June 2007 – Page 3 – David Bradley

Nuclear Chemistry and Web 2.0

Berkeley nuclear chemist Mitch AndrÃ© Garcia is very much a modern chemist. He is not content with the staid old laboratory notebook and blotchy ballpoint in his labcoat. No! Garcia is a web-chemist.

Aside from his excellent work on the chemistry of the element rutherfordium, he has created a network of chemistry websites that provide answers to an almost unthinkable number of questions about the science (actually, there are about 1000 Q and A), offer hundreds of fellow chemists and students the chance to share their thoughts online, and a couple of weekends ago, he knocked together a new website that works like the voting system on Digg, the social bookmarking site, but for chemistry research papers rather than random news and images, ChemRank.

I interviewed Garcia for the June issue of chemistry webzine Reactive Reports. I asked him whether a growing online presence might present a problem for chemists, who traditionally work in a very physical science. “A complaint or compliment I frequently get from my colleagues is that I already seem to live online,” he told me, “Aside from rogue chemical developers like myself, there will always be room for glassware in a chemist’s life in our ever increasing in silico lives.” Read the full interview in Reactive Reports.

Five Dimensional Online Gifts

Online communities Different social media, such as wikis, MySpace, Flickr, and various forums have different ways for people to give and receive gifts, according to Swedish scientists.

To fully understand online gifting and the successes and failures of online communities, we need to consider the question “who gives what to whom, how and why?”

Every day, more and more people join online communities, such as MySpace, FaceBook, and Second Life, and use file sharing systems like BitTorrent. In these virtual spaces they can reinvent themselves, make new friends, and share information and resources with others. Understanding how people give and receive digital items, “gifts”, online is key to understanding the successes and failures of countless online communities.

Now, computer scientist JÃ¶rgen SkÃ¥geby of LinkÃ¶ping University in Sweden writing in the International Journal of Web Based Communities, explains how there are five dimensions to the way people give and receive gifts online, whether those gifts are information, mp3 files, photos, or illicit file shares.

Initiative – spontaneous giving and sharing, e.g. SourceForge.net and flickr.com
Direction – the path the gift follows
Incentive – exploited in point-scoring systems such as BitTorrent networks
Identification – anonymous or recognised
Limitation – access control

Gifting is a central human activity in many communities, both offline and online, explains SkÃ¥geby, “As more and more of human social activities will be copied or migrate entirely to online, we need to consider what dimensions are central to these activities, so that we can analyse their long-term impact on individuals and society.”

SkÃ¥geby’s work is reported in Int. J. Web Based Communities, 2007, 3, 55.

Power Down to Save the World

According to the UK’s Energy Savings Trust we have at least 12 gadgets on standby or recharging at any one time, including TVs, mobile phones, mp3 players, which adds up to a cost of about 40 pounds ($80) a year on domestic electricity bills. There is a strong call from environmental lobbyists for us to power down our electrical devices and now John Clare, outgoing head of one of the UK’s biggest high street electrical retailers, is calling on manufacturers to eradicate the “standby” button from devices such as DVD players and TVs.

According to Clare, when given a choice between a less efficient and a more energy efficient product, customers choose the least costly option. “Standby buttons costs so much money and produce carbon emissions,” he told BBC Radio 4’s Today show, “of which many consumers are not aware.” He suggests that because our modern lifestyles demand so many electrical gadgets that the onus should be on the manufacturers to produce more energy-efficient products and for retailers to keep the consumer informed of the energy ratings of these devices and not just the “white goods”, such as washers and dryers which already have an efficiency code.

The interviewer pointed out to Clare that the standby mode on a television is very important to the elderly and those of limited mobility. Clare responded by saying that such people can “use remote controls”. At this point, I got rather confused. He is advocating that manufacturers get rid of the proverbial “standby button”, which means that a device would be fully powered down to save energy. That’s fine, sounds sensible. But, if there is no standby mode and the device is fully “off”, how will a remote control help the elderly person who may not be able to clamber from their chair, bend to switch the TV on? Doesn’t the remote control require the device to be in a ready, “standby” state before it will function.

Clare then back peddled slightly and said that the standby button could perhaps be a kind of optional accessory that those of us capable of bending to reboot our TVs could have so that we might save that $80 or so a year. But, generally the elderly are those who might benefit the most from such an annual saving, and they would essentially be excluded by having to choose the standby button option.

It is true that the dreaded standby button is wasting energy, there are claims of their using up to 8% of total device consumption. But, there is evidence that hard powering devices on and off reduces their lifespan considerably compared to standby mode.

Regardless, the “Western” lifestyle, overall is far more of a problem. The amount of energy wasted by standby mode is trivial compared to the amount of energy wasted in using a washer-dryer several times a week. Even the “A” class, most energy efficient white goods use vast amounts of water (which costs energy to produce) and electricity, and the juice pulled by a standard television when in use far outweighs even the most inefficient standby mode. The Energy Saving Trust asserts that we should power down fully and switch off our chargers (presumably that includes those that don’t have trickle mode and so use no electricity when charged to capacity!).

The real problem is not standby mode at all. It is our attitude to consumption in general. Admittedly, there is an old adage that we should look after the pennies, and the pounds (dollars) will look after themselves. But, when it comes to power and water consumption, this is simply not true. Save a few milliwatt hours by unplugging your charger every day is not going to offset the consumption inherent in running a mobile phone network (all the construction and maintenance and operation of powered masts and exchange systems) nor the same for TV.

It makes sense to power down properly, but do not think it will save the world. Getting rid of your electrical laundry goods, TV, and car, might. But eradicating the standby button most certainly won’t.

Extracting the Urine

According to a recent report in Wired, agents at the FBI labs in Quantico, Virginia, have discovered that chilled samples of urine can spontaneously produce the drug GHB (gamma butyrolactone), commonly known “liquid E” and a well-known date-rape drug involved in an increasing number of what the FBI terms “drug-facilitated sexual assaults”, or DFSA. However, certain observers suggest that the while GBH is infamous its use in DFSA is far less common than law-enforcement agencies would have us believe; alcohol is a much guiltier party in DFSA than any other substance. The findings, based on GC-MS (gas chromatography-mass spectrometry) suggest that suspects could give a false positive result even in the toughest FBI forensic test.

Writing in the journal Forensic Science International, the FBI team, lead by Marc LeBeau, explains that, “Our study suggests in vitro production of GHB may increase the apparent GHB concentrations in urine during storage. To minimize this production, it is suggested that urine specimens be maintained in a refrigerated or frozen condition and analyzed as quickly as possible. This is particularly important, because GHB analyses are relatively infrequent requests in many laboratories. Therefore, specimens are likely to be stored for some extended period of time before the analysis is carried out.”

Earlier studies had hinted at increasing concentrations of GHB, GBL, or 1,4-BD in the urine of abusers of these comppunds. “It is generally accepted that urine is the most valuable specimen in DFSA cases,” explains LeBeau, “and that 10 micrograms per milliliter be used as the cutoff concentration to differentiate between endogenous and exogenous GHB in urine.”

The FBI team admits that it does not yet know what causes increasing concentrations of GBH in urine samples. It could be microbial activity, but it is probably not straight putrefaction. “Whatever the cause of these small artificial increases in endogenous GHB [in urine samples], the modification is likely driven by time, temperature, and/or changes in pH,” they say. But, also in taking the wind out of Wired’s sails, not only is GBH not considered a date-rape drug, the FBI team adds that, “It should also be noted that none of the samples in this study ever exceeded the recommended urinary endogenous GHB cutoff of 10 micrograms per milliliter.

InChI=1/C4H6O2/c5-4-2-1-3-6-4/h1-3H2

Chemical Precedent

Readers with a fairly long memory will remember ChemWeb preprints. The pioneering site , which hosted my weekly Alchemist column from pilot issue till final closure and takeover by CI now hosts a fortnightly newspick from yours truly. As to the preprint server it attracted a lot of interest but never took off in the way that the physics preprint service at LANL did, unfortunately. It seems that now nature publishing group is hoping to step into the fold.

Nature Precedings (Geddit?) will cover chemistry, biomedicine, and earth sciences ) will host a wide range of research documents, including preprints, unpublished manuscripts, white papers, technical papers, supplementary findings, posters and presentations. All submissions will be reviewed by staff curators and accepted only if they are considered to be legitimate scientific contributions. The papers will not be peer reviewed. So, it’s almost exactly the same as ChemWeb preprints, but with the addition of biomed and geo. I hope it goes well, it is an interesting experiment, but one that did not produce the desired yield for ChemWeb despite that organisation’s peak membership being higher than the American Chemical Society. It takes more than a snappy name and some Web 2.0 graphics to win scientists over with novel Internet applications…thankfully.

Academic Rebellion

Science nature microsoft Science is revolting! A revolution is underway and the battles are taking place on the Microsoft Office frontline. Science, the journal of the America Association for the Advancement of Science (AAAS), is ditching support for Microsoft format office documents. In its notice to authors it advises that:

“Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”

There is also a warning that Microsoft Word 2007 is no longer acceptable in revision documents because of problems with incompatibilities with Equation Editor.

But, it is not just hefty Science magazine, Nature has also weighed into the battle:

“We currently cannot accept files saved in Microsoft Office 2007 formats. Equations and special characters (for example, Greek letters) cannot be edited and are incompatible with Nature’s own editing and typesetting programs.”

Thanks to An Antic Disposition for bringing the S and N issues to our attention. But, is this the only evidence of a rebellion? Certainly not. While Science and Nature are ditching the various Microsoft proprietary formats for technical reasons but staff and students at Imperial College London are truly up in arms over the imposition their institution makes on them to use Microsoft products.

The Software Freedom for Imperial College is hoping to persuade IC to implement a college-wide policy that ensures students are not coerced into purchasing M$ products in order to complete their studies. At present, many tutors and professors ask for Word format files, Powerpoint presentations, and Excel spreadsheets. All of which are infinitely more expensive than the Open Source equivalents of these Office products which are widely available and widely accepted in many quarters.

The movement also hopes to discourage the use of Microsoft products for email attachments and to preclude Microsoft’s awful winmail.dat (workaround here). They want IC to ensure that all web services are standards-compliant and fully functional in all major web browsers, not just the dreaded IE. And finally, they want to see the use of free and open source software for services when high quality and reliable alternatives exist.

Several top universities have already made the move to OS and ditched Microsoft either completely or partially. In fact, IC is the only one of the Top 20 academic centres of excellence around the world that still uses a proprietary web server that is not 100% standards compliant. This resulted, according to the site in 313 errors during testing compared to University of Cambridge: 0, University of Oxford: 0, MIT: 0, and Yale University: 1 error. SFIC hopes to negotiate with IC to rectify the problems. The main issue is probably inertia, even within academic science, Word, Powerpoint, Internet Explorer, Outlook, are all considered pretty much standard the world over.

There are viable and better, free alternatives to almost all Microsoft products, such as Thunderbird email, Firefox, Safari, and Opera web browsers, OpenOffice etc etc as well as countless non-proprietary server systems.

Kitty cat crack

TL:DR – Catnip, catmint is often referred to as cat crack. It is thought to have a weakly psychoactive effect in cats and sedative and euphoria-inducing effects.

Over on the excellent Instructables site, talbotron22 (aka Logan Sandmeyer) has found a way to extract the active ingredient, nepetalactone, from catnip (Nepeta cataria, also known as catmint) and so create a product that is essentially skunk for cats. As you may or may not know, half of all cats , are overwhelmingly intrigued by the scent of catnip. No one knows quite why, but the active compound is known to be weakly psychoactive, triggering sedation and euphoria, so it could simply be that your pussy cat wants to get high.

talbotron22 suggests that the use of his concentrated catnip extract could make him something of a cat god. But, if catnip is the feline equivalent of hash, and he is cooking up some skunk, or worse still cat-crack, then doesn’t that make him some kind of pusher? Well, he does provide a safety disclaimer that should keep his name clean:

“Yes, it is safe to use this extract on cats. I have looked into it, and there are a number of studies (very interesting in their own right) using pure nepetalactone on cats in experiments trying to figure out why it causes them to go bonkers. The upshot is that it’s pretty safe. In the last of the references below, the LD50 of nepetalactone was determined to be 1550 mg/kg (about the same as aspirin), meaning you would have to force feed your average 5 kg cat ~8 grams in order to cause it any harm. So as long as you are reasonable with the extract it should pose no harm.”

Moreover, his extraction process produces very pure nepetalactone but only a small yield, even the most determined feline drug peddler would have to spend days on the project just to keep kitty happy.

InChI=1/C10H14O2/c1-6-3-4-8-7(2)5-12-10(11)9(6)8/h5-6,8-9H,3-4H2,1-2H3

Attractive Science and Nickel Shots

Magnetic carbon The latest issue of my Spotlight column for the science search and tutorials portal Intute is now online. In it I report on:

Elemental magnetism – Carbon is the element of life, without it we simply would not exist, despite the sci-fi penchant for silicon-based life forms. It is indeed a unique element with many apparently anomalous properties. However, one phenomenon that has not been observed unambiguously in carbon, until now, is magnetism. US and German researchers have used a proton beam and advanced X-ray techniques at the Stanford Linear Accelerator Center (SLAC) to put to rest finally any doubts about carbon’s elemental magnetism.

I asked team leader Hendrik Ohldag about the prospects of utilising magnetic carbon in technological applications. “At the moment only very small quantities of magnetic carbon can be produced,” he conceded, “Also, the magnetic moment of such a spot is still very small.” However, he further explained that the proton bombardment technique not only induces magnetism in the carbon particles but can be used to reveal the underlying process of converting this ubiquitous material into a magnetic material. “We might even find ways to make carbon magnetic without proton bombardment, which is admittedly not very suitable for technological applications,” he added.

Also in the latest issue:

To the tower! – Pollution regulations aimed at protecting human health are having an unexpected effect on the London skyline. Buildings such as the Tower of London complex were soot encrusted from as early as the thirteenth century because of fires and industrial smoke. Today they are turning yellow-brown because of biological activity on the surfaces of the buildings facilitated by the low-sulfur atmosphere of modern London.

Nickel shots and stellar nurseries – A chemical analysis of meteorites almost as old as the Solar system itself suggests that rather than forming from the remnants of a supernova explosion our Solar system was formed from the wind of a nearby star some thirty times the mass of the Sun in a violent stellar nursery. One of the teams involved is led by Rick Carlson, I caught up with him today and he explains the implications of isotopic compositions.

“Our paper showed that C-chondrites and the Earth have a slightly different isotopic composition,2 he told me. “The implication is very much along the lines of the work presented by the Bizzarro paper discussed in your news article on Spotlight, that newly synthesized elements, of unusual isotopic composition, were injected into the Solar nebula so shortly before its collapse to form the solar system, that these new elements did not have the chance to mix perfectly with the preexisting material.” Carlson’s work uniquely revealed that the C-chondrites contain a slight excess in r-process and p-process Ba, Nd and Sm isotopes, both of which are likely made in a supernova.

Ordinary chondrites, however, have the same Ba and Sm isotopic composition as the Earth. The small difference in niodymium-142 isotopic composition between ordinary chondrites and Earth therefore most likely reflects the decay of now extinct radioactive samarium-146. “This provides evidence that the Earth underwent a chemical differentiation event while 146Sm was still alive (likely < 100 Ma after collapse of the solar nebula)," Carlson adds.

Measuring Up Size Comparisons

After such a long, serious, and scientific post on genetics and disease yesterday, I thought it was time to post a slightly less serious, shorter, but hopefully useful item on length. As a science journalist, I often need to explain the scale of nanometres, picometres, and very, very rarely yoctometers (okay never) to a non-scientific audience in my writing. Similarly, visitors to this site often ask questions relating to size and the relative scale of something like a femtometer. For more on the definitions of the prefixes you can check out this earlier article on yotta to yocto. Meanwhile, here’s a digest of some of the more common size comparisons:

One metre (1 m), that’s about the length of our dog, the height of a two-year old toddler, or roughly the length of a six-foot adult male’s arm, give or take a couple of inches.

One millimetre (1 mm) a sheet of fairly stiff, but plain, cardboard is about 1 mm. A pinhead measures up to approximately 1.7 mm.

One micrometre (1 um, the u should be a Greek letter mu) is the size at which things start to get a bit tricky. Because of the “micro”, these things are by definition microscopic: a grain of pollen, a red blood cell, are 1 micrometre across. A human hair is about 200 micrometres thick, for comparison.

One nanometre (1 nm). Now comes the really interesting bit, a nanometre is a billionth of a metre, viruses are on this scale as to are the breadth of a strand of DNA. Cell membranes too are about one nanometre thick. However, when researchers talk about nanotechnology, the scale of the objects they are discussing can stretch from this very large molecule size all the way up to several hundred nanometres…which strictly speaking is probably better thought of as a few tenths of a micrometre instead.

The Sense of Scale site has some additional comparisons, although they seriously let themselves down by talking of flourine, as opposed to fluorine atomic nuclei. Nevertheless, they do offer some interesting size comparisons, such as 260 nm being the length of the smallest transistor in a Pentium 3 chip. A Pentium 3 chip, you say? Well, presumably the site was produced when those chips were cutting edge and long before 65 nm and 45 nm processes in microelectronics had become reality. A grain of salt is about 100 micrometres, meanwhile, which given it is a near-perfect cube means it is a million cubic micrometres.

All of this relates, of course, to the orders of magnitude primer on Sciencebase some time ago, which is visualised very well in the FSU’s Powers of Ten movie. The interactive clip stretches from 100 attometres (10 to the minus 16 metres) to 10 million light years (10 to 23 metres, which is a tenth of a yottametre).

Of course, I’ve only touched on length in this post. Sometimes I need size comparisons for mass, time, density, in fact most physical properties. If you have any good indicators, leave a comment to tell us about them.

Social Scientists Don’t Do Chemistry

To show scientific information flow between disciplines, Columbia University’s W. Bradford Paley and colleagues categorized about 800,000 papers into almost 800 areas based on citations of each in other papers. They produced a map of nodes in which node size is proportional to citation frequency and color distinguishes between 23 broader areas of scientific inquiry, from mental health to fluid mechanics.

A write-up outlining the details appeared on the Discover Magazine site recently and the number 1 section heading announced that “Social Scientists Don’t Do Chemistry”. Presumably, the reverse is also true as the relationships between disciplines are mutual in Paley’s map. So, what I’d like to know is aren’t there examples of social scientists studying the impact of chemistry on our lives, perhaps touching on chemophobia and other phenomena and what about those chemists who take a philosophical view of their science considering its wider sociological implications in their work. If you have any examples or thoughts on this please leave a comment.