David Bradley – Page 293

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cover chemistry, biomedicine, and earth sciences ) will host a wide range of research documents, including preprints, unpublished manuscripts, white papers, technical papers, supplementary findings, posters and presentations.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.

Genetic Research Hits Pay Dirt

DNA The budget for the Human Genome Project and all that post-genomic, proteomic, metabonomic, immunomic…research was almost on a par with defense spending; it was almost c-omical really. Well, maybe not quite, but it stretches out with a lot of zeros nevertheless. At the time the grants were written and the funding given, we, as a society, were promised all kinds of medical miracles from gene therapies and new treatments to cure all those nasties – cystic fibrosis, sickle cell, thalassemia, cancer, heart disease and more.

We were promised personal medicine courtesy of pharmacogenomics. This would allow your doctor to profile your genome and tailor your medication to the particular set of enzymes running in your liver and whether or not you were likely to respond positively, suffer adverse effects, or simply not respond at all. We have even seen, this last few days, the sequencing of James Watson’s genome; an effort that cost less than $1m and took under four months. But do any of these promises add up to very much beyond myriad PhD theses and thousands of biotech startups many of which have already crashed?

Hopefully, the answer is yes. In the next few years, gene science will hit pay dirt as genes finally give up their real secrets and the true meaning of so-called junk DNA will become clear. Our understanding and ability to treat a wide range of disease from breast cancer and obesity to hypertension and bipolar disorder will come of age and perhaps finally succumb to all this genetic scrutiny and manipulation.

Nature, Science and the Wellcome Trust provided a useful summary of the genetic state of the art for a recent Times report by Mark Henderson on our genetic future. In the summary Henderson highlighted the latest “in press” results, most of which are now online, so I am providing here the hyperlinked executive summary:

Breast cancer – Three papers published in Nature and Nature Genetics at the end of May reported four new genes and one genomic region associated with increased risk. 10.1038/nature05887, 10.1038/ng2075, 10.1038/ng2064

Obesity – An obesity gene, the FTO gene, was published in Science in April and reported in Sciencebase at the time.

Diabetes – Again in Science (and 10.1126/science.1142382 and 10.1126/science.1142358, three common genes for increased diabetes type 2 risk were reported, bringing the total known genes associated with diabetes to nine.

Alzheimer’s disease – New results also published this week in Neuron discuss an Alzheimer’s gene

Data that were still under press embargo at the time Henderson’s feature appeared in The Times, however, meaning he could only hint at the true potential of human genome results were revealed today.

The largest ever study of genetics of common diseases in which almost 10 billion pieces of genetic information were analysed were published just one minute ago, so I can now outline the findings in a little detail. The new study compared 2000 cases each of seven common diseases with 3000 shared control patients, and reveals new genetic associations with these disorders. A pair of related papers in Nature Genetics (a and b) offer further insights into two of the seven diseases investigated.

In the Nature article, scientists from the Wellcome Trust Case Control Consortium report genetic variants associated with the development of bipolar disorder, Crohn’s disease, coronary heart disease, type 1 and type 2 diabetes, rheumatoid arthritis and hypertension. This is the first study from this large scope and it, the scientists found one genetic region newly associated with bipolar disorder, and another with coronary artery disease. A separate group of three markers have been found to be associated with rheumatoid arthritis. The researchers also identify nine new genetic associations for Crohn’s disease and ten chromosome regions that contain genes related to diabetes.

These new results would suggest a medical revolution is at hand and that the Human Genome Project and its spinoff -omics really are about to hit pay dirt. But, are we really on the verge of a new era in medicine, or are the various genetic revelations simply more grant-baiting hyperbole?

Testing your rotten organics

Tobacco sky Will your molecules rot, is biodegradability an intrinsic property of those chemicals you handle on a daily basis? A study published today in the journal Molecular Systems Biology reveals whether or not thousands of chemicals will be biodegradable. The work could help in environmental risk assessment of production, transportation and disposal of organic compounds.

Biodegradability is determined primarily by whether or not there are microbes in the environment that can diget any given compound. Victor de Lorenzo and colleagues at the National Biotechnology Centre in Madrid, Spain, used a database of all known microbial metabolic reactions to train a computer algorithm to distinguish between the biodegradable from the recalcitrant compounds. With this in silico test kit they looked at almost 10000 chemicals.

This automatic predictive approach to assessing biodegradability could help researchers evaluate the potential of new compounds to pollute the environment and help in the implementation of international regulations on the use of new chemicals.

Perhaps not surprisingly, the press release associated with this work focused on those compounds, including herbicides, that are most resistant to biodegradation, but fails to mention the even larger group of compounds that are intrinsically biodegradable. The usual news write-ups about toxic chemicals and the environment 9999 times out of 10000 will inevitably highlight those that are the nastiest.

The huge benefits of the thousands of organic compounds used in the pharma, biotech, plastics, and other industries as well as medicine and agriculture will simply be ignored whether or not those compounds accumulate in the environment or not. Biodegradation is only one route by which thousands of compounds are destroyed naturally in the environment (heat, light and interaction with other non-living materials, are others). The predictive system will be useful, certainly, but its wider applicability should consider these other routes and the risk factors and toxicity associated with any particular chemical, rather than tarnishing all entries in the database simply on the basis of whether or not a microbial enzyme exists to digest it.

The original research paper can be read here.

Down to Earth Spectroscopy

Cheminformatics could help save forests from the damage caused by runaway widlfires. As long as there have been forests, there have been forest fires, from the bushfires of the Australian outback, across Africa, Asia, and Europe, to the Americas. Such fires often thought of has having a regenerative effect on old woodland, but predictions of an increasing frequency and intensity of wildfires because of climate change could lead to loss of forest and soil erosion rather than dendritic rebirth. Spanish researchers have now used near infrared spectroscopy, a simple calibration technique and cheminformatics analysis of their spectra to determine a key parameter of soil damage – the MTR, or maximum temperature reached. You can read the full story in the latest issue of SpectroscopyNOW.

Spiked innovations

Some time ago, the editors at Sp!ked-Online asked me to suggest what I thought was the greatest innovation of all time. I tried to be a bit esoteric and opted for the inorganic chemistry of ammonia and sulfuric acid, certainly not the most exciting sounding of entries in the sp!ked innovation survey, but I hope the chemists among their readership would appreciate it among all the more electrical technological suggestions and the tools of molecular biology.

It seems I was among some eminent participants, “key thinkers in science, technology and medicine” allegedly with some half a dozen Nobel laureates in their number. The survey aimed to identify the greatest innovations and a live discussion is scheduled to take place in London on June 6.

Surveying the responses, Mick Hume, sp!ked’s editor-at-large, says the survey “Provides some illuminating insight both into the important developments of the recent and more distant past, and into the way those involved at the cutting edge see the issue of innovation today.” My colleague Philip Ball, a fellow freelance science writer with a chemical bent, also stuck up for chemistry in his submission opting for innovations in analytical chemistry, including NMR spectroscopy and X-ray crystallography.

Among the other innovations suggested were The Internet, the alphabet, the discovery of nuclear fusion, X-rays, the brick, rockets, the eraser. I surely must posit that without sulfuric acid and ammonia not one of those innovations would ever have reached its full potential. Maybe I should also add an upside down exclamation mark, just to emphasize my point!

Among the other contributors to the event are Anjana Ahuja, science columnist, The Times, Ken Arnold Head of Public Programmes, Wellcome Trust, Peter Cochrane co-founder of ConceptLabs, and former chief technologist at BT, Marcus Du Sautoy professor of mathematics, Wadham College, Oxford, Sir Tim Hunt (FRS) principal scientist, Cancer Research UK, and David Roblin VP, Clinical R&D, Pfizer Global Research & Development.