David Bradley – Page 285

Could World of Warcraft Fight Disease?

Corrupted blood

In September 2005, about 4 million World of Warcraft gamers saw a new and unexpected challenge in the game. Players exploring a new area within the game encountered an extremely virulent, highly contagious disease, known as Corrupted Blood, which had been introduced in an update on the 13th of that month. The disease quickly spread, like the Black Death, to the population centres of the fantasy world, killing many and causing social chaos. But, who, other than the gamers themselves should care about virtual deaths and digital disease?

Well, according to Eric Lofgren of Tufts University School of Medicine, in Boston and Nina Fefferman of Rutgers University, in Piscataway, we all should care because the virtual epidemic could provide a very useful model of how diseases spread, how individuals and groups respond to the presence of a killer disease, and what we might do to control an outbreak, of bird flu or a SARS-type disease, in the real world. Writing in the journal Lancet Infectious Diseases, the team explains how simulation models are very useful in studying the spread of disease, epidemiology. However, validating the models or tailoring them to particular human behaviour patterns is next to impossible. The World of Warcraft incident, known as the Corrupted Blood outbreak, on the other hand, “provided an excellent example of the potential of such systems.” They explain that while data from the Corrupted Blood outbreak were not gathered scientifically at the time and so represent a missed opportunity, there is the potential for deliberately engineering such gameplay into other virtual worlds. “Virtual outbreaks designed and implemented with public-health studies in mind have the potential to bridge the gap between traditional epidemiological studies on populations and large-scale computer simulations,” the researchers say, “these would involve both unprogrammed human behaviour and large numbers of test participants in a controlled environment where the disease parameters are known.”

The use of distributed networks to help solve scientific and medical problems is not new. many Internet users will have heard of the likes of SETI@home. This system is essentially a program you install on your computer which uses idle time to search for signs of extra terrestrial life in downloaded astronomical data.

SETI@home is just one of a group of applications based on BOINC, the Berkeley Open Infrastructure for Network Computing. You can use your Windows, Mac, or Linux machine to help find cures for disease, study climate change, discover pulsars and solve various other problems in earth sciences, astronomy, physics, biology, medicine, mathematics and strategy games. You can find a full list of projects here.

A recent paper in the International Journal of Web and Grid Services (2007, 3, pp 354-368) reviewed the state of the art in such distributed applications the world over. According to Bertil Schmidt of the University of New South Wales, Australia, desktop grid computing, as these kinds of distributed applications are known technically, is a relatively new technology but can nevertheless provide massive computing power for a variety of applications. He points out that the cost is low for the researchers, given that once set loose in the wild, the running costs of the program are themselves distributed to the downloaders’ computer and the costs to the researchers are then only in terms of retrieving results from those machines as and when necessary and analysing the incoming data.

Schmidt explains how BOINC provides “a proven open-source infrastructure to set up such projects in a relatively short time” and surveys the scientific projects, e-science, that have adopted this strategy. “The power and mass appeal of desktop grid computing for implementing task-parallel problems have been demonstrated in projects such as SETI@home,” Schmidt explains, pointing out that as of April 2007, the average performance of SETI@home was around 250 teraflops. A teraflops (sometimes teraFLOPS), is a million million floating point operations (or instructions) per second. The combined average performance of all BOINC-based projects was around 0.5 petaflops spread over more than 400 000 active CPUs, which is more powerful in total than IBM’s BlueGene/L, which peaks at 0.280 petaFLOPS. By comparison, the next generation supercomputer, Blue Gene/P, will run at 3000 teraflops, or 3 petaFLOPS, so this distributed power represents a vast resource for e-science and is as yet only very partially tapped.

Personally, I have the World Community Grid running on my computer. This application allows you to help out in the fight against Dengue fever, AIDS, and phase 2 of the human proteome folding project. At the time of writing, teh project has 318,888 members and is running on 715,025 devices amounting to a total of 107,837 years of computing time so far. You can view the latest stats here.

If you have a fast computer and are not running CPU or memory intensive applications, then you could do even more with any of those e-science projects, allowing the BOINC application to run even when your machine is not idle. You will not only accrue more “credits and kudos” on your chosen project but you could just solve one of the problems facing humanity.

Diamonds Almost Forever

Diamonds almost as old as the Earth itself have been found locked in ancient crystals of zircon from the Jack Hills region of Western Australia, according to scientists writing in Nature this week. The diamonds could provide unique insights into the early evolution of our planet’s crust.

Zircons are tough and resist heat and some samples have been shown to be several billion years old. As such, they retain vital clues about the Earth’s geological evolution, at least as far as the crust and mantle are concerned. Recent studies of these ancient crystals have suggested that the Earth may have cooled much faster than previously thought, with the continental crust and oceans forming some 4.4 billion years ago.

Now, Martina Menneken and colleagues at the Westfaeische Wilhelms-Universitaet Muenster, in Germany, have investigated mineral inclusions within zircons and found that some of them contained small diamonds. The zircons have been dated using uranium and lead isotopes and found to be over four billion years old,” almost one billion years older than the previous oldest-known terrestrial diamonds, and present in material that crystallized within 300 million years of the formation of the Earth itself.

The authors suggest that these diamond inclusions formed under ultrahigh-pressure conditions, which implies that the Earth had a relatively thick continental crust and crust-mantle interaction at least 4.25 billion years ago. Diamonds are formed in the earths interior, where they are brought to the surface by volcanoes and it is known as one of the hardest materials on earth.

Azadirachtin Done

Steve Ley and his team (some 40 PhD students over the last two decades) have finally cracked the total synthesis of the natural insecticide azadirachtin. This hugely complex natural product extracted from the Indian neem tree put up quite a struggle from the year it was isolated (1968) till its structure was unequivocally elucidated (seventeen years later) till the publication of Ley’s paper in Angewandte Chemie outlining the 64-step strategy for making it from standard starting materials. Check out the Angewandte press site for a more detailed write-up and the paper itself for full details of the completion of these chemical odyssey.

Why Do We Yawn?

Yawning

No one knows why we yawn. There are lots of theories, some talk about it signalling tiredness or getting oxygen to the brain, others mention clearing out stale air from the lungs and reducing blood carbon dioxide levels. Most are baloney. But, one thing that is certain, yawns can be infectious. Catch sight of someone yawning, and nine times out of ten, you will yawn yourself within a few seconds. But, that still doesn’t really answer the question, why do we yawn? Is such an infectious yawn a message to others in the group that it’s time for bed? Probably not, otherwise why yawn first thing on getting out of bed? Either way researchers have found that people with autism spectrum disorder don’t tend to succumb to an infectious yawn.

Atsushi Senju of the Centre for Brain and Cognitive Development at Birkbeck, University of London has shown for the first time that children with some degree of autism are not susceptible to contagious yawning. Autism Spectrum Disorder is a developmental disability that severely affects social interaction and communication including empathy. Report published in the August issue of the Royal Society journal Biology Letters.

This would seem an obvious result given that contagious yawning is thought to share similar cognitive and neural mechanisms as empathy.

Senju and colleagues from the University of Tokyo showed videos of people yawning or making mouth movements to 24 children with autism spectrum disorder and to 25 non-ASD children. Both groups of children yawned the same number of times while watching the video of general mouth movements, but the non-ASD children yawned more when watching the video of people yawning.

“This is the first report that a neuropsychological or psychiatric condition can selectively impair contagious yawning, sparing spontaneous yawning,” explains Senju, “Our study confirms the prediction of ’empathy theory’, by demonstrating that individuals with autism, who show atypical developments in empathy, also show selective impairment in contagious yawning.”

None of this answers the question of why do we yawn in the first place? Apparently, yawning becomes contagious at around one to two years of age, although unborn fetuses also yawn (presumably not contagiously though!) and can be triggered in animals by stimulating the hypothalamus in the brain with injected dopamine, excitatory amino acids, nitric oxide, and neuropeptides. None of this really explains why we yawn. The empathy angle perhaps points to an ancient benefit in group behaviour, but what that benefit is, science does not yet know.

For more on simple experiments and the power of yawn, check out the neuroscience for kids page at Washington U.

By the way, did you notice while reading this whether you yawned? Hopefully, it was not merely boredom that did it…

Antibodies Online

antibodies-online launched in April 2006 and calls itself the marketplace for research antibodies providing scientists in Germany, Austria, and Switzerland with invaluable assistance in finding antibodies quickly and easily, a task that was once very time-consuming when predominantly paper-based catalogues were the only resource for searching available.

The company also acts as a kind of immunological broker allowing antibody distributors and producers to ply their trade online at low costs and no risks. The reason I mentioned it on ChemSpy.com is that the their site provides access to information on some 60,000 antibodies in a database, with that number growing every day. Such a resource could prove invaluable to many researchers working in silico let alone in vitro and in vivo. antibodies-online.com claims to be one of the largest vendor-independent platform for research antibodies in that region and plans to increase its product portfolio to more than 100,000 antibodies by Spring 2008, which could make it an even more useful resource.

Quantum Dots and Spin Pumps

Spin pumped quantum dot It is not so long ago, that the first thing that sprang to mind when one read the phrase ‘quantum dot’ was the idea of some rather esoteric and complicated aspect of avant garde physics. This is still partly true, there is some rather complex experimental work underway underpinned by even more complex theoretical work investigating the bizarre properties of tiny devices that can trap a single electron in zero-dimensions.

Practical applications of quantum dots have emerged recently in sensor science but US and Brazilian researchers hope to exploit them in a new kind of electronics, known as spintronics where electron charge and quantum spin add an extra dimension to electronic operations and computation. Spin currents might also be used to allow quantum communications take place “in-chip” in devices so small that light propagation is not practical. Such developments will open up quantum dots that can increase processing speed, storage capacity, and functionality of conventional electronics, communication, and computations and technologies.

Eduardo Mucciolo of the Department of Physics at the University of Central Florida, Orlando and Caio Lewenkopf of the Department of Theoretical Physics at State University of Rio de Janeiro, Brazil, are investigating lateral semiconductor quantum dots. They believe that such devices could be used as pumps to produce spin polarised currents, by exploring quantum phase coherence phenomena. The effect, called pure spin pumping, is analogous to charging a battery in conventional electronics. Such a spin pump might provide the much-needed circuit element for spin-based electronics.

Writing in the International Journal of Nanotechnology (2007, 4, 482-495), Mucciolo and Lewenkopf describe a lateral semiconductor quantum dot. In these systems, electrons within a two-dimensional gas are trapped within small puddles by the application of a voltage; applied voltages control the shape and size of these puddles. Electrodes can be used to vary the width of the point contacts between the electron puddle and the 2D gas. Controlling these point contacts allows quantum dots to be “opened” and “closed”.

Controlling these point contacts allows them to “open” and “close” the quantum dots. This effect dates back to the early 1990s, points out Mucciolo. “Closing and opening the propagation through a constriction, the point contact, can be used to detect spin-polarized currents,” he explains, “This is how Susan Watson and colleagues at Middlebury College managed to see spin currents coming out of their quantum dot pump in 2003.”

“Recently, our spin pump proposal passed its first experimental test,” say the researchers, who now hope that other teams will take up the challenge and investigate the potential of spin pump quantum dots.

“The main idea behind the spin pumping mechanism was actually published for the first time in Physical Review Letters in a paper I co-authored with Claudio Chamon (Boston University) and Charles Marcus (Harvard University),” adds Mucciolo. The main development since that earlier work presented in the current paper with Lewenkopf is that now they have carried out a much more detailed analysis to demonstrate the precise details, this was entirely missing from the PRL paper, Mucciolo told us. “In the J Nanotech paper we also develop a general formalism that could serve as a basis for the theoretical investigation of several aspects of spin pumps which, albeit important, have not yet been considered in the literature,” Mucciolo adds.

Growing Nano Journals

The American Chemical Society is following up the success of its preliminary reports publication Nano Letters with a full-blown journal – ACS Nano. Penn State’s Paul Weiss will be Editor and the journal will publish monthly in print and online.

The inaugural issue features work from David Allara, Hongjie Dai, Prashant Kamat, and Frank Caruso, as well as a conversation with Nobel Laureate Heinrich Rohrer, and an editorial from Weiss. A news ection, NanoFocus, will also feature.

If you’re an institutional subscriber you can access Nano at no extra charge for the remainder of 2007 at www.acsnano.org.

Wound Healing and Super Cabbage

This week in The ChemWeb Alchemist, I report how Illinois chemists have developed a novel catalytic approach that side-steps functional group modifications to streamline organic syntheses. The Alchemist also discovers that a serendipitous finding leads to a bright spot in observing electron transfer in single molecules under the scanning tunneling microscope. While mixed signals appear in C&EN regarding the safety of bisphenol A.

In Africa, extracts of the leaves of the so-called hemorrhage plant could provide medical science with a new approach to faster, cleaner wound healing. Finally this week, upping the glucosinolate content of an entirely different group of plants, brassica crops, might not only help cabbage, broccoli, and cauliflower ward off pests and so save on pesticide use, but could also boost the cancer-fighting powers of these foods for people who eat them.

Speedy synthesis – University of Illinois chemists hope to meet the efficiency challenge in organic chemistry by exploiting a newly developed class of carbon-hydrogen catalyst. Christina White and her colleagues are creating a new chemical toolbox of highly selective and reactive catalysts that are tolerant of other functionality. “By offering fewer steps, fewer functional group manipulations and higher yields, this toolbox will change the way chemists make molecules,” White claims. A palladium/sulfoxide catalyst provides the team with a selective method for directly inserting nitrogen functionality into relatively inert C-H bonds without having to manipulate functional groups. The team has reported streamlined syntheses of various compounds, including a peptidase inhibitor drug candidate, a nucleotide-sugar L-galactose, and the chemotherapeutic reagent acosamine. She and her colleagues are currently applying the technology to synthesizing the antibiotic erythromycin A.

Read this week’s Alchemist for summaries and direct links to all featured chemistry news

Short Chicken Wire Roll Up

Double wall chickens

In a past life I was deputy editor on the RSC journal Chemical Communications and recall the excitement and tension around the time we published Sir Harry Kroto’s pioneering fullerene paper. At the time, there were all kinds of imaginative plans emerging for what might be done with these odd all-carbon soccerball shaped molecules.

However, it was not the spherical, nor the spheroidal, fullerenes that became the darlings of materials scientists and nanotechnologists the world over. Instead it was their stretched cousins – the carbon nanotubes. Resembling a sub-microscopic roll of chicken wire, these long, hollow molecules have been touted as potential components for the future of microelectronics, as conducting connectors for nano devices, as catalysts and even as smart drug delivery agents.

Chemical scientists have developed various methods for synthesising nanotubes that are just a single atom thick, others that have a double wall, like two layers of rolled up chickenwire, all just a few nanometres in cross-sectional diameter. However, according to researchers writing in the International Journal of Nanotechnology (2007, 4, 618-633) there are no widely accepted techniques for producing useful quantities of short nanotubes of a specific length.

Simon Smart, G.Q. Lu, and D.J. Martin of the Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Australia, and W.C. Ren and H.M. Cheng of Shenyang National Laboratory for Materials Science, of the Chinese Academy of Sciences, have now devised a production method for making shortened double-walled carbon nanotubes using by high-energy ball milling.

On the everyday scale of things, a ball mill is type of cylindrical grinder within which are loose balls (ceramic, steel, or flint pebbles, commonly) and to which is added the material to be milled. The ideal technique for shortening nanotubes has to have three characteristics, say the researchers. First, from a practical point of view, it should be able to produce gram quantities of individual samples. Secondly, it has to be able to shorten the nanotubes without significantly impacting on their purity of destroying the nanotubes entirely. Finally, the method has to be controllable so that it can shorten the nanotubes reproducibly and accurately.

Other researchers have attempted to shorten nanotubes using ultrasonic agitation, chemical cutting techniques, and ball milling. Ultrasound is not particularly controllable in terms of producing large quantities of nanotubes of a similar length while chemical methods are convoluted and can damage the nanotube walls. So, Smart and colleagues have focused on ball milling. This technique requires no chemical additives and can have a high throughput.

The team tested the shortened nanotubes using transmission electron microscopy (TEM), scanning electron microscopy (SEM), Raman spectroscopy, thermogravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS).

The researchers now plan to use their ball-milled carbon nanotubes in novel polymer nanocomposite materials and to carry out toxicological studies. It should be possible to disperse these shorter nanotubes much more effectively in composite materials, explain the researchers, because they do not form bundles so readily as long nanotubes but would still endow the nanocomposite with novel strength and flexibility properties. “In fact, early results are showing that in polyurethane elastomers, the shorter nanotubes out perform the longer ones,” Smart told Sciencebase. He adds that, “These materials are most suited towards polymer nanocomposite materials. The presence of
carbonyl functional groups on the sidewalls does lend itself towards further chemistry and possible applications in drug delivery or sensing applications. However, at this stage of research, the ball milling process induces too many defects for use in applications that utilize the nanotubes
unique electronic properties.”

Giving good head line

Giving good head line I was discussing press releases and headline writing recently with a technology writer friend. One thing that many first-time authors and the people they write about are blissfully unaware is that magazines and newspapers usually employ specific people, sub-editors and headline writers, to chop up any author’s glorious prose and to stick an entirely different title up-top and call it the headline. This is not a criticism, it’s just a fact of journalism.

However, it often comes as a shock to many new writers who may have imagined their witty strapline needed no tweaking or editing all. A shock, you say? Well, certainly. The headline is designed to both grab your attention and primarily make you want to buy the publication with the intention of reading the article. If it is left as a flat abstract or esoteric phrase who’s going to grab the paper?

Compare and contrast: “Member of royal household indulges in illicit substance by inhalation” with “Dopey Prince”

The former is obviously a ludicrously overblown working title that an author might cut down to something like “Royal admits to smoking cannabis”, but a subbie would prefer something even crisper, with a deliberate ambiguity about whom the article is talking. Is it the artist formerly known as Prince and now known as Prince again but giving it away for free? Or is it one of the Royal Family? If so, which one? Intrigued? You will be. Subeditors and headline writers are the royals of keyword use, they are now and always were, even before we were all worrying about link bait and search engine optimisation online.

Anyway, the upshot of this discussion was that I thought I would dig out some of my old cuttings from the The Grauniad and elsewhere and do a comparison of the titles I originally gave the article and the final headlines used by the paper…if there’s an online link to them, I’ll point to those too, so you can get to read what I had to say (assuming the headline grabs you). In fact, now that I think of it, maybe I should not say which one is which and simply link to the online article (where there is one) from both my title and the final headline. You can guess which you think it will be and find out when you make the click.

A blue light for change – Guardian – The butterfly effect

Be of good cheer – Guardian – Bread and stuffing chemistry

The Genome Chose Its Alphabet With Care – Science – Genetic alphabet soup

A cup of tea is no mug’s game – Guardian – Tea – best drink of the day for diabetics

Sweaty way to beat stress – Guardian – Sweaty stress busters

Shy Chemicals Offer a Solution – Science – Greening chemistry with non-stick molecules

The dating game – Guardian – A trunk call to be sniffed at

Finally, sometimes the sub-editor merely tweaks a title as in the case of my article in the July-August issue of StarDate magazine:

Cosmic Efforts Shed Light on Dark Universe – Cosmic Efforts Shed Light on Dark Energy

I’ll add a few more when the opportunity arises. I have dozens in the archives but will have to dig out backup discs to find the original pre-edited article and accompanying title.