David Bradley – Page 289

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.

Did Strychnine Kill the Dinosaurs?

Strychnine seems to be a commonly searched entry in the ChemSpider database. I am not sure whether that means there are poisoners among the users or whether it is people hoping to find out more about the recent case of a man accused of poisoning his neighbors’ dogs with a gopher bait pesticide containing strychnine. Alternatively, it could be people hoping to learn more about recent research into the unusual poses struck by dinosaur fossils.

Dinosaur fossils always seem to show the creatures “voguing”, as if there were some Jurassic equivalent of the 90s dance craze kicking off some time BC. But, the odd postures of these long-dead animals would actually suggest that they had an agonized death – the wide-open mouth, head thrown back and recurved tail – all point to poisoning, disease, or asphyxiation, according to two Berkeley paleontologists.

The usual explanation for the postures is that the dinosaurs simply died in water and currents dragged their bones into these odd positions and they were frozen in time as sediments settled and fossilization began.

Berkeley veterinarian-turned-paleontologist Cynthia Marshall Faux has seen a lot of animals that have been poisoned, hit by vehicles, or died of painful disease. They often arrive displaying the same postures as these fossils. She believes that the posturing dinosaurs may have met unnatural deaths, choking on volcanic ash, diseased, or poisoned.

The very same posture is seen in several disease states as well as in strychnine poisoning. Srtychnine is a highly bitter alkaloid found in several plant species, but it is its LD50 of approx. 10 mg per kilogram of body weight that points to its highly toxic nature. Strychnine causes muscular convulsions and eventually death through asphyxia or sheer exhaustion. Virtually all articulated fossils of Archaeopteryx have been found with the characteristic posture of the strychnine poisoned. We may never know exactly how these creatures died, but could it be that there was a dinosaur poisoner in the wild during the time of the dinosaurs?
InChI=1/C21H22N2O2/c24-18-10-16-19-13-9-17-21(6-7-22(17)11-12(13)5-8-25-16)14-3-1-2-4-15(14)23(18)20(19)21/h1-5,13,16-17,19-20H,6-11H2

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.

Funding the All-electric Aircraft

Superconducting motor Today, Philippe Masson of the FAMU-FSU College of Engineering and Center for Advanced Power Systems and colleagues at NASA and Georgia Tech publish details of an entirely new class of aircraft engine that, if it takes off, could lead to an all-electric aircraft that would cut airport pollution and reduce aircraft vapor trails to a distant memory. You can read my write-up about the work on the AlphaGalileo site here.

Unfortunately, while the science is sound, no one is yet beating a path to the inventors’ door, despite NASA backing. I asked Masson why he thought this was the case and his answer provides some cutting insights into the nature of the transport industry and the manufacturers that currently underpin it.

First off he pointed out that, “Conventional jet engines (turbofans) are very reliable and can still be improved: people are still working on NOx and noise reduction (including as part of our NASA sponsored project),” he says, “Therefore, there is a lot of inertia and imposing a new and totally different technology would be very difficult.” The major advantage of using electrical power is environment preservation because the performance of an all-electric aircraft would be unchanged unless one takes into account increased controllability and decreased maintenance requirements.

Masson’s electric jet is based on using zero-resistance superconducting materials as the magnetic components of the turbo-driving motor, but he points out that these, and cryogenic support systems needed to make them work, are still very expensive thus making funding difficult to find. It is possible that mass production would reduce costs to an economically viable level, but that is probably not going to happen any time soon.

“The motor designs we proposed can exhibit impressive power densities that would unfortunately almost only benefit airborne applications, there are no other applications with critical constraints in terms of weight and volume,” he told me, “As for the car industry in which combustion engine manufacturers are putting a lot of pressure to prevent new clean technologies to take off, jet engine manufacturers would not be happy to see electrical propulsion systems becoming a new standard.”

“An all-electric aircraft prototype is feasible,” he adds, “but imposing this technology as a replacement to gas turbines would still require a lot of research and development to meet flight requirements in terms of reliability.” However, Masson asserts that the appearance of increasingly electrical airliners from both Airbus and Boeing could hint at a future of all-electric aircraft. “I am convinced that one day in a not so far future we will see small electrically powered aircraft,” he says. He concedes that, “It will be years, probably tens of years, before we can see a truly all-electrical aircraft as all the components require extensive testing and a very high reliability before being implemented in airplanes.”

Masson and his colleagues have approached several companies and aircraft manufacturers and have not yet been successful in getting funding to build a prototype of their superconducting propulsion motor for which patents are pending. “We are still hopeful and will keep looking for funding,” he says.

Science in the Movies

Some time ago, I wrote a feature for the long since scuppered HMS Beagle on BioMedNet.com on the subject of science in the movies. I interviewed various scientists and people in the movie industry about the role of experts in advising on plot lines and details. It was quite a departure from the usual research reporting and was part of my once-monthly “Adapt or Die” column for the webzine. Sadly missed, for a short time, by many life scientists.

One thing that strikes me repeatedly is the lack of chemistry in the movies, other than the chemistry of weapons of mass destruction, of course. Carl Djerassi attempted to bring chemistry to the fore in his Nobel play, Oxygen, but that was a one-off and was in a sense a test-bed for his ethical and moral debates which he embeds in many of his science in fiction scripts. UPDATE: Of course, there was the wonderful Breaking Bad that came much later than this blog post from 2007!

Living Chirality

Yet another possible explanation for the bias in life’s handedness – the fact that nature uses mainly only form of the building blocks of proteins – comes from Dutch chemists experimenting with the sublimation of amino acids.

Writing in the latest issue of my alma mater Chemical Communications, Ben Feringa and colleagues at the University of Groningen have demonstrated significant enantioenrichment of a variety of amino acids by sublimation in which preferential evaporation of the predominant enantiomer occurs from a mixture of low ee amino acids. They lay claim to this process as being a possible mechanism for the presence of ee of amino acids under the conditions found in space.

Theories abound as to why life on earth predominantly uses L amino acids. Most rely on some obscure initial set conditions and a convoluted route from a small excess in outer space to the seeding of amino acids on earth. While Feringa and colleagues discuss their findings in terms of interplanetary conditions it may be just as possible that their process had some counterpart on the primordial earth.

InChI=1/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/f/h8H

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.

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.