Chemistry – Page 30 – David Bradley

Chemical Crocodile Clips

I hate having to download standalone video players to enable playback of video content. Google Videos/Youtube are both guilty, although obviously you can view online, but then you have to have an internet connection to do that unless you save the file to your hard drive and download the player…

Crocodile Clips provides simple simulation software and, you’ve guessed it, they have their own proprietary player. But, I can excuse them, because their player is not a simple video rendering application but a simulator that allows educators and students alike to work with data and generate simulations of a whole range of processes from titration to animation. For ChemSpy.com users, the chemistry simulations and tutorials will probably be of most interest.

With the snappy Crocodile Chemistry, you get a simulated chemistry laboratory where you can model experiments and reactions, without all the hassle of fume cupboards and safety goggles. Drag chemicals, equipment and glassware from the toolbars at the side of the screen, and combine them as you wish. Choose whatever quantities and concentrations you like: reactions are modelled accurately as soon as you mix the chemicals. Plot graphs to analyse data from your experiment, and view mechanisms using 3D animations.

Moreover, if you really cannot face downloading yet another applet for viewing something, then they also have a section on pre-simulated videos ready for showing that are targeted at training potential users, but only if you’re online and only in their proprietary video format.

Chemweb Chemistry News

The Alchemist this issue takes a look at colorful nanoparticles and how to control them with a magnet, a platinum wrap that could improve the efficacy of certain types of anticancer drug, an answer to why trucks cannot crush mother-of-pearl, and the chemistry behind plans for a liquid telescope destined for the moon. Also, this week, the discovery of a new type of electron wave that exists on metal surfaces could provide a new foundation for theoretical studies of chemical reactions. Finally, a princely sum is shared by the journals Nature and Science for excellence in science communication.

Also new on the ChemWeb site this week: The Events Calendar at ChemWeb.com lists conferences, seminars, trade shows, user group meetings, webinars and many other events of interest to ChemWeb members.

Chemistry of Sex, Toothpaste, and Armpits

John Emsley book I started a book on the chemistry of sex once…didn’t get very far, it was too distracting and working from home with my wife meant one thing led to another too often for us to knuckle down to the online research. TMI? Sorry.

Anyway, my good friend John Emsley who has been pounding the chemistry writing beat a lot longer even than me has just published another fascinating title on the chemistry and chemicals that underpins cosmetics, grooming, health, food, and, of course, sex.

In Better Looking, Better Living, Better Loving takes the novel tack of introducing each chapter with a mock news item about the next big thing in the various areas he covers, explaining how near-future chemistry used to develop the perfect toothpaste might develop and put dentists out of business, for instance, or a deodorant that could biochemically convert armpit odors into attractant pheromones. His news items are certainly tongue-in-cheek, but they do point to the very real ways in which chemistry impacts on almost every aspect of our lives.

Emsley tours plenty of the recent advances in chemistry, taking in the cosmetic factory, the pharmacy, the grooming salon, the diet clinic, the power plant, the domestic cleaning company, and the art gallery along the way. The tour is for anyone wanting to know more about the true impact of chemical products on our everyday lives, not just the nasties of tabloid scare-stories. Indeed, Emsley puts to rest several of the more ludicrous claims made for the effects of certain chemicals on our health and the environment.

He covers whether homeopathic medicines really work (you can probably guess his answer), the myth of date rape drugs, how the toxic chemical acrylamide gets into our food, and whether great
artists were affected by the poisonous pigments they used in their masterpieces.

With his informal, if deadpan, style, Emsley links his incredibly strong chemical knowledge to fun
situations, with a sneaky sideways glance or a roll of the eyes. Anyone suffering from chemophobia should read this. Anyone already singing with the chemical choir should read this. In fact, everyone should read this. Chemicals impact on all our lives, mostly in a positive way, rarely in a negative way (seriously). Emsley will help you understand the arguments on both sides, weigh up the risks and benefits, and make your own decisions about the chemistry of food, cosmetics, health, and, of course, sex.

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?

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.

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.

YASSE – Yet Another Science Search Engine

A new global science gateway – I’m sure they’d prefer me to display that phrase in blinking bright green text on a red background, but I won’t – has been launched by the US Department of Energy (DOE) and the British Library. The aim is in “accelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases.” Yeah, okay. But, isn’t this just yet another science search engine portal? Apparently, subsequent versions of WorldWideScience.org will offer access to additional sources as well as enhanced features.

That’s what they all say. I’m sure it’s a very worthy search tool and would like to hear from Chemspy visitors who have tried it out and found its results useful/useless (del. as applic.)

Incidentally, the webmaster risks a duplicate content penalty because the two canonical forms of the web address (WorldWideScience.org and www.WorldWideScience.org) both return “200 OK”. One of them should have a 301 redirect applied.

Ptaquiloside Redux

Almost ten years ago, I wrote a feature article on the cancer risk associated with the bracken toxins known as ptaquiloside for ChemWeb. The article was updated and mirrored on Paul May’s Molecule of the Month website at Bristol University, and quite bizarrely still draws a few readers to the Sciencebase site via my byline on the article. I suppose the reason it is still popular is that it makes it to page on in Google should you search for the word bracken.

Anyway, this article occasionally triggers some rather interesting correspondence with readers. Most recently, John Nayler emailed me to ask whether or not toxic chemicals from bracken might leach into groundwater beneath bracken-infested areas. I had to admit I did not know, but a paper published recently in the journal Chemosphere (2007, 67, 202-209) discusses the microbial degradation and impact of ptaquiloside on soil microbes themselves, which sheds some light on the potential impact of this carcinogenic toxin.

Another of Nayler’s concerns regards whether or not bracken is not simply an unpleasant weed with a cancer risk associated with eating the “fiddle heads” (a delicacy in Japan), but whether or not landowners, whose land is infested with bracken might be liable for public health lawsuits should those with a right to roam on their land be exposed to bracken spores. The risk may be small but that never stopped an ambulance-chasing lawyer in the past.

Cancer Research UK has a FAQ on the cancer potential of bracken. Despite isolated ptaquiloside coming up positive in carcinogenicity tests a decade ago, the latest research, according to Cancer UK is that there is no risk of cancer associated with eating bracken fiddlehead greens. So, what about those spores. Studies have shown bracken spores to cause cancer in mice, but those mice were given a lot of spores and to extrapolate to human cancer risk is (death)wishful thinking. A walk among the bracken is more likely to trigger a sneezing fit if the spores are high than anything else, and as CRUK points out, diet and smoking are far greater risk factors than bracken for cancer.

Search on Steroids

Researchers at Xerox Corporation have developed new text mining software that goes beyond conventional keyword search, enabling it, in effect, to hone in on the one or two golden nuggets among the trash in the garbage pit. I asked the developers how applicable the system might be to science searching as it is originally aimed at administrative, legal and business type environments. Apparently, the FactSpotter software will be just as well matched to searching out elements of risk in scientific documents, for instance.