.<br />
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It starts off boldly with a section on waste in all of its taboo-challenging senses, looking at how the technology and social norms around sanitation have shaped and entrenched each other, replacing - but later being challenged by - more sustainable, closed-loop approaches. This eyebrow-raising material jostles with technological approaches to reuse such as waste-derived plastics and whimsical artistic projects, like a conceptual restaurant built around the micro- and macro-organisms that quietly feed on people.</div>
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A similarly balanced meal appears in each of the sections on farming, trade, packaging and ultimately cooking and eating, meaning there's something to be enjoyed here whether you're looking for ways to challenge the agribusiness hegemony or just want to have a bit of fun with unconventional table settings. The way we engage with food is so fundamental that even acknowledging our norms and conventions can seem transgressive - just look at how people react to veganism - but viewing at them from a distance in this playful, thoughtful way makes these big ideas very accessible.</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-21507943195847466082018-01-04T19:44:00.001+00:002018-01-04T19:44:57.468+00:00ChangesOh boy have I neglected this blog.<br />
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Since my last updates, I've become a publishing editor for the Royal Society of Chemistry, which is interesting work I'll probably talk about more in the future. In fact, you can <a href="http://my.rsc.org/blogs/119/1834">read about my recent experiences at a Faraday Discussion on the RSC Publishing Editor Blog</a> right now.<br />
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I have apparently also let my domain name stop working so update your links I guess? I'll see if I can fix that.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-13638911808103390492018-01-04T19:34:00.002+00:002018-01-04T19:34:15.655+00:00December BooksI've spent my Christmas break binge-reading the various books in my to-read pile. This means I finally got around to Gregory Benford's "Deep Time", which I picked up this summer. It's a discussion of how we pass information down over extreme time scales, generally at least the ten-thousand-year span of human civilisation. There are plenty of ways this could be made into an abstract slog, but the book is nicely grounded by the perspective Benford is writing from: three of the four chapters are built on "deep time" related projects that he worked on, and the technical and social implications are well-balanced by his personal accounts. Sending messages to our future selves requires us to overcome our inherently short-term view of the world but also, it transpires, our bureaucracy.<br />
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The book's introduction is such a broad-reaching and detailed discussion of the theme that it probably should have been published as a feature article in a popular science magazine. (Was it, I wonder?) Stage set, the first and most romantic chapter addresses the Waste Isolation Pilot Project, and in particular its warning markers, which must communicate specific and (ideally) quite technical ideas to humans thousands of years in the future. The second discusses a never-constructed diamond message disk for the now-expired Cassini-Huygens probe, and gets deeply into the idea of communicating with non-humans in ages to come and upper management in the present. The third and fourth chapters consider biodiversity and the Earth climate as messages we are inadvertently writing for future generations, and how we can make the best of them.<br />
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The book came out in 2000, and there don't seem to have been any updated editions, so it makes for quite an apt capsule of the time in which it was published. There's a good perspective on these projects from when they were initiated, which can be contrasted with their current situation (farewell, Cassini!) but changes in broader concerns and themes are also noteworthy. Ecological issues here come across as more prominent and more urgent than climate change, although that was already a significant concern as seen in the final chapter. Those seem to have swapped over. The little details amuse: Benford is dubious at the suggestion of scattering CD-ROMs as a way of sending a message down the centuries, and sure enough notebook manufacturers started taking optical drives out of laptops within a decade, never mind the information security implications.<br />
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If you happen across a copy of this and the theme intrigues - it seems to be out of print - I'd highly recommend it.<br />
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I also received "Arrival" (previously published as "Stories of Your Life and Others") as a gift, a collection of short stories by Ted Chiang. Obviously the big draw here is "Story of Your Life", which was the basis for the 2016 movie after which this story collection was renamed. How we perceive the world and the quiet tragedies that arise with abrupt shifts in understanding are a common theme, naturally, but the collection also has an interesting line in taking religious concepts and playing them straight as science fiction premises. The overlap of the three is thought-provoking territory and Chiang is a first-rate storyteller. They're not all classics - there are a couple of stories where the ideas start to take over - but this was an excellent read. This may be my bias; the protagonists are almost invariably technical people (or think like them) and therefore some of the events struck me quite strongly.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-39896746079551289012016-03-31T09:21:00.003+01:002020-06-11T08:24:52.935+01:00How not to cut cakeWhen my wife pointed out Francis Galton's method for cutting a cake to minimise the exposed surface and therefore improve its lifespan, I of course implemented it immediately. I hate stale cake. (I eat it anyway.)<br />
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<a href="http://4.bp.blogspot.com/-qkfbcx8tq5E/Vvza_KNpvEI/AAAAAAAAAgc/IC_Es-WmDIAsh0HE3aAtFS27DVxHpNBRQ/s1600/Capture.JPG" imageanchor="1"><img border="0" src="https://4.bp.blogspot.com/-qkfbcx8tq5E/Vvza_KNpvEI/AAAAAAAAAgc/IC_Es-WmDIAsh0HE3aAtFS27DVxHpNBRQ/s400/Capture.JPG" /></a><br />
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Galton, <i>Nature</i> <b>75</b>, pp. 173-173 (1906) <a href="http://www.nature.com/nature/journal/v75/n1938/abs/075173c0.html">doi:10.1038/075173c0</a><br />
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The basic principle is that you remove slices from across the middle of the cake, and then press the remaining pieces together so that there is no exposed surface to get stale.<br />
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<a href="http://4.bp.blogspot.com/-e-9CYHpsJkM/VvzdjpMz-rI/AAAAAAAAAgo/eq5g25_cIrUbCLFKQS0BPF8OvCq3xaMag/s1600/2016-03-27%2B20.57.20.jpg" imageanchor="1"><img border="0" height="239" src="https://4.bp.blogspot.com/-e-9CYHpsJkM/VvzdjpMz-rI/AAAAAAAAAgo/eq5g25_cIrUbCLFKQS0BPF8OvCq3xaMag/s320/2016-03-27%2B20.57.20.jpg" width="320" /></a><br />
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There's an immediate drawback to this method: each progressive slice is taken from a smaller cake of a different shape, so it's hard to judge portions. It's also difficult to make even-sized pieces for multiple guests. (Galton's original publication was meant to maintain the lifespan of a cake that was only being eaten by two people.) The slices are at least neatly cuboid which solves the age-old problem of how to eat a wedge of something with a fork<br />
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<a href="http://3.bp.blogspot.com/-xaJAB132Cu8/VvzdoawLQwI/AAAAAAAAAgw/BUWtXHnydZs-mZ59BAwfSR6fPQV5leGmg/s1600/2016-03-27%2B21.00.30%2BHDR.jpg" imageanchor="1"><img border="0" height="239" src="https://3.bp.blogspot.com/-xaJAB132Cu8/VvzdoawLQwI/AAAAAAAAAgw/BUWtXHnydZs-mZ59BAwfSR6fPQV5leGmg/s320/2016-03-27%2B21.00.30%2BHDR.jpg" width="320" /></a><br />
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The bigger problem is that this method is wholly counterproductive when applied to my wife's delicious coffee and walnut cake. It's simply not possible to produce sufficiently crisp parallel edges so that the different sides fit together and exclude the air. In fact, this method results in a greatly increased exposed surface area compared to just cutting out a wedge.<br />
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<a href="http://3.bp.blogspot.com/-pHbqEwr5e2o/VvzdtuoqHfI/AAAAAAAAAg4/kHVyf3X8lKI3j3bU-W91CVNLqng-fuXIg/s1600/2016-03-28%2B16.30.21.jpg" imageanchor="1"><img border="0" height="320" src="https://3.bp.blogspot.com/-pHbqEwr5e2o/VvzdtuoqHfI/AAAAAAAAAg4/kHVyf3X8lKI3j3bU-W91CVNLqng-fuXIg/s320/2016-03-28%2B16.30.21.jpg" width="239" /></a><br />
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Galton's original method is applied to a Christmas cake, which has a firm texture that might be more conducive to clean edges, but I still think you're going to have difficulty getting a nice tight interface between the two exposed surfaces, even with his suggested rubber band.<br />
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Galton is known as the originator of eugenics, so perhaps it's unsurprising that this idea proves to be counterproductive. I'll stick to using the plastic cake cover.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-72468628001418578062016-03-08T19:05:00.001+00:002016-03-08T19:05:08.757+00:00Melting points and The French ConnectionI was watching the classic 1970s crime film <i>The French Connection </i>recently (which is a masterpiece, by the way) and was surprised to see a bit of ordinary undergrad chemistry appear at about the half-way mark.<br />
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<span style="font-size: x-small;"><i>In lieu of the screencap that Netflix won't let me take, you'll have to load up your own copy and fast forward to the 52-minute mark.</i></span><br />
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The gang are having their chemist confirm the purity of the heroin shipment around which the whole movie revolves. He's watching for the temperature at which the compound melts - the higher, the purer, with completely pure "product" melting at its own specific melting point. I was really chuffed that the movie went to such lengths to get the technique right, which is just going to be a background detail to most viewers. It really adds to the verisimilitude.<br />
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At the end of my undergraduate organic chemistry labs, we would do a similar procedure to show that we'd done a good job of making whatever compound we were supposed to be making. The hardware was a little different, but we were still tapping the compound into a little glass tube, heating it up, and watching for the temperature at which it melts.<br />
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<a href="http://4.bp.blogspot.com/-k0iWH5ORuhY/Vt8f35cnDNI/AAAAAAAAAgE/sT6k4JdQKmE/s1600/grad%2B184.jpg" imageanchor="1"><img border="0" height="240" src="https://4.bp.blogspot.com/-k0iWH5ORuhY/Vt8f35cnDNI/AAAAAAAAAgE/sT6k4JdQKmE/s320/grad%2B184.jpg" width="320" /></a><br />
<i><span style="font-size: x-small;">Many a lab session ended with me squinting into these machines. A thermometer and a sample tube go in the top.</span></i><br />
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You might rightly wonder why impurities lower the temperature at which some chemical compound melts. The intuitive answer is that the molecules of the compound have to fit together like little lego bricks, and impurities get in the way of the molecules bonding (fitting) together, and therefore it melts more easily.<br />
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It's intuitive but it's wrong!<br />
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Actually, the bonding isn't weakened all that much by the presence of impurities. The real reason has to do with entropy.
Understanding this from first principles involves a bit of thermodynamics, but I can cut to the chase a bit and introduce you to one of the neater ideas in physical chemistry.<br />
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A process in chemistry happens when the "free energy" <i>G</i> is lower after the process than before. So to melt, the liquid substance has to have a lower free energy, <i>G</i>, than the solid. <i>G</i> has two parts, the enthalpy <i>H</i>, which has to do with things like how strongly molecules are bonded together, and the entropy <i>S</i>, which is to do with the system's capacity for disorder. (Measured by the number of different ways we can arrange the molecules.)<br />
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<i>G = H - T </i>x<i> S</i><br />
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The entropy <i>S</i> is multiplied by the temperature as you can see, so it has an additional property that its contribution to the free energy gets larger as the temperature increases.<br />
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For a process like melting, the enthalpy <i>H</i> has to increase. The compound is always going to be more stable locked into a neat little solid than with the molecules free to move. So this is a penalty against forming the liquid. (This is known as the enthalpy of fusion.)<br />
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However the entropy <i>S</i> will increase upon melting, because we can arrange the molecules in many more different ways in the liquid than in the solid. The entropy increase can be viewed as a sort of a discount on the enthalpy penalty, and because <i>S</i> is multiplied by the temperature, the total discount <i>T</i> x <i>S </i>is<i> </i>bigger at higher temperatures. Melting happens when you reach a sufficiently high temperature that entropy discount <i>T</i> x <i>S</i> is equal to the enthalpy penalty <i>H</i>.<br />
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So what happens when we add impurities? Well, the entropy <i>S</i> of the solid is a bit higher than before, because there are now even more different possible arrangements of molecules. However the entropy of the liquid is much higher than before. That means that the entropy increase associated with melting is larger, and therefore the discount we get from the entropy is bigger. Seeing as the enthalpy part <i>H</i> stays more or less the same, the temperature at which the entropy overbalances the enthalpy is lower.<br />
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Thinking about chemical processes in terms of thermodynamics isn't always intuitive, but it reveals a lot of subtleties that aren't immediately obvious. Kind of like a good movie.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-76724872843007207362016-02-25T18:00:00.000+00:002016-02-25T18:00:34.599+00:00Guillermo del Toro on getting ideas off the groundIn a recent discussion with game director Hideo Kojima (moderated by Geoff Keighley), the film director Guillermo del Toro offered the following regarding how he chooses projects:<br />
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I wish I could command the movies I want to make. The movie that gets made gets made because it's right at that time, and it doesn't matter. Anything else is completely haphazard. When people say why do you have six, seven things going at the same time, it's because <i>one</i> of them happens, not the seven, not the six. And I learned this the hard way. When you think about projects you think about something that came out in a dream. That's it. When you hear about it, and whether it happens or not, in between [those points] I work three, four, ten years on that thing. And sometimes, most of the time, they don't come through.</blockquote>
While del Toro is talking about films, I think this is good advice for anyone who's dependent upon outside support to get a project off the ground, such as scientific grants. You need to have enough ideas in progress that when the circumstances are right in terms of collaborations, funding, and the general mood of the research community, one of them can move along and give a finished result. As a corollary I'd argue that one of the things that distinguishes the really successful creative people is simply having enough ideas to be able to discard all but the best.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-83857422772500847942016-02-24T00:00:00.000+00:002016-02-24T00:00:00.151+00:00A second mechanism for Sn2The S<sub>N</sub>2 mechanism is a favourite of first-year undergraduate organic chemistry lectures. It's chunky and easy to understand, but there's a lot of subtlety in there, and it comes up all over the place. It's supposed to be well-understood (as first-year stuff it better be) but a collaboration of physicists at the University of Freiburg and Texas Tech has <a href="http://pubs.acs.org/cen/news/86/i02/8602notw1.html">found another mechanism for it.</a> (Check out the animations in the link - it makes what I'm about to prattle on about a lot clearer.)<br />
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What's S<sub>N</sub>2? Suppose you have a molecule of methyl iodide, CH<sub>3</sub>-I, but really you want a bromine atom, Br, in there instead of the iodine. Bromine and iodine are both in the same chemical group (the halogens) so it seems like a fair swap. You do this by shoving in some bromide anions (bromine atoms with a negative charge). The iodine that was originally in the molecule comes out as an iodide anion (which is just an iodine atom with a negative charge), balancing things out.<br />
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<span style="font-size: small;">Br<sup>-</sup> + CH<sub>3</sub>-I --> Br-CH<sub>3</sub> + I<sup>-</sup><br /></span><br />
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<span style="font-size: small;">This process turns the CH<sub>3</sub> part of the molecule inside-out, like an umbrella.</span> This mechanism makes a lot of sense, and explains a lot of things seen in experiment - with more complicated molecules, you can see the inverting process happening around that particular carbon atom. And of course there has to be room for the attacking nucleophile to approach - if you stick really big bulky things on that carbon, the nucleophile can't attack, and suddenly the reaction won't go.<span style="font-size: xx-small;"><sup>[1]</sup></span><br />
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Looking at S<sub>N</sub>2 this way makes it easy to understand what's going on. However it always pays to check your assumptions rigorously, which is how the new mechanism was exposed. The researchers set up an idealised S<sub>N</sub>2 reaction. They fired a beam of pure Br<sup>-</sup> into a beam of pure CH<sub>3</sub>-I molecules, so they know exactly how things are flying together. They monitored what direction and speed the iodide ions were coming out after the swap with in order to figure out what was happening.<br />
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In a minority of cases, rather than the bromide whalloping in one side and iodide flying out opposite (as you'd expect from the normal mechanism above), the bromide smacks into the methyl group from an angle. This sends the methyl iodide molecule spinning. The bromide can then snag the methyl part away, leaving an iodide ion. The substrate and products, and even inversion around the attacked carbon are the same (as you can see on the animation on the website).<br />
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It's a really neat idea, although the spinning action kind of depends on you having big, heavy atoms to swap in otherwise fairly light little molecules. And the new mechanism only becomes important when the collisions are happening with a lot of energy. It may seem pedantic, but exploring little oddities like this can explain odd behavior.<br />
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<span style="font-size: small;"><span style="font-size: xx-small;"><sup>[1]</sup>This kind of reaction is a <i>nucleophilic substitution</i> - the iodide and bromide are nucleophiles (they chase positive charges) and we're swapping one for the other. In this case, if you sit down and monitor how the reaction's speed changes with the concentration of methyl iodide or the amount of bromide, then you see that both matter - this suggests that both the attacking group and the substrate come together in one step to make the reaction go. We say that the process is <i>bimolecular</i>. That's where the odd name comes </span></span><span style="font-size: xx-small;">from - S</span><span style="font-size: xx-small;">ubsitution<sub>Nucleophilic</sub>2</span><span style="font-size: xx-small;">(Bimolecular).</span><br />
<span style="font-size: xx-small;"><br /><a href="http://www.sciencemag.org/cgi/content/summary/319/5860/168">Original paper. (<span style="font-style: italic;">Science</span>)</a></span></div>
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Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-49421131805083710452016-02-23T00:00:00.000+00:002016-02-23T07:35:05.006+00:00Antoine Lavoisier and the Musee des Arts et MetiersAntoine Lavoisier was one of the founders of chemistry. His work demonstrated the idea of "stoichiometry", that chemical compounds react in particular ratios. He's rightly enshrined as a hero of chemistry, and you can see his equipment in the excellent <a href="http://www.arts-et-metiers.net/musee/visitor-information">Musee des Arts et Metiers</a> in Paris:<br />
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<a href="http://3.bp.blogspot.com/-nwDKN5k7j3E/VstBzw3WWDI/AAAAAAAAAes/p0DLSd7aJ74/s1600/2013-10-10%2B19.59.15.jpg" imageanchor="1"><img border="0" height="239" src="https://3.bp.blogspot.com/-nwDKN5k7j3E/VstBzw3WWDI/AAAAAAAAAes/p0DLSd7aJ74/s320/2013-10-10%2B19.59.15.jpg" width="320" /></a><br />
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It's a great museum of science, with all sorts of interesting hardware from different eras.<br />
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<a href="http://2.bp.blogspot.com/-nbkGZtVhmTg/VstCDuWKCvI/AAAAAAAAAe0/g28cOuv4pvE/s1600/2013-10-10%2B20.21.39.jpg" imageanchor="1"><img border="0" height="320" src="https://2.bp.blogspot.com/-nbkGZtVhmTg/VstCDuWKCvI/AAAAAAAAAe0/g28cOuv4pvE/s320/2013-10-10%2B20.21.39.jpg" width="320" /></a><br />
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It also had some historical technological figures of a different type during my visit, as part of a temporary exhibition.<br />
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<a href="http://2.bp.blogspot.com/-kb2BRc61ONc/VstCbVgTE-I/AAAAAAAAAe8/DTqazHZvrdw/s1600/2013-10-10%2B20.41.59.jpg" imageanchor="1"><img border="0" height="320" src="https://2.bp.blogspot.com/-kb2BRc61ONc/VstCbVgTE-I/AAAAAAAAAe8/DTqazHZvrdw/s320/2013-10-10%2B20.41.59.jpg" width="239" /></a><br />
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As for Lavoisier, he was executed during the Terror, but is remembered with justifiable pride by his countrymen. Look closely, and you can find his name on the Eiffel Tower.<br />
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<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-56157229433830659282016-02-22T17:12:00.000+00:002016-02-22T17:57:23.891+00:00Coulomb explosions in alkali metalsThe reaction of alkali metals with water is one of the all-time classic chemistry demonstrations: a pellet of sodium or potassium is dropped onto the surface of water, where it reacts to produce hydrogen gas and a lot of heat. The heat ignites the hydrogen and melts the metal into a little ball which then jumps around on top of the water trailing flames and steam.<br />
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<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/eaChisV5uR0" width="560"></iframe><br />
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The basic chemistry is a reduction-oxidation reaction, that is, a reaction involving exchange of electric charges. Water isn't just a bunch of neutral water molecules H<sub>2</sub>O. It also contains fragments in the form of positively charged hydrogen ions H<sup>+</sup> and the negatively charged remainder called hydroxide OH<sup>-</sup>.<br />
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H<sub>2</sub>O --> H<sup>+</sup> + OH<sup>-</sup><br />
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The alkali metals are holding onto their last negatively charged electron very weakly, and give it up very easily to the positively charged hydrogen atom. The neutral potassium atoms become positively charged potassium ions, and the positive hydrogen ions become neutral hydrogen atoms:<br />
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K + H<sup>+</sup> --> K<sup>+</sup> + H<br />
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Those neutral hydrogen atoms can then pair up to form hydrogen molecules, while the charge of the new positive potassium ion is balanced by the negative hydroxide ion:<br />
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K<sup>+</sup> + OH<sup>-</sup> --> KOH (in solution)<br />
H + H --> H<sub>2</sub> (gas)<br />
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This is, of course, a gross simplification, but it gives you an overall idea of the processes involved. The upshot is that neutral hydrogen forms a gas that is ignited by all the heat released by the reaction, leaving behind potassium hydroxide KOH, also known as potash. This is an alkali.<br />
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However one of the great pleasures of science is checking to see what <i>really</i> happens. A group of researchers at the Academy of Sciences of the Czeck Republic and the Technische Unversitat Braunschweig <a href="http://arstechnica.com/science/2015/01/high-speed-camera-reveals-details-of-potassium-water-explosion/">studied the reaction between potassium and water using a high-speed camera</a>, and they found that the metal bursts apart in a ball of spikes:<br />
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<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/c3oyzHS9N3E" width="560"></iframe><br />
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What's going on here? Well, remember that the first step in the reaction is that each potassium atom loses an electron to the water. That leaves all the atoms at the surface of the potassium with a positive charge. Similar electric charges - like matching poles on magnets - repel each other. Potassium is a pretty soft metal, so once all those surface atoms turn into charged ions, and before they have a chance to dissolve into the water, the repulsion between the ions is enough to cause the ball to blast apart into spikes. This is called a "Coulomb explosion" - Coulomb from the Coulomb force between electrical charges, and explosion because it's an explosion. The researchers performed highly sophisticated computer simulations to verify that this was indeed what's happening - no mean feat, given that they have to accurately consider the movement of electrons, metals, and water molecules.<br />
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Coulomb explosions show up in other parts of chemistry. A Mass Spectrometer which measures the masses of charged molecules flying through the instrument, so you can figure out what they are, or measure how much of a known molecule is in a mixture. However first you have to get the molecules out of the mixture so they're floating around freely, and put an electric charge on them. A classic way of doing this is to run a stream of your mixture into a powerfully electrically charged nozzle. By dumping a big charge on the mixture, you not only give the molecules the right electric charge, but you cause all of the different molecules to repel each other rapidly until you've got just individual molecules floating around in space.<br />
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I did some research work on that process in my undergraduate years. It's always great to see how universal these processes are.<br />
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Bringing this obviously ancient draft post up to date, here's Periodic Videos putting a light alkali metal - lithium - into 7-Up. The results are less spectacular, because the reaction is less aggressive.<br />
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<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/ofNN1b7xzFw" width="560"></iframe>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-24254062968039756672016-02-22T16:51:00.002+00:002016-02-22T16:51:45.442+00:00"Here's Your Damn Jetpack"A while ago I wrote a post about <a href="http://www.chemistintheory.com/2008/09/ligoland.html">visiting LIGO</a>, the Laser Interferometer Gravity Observatory. Actually that visit kicked off a little Tumblr project of mine, a response to people's cynicism about technological progress. No, we don't have jetpacks and flying cars, but we have scientific instruments that can detect distortions in space-time to a mind-crushingly exacting degree, portable data devices that shame the Star Trek PADD, and an impending flying robot problem.<br />
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That project ended a while ago but the <a href="http://www.nature.com/news/gravitational-waves-how-ligo-forged-the-path-to-victory-1.19382">recent announcement that aLIGO had detected gravitational waves</a> jogged my memory and I decided it'd be nice to share it here. Enjoy "<a href="http://damnjetpack.tumblr.com/">Here's Your Damn Jetpack</a>".Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-80099166415035679732014-01-05T16:16:00.001+00:002014-01-05T16:16:31.779+00:00Superhydrophobic sand<a href="http://cheezburger.com/7980373504">This gif</a> has been blowing a few minds lately. It's superhydrophobic sand. You know how oil and water won't mix? Oil is known as a "hydrophobic" material as a result, it's "afraid" of water and the two will try to separate. As it happens, you can engineer other materials with the same property, often by sticking little oily molecular chains onto them. That gives you a material where - for example - water will roll right off it. Silica is a great substrate for this, and sand is essentially silica. <div>
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So you can get some sand, treat it appropriately, and when it's poured into water the two simply won't mix. The water can't even get into the tiny spaces between the sand grains, so the air that's mixed in with the sand stays there as a big bubble, giving it that shiny appearance.</div>
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Now, just how hydrophobicity works is an interesting subject in and of itself. It's important not just in waterproofing, but how the proteins that your body uses can arrange themselves, and how certain drugs work. I'll be writing about that in the near future.</div>
Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-7007692219029283524.post-26550917051666052042013-11-24T16:22:00.003+00:002013-11-24T16:22:54.572+00:00Fun with Jablonski diagramsKenneth Hanson over at Chemistry-Blog <a href="http://www.chemistry-blog.com/2013/11/09/rethinking-the-jablonski-diagram/">set his students the task of re-inventing the Jablonski diagram</a>, a kind of schematic used in chemistry to show how molecules become excited and de-excited. Those processes drive things like phosphorescence ("glow in the dark") and fluorescence ("day-glo") and are really important to organic solar cells and organic LEDs. (If you've seen the first-generation PlayStation Vita's eye-popping display, you can thank the latter technology.) Having a good, clear way of conveying this information is important, which is why the Jablonski diagram has hung around for the best part of a century - it works!<br />
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To come up with their own versions, the students had to really understand what's going on behind the diagram, so this is a great teaching exercise. If you're at an early stage of your chemistry career, take it from me: nothing gets your brain going on a problem like trying to describe and explain it to someone else. Quite aside from that though, they're all really imaginative. I wish I could have a go on Jablinko.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-81630539933923375102013-08-25T18:24:00.000+01:002013-08-25T18:24:18.839+01:00Calculating CarbyneA group of researchers at Rice University have performed some nice calculations on carbyne, or linear acetylenic carbon, determining its mechanical properties and lots of other fun stuff. Carbyne is a carbon chain with alternating single and triple bonds, and therefore there's plenty of reason to expect that it'd have some interesting mechanical properties like being really strong. Of course, being basically a whole lot of acetylene molecules spaced apart by ethane, it's <a href="http://www.rsc.org/chemistryworld/Issues/2010/November/CarbyneOtherMythsAboutCarbon.asp">supposedly be really reactive</a>, and it's strongly suspected that it'd cross-link to death if left to its own devices. (Alternatively, it could be double bonds all the way down; more on that later.) <br />
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The group did periodic DFT calculations in VASP to calculate the material's strength - when it breaks - and Young's modulus, a measure of its resistance to stretching. If you're not familiar with periodic boundary conditions, imagine a Pac-Man or Asteroids game board. Everything that goes out one side wraps around to the other. So a snippet of the molecule sees an image of itself continuing at each of its own ends, and those ends in turn see their own duplicates, and so on. This is an excellent model of an infinitely long chain that doesn't change anywhere along its length. This model of an infinitely long chain is, itself, is a good approximation of a really long, but finite carbyne molecule - and by stretching that chain they could measure its Young's modulus.<br />
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They also did some molecular calculations on some rings of the material to estimate its resistance to bending, and on finite-length carbyne molecules (capped at the end with different functional groups) to measure its resistance to twisting. To finish it off they determined the energy barrier to cross-linking when two molecules come together, how well it conducts electricity, and whether the single-triple or double-double bond structures are preferred.<br />
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Thorough work!<br />
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It transpires that it's not only really rigid but spectacularly strong. Its Young's modulus is double that of the next stiffest material, <i>graphene</i>, and three times that of diamond. It's also comfortably stronger than either. That's right, if you're looking for something to build a space elevator cable out of, miles of nanotubes are no longer the cool hypothetical material to go for. Its resistance to bending and twisting are on a similar order of magnitude to <i>double stranded DNA</i>, a whopping great hydrogen- and covalent-bonded monster of a material. (Interestingly, carbyne's properties are strongly dependent upon what capping groups are used, which could make for some interesting fine-tuning.)<br />
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Fun stuff. The real question is, will it hang around when you make it?<br />
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Well by these calculations, when bringing two chains together there's an energy barrier of 0.6 eV to them cross-linking. That's pretty substantial. On the other hand, it's very unlikely that two carbyne molecules would just benignly wander up to each other like this. I suspect that when you put the molecule into a real-world soup of radicals and ions, it's not going to have a hard time finding a way around that wall. They also determined that two carbyne chains won't cross-link together down their whole length; the difficulty of pulling the two chains alongside means that there are alternating stretches of untouched and cross-linked carbyne. Again, I'm not sure that carbyne would behave itself quite so well in the messy real world, but it's promising.<br />
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You can read the paper at Arxiv, <a href="http://arxiv.org/ftp/arxiv/papers/1308/1308.2258.pdf">"Carbyne from first principles: Chain of C atoms, a nanorod or a nanorope?"</a> by Mingjie Liu, Vasilii I. Artyukhov, Hoonkyung Lee, Fangbo Xu, and Boris I. Yakobson; a quick Google News search for Carbyne should give you plenty of news coverage.<br />
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As always, all errors here are my own, and I would be really grateful for any corrections you might want to send my way.Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-7007692219029283524.post-23250798137267241172013-08-20T20:53:00.001+01:002016-02-22T19:14:15.686+00:00When someone says "formula for the perfect", I reach for my red penSince this morning, I've upgraded my reaction to the RSC's <a href="http://www.rsc.org/AboutUs/News/PressReleases/2013/formula-perfect-cheese-on-toast.asp">formula for the perfect cheese on toast</a> from "not impressed" to "deeply not impressed".<br />
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It starts off pretty well. They actually did some experimentation, which is a far cry from most "formula stories" <a href="http://www.theguardian.com/science/2009/sep/02/perfect-formula-festival-science">cut from whole cloth at a PR firm's behest</a>, many of them from <a href="https://www.google.co.uk/search?q=%22david+holmes%22+%22formula%22">the same few</a> <a href="http://www.theguardian.com/science/2006/dec/16/badscience.uknews">chronically underworked researchers</a>. By carefully varying the amount and type of cheese, the thickness and type of bread, and the distance from the heat source, they determined the combination most appealing to a panel of experts. That's how science is done! Science is about thinking and experimentation, which are really, really accessible, so a cheese on toast experiment was a great idea. People could recreate this test at home. (And I encourage you to!) Great job RSC.<br />
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Then they present the results like this:<br />
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<a href="http://www.rsc.org/images/Formula-for-the-perfect-che_tcm18-233990.jpg" imageanchor="1"><img border="0" src="http://www.rsc.org/images/Formula-for-the-perfect-che_tcm18-233990.jpg" /></a><br />
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That's not okay!<br />
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By cloaking their results it in a mish-mash of confusing abbreviations, the formula just continues the message that science is an opaque and needlessly complicated field, making grand prognostications about topics in which it is hardly the be-all and end-all of judgement. You wouldn't actually write a reaction like that in a report, anyway - it would defeat the purpose. They take less space to simply tell us how to make the cheese on toast, and with more clarity, than the diagram occupies. So it's not just complicated, it's inauthentically complicated!<br />
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Outreach efforts like these should show that science is an activity for everyone, and do their best to explain that when scientists use jargon, it's only when needed for clarity or precision. Science can be, and should be, universal. Science is about trying things out, testing and iterating. We can all do that, even if we're just trying to figure out the best way to make our favourite snack.<br />
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Here's an equation I think we can all get behind:<br />
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Cheese + bread ---SCIENCE---> Deliciousness<br />
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For good articles on bad formulas, you could do worse than start with these:<br />
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<a href="http://www.badscience.net/2008/12/transparent-excuse-for-printing-a-nice-pair-of-hooters/">"Transparent excuse for printing a nice pair of hooters"</a> by Ben Goldacre<br />
<a href="http://www.howtospotapsychopath.com/2008/12/13/xyz-bs/">"X+Y/Z=BS"</a> by Dan Rutter<br />
<a href="http://www.improbable.com/2007/12/27/formulaic-fashioning-of-fun-formulas/">"Formulaic fashioning of fun formulas"</a> by Marc Abrahams<br />
<a href="http://www.andrewt.net/blog/tag/stupid-formulae/%3E">"Stupid formulae"</a> by Andrew Taylor.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-30916548789609418382013-08-05T20:07:00.000+01:002013-08-05T20:08:53.341+01:00A Chemical ImbalanceProfessor Polly Arnold of the University of Edinburgh department of chemistry is launching a campaign to understand and improve gender equality in science titled "A Chemical Imbalance" which the BBC <a href="http://www.bbc.co.uk/news/uk-scotland-23567476">have written a story about</a>. She's taken Rosalind Franklin award funding and used it to produce a free movie and eBook, hosted on the <a href="http://chemicalimbalance.co.uk/">Chemical Imbalance web site</a>. Full disclosure, I'm knackered and preoccupied with work right now so I've not had a chance to check out either in any depth. However the campaign clued me in on an Edinburgh science story that feels familiar (perhaps via the Surgeon's Hall museum) but I never learned about in any depth: the Edinburgh Seven.<br />
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The Seven were a group of women, led by Sophia Jex-Blake, who banded together so that they could be allowed to study for degrees at the venerable old University of Edinburgh medical school in the late 1800s. Despite their successful studies, performed in the face of opposition from science notables like Alexander Crum Brown - later president of the RSC - and an actual riot about their anatomy exams, the university refused to allow them to graduate. Most of them ultimately went on to be granted medical degrees by more progressive institutions, and blazed a trail for future equality in education and medicine. You can read more about them in the eBook on the site, or if that's too long, <a href="http://en.wikipedia.org/wiki/Edinburgh_Seven">Wikipedia</a> and <a href="http://iainthepict.blogspot.co.uk/2011/11/edinburgh-seven.html">this blog</a>.<br />
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With a wonderful sense of cosmic justice, Professor Arnold is now the Crum Brown Chair of Chemistry, while Professor Lesley Yellowlees was not only the first female head of chemistry at Edinburgh, but is now the first female president of the Royal Society of Chemistry, a position once held by Crum Brown himself.<br />
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Such overt discrimination has waned in much of the world, but the gender balance in the sciences is still ridiculous. The chart on the site shows the ridiculous drop-off rate between undergraduate, where it's nearly equal, and professor, where it's ten to one. Worse, as Prof. Yellowlees relates in the BBC article, outward contempt for female scientists is still depressingly extant. I'm not sure what I can do to help, but passing it along, reading the book and watching the documentary seem like a good start.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-2495439099647346412013-07-27T10:53:00.000+01:002013-07-27T15:45:54.298+01:00The Signal and the Noise<span style="font-family: Verdana, sans-serif;">I'm working on getting the blog back up and running; rather than the ad hoc approach of last time I'm planning out a writing project that should keep the blog fed with content at least once a month. I'll fill you all in in due course. In the mean time, I've finished reviewing Nate Silver's The Signal and the Noise, which I've attached below. </span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">Nate Silver has shot to fame as the oracular figure who decoded political polling data into plain English and successfully predicted the US election. His debut book brings him back down to earth, using familiar examples as diverse as moneyball and warfare to demonstrate the sore lack of and need for better prediction in our lives, and the path to improvement through critical thinking and Bayesian reasoning.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">Each chapter uses a particular area of prediction to teach broader lessons. The book opens with great momentum, using the financial crisis as a set of unambiguous examples of how not to make predictions before drilling into the all-too-human reasons that political commentators make poor election forecasts. There are good lessons here about how the need to feel confident and a single-minded focus on a few issues can lead one astray; he turns back to the financial crisis to emphasise the same failures there.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">It's not all about the human factors, though, and Silver then turns to "moneyball" - statistics-based sports recruitment - to provide an overview of the more technical aspects of the art of prognostication. The idea of a predictive model is well articulated and applied to common-sense issues with surprising complications. With the reader warmed up, he spends several chapters digging into the fundimental reasons why level-headed and critically thinking scientists are unable to predict earthquakes. Some things - weather, disease, tectonic plates - are inherently challenging to forecast for interesting reasons, and he is equally quick to emphasise the technical traps that researchers can fall into in building their models.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">The heart of the book, however, is Bayesian reasoning: the idea that we should take new predictions as adjustments to whatever our existing prediction said, as a sort of rolling improvement to our models. As a simple illustration, a test result indicating that one may have a rare disease should be combined with the low probability that one had the disease before the test results were in. Even if the test is 95% accurate, if the disease only affects one in a million people then the odds are far, far lower than 95% that one actually has the condition.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">This is the tool Silver uses in the latter half of the book to show the way to better predictions, while still taking the time to illuminate other forecasting challenges. Whether it's poker or chess, the stockmarket or the battlefield, making a good model and refining it with new data is the key to victory. He lays out how the problems rise in these fields, be it a new raft of human frailties or the hefty challenge of trying to beat the "wisdom of the crowds", sets out how these failures in prediction can be capitalised by good agents or bad, and suggests Bayesian solutions.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">A chapter on climate change in a book aimed at at those in big business has a huge potential to be a train wreck but Silver manages to weave a fairly acceptable course through the problem. This chapter acts to draw the book together, forcing together issues of complex models, noisy new data, and incentives to mislead, with Bayesian reasoning as the knight in shining armour. The overall theme is that climate models are difficult to make for fundamental reasons, and the warming consensus that has come out from those models has stood up to new results - despite the claims of think tanks who wish it otherwise.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">This section has annoyed commentators on both sides of the issue. Silver manages to make good points without falling into the many huge rhetorical traps that the denialist movement has laid in any writer's path, but he's never particularly strong on the issue either. I liked the unspoken conclusion that less-confident predictions - 95% confidence rather than 99%, say - are more resilient to contradictory data in a Bayesian world, and Silver does not make false equivalencies and is unambiguous in supporting global warming. However this is not a strong introduction into climate science, or a real challenge to many of the incorrect claims made by denialists.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">Truth be told this is a deliberate stylistic choice and potential issue throughout the book. Silver avoids bringing in controversies in the fundimental results that feed forecasts, except where it is directly relevant to a chapter's lesson. In the section on the financial crisis, human incentives are raised as a source of bias, but the humans responsible are hardly taken to task. If you want to find out about the failures of reasoning that permitted the 9/11 attacks, you'll have to read elsewhere. (Donald Rumsfeld appears but only as a lead into the "unknown unknowns" idea.) The implications of Scott Armstrong's work with the notoriously vociferous anti-climate-change Heartland Institute are left for the reader to find out about on their own.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">This will variously come across as refreshingly expedient, frustratingly wishy-washy, focussed or cowardly depending on your reading preferences and ideological views. Consider yourself forewarned and take the book on its own terms.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">The Signal and the Noise is certainly cleanly written and well-structured. Silver's introduction sets the book up as a toolbox, first outlining the failures of prediction and their causes before moving onto the successes and the processes that enable them, but in truth he allows the book to digress around the broader themes raised in each chapter, be it the problems and benefits of the "wisdom of the crowds" or the failure to properly, quantitatively account for the uncertainty in the prediction. These digressions are brief and enlightening, and echo back and forth between the chapters to make a more cohesive whole.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">With the aforementioned caveat this is a superb route into the whole issue of modeling and forecasting. It's accessible, clearly written, technically sound and meticulously reasoned. It's recommended as reading on a difficult subject, although it's probably not going to prove to be the definitive work.</span><br />
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<span style="background-color: white; font-family: verdana, arial, helvetica, sans-serif;">(If you want an primer to thinking about statistics before you dig into this I strongly recommend Darrell Huff's "How to Lie with Statistics". It's inexpensive, funny, brief, and makes a good companion piece.)</span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-61346939785381384102011-10-09T17:19:00.005+01:002011-10-09T17:49:44.449+01:00Climate denial's next top modelI'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 <a href="http://dansdata.blogsome.com/2011/09/15/stop-worrying-and-love-the-global-warming/#comments">at comment #29 here</a>, or <a href="http://science.slashdot.org/comments.pl?sid=2424826&cid=37385586">this</a>).<br /><br />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.<br /><br />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 <a href="http://en.wikipedia.org/wiki/Standard_Model">standard model of particle physics</a>, 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.<br /><br />So we're left with empirical or theoretical models. Approximations. <i>Good</i> 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.<br /><br />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.<br /><br />Deal with it.<br /><br />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:<br /><br /><iframe width="560" height="315" src="http://www.youtube.com/embed/KUA7C5s7WgE" frameborder="0" allowfullscreen></iframe>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-74212317221002995992011-06-03T09:04:00.003+01:002011-06-03T09:18:03.087+01:00How the Syrian opposition charges its batteries?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?<br /><br />"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."<br /><br /><a href="http://www.npr.org/2011/06/02/136879259/opposition-tries-to-define-syrias-political-future">Original here.</a><br /><br />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.)Unknownnoreply@blogger.com2tag:blogger.com,1999:blog-7007692219029283524.post-28267788955741516672011-03-01T22:08:00.004+00:002011-03-01T22:33:22.547+00:00Regarding the Pfizer Sandwich closure<a href="http://www.bbc.co.uk/news/business-12335801">Pfizer is to close its historic research facility in Sandwich, Kent</a>. 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.<br /><br />I'm not really qualified to talk at any great length about the state of the pharmaceutical industry - I will defer to whatever <a href="http://pipeline.corante.com/">Derek Lowe</a> 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.<br /><br />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.<br /><br />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.<br /><br />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.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-78098384455387312172010-12-21T08:57:00.003+00:002010-12-21T09:06:45.599+00:00Fearless woman's life in scienceScience Friday had a segment last week on <a href="http://www.sciencefriday.com/program/archives/201012174">Prof. Daniel Tranel's research with a woman known as "SM" who experiences no fear</a> 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.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-19291770635900183682010-11-30T08:39:00.004+00:002010-11-30T08:50:20.094+00:00On FuturismIt strikes me that the problem with futurism (see: <a href="http://spectrum.ieee.org/computing/software/ray-kurzweils-slippery-futurism/0">Kurzweil</a>) 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.<br /><br />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.<br /><br />Knowing all of the elements does not grant one a total understanding of chemistry.<br /><br />(See also <a href="http://www.popsci.com/science/article/2010-10/fyi-what-would-happen-if-every-element-periodic-table-came-contact-simultaneously">this</a> thought experiment.)Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-8134800092805567712010-05-31T16:09:00.010+01:002010-05-31T16:52:52.494+01:00Evan Harris on Royal Free and Lancet culpability in Wakefield case<a href="http://www.bmj.com/cgi/content/full/bmj.c2829">"After Wakefield: the real questions that need addressing"</a> 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 <a href="http://www.chemistintheory.com/2010/02/huffpo-blame-gmc-not-wakefield-for.html">discussed this previously</a> 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.<br /><br />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.<br /><br />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.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-23632022130795139502010-05-03T15:52:00.001+01:002010-05-03T15:53:49.236+01:00Coming soon!Sorry for the absence of updates recently. In the mean time I've punted the "Free Radicals" posts over to a twitter feed <a href="http://twitter.com/alexacit">@alexacit</a>.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-7007692219029283524.post-41721962911387299072010-03-04T00:30:00.001+00:002010-03-10T10:09:54.413+00:00Free Radicals Feb 2010The best of the past month in my RSS feed:<br /><br /><u>Chemistry</u><br /><br /><a href="http://pubs.acs.org/cen/news/88/i07/8807notw3.html">"Very Cool Chemistry"</a> at ACS Chemical & Engineering news: ultra-low temperature chemical reactions dominated by quantum mechanics.<br /><br />A gorgeous article on <a href="http://pubs.acs.org/doi/abs/10.1021/ar900288m">"Crystals in Light"</a> at Accounts of Chemical Research.<br /><br />Mismatched DNA base pairs may have <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000132000008085102000001&idtype=cvips&gifs=yes">a detectable magnetic signature</a>, at JCP. I wonder, do any of the cell's DNA repair systems operate on this principle, or is it electronic?<br /><br />A nifty <a href="http://www3.interscience.wiley.com/journal/123300143/abstract">molecular syringe</a> for metal ions.<br /><br />A fairly pure solution of left-handed molecules is jumbled into a mix of left and right mechanically <a href="http://pubs.acs.org/doi/abs/10.1021/ja910716s">using ultrasound</a>, rather than chemistry.<br /><br /><a href="http://www.sciencemag.org/cgi/content/full/327/5968/923-d">Maintaining spins for memory for a quantum computer,</a> and <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000132000007074105000001&idtype=cvips&gifs=yes">maintaining alignment of molecules with laser pulses.</a><br /><br />A silicon analogue of a substituted benzene <a hre="http://www.sciencemag.org/cgi/content/abstract/327/5965/564">with some kind of aromaticity</a>. And it's green!<br /><br />Watching guanine structures swap back and forth <a href="http://www.nature.com/nchem/reshigh/2010/0210/full/nchem.594.html">under an electron microscope</a>.<br /><br />Not <a href="http://www.sciencemag.org/cgi/content/abstract/327/5963/308">one</a> but <a href="http://www.sciencemag.org/cgi/content/full/327/5963/280/">two</a> papers on how the water networks surrounding molecules control reactivity. <br /><br />Collapsing bubbles create <a href="http://www.sciencemag.org/cgi/content/full/327/5966/625-b">incredible temperatures and unique reaction conditions</a>.<br /><br />Paper titles don't get much more descriptive than <a href="http://www.sciencemag.org/cgi/content/abstract/327/5966/672">"Water Freezes Differently on Positively and Negatively Charged Surfaces of Pyroelectric Materials".</a><br /><br />Make Magazine has some neat links in its story on <a href="http://blog.makezine.com/archive/2010/02/microfluidics_with_cotton_thread.html">microfluidics using thread</a>; the article itself is <a href="http://pubs.acs.org/stoken/presspac/presspac/full/10.1021/am9006148">here</a>. It turns out that <a href="http://pubs.acs.org/stoken/presspac/presspac/full/10.1021/am9006148">hairspray</a> is useful in making micro-electrodes, too. <br /><br />Imagine hydrogen peroxide, but instead of hydrogen, you've got fluorine. That's <a href="http://pipeline.corante.com/archives/2010/02/23/things_i_wont_work_with_dioxygen_difluoride.php">dioxygen difluoride</a>, which is about as insane as it sounds.<br /><br />A new paper on <a href="http://pubs.acs.org/doi/abs/10.1021/jp100374x">non-thermal chemical effects from microwaves</a>, a few months after it seemed <a href="http://pipeline.corante.com/archives/2009/09/30/microwaves_arent_magic.php">pretty much settled</a> that they didn't exist. (<a href="http://www3.interscience.wiley.com/journal/122609615/abstract">Original paper.</a>)<br /><br /><a href="http://pubs.acs.org/doi/abs/10.1021/ja909769a">The formation of large crystals involves an intermediate step in which nano-crystals aggregate and order over surprisingly long distances in solution.</a><br /><br />A copper complex goes for a <a href="http://www3.interscience.wiley.com/journal/123277762/abstract">bumpy ride over a hot surface</a>, providing some insights into how the hot surface controls chemistry on the way.<br /><br /><br /><u>Biology</u><br /><br />New Scientist goes for the pop-culture jugular with <a href="http://www.newscientist.com/article/mg20527493.800-the-real-avatar-ocean-bacteria-act-as-superorganism.html">"The real Avatar: ocean bacteria act as 'superorganism'"</a>, also at <a href="http://pubs.acs.org/cen/news/88/i09/8809news6.html">C&EN</a> and the original paper at <a href="http://www.nature.com/nature/journal/v463/n7284/full/nature08790.html">Nature</a>. Undersea bacteria use electron transfer to share energy around their colony.<br /><br />Childhood stress may echo long into adulthood, according to <a href="http://dx.doi.org/10.1523/JNEUROSCI.4470-09.2010">a mouse study in the Journal of Neuroscience</a><br /><br />Wonky address labels may have a role to play in <a href="http://dx.doi.org/10.1083/jcb.200911115">the degenerative effects of prions</a>, thanks to <a href="http://www.nature.com/nature/journal/v463/n7284/full/4631002f.html">Nature</a> for making sense of this one. Over in Science it turns out that <a href="http://www.sciencemag.org/cgi/content/full/327/5967/869">prions may evolve by a darwinian mechanism</a>.<br /><br />SCIAM discuss <a href="http://cancerres.aacrjournals.org/cgi/content/short/70/5/1981">recent research</a> proposing that arsenic's tumour-causing ability is due to <a href="http://www.scientificamerican.com/blog/post.cfm?id=dangerous-drinking-water-arsenics-t-2010-02-23">meddling with the ubiquitous hedgehog gene</a>.<br /><br />Here's an RNA that binds to a protein that normally acts on DNA, <a href="http://www.sciencemag.org/cgi/content/full/327/5968/917-f">to inhibit its activity.</a><br /><br />Aetiology's guest blogger Zainab Khan <a href="http://scienceblogs.com/aetiology/2010/02/what_is_the_hygiene_hypothesis.php">on the "hygiene hypothesis"</a> that hyper-cleanliness may lead to allergies and other conditions. Also, a treatment for <a href="http://www.guardian.co.uk/science/2010/feb/21/peanut-allergy-clinical-trial">peanut allergies</a> might be on the cards.<br /><br />Individuals in the same plant species <a href="http://www.sciencemag.org/cgi/content/full/327/5969/1055-a">diversify to partition up the environment and use resources </a>.<br /><br /><a href="http://www.scientificamerican.com/video.cfm?lineup=1406165298&id=67975965001">Earthworms cheese it when a mole's on the loose</a> (video).<br /><br /><br /><u>Physics</u><br /><br />I was surprised to discover that there's a <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000132000008084110000001&idtype=cvips&gifs=yes">nuclear exchange interaction</a>, which can be neglected using a Hartree product wavefunction in a similar way to neglecting the exchange interaction in electrons.<br /><br /><a href="http://www.nature.com/news/2010/100223/full/4631008a.html">Nature asks: does the LHC have serious inherent engineering flaws?</a><br /><br />Active galaxies perhaps aren't as important in the production of <a href="http://www.nature.com/news/2010/100222/full/4631011a.html">high-energy cosmic rays</a> as was previously thought.<br /><br />The effects of general relativity tested with a wonderfully elegant <a href="http://www.nature.com/news/2010/100217/full/463862a.html">tabletop experiment</a>. <br /><br /><br /><u>Computing</u><br /><br />Philip Ball presents the <a href="http://www.nature.com/news/2010/100222/full/news.2010.86.html">"Wisdom of the fool's choice"</a>, on automatic recommendation systems such as Last.fm and Amazon.<br /><br />How could scientists cope without Google? <a href="http://www.nature.com/news/2010/100224/full/4631012a.html">Nature addresses this in the context of China and Google's recent spat.</a><br /><br />Roger Ebert is getting a synthetic version of <a href="http://rogerebert.suntimes.com/apps/pbcs.dll/article?AID=/20100226/PEOPLE/100229986/-1/">his own voice</a> thanks to an Edinburgh-based company. I didn't realise until after I'd <a href="http://www.oprah.com/oprahshow/See-How-Technology-Gave-Roger-Ebert-His-Voice-Video">heard the results</a> that I've never actually heard his voice before. The Roger Ebert I know is entirely prose. CereProc has some interviews <a href="http://www.cereproc.com/node/313">on its own site</a>, and for context there's <a href="http://www.esquire.com/features/roger-ebert-0310">Esquire's recent piece</a> on Ebert and <a href="http://blogs.suntimes.com/ebert/2010/02/roger_eberts_last_words_cont.html">his own thoughts.</a><br /><br /><br /><u>Teaching</u><br /><br /><a href="http://thescotsman.scotsman.com/news/39Dubious39--university-research-should.6078148.jp">"'Dubious' university research should be scrapped"</a> and <a href="http://news.scotsman.com/news/Claims-of-39dubious-research39-could.6082436.jp">"Claims of 'dubious research' could deter vital academic investment"</a> 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.<br /><br /><a href="http://www.nytimes.com/2010/02/22/business/media/22textbook.html">"Textbooks That Professors Can Rewrite Digitally"</a> at the New York Times. Macmillan proposes lecturer-editable electronic textbooks.<br /><br /><br /><u>Politics and society</u><br /><br /><a href"http://www.nature.com/news/2010/100224/full/news.2010.91.html">"Concessions over science advice principles"</a> at Nature: government drops proposed requirement that scientific advisors must meet them in the middle on politically-sensitive issues.<br /><br />Turkey's GMO-control rules, which Nature dub <a href="http://www.nature.com/nature/journal/v463/n7284/full/4631000a.html">"An absurd law"</a>, may fail to accommodate research.<br /><br />An attempt to study avalance effects with <a href="http://www.nature.com/nature/journal/v463/n7283/full/463877a.html"> tranquillised pigs</a> is abandoned after public outcry.<br /><br />A model Mars mission falls down as <a href="http://gizmodo.com/5476462/fake-mars-mission-befallen-by-real-drama">participants fail to read their own manuals</a>. I'll be having fun digging through the logs <a href="http://desert.marssociety.org/mdrs/fs09/">here</a>.<br /><br />A simple model partitions the United States into regions <a href="http://www.weathersealed.com/2010/02/23/a-disturbance-in-the-force/">controlled by different fast-food joints</a>. 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.Unknownnoreply@blogger.com4tag:blogger.com,1999:blog-7007692219029283524.post-58625345149928765682010-02-17T13:25:00.011+00:002010-07-22T09:10:40.998+01:00Peter Atkins on textbooks, eBooks, and interactivity.Nature recently published an <a href="http://www.nature.com/nature/journal/v463/n7281/full/463612a.html">interview with Peter Atkins</a> (probably subscribers only) on textbook writing. Atkins' <i>Physical Chemistry</i> and <i>Molecular Quantum Mechanics</i> are deserved classics in their field, and I greatly enjoyed his <i>Four Laws that Drive the Universe</i>, a slim text which discussed thermodynamics from first principles, although I sometimes find his explanations a little opaque.<br /><br />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.<br /><br />Atkins proposes the following:<br /><br /><i>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.</i><br /><br />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 <a href="http://www.destructoid.com/ea-complains-about-second-hand-games-tries-to-curb-them-101567.phtml">videogame</a> 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.<sup>[1]</sup><br /><br />Non-transferrability raises subtle issues. If I can purchase <i>Physical Chemistry</i> 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.<br /><br />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 <a href="http://www.springer.com/ebooks">PDF text books can be downloaded for free using an institution's site licence</a>, 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.<br /><br />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, <i>etc.</i>), 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.<sup>[2]</sup><br /><br />Returning to the article, Atkins is clearly considering the potential in interactive texts, such as those <a href="http://www.wired.com/epicenter/2010/02/the-wired-ipad-app-a-video-demonstration/">headed for the iPad</a>:<br /><br /><i>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><br /><br />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 <i>Organic Chemistry</i> here which packs a plethora of paired 3D structure images and <a href="http://en.wikipedia.org/wiki/Stereoscopy">stereoscope</a>. My model kit is never far away. I use generate intricate visualisations of data. I prefer to discuss my results by talking around charts.<br /><br />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.<br /><br />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.<br /><br /><sup>[1]</sup>Electronic distribution has its own advantages in prolonging sales which I won't get into here.<br /><sup>[2]</sup>Out in the non-academic world, Sony's <a href="http://gizmodo.com/5345112/sony-daily-edition-reader-3g-7+inch-touchscreen-in-december">Daily Reader</a> 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.Unknownnoreply@blogger.com1