Chemistry – Page 31 – David Bradley

White Biotech

Is it just me or is the title of the latest paper published on Chemistry Central rather unfortunately politically incorrect when taken out of context? I suspect it is just me, as Google throws up almost half a million entries for “white biotechnology” and the phrase itself was apparently coined in 2003 or thereabouts.

Anyway, the paper’s full title is “Relevance of Chemistry to White Biotechnology” and it is authored by Munishwar Gupta and Smita Raghava of the Indian Institute of Technology in Delhi. They discuss the emergence of novel biotechnological approaches to the bulk production of fine chemicals, biofuels, and agricultural products. It is, as the authors say, “a truly multidisciplinary area” with “further progress depending critically on the role of chemists.” The authors outline the state of the art and in so doing hope to encourages chemists to take up some of the challenges thrown up by this area of chemical science.

You can read the pre-press version of the paper here (as a pdf).

Borromean Tales and Chemical Complexity

I got a chance to see pioneering supramolecular chemistry supremo, Professor Sir Fraser Stoddart of UCLA on the Cambridge leg of his UK tour on Monday. Sir Fraser took us on a whirlwind tour of the last quarter century of interlocking ring-shaped compounds, molecular dumbbells and the potential of collections of such entities to bring us the next generation of computer memory that could be fast, high density, and even error self-correcting.

He also took us on a spin through the synthetic tales of how to make Borromean rings on the molecular scale and ways to tie a Solomon knot with chemistry. It was visually and synthetically beautiful chemistry, told as eloquently and with the same dry wit as the last time I heard him speak. At that time he and his colleagues had designed the ultimate Olympic symbol from four interlocked molecular rings, something the UK’s Olympic designers should have perhaps taken to heart with their publicity materials.

However, aesthetics aside, Sir Fraser’s real take-home message is that chemistry is not yet the mature science many of its number would suggest. Over the last 150 years chemistry has gathered together many words and even begun putting them together into simple phrases, such as Sir Fraser’s own catenanes and rotaxanes. But, this maturity can be likened to the “maturity” of a toddler, he said. It is now time to stop trying to mimic nature with our chemical structures, turn up the complexity by at least an order of magnitude and Make, Measure and Model.

Resistant to Base

It has been some time since we had a video interlude on Sciencebase, but I just could not resist this one. It’s definitely one for fans of the late, great Robert Palmer and synthetic organic chemists everywhere.

The lights are on, but you’re not home
You’re in the lab, work-ing alone
Your synthesis, is nearly done
Just add a chain to that car-bon

Don’t you know its resistant to base? The pH is past 14 and your stirring bar is dissol-ving! Dig those shoe covers and the impromptu appearance of a mop head. The only song in the world to rhyme potassium t-butoxide and ammonium hydroxide.

Thanks to Chemistry Central blog to bringing this one to our attention. Bryan Vickery has gathered together several chemistry covers on the site.

Thumbing Scientific Papers

A rather eye-catching paper was posted on the ChemRank site recently entitled: How to write consistently boring scientific literature. The paper is a parody on the art of writing a research paper by biologist Kaj Sand-Jensen of the University of Copenhagen. And begins, “Although scientists typically insist that their research is very exciting and adventurous when they talk to laymen and prospective students, the allure of this enthusiasm is too often lost in the predictable, stilted structure and language of their scientific publications. I present here, a top-10 list of recommendations for how to write consistently boring scientific publications. I then discuss why we should and how we could make these contributions more accessible and exciting.” Are you enticed by Sand-Jensen’s intro? Me neither. It just seems it would be as terse and as inaccessible to a lay reader as any of the papers he parodies. You can give it the thumbs up or the thumbs down on ChemRank.

Atomic Chips

Atomic chip schematic Laboratory spectrometers are great lumbering beasts, essentially tied to the bench and useless for slipping into an overnight bag and heading off for a spot of analytical field work. Thankfully researchers are working on changing all that, at least in the area of atomic spectroscopy.

Holger Schmidt of the University of California, Santa Cruz and Aaron Hawkins at Brigham Young University and their colleagues have found a way to build an atomic absorption spectrometer on a chip just a few centimetres across. I report on their work in more detail in the latest issue of SpectroscopyNOW.

Schmidt told me that the new instrument could be used not only in gas sensors and other portable analytical devices but also to stabilize the frequency of lasers and even in the future world of quantum information processing, which will revolutionize computing and telecommunications.

“Frequency stabilization could be implemented within a couple of years,” he says, “while quantum communications applications are definitely further out, at least ten years, that work is in the fundamental science stage which makes it very exciting for us.”

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.

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.

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.

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.