David Bradley – Page 288

Data Mining Prominent Scientists

Authoratory is a unique database that provided contact information, professional interests, social connections and funding for almost 300,000 leading scientists (The site quoted 289,943 as the actual figure, at the time of writing). So, what makes this database so unique? Well, The content is generated by data mining the millions of articles indexed by PubMed. Published papers are inspected and a personalized report built. You can hook out the most prominent expert in almost any field reported by PubMed and the site will tell you how many papers they published, their research affiliations collaborators, and list any NIH funding.

Researchers listed have to be US, UK or Canada based and have to have published at least three papers a year. 2,129,859 papers with almost 2,699,772 unique authors have been mined, the site claims, but only ten percent of those are considered worthy for inclusion in the Authoratory release.

I am sure someone adept at Yahoo Pipes could exploit this database in a mashup of chemistry papers and feeds and the Authoratory database. Mitch?

A space-age search engine

eZipSky Want to know what time the moon will rise in your neck of the woods, which planet is in which constellation tonight, or when the Internation Space Station will next be overhead? There is not much stargazing going in England at the moment, too much H20 falling from the sky, but eZipSky’s free service for amateur astronomers in the US, is a kind of search engine for heavenly bodies.

The eZipSky recently announced its Interactive SkyEngine, possibly the simplest way to search for many common features of the sky at night. Enter your zipcode and an object of desire – the moon, ISS, a planet, constellation – and the SkyEngine returns that object’s location or tells you when it will next be visible from your location.

Available sky objects include the sun, the moon, the naked-eye planets, the constellations, the 150 brightest stars, the brightest star clusters and galaxies, and upcoming meteor showers. It also provides hits for the International Space Station, the Hubble Space Telescope, more than 100 other earth-orbiting satellites, and, when it’s in Earth orbit, the Space Shuttle.

Imagining I was in Cambridge, MA, as opposed to Cambridge, UK, I tried out the zipcode for Harvard Science, 02138, and apparently I should “Look for the Andromeda Galaxy after it rises tonight at 20:51 and before sunrise tomorrow morning at 5:14.” The results provided also offer tips on what to search for next, so following their lead I ran a search on Mars and got a similar pair of times to watch out for it. Something that was lacking when I first visited the site was reference compass points to help newbie amateur astronomers pinpoint their objects of desire and not spend all night looking at some random twinkling object rather than the ISS, Mars, or a neighbouring galaxy.

I mentioned this to eZipSky’s Peter Busch and he tells me that the web team has now implemented my idea. Now, that’s service for you!

Free cure-alls

Free cure-alls As I think I’ve mentioned before, I get a lot of emails from people claiming to have solved all the worlds environmental problems through some perpetual motion device or similar. These are not the usual run of the mill spam messages, they are usually targeted at me as a science journalist and talk of big solutions and the potential for a Time cover, a Pulitzer or some other grand prize. If they were sent by snailmail I suspect the majority would be written in lurid green ink.

Some of these claims seem to reach global proportions as we’ve seen with the Steorn research, which is yet to bear fruit, although on July 4, Steorn announced it was planning to demo its results publicly; they are yet to materialise, in fact they were delayed to July 5, and at the time of writing had still not been shown.

For some of the more intriguing of these emails, I created a new section on SciScoop to cover and discuss just such controversial conjectures. I have also highlighted several odd scientific claims some time ago on Sciencebase too, purely for your amusement.

Anyway, those emails continue to arrive, within the last week or two I have had one claiming the amazing powers of an electrical device that seems to create energy from nothing. It strikes me and several energy scientists I spoke to as being nothing more than the electrical equivalent of Bhaskara’s wheel, although the inventor has every faith in his product. Good luck to him, I hope it works out.

I know several academics who are always more than willing to assist inventors with bizarre claims…for a fee. They delight in showing up the obvious flaws in an argument. I should send a pharmacology professor the most recent message I received, which claims to cure almost every form of cancer, despite cancer being simply an umbrella term for a massively diverse range of diseases. The email told of a very simple, small molecule, there is no targeting, and no clue as to a mode of action. I suspect the research runs along the lines of another unrelated compound that was popular on bad medicine sites about five years ago. I won’t name either compound for fear of giving them some kind of credence here or inspiring anyone to go looking.

Many of these emails claim that the invention precludes understanding, somehow lies beyond current scientific understanding, and often defies well-proven laws of nature.

Science and medicine do occasionally enter the realms of paradigm shifts, big changes to theory arise, but despite the popular perception these do not often, if ever, come in a single Eureka moment; even the eponymous event concerning Archimedes in his bath is almost certainly apocryphal and a brilliant piece of science popularisation. Moreover, no apple fell on Newton’s head, instead years of observations and the development of a new theory gave rise to his theory of gravitation. Likewise, although Einstein is credited with the theory of relativity, there were other theories around and he built his work on the solid experimental results from the latter half of the nineteenth and early twentieth century to gradually evolve Newton’s ideas at the cosmic scale.

It would perhaps be nice to imagine that there is a quickfix to our energy needs, a universal panacea for our ills, a maverick theory that explains life, the universe and everything, free cure-alls for everything, in fact. But, there isn’t. While, I occasionally draft a quick write-up for Sciencebase on the basis of some of the more plausible of those tantalizing emails with extravagant claims, more often, input from well-respected contacts in academia directs me, once again, to the overflowing Controversial Conjectures folder. Such emails are ultimately filed here for posterity. Whether or not the Steorn case turns out to be fit for this slot, we will have to wait patiently to see. As I said, their advertised demo is not yet available for display and their “offices” are closed for technical reasons. The latest word on the Steorn site is that overhead lighting caused device heating problems and Steorn has now decided to postpone the demonstration until further notice.

Anyone care to draw the obvious conclusion from that?

Captain Jack and the Large Hardon Collider

Doctor Who’s maverick side-kick Captain Jack, played by big show-tunes fan John Barrowman, took time out from his busy schedule to indulge a passion for mini big bangs with a visit to CERN, the world’s largest
particle physics laboratory and home of the large hardon collider (LHC). I suspect that Barrowman has not read my earlier post on the LHC and misread the title, but you never know.

Anyway, Barrowman took Manchester-CERN high-energy physicist, Brian Cox, along for the ride, and yes, there really are just far too many lewd puns to be made in the context of Cox, hadrons and Barrowman to be worth the effort. Actually, Cox was a ray of Sunshine, he was one of the scientific advisers on the recent sci-fi flick of that name. Barrowman, apparently, is genuinely interested in exploring the boundaries between science fact and science fiction. His fascinating response when confronted with the notion that a speeding proton in the particle accelerator experiences every second of our time as a seven thousandth of a second is illuminating to say the least – “Holey Moley”, he exclaimed. But, at least he went and donned the hard hat in the name of science.

Check out the video. Dig the groovy tune. And if you’re into that kind of thing you get to see Barrowman’s teeth, which are a miracle of modern science in themselves.

PubChem Statistics

In March 2006, I interviewed PubChem’s Steve Bryant for the Reactive Reports chemistry webzine and he revealed some of the inner workings and the aims of the PubChem chemistry database. Ever since, I’ve been rather curious about the growth of the site. How many scientists are using it. Unfortunately, Bryant tells me, getting a handle on that kind of data is difficult. “It’s a very tricky business to accurately condense all the raw log info on hits and IP addresses into an accurate summary of who’s using a given resource and how,” he explains.

However, there are a few tips you might use to extract some useful information from the site nevertheless. There is an easy way to look at current contents of the databases, for instance. The best trick is to go to the “global query” page:

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

Then enter “all[filter]” (no quotes) in the search box. This gives counts of how many records in each database, e.g. 10,358,219 PubChem compounds, 552 assays, etc. There is also a summary of contributors to PubChem, that lists numbers of substances or assays by organization:

http://pubchem.ncbi.nlm.nih.gov/sources/sources.cgi

Now, obviously that doesn’t provide usage stats, but it does highlight a newsworthy aspect of developments at PubChem. Over the past year, there has been an increasing number (and diversity) of the screening assay results. “We’re now up to over 10 million substance test results (sum of the number of substances tested in each assay, across all assays),” says Bryant, “We’ve also put some work into structure-activity analysis tools. For example, from the first
assay answering the all[filter] query (AID 728, Factor XIIa Dose Response Confirmation), try “Related BioAssays | Related BioAssays, by Target Similarity”, the “Structure Activity Analysis”.”

Bryant points out that this “heatmap” display isn’t useful to all users. However, screeners who want to check on the selectivity of their “hits” are using these tools more and more, he says.

Master AND commander

Master commander An fMRI scan of the upper echelons of the human brain, reveals that there are apparently two commanders at the helm, according to US neuroscientists; it is as if Russell Crowe were joined by his twin brother to captain the ship. The work may suggest new insights into behavioural problems that occur following brain injury.

Neuroscientist Steven Petersen and his team at Washington University School of Medicine in St. Louis also found that these two captains at a single helm do not consult each other in the control of voluntary, goal-oriented behaviour. Such behaviour encompasses a vast range of activities from reading and surfing the net to singing a song or even sailing a ship. In contrast, involuntary behaviour, such as pulse rate, breathing, and digestion are not controlled in this way.

You can read the full story in my SpectroscopyNOW column in the MRI channel.

Fire-extinguishing Grenades and Laser Remotes

Fire fighting grenade A fire-extinguishing “grenade”, a “laser finger” remote control for quadriplegic individuals, and a pocket-sized water purifier. A stack of cutting-edge innovations that have not come from a hi-tech thinktank but from teams of high school students in the US.

Twenty InvenTeams recently showcased these and other inventions at the 2007 Odyssey event at the Massachusetts Institute of Technology. The teams are set to receive grants of up to $10,000 in October to help them develop an invention prototype.

Among the other amazing creations are:

Solar-powered biodiesel processor
Driver Awake dozing driver waking system
Underground locator and communicator

Organising spokesperson Sarah Piperato told me that, “These high schoolers’ inventions show great innovation. This is what ambitious American teens are accomplishing with science and technology.” Now, these truly are winning science projects that put things like squeezing a boiled egg into a bottle to shame. That said, not everyone can be a Faraday, Edison, or a Lovelace.

Pirouetting DIABN

It seems to be no coincidence that tens of thousands of molecules line up to pirouette around a photochemical reaction centre, according to German researchers, given the superficial resemblance of the molecule, 4-(diisopropylamino)benzonitrile (DIABN), to a ballet dancer en pointe. They have shown, for the first time, that the ultrafast intramolecular electronic charge separation that takes place during a photochemical reaction leads to light-induced reorientation in an organic molecular crystal.

Whether or not the same will apply to other molecular crystals remains to be seen. The results appear in Phys Rev Lett and you can read David Bradley’s write-up in the latest issue of the SpectroscopyNOW X-ray ezine. This and related studies could pave the way for investigations of more complex systems including crystalline biological macromolecules.

InChI=1/C13H18N2/c1-10(2)15(11(3)4)13-7-5-12(9-14)6-8-13/h5-8,10-11H,1-4H3

Yoga Stretches Brain Chemical

GABA yoga posture US researchers have used a specialist brain scanning technique, magnetic resonance spectroscopic imaging, which is effectively an MRI scan carried out at the molecular level to reveal the effects of yoga practice on the brain. Specifically, they have investigated how concentrations of the feel-good compound gamma-aminobutyric (GABA), an inhibitory neurotransmitter, change after regular practice of yoga postures.

Eric Jensen and colleagues at Harvard Medical School looked at eight subjects prior to and after one hour of yoga as well as eleven control subjects who read a book rather than undertaking the yoga exercises. Although the samples are very small, they saw a marked difference in GABA levels in the yoga practitioners compared to the readers. Their findings suggest that yoga, and perhaps other forms of exercise, should be investigated as a complementary treatment for depression and anxiety disorders, which are commonly associated with low levels of GABA.

You can read more on this in my write-up over on SpectroscopyNOW.com. Click here for the Sciencebase complementary medicine roundup

Alchemy and Infamy

This week, I filled my regular fortnightly slot on ChemWeb with some applied chemistry, chemical engineering, and more:

volunteer work gets rewarded right from the top at the American Chemical Society, a novel approach to coupling unreactive arenes solves a century-old problem, sidesteps several synthetic steps and cuts down on waste, while a Stanford chemist reveals a PUG that can hack the PubChem database. Also, this week The Alchemist discovers that forests of nanotubes can be bundled together like so many logs in a molecular scale timberyard and new European regulations on chemicals came into force at the beginning of June, but may not reach consumers for years. Finally, yet another answer to the problem of binge-eating and obesity, a synthetic version of the hormone amylin gives positive rewards in the latest clinical tests.