YACJ – Nature Chemistry

April 2009 sees the launch of yet another chemistry journal, this one coming from Nature Publishing Group. It will, apparently, “provide a unique forum for the publication of high-quality research in all areas of chemistry.” Well, they would say that, they’re hardly going to tell us it’s a run-of-the-mill publication offering tedious and dead-end research, are they?

The launch site usefully reminds us that, “Chemistry is concerned with the study of matter on all levels, including its composition, structure, properties and how it can be transformed in chemical reactions.” Again, they’re not wrong there. But, speaking of definitions of chemistry, I thought Walt’s definition in Breaking Bad was pretty good.

If you don’t know about Breaking Bad (It’s not on UK TV yet, for instance), the plot involves a stressed-out, 50y old, high school chemistry teacher, who’s moonlighting at a carwash to make ends meet when he discovers his wife is pregnant and he’s dying of lung cancer. In desperation he hooks up with a crystal meth pusher and starts cooking up some highly pure and enormous crystals in the back of an RV. Needless to say the local dealers don’t like him muscling in on their patch, and he attempts to murder them (in the back of the RV) by pouring powdered red phosphorus on to a pan of boiling methanol. A quick lesson in the incredible corrosive properties of hydrofluoric acid – it burns through metal, rock, ceramic, but not polythene – all adds to the fun and games.

Anyway, Breaking Bad, with its periodic table credits, is a lot more entertaining than yet another chemistry journal. Although I am sure the Nature effort will turn out not to be YAFCJ at all but instead a major success, nudging JACS, Chem Comm, and Angewandte a little further along the virtual shelving.

Meanwhile, thanks for Chemistry Lab Notebook for the tip-off.

Beer or Wine?

Beer or Wine? The choice is yours!In the good-old days there was no choice, if you were posh you drank wine, if you were not you drank beer. Same goes for the Beatles-Stones debate. The Beatles were the nice clean-living, fun loving beat combo, whereas the Rolling Stones were the scare-your-mom hairies. But, making the choice between beer vs wine, Beatles vs Stones led to a societal bifurcation, it split us down in the middle, in other words.

What are the two tribes of today? Burberry vs Barbour? Twitcher vs Birder? Bling vs Blong? Do those sociopolitical barriers between groups still exist? Here’s a short list of the key life choices you must make to help you decide on which side of the fence you sit, in whose camp you reside, and whether you’re a “Lager Lout” or a “Winebar Winker”. Check through this highly scientific list and then cast your vote in the most important blog poll ever!

Lager Louts

  • PC
  • Star Wars
  • Snapshot
  • Windows
  • Electric
  • Pr0n
  • Rock
  • Stones
  • Jogging
  • Cook
  • Ford
  • Manchester United
  • Coffeetable book
  • Pop Tart
  • Atheism
  • Walmart
  • Constable
  • Cup of char
  • Fingers
  • Big Bong
  • Plastic bag
  • Pizza
  • Camper van
  • French fries
  • Staples
  • Tourist
  • Alpha

Winebar Winkers

  • Apple
  • Doctor Who
  • RAW Image
  • Linux
  • Acoustic
  • Erotica
  • Jazz
  • Beatles
  • Yoga
  • Chef
  • Chevy
  • Manchester City
  • MySQL Manual
  • Pop Art
  • New Age
  • Harrod’s
  • Warhol
  • Lapsang Souchong
  • Knife & fork
  • Big Bang
  • Luis Vitton
  • Pasta fresca
  • Penthouse suite
  • Morrocan couscous
  • Red paperclip
  • Traveler
  • Omega

Okay, now it’s time to vote on the single most important deciding factor in our sociopoliticoeconomico experiment. Forget Star Wars v Doctor Who. Forget jogging or yoga. Forget even the pr0n-erotica debate. On which side of the fence do you sit? When it comes to Beer or Wine?

Full Spectrum Science News

Musical molecules

Musical molecules, bright fibres, polarised brain chemistry, and cholesterol regulation, all feature in my SpectroscopyNOW column this week.

Musical molecules – What do Schroedinger’s equation and Schoenberg’s expressionism have in common? Not a lot you might think. However, researchers in Germany and the US have now modelled the hydrogen molecule, the archetypal subject of molecular modelling, using a theory of behaviour that emerges from music. The study demonstrates how a hydrogen molecule responds to laser pulses as if the molecule’s vibrational motions, its quantum states, were the notes making up a changing musical chord and offers the opportunity of laser-controlled chemical reactions.

Fibre, fibre burning bright – A European research team has developed novel strategies for the rapid trace element analysis of metals in polyamide synthetic fibres by graphite furnace atomic absorption spectrometry and inductively coupled plasma mass spectrometry. Their method allows the accurate determination for quality control of polyamide products containing titanium dioxide as an optical brightener.

Bad cholesterol regulator – US researchers have discovered exactly how a destructive protein binds to and interferes with one of the molecules involved in removing low-density lipoproteins (LDL), the so-called “bad” cholesterol, from the blood.

Bipolar disorder – Spectroscopic studies of post mortem brain chemistry reveals that sufferers of bipolar disorder (often referred to as manic depression) have a distinct chemical signature linked to this mental illness. A collaboration between researchers in the UK and US also suggests a possible mode of action for the mood stabilisers used to treat the disorder and how they counteract changes in brain chemistry.

Technological To-Do List

Technological To-Do ListA panel of eighteen apparently maverick thinkers was charged with coming up with a to-do list for the twenty-first century by the US National Academy of Engineering (NAE). The maverick panel includes such notables as former director of the National Institutes of Health Bernadine Healy, Google co-founder Larry Page, geneticist and businessman Craig Venter, Nobel Chemistry Laureate Mario Molina, climate change expert Rob Socolow, and ‘futurist’ Ray Kurzweil.

I am sure some of these sci-celebs are mavericks in their own way, but if that’s the case why do some entries on their list of 14 technological challenges for our age read like the section headings from a college student essay or worse still a beauty pageant winner’s wishlist?

  • Engineering better medicines
  • Advancing health informatics
  • Providing access to clean water
  • Providing energy from fusion
  • Making solar energy economical
  • Restoring and improving urban infrastructure
  • Enhancing virtual reality
  • Reverse engineering the brain
  • Exploring natural frontiers
  • Advancing personalized learning
  • Developing carbon sequestration methods
  • Managing the nitrogen cycle
  • Securing cyberspace
  • Preventing nuclear terror

Okay, don’t get me wrong, world peace and universal wellness are noble aims and avoiding nuclear terror should be a priority. Moreover, even beginning to approach some of these problems will take a maverick or two, and many will probably remain intractable well beyond the twenty-first century. Despite advances in functional MRI, I don’t think we’re that close to reverse engineering the brain, for instance. We are really not going to come close to “managing” the nitrogen cycle any time soon either; we cannot yet make perfectly accurate weather or climate forecasts let alone find ways to control the global flux of atmospheric gases.

Another worrying property of the list is that in some sense a few of the entries are redundant. If we have access to solar power, why would we need fusion power? Even if we get to grips with fusion, building fusion reactor power stations is going to be incredibly expensive and difficult to do at least compared to the solar option. Some people would argue that CO2 is not an issue and others would suggest that the threat of nuclear terrorism is not what the scaremongers would have us believe, so maybe those list entries are also redundant.

Socolow admits in an interview that the challenge of coming up with 14 must-do technological developments was “crazy”. “We came up with broad categories of the challenges that lie ahead and within those categories identified specific initiatives,” he says.

The panel didn’t actually rank the 14 challenges in any particular order. It was obviously a tough call to decide whether advancing health informatics is any more or less important than advancing personalized learning. However, preventing nuclear terror should come well above reverse engineering the brain and perhaps even above engineering better medicines, surely?

Likewise, enhancing virtual reality and exploring natural frontiers will allow humanity to advance way beyond the claustrophobic confines of our current mindset, but if millions of people are without clean water, then we might as well be in the dark ages.

Apparently, the panel released its report in Boston at the annual meeting of the American Association for the Advancement of Science (AAAS), so I suspect it was more than a little tongue in cheek in some respects, especially given some of the personal reports I’ve heard from fellow science journalists about the quality (or lack thereof) of this year’s meeting.

CO2 Refusenik to Win Pulitzer

Polar bear

Polar bears are not quite the enormous white climate canary of frozen climes that we have been led to believe. In fact, they’re more likely to turn out to be the elephant in the room, when in fifty years time their numbers have grown despite Gory warnings.

Anyway, in the spirit of being contrary almost for the sake of it, but more seriously for the sake of science, I’d like your thoughts on the following article. It was published on ScienceandPublicPolicy.org, which is controversial enough, with the organisation’s Chief Science Advisor being Willie Soon, who along with Sally Baliunus, suggests that climate change is down to non-anthropogenic phenomena.

Anyway, the SPPI article highlights how some scientists have apparently now broken ranks to proclaim that anthropogenic carbon dioxide is not quite the forceful climate change driver those who advocate a global carbon tax would have us believe. After all, if George W Bush is suddenly on-message when it comes to the environment, then something is surely wrong with the world. Of course, I’d want the full insider details and to know if there are any conflicts of interest before taking any refusenik too seriously.

The post’s author Jerry Carlson suggests that a brave journalist who stands up against the carbon conspiracy might be in line for a Pulitzer by 2010. There are a few out there who are making waves including at least one NYT writer, he tells us. Carlson suggests that in order to take the Prize, that enterprising investigative journo will have to find answers to an intriguing pair of questions. I’m sure the folks at RealClimate.org will be readying their riposte right now, if they haven’t already, but here are Carlson’s queries for the record:

First, he asks, why don’t those who suggest we reduce atmospheric CO2 emissions and sequester carbon ever mention the enormous opportunities for feeding the world that might come from longer growing seasons and higher carbon availability for crops? Historically, civilisation has seemingly thrived when the climate has been warmer and wetter and agriculture more prolific. One might also tack on to the CO2 question the issue of water vapour being a much broader and potent greenhouse gas than CO2 as well as a dozen other apparently unaddressed issues within the climate change models.

The second Pulitzer-winning question Carlson offers is: Why is the IPCC’s projected future global warming almost linear or accelerating, when it is well-known that the greenhouse-gas impact of CO2 fades sharply with each incremental increase of CO2 in the atmosphere?

My own additional question to IPCC would ask about that 10% uncertainty in their initial report that suggested we are 90% certain that humans are responsible for rising temperature trends. 9 to 1 against is long odds, but not lottery impossible and mean that there is a chance (albeit just one in ten) that our carbon emissions are not to blame. If they’re not to blame, then rather than asking what is perhaps it’s time we checked the climate change data and took a more rigorous look at the historical and prehistorical trends, before it’s too late.

We live in an ice age, by definition; there is ice at the poles and that defines it as such. But, despite measurable volume changes in the Arctic ice sheet, NASA satellite images show without doubt that the ice cap is growing. Couldn’t that cause cooling because of increased reflectance? It has been said before, but what if we actually manage to reduce CO2 levels only to discover that the earth’s natural cycle is about to take us into a deeper ice age? We’ll regret meddling with atmospherics if it does. But, at least the growing polar bear population will be happy.

Drug Design on the Playstation

Serious drug design researchers are apparently hacking their PS3 machines to turn them into drug discovery workhorses. At least that’s according to my alma mater New Scientist magazine. It’s the kind of catchy subject they cover and is a classic from Mike Nagle.

The PS3 console uses a Cell chip, made by IBM, Sony and Toshiba, which is composed of a CPU and eight slave processors that run on Linux. According to NS, this chip is prized by chemists and physicists alike because the same kind of calculations it uses to produce the stunning, high-quality PS3 graphics for gaming are just about the same those needed to simulate reactions between particles, ranging from the molecular to the astronomical (apparently, you can do black holes with it too).

But, when we say they’re hacking the PS3, it’s not like these scientists are just plugging in a data cable and running their lab. According to NS, University of Massachusetts astrophysicist Gaurav Khanna has actually strung together 16 PS consoles to simulate the gravity waves that to occur when two black holes collide. While University of Illinois chemist Todd Martinez is running particle simulations on a Playstation, with 1000 atoms (a small protein in other words) that can be done 130 times faster than on an ordinary PC.

It’s all quite twee really, what with the surgeons cannibalizing their Wii consoles to do virtual operations and chemists latching on to the power of virtual world Second Life too. One can almost imagine the response of the peer review panels as the grant applications start to roll in with instrumentation inventories listing costs for 32 PS3 consoles, 20 Wii controllers, a couple of PSPs, and a dozen iPhones. The real test will come though if they can get away with tacking on a few copies of World of Warcraft and Nintendogs Labrador Retriever & Friends.

Watery Typo Leads to Salvation

Water salvation, photo by David Bradley

In the realm of physical chemistry (or is it chemical physics?) there was almost theological interest in this week’s Alchemist. Having written about water glass and how low-temperature studies of aqueous phase changes are helping scientists to explain this anomalous and yet ubiquitous material it was a simple spellcheck-induced typo that drew the most interest from The Alchemist’s email newsletter readers.

Wave after wave (pardon the pun) of correspondents got in touch almost as soon as the newsletter was dispatched to point out that I, Uberpedant Taskmaster General had been hoist by my own petard. In describing water’s fascinating properties I described its ability to interact act at a fundamental level with many other materials as being related to its “powerful salvation properties”. Like I said, my petard was well and truly hoist. Of course, some would say it was a baptism of fire to describe water thus, but that would be nothing but hot air with an earthy stench. Thus having shoehorned allusions to all four classical elements into that last sentence, I stand before you hands up and head bowed, seeking solvation!

Meanwhile, back with the chemistry news. I also report in The Alchemist on a new approach to engineering goats to produce medicinal milk which has been devised in Pennsylvania. The research could be good news for people with diabetes. Then there’s the finding that a well-known anticancer compound also used as an antiparasitic drug could turn out to be an even better multitasker operating as it does as an effective antiviral against HIV.

Also this week, a multitude of awards from the National Academy of Sciences for diverse chemical discoveries. You can read the list of winners on the Chemweb site, together with links to the juicy bits on how much money they got, in other words.

Finally, in the legendary world of organic synthesis a wartime effort to synthesize quinine may have been vindicated while Canadian chemists have constructed nanoscopic gas cylinders from barium organotrisulfonate that come with temperature-controlled valves for trapping hydrogen and carbon dioxide. And, speaking of which, I have a hopefully typo-free but far more controversial item on the whole issue of carbon footprints, climate change now live on the Sciencebase blog.

Search and Cite for Science Bloggers

Crossref for WordPress

A couple of weeks ago I was reading a post by Will Griffiths on the ChemSpider Open Chemistry Web blog about how the DOI citation system of journal article lookups might be improved. The DOI system basically assigns each research paper a unique number depending, with an embedded publisher tag. Enter a DOI into a look up box (e.g. the DOI lookup on Sciencebase, foot of that page) and it almost instantaneously takes you to the paper in question. I use the DOI system for references in Sciencebase posts all the time.

There are a few cons that counteract its various pros, for instance, not all publishers use it and among those that do there are some who do not implement the DOI for their papers until they are in print, as opposed to online. Despite that it is very useful and commonly used. Having read Griffiths’ post about OpenURL a non-proprietary DOI alternative, I thought maybe it would be even more powerful if the concept were taken back another step the author level and I came up with the concept of a PaperID, which I blogged about on Chemspy.com. PaperID, I reasoned could be a unique identification tag for a reasearch paper, created by the author using a central open system (akin to the InChI code for labelling individual compounds). I’m still working out the ins and outs of this concept and while a few correspondents have spotted potentially fatal flaws others see it as a possible way forward.

Meanwhile, CrossRef, the association behind the publisher linking network, has just announced a beta version of a plugin for bloggers that can look up and insert DOI-enabled citations in a blog post. I’ve not investigated the plugin in detail yet, but you can download from a Crossref page at Sourceforge.net. the Crossref plugin apparently allows bloggers to add a widget to search CrossRef metadata using citations or partial citations. The results of the search, with multiple hits, are displayed and you then either click on a hit to go to the DOI, or click on an icon next to the hit to insert the citation into their blog entry. I presume they’re using plugin and widget in the accepted WordPress glossary sense of those words as the plugin is available only for WordPress users at the moment with a MoveableType port coming soon.

According to Geoffrey Bilder, CrossRef’s Director of Strategic Initiatives, “CrossRef is helping jumpstart the process of citing the formal literature from blogs. While there is a growing trend in scientific and academic blogging toward referring to formally published literature, until now there were few guidelines and very few tools to make that process easy.” Well that reference to a jumpstart sounds like marketing-speak to me, as Sciencebase and dozens of other science blogs have been using DOI for years.

Whether or not I will get around to installing what amounts to yet another WordPress plugin I haven’t decided. I may give it a go, but if it works as well as is promised you will hopefully not see the join. Meanwhile, let me have your thoughts on the usefulness of DOI and the potential of OpenURL and PaperID in the usual place below.

Sciencebase Upgraded

UPDATE: Since I wrote this post back in February 2008, WordPress has gone through many changes, updates on Sciencebase are automated these days too, which is marvellous.

I finally upgraded the Sciencebase site to the very latest version of WordPress, it had been languishing at version 2.1.3 (can you believe it?) for far too long. There had not only been dozens of security upgrades since that version and the current version 2.3.3 but various new features that the site was not making full use of.

It was a post by Wayne Liew WayneLiewDot.com that persuaded me to do the necessary and his recommendation for using a plugin that automates that whole process was the tipping point I needed.

Having carried out the upgrade (more on the actual WordPress upgrade process here) and found only a few minor problems, like a disordered sidebar, a couple of out-of-date plugins and just one irrelevant dead plugin, and fixed those as best as I could, I figured it was time for a weekend break. So my wife and I headed off to the seaside, abandoned the children with their grandparents and took off with the dog for a well-earned break at an artsy country town on the Suffolk coast. (Photos will appear soon on the Sciencebase Flickr account). Hence this trivial and possibly pointless post.

Back with a more substantial science based post later this week.

Giving the Ghetto Blaster Retro Chic

iPod Ghetto Blaster

The ongoing quest for bigger, better, smaller, faster gadgets and other consumer products is not environmentally sustainable and must be replaced by an approach to design that builds on the products of contemporary mass-produced culture by re-working them for current desires. That is the simple message offered by Stuart Walker of the Faculty of Environmental Design, University of Calgary, Canada, currently Co-Director of Imagination@Lancaster at Lancaster University, UK, writing in the current issue of the International Journal of Sustainable Design.

Walker points out that it is critical that we address issues of sustainability more substantially than has been done to date. The throwaway culture of the mp3 generation is not only filling landfills with mass-produced and almost disposable products, but wasting vast quantities of potentially recoverable materials, including precious metals. Moreover, the continued greed for novelty means that countless perfectly useful gadgets and other products are being discarded in favour of the next version much sooner than they need be given the robustness of many well-designed products today.

He adds that if design is to contribute to human culture in a more meaningful way then it has to move beyond the often shallow, style-based notions of product design that have become so prevalent over the last 50 years.

If the creation of new products is part of the problem rather than the solution to sustainability in a world of climate change, overburdened landfills and dwindling supplies of inexpensive mineral resources, then does the designer have a role if consumerist society were to desist from its quest for novelty?

“On the face of it, and within the conventional parameters of product design, it would seem that the answer would be no,” says Walker, “or at most, relatively little.” However, he suggests that a broadening of definitions of what design involves could lead to a new generation in design that exists not simply to create novel products but to use the creative skills of individuals to re-work old products.

Walker takes as a case in point the “old-fashioned” stereo radio-cassette player, which had its heyday in the ghetto blasters of the 1980s. Countless ghetto blasters will have hit landfills in the decades since and yet, with a little imagination, a once prized possession could become a new outlet for a portable mp3 player with a simple rewiring of the input circuitry.

Such re-purposing may not be fashionable, there is not at present any cachet nor retro-chic associated with the ghetto blaster as generation after generation of sleek touch-sensitive portable media gadgets hit the market month in, month out. And yet it would take only a few cultural innovators seeing the potential of this and other examples for rebuilding and repurposing to lead to a consumer tipping point in which such a primal approach to recycling became the height of fashion. Being an early adopter need not mean buying the latest gadget, it could simply mean repurposing an old one.

More information on Walker’s potentially revolutionary proposals can be found in “Extant objects: designing things as they are” Int. J. Sustainable Design, 2008, 1, pp 4-12

You can leave ideas for other potentially retro chic repurposed gadgets and products in the comment form below.