PubChem molecular structure search

Pubchem is fast growing into one of the most useful repositories of small molecule information on the net and best of all it’s free. The service not only gives you the molecular formula and structure but also provides information on the biological activities of millions of small molecules. It is a component of NIH’s Molecular Libraries Roadmap Initiative.

NIH provides its own help resources here, but US chemical information aficionados Gary Wiggins and Dana Roth offer their own help sheets on how to search Pubchem most effectively and find the chemical information you need quickly.

So check out their info and get searching. PubChem allows searching of unique chemical structures using names, synonyms or keywords and provides links to available biological property information. You can also search by PubChem BioAssay using terms from the bioassay description, for example “cancer cell line”. But, most useful for many scientists will be the ability to search using a standard structure format sketched using SMILES, MOL files, or other formats. The main Pubchem landing page is here.

For those who need more help with PubChem, why not join the PubChem discussion group.

Firefox 2 launched

Version 2.0 of the alternative web browser Firefox, has now been launched. The latest browser has many of the features of version 7 of that other browser, including a pop-up blocker, safer surfing, virus protection, tabbed browsing, and better handling of newsfeeds. One thing it will hopefully lack is the never-ending release of security patches that other browser seems to need on a regular basis.

I’m loathe to say that Sciencebase is optimised for Firefox. It’s not. In fact, it’s not optimised for any specific browser at all. It’s set up to hopefully adhere to the general W3C web standards rather than favouring any particular browser, so that it is compatible with them all. That said, I personally tend to use Firefox as my day to day browser and drop out to MSIE only to check formating of this site and others with which I work. Even if you have IE only sites you visit, there’s a plugin for Firefox that runs IE in a Firefox browser tab so you don’t even need to switch programs. Unless you’re smitten with Mr Gates’ turtleneck sweaters, I’d go for something bushier.

You can download version 2 officially from the Mozilla site from Tuesday October 24, although if you view the cache of this post you will see a set of pre-release links.

Australian Produce Banned by US

Vegemite banAnd you thought Brussels was crazy for banning bananas that were too curved, for forcing manufacturers to relabel brandy butter as “modified distilled wine spreadable fat product”, and for limiting pizzas to an eleven-inch standardised diameter only! Now, the US is searching Aussies coming into the country to make sure they’re not bringing that most infamous of products with them – Vegemite!

According to News.com.au, the iconic spreadable brown stuff in a jar is faithfully carried around the world by travellers from down under. But, a legal technicality in the US means that only breads and cereals are allowed to contain added folic acid (aka folate or vitamin B9), so Vegemite has become hot outlaw property.

A spokeswoman for the manfacturer Kraft, Joanna Scott said: “The (US) Food and Drug Administration doesn’t allow the import of Vegemite simply because the recipe does have the addition of folic acid.” She added that the US is actually only “a minor market” for Vegemite.

Presumably, the reason the folate law exists is to prevent manufacturers of other products from cashing in on folate health publicity surrounding folic acid and campaigns aimed at women hoping to get pregnant but reduce the risk of their child having spina bifida. But, Vegemite, Australians will tell you, is almost as old as toast itself. Its certainly something most will be very reluctant to give up in the final count. If the “ban” persists one can anticipate a rather rapid decline in quality bar staff across the US, especially among those who can mix a Singapore sling and play the digeridoo. Or, maybe the whole story is simply a PR campaign in itself aimed at boosting the Vegemite share price and Aussie bar staff will be able to cope just fine!

You Are a Monkey

Do you think of yourself as more than a monkey? I say monkey, but of course I mean ape, and so do the guys who made this video…but as they point out, monkey, ape, are just words to try and elevate the position in the universe of the monkey that happens to have the biggest and most well connected brain. I suspect Richard Dawkins would enjoy this video. It really does tell it like it is:

Check out this post for a brief review of Dawkins’ latest book, The God Delusion, and his interview with Paxman on Life, the Universe, and Teapots.

Sciencebase wants your blog

A couple of the recent additions to the Sciencebase science links were research-based blogs rather than the more familiar commentary type (like this one). The chat and waffle sites can be informative and entertaining but sites like the Usefulchem blog are more, well…useful, providing as they do insights into the processes of scientific research and potential offering new solutions through discussion. So, if you’re a scientist running a research-type blog, please get in touch. If there’s enough interest, I’ll create a separation links section dedicated to total syntheses, telescopic adjustments, physical fine-tuning and other research matters.

Please send your links in by email or add a comment to this post.

Richard Hammond Explodes (Microwave Ovens) Again

Probably a really, really good idea to take Brainiacs presenter Richard Hammond’s advice NOT TO TRY THIS AT HOME. The Brainiacs team set up two microwave ovens and stuffed in all the stuff they’d already tested in microwave ovens on previous shows (as a serious experiment so that you don’t have to do it at home). Beer, CDs, soap, petrol, champagne, wire wool and much more leads to some pretty lights and them some serious damage.

Are we running out of oil

Are we running out of oil? It’s a question that has vexed drivers the world over since the first major oil crisis three decades ago. Oil experts have been telling us for years that supplies are dwindling and that within another few decades the petrochemical legacy left by ancient life will have all but gone.

But, Eric Cheney economic geologist at the University of Washington thinks this notion is nonsense. “The most common question I get is, ‘When are we going to run out of oil,’ he says, “The correct response is, ‘Never!'” He says that there might come a point when we are paying $100 a gallon, that’s gallon, not barrel, but, he says, changing economics, technological advances and efforts such as recycling and substitution make the world’s mineral resources virtually infinite.

Is that a reasonable assumption? Recycling isn’t going to save us, it costs energy, and unless we have some kind of renewable power to drive the recycling “machines” that is almost always going to fall short of 100% efficiency and leave us with a net loss.

However, he does have a point about untapped oil deposits. Forty years ago, the technology did not exist to extract oil from tar sands, for instance, and organic matter or coal is now worth manufacturing. Of course, processing costs will rise, but that’s the price we will pay to drive our vehicles and power our industries.

“Mineral resources are vitally important to our industrial and service economy,” Cheney says, but speaking at the Geological Society of America annual meeting this weekend in collaboration with Andrew Buddington of Spokane Community College he will point out that gas prices today, adjusted for inflation, are about what they were in the early 20th century. Today’s prices seem inordinately high, he said, because crude oil was at an extremely low price, $10 a barrel, just eight years ago and now fetches around $58 a barrel and has been as high as $78.

As major economies, such as those in China and India, develop and are on the verge of greater demand for mineral resources because of increasing road use, he said, it is an opportune time for universities to train a new crop of resource geologists who can understand the challenges and help find solutions. He believes that popular but misguided notions about mineral resources might be hampering students from entering the field.

So that’s alright then. We can carry on pumping out exhaust gases to the contentment of our cars and concreting the countryside as long as we teach our students how to reach the unreachable.

American ice

A press release arrived yesterday from the American Chemical Society that said, “Japanese scientists have reported the discovery of an additive that can speed up the formation of methane hydrates, literally ice that burns.”

Literally ice that burns?

I know what they mean, but it’s not literally ice that burns is it? That would be a mythical substance composed of flammable frozen water, surely?

Anyway, these not-literally-ice-that-burns materials have some interesting properties not least because they could act as a potential new energy resource to boulster apparently dwindling fossil fuel supplies. Methane hydrates are found in vast natural deposits beneath the seafloor in coastal areas of the United States and certain other parts of the world. Estimates suggest that known hydrate deposits contain enough natural gas to meet demand for centuries. Of course, the carbon-containing component of methane hydrates is one of the most potent greenhouse gases we know, and climatologists have serious concerns about the release of vast quantities into the atmosphere as frozen stores begin to melt as global temperatures rise.

So, an additive to speed up their formation might be useful in helping us sequester enormous volumes of greenhouse gases.

But, how does this sit with the idea of using the stored methane in natural reserves as an alternative to other natural gas sources? Burning this aqueous methane will release its carbon content just as readily as burning methane without the aq. We’ll be able to propel our vehicles and heating our homes, of course, but we’ll be adding just as much carbon to the atmosphere as we would otherwise do with fossil fuel sources. With the added problem of having to build energy-intensive manufacturing plants to synthesise the “additive” to help is produce methane hydrates for burial at sea.

It just doesn’t add up. Faced with a putatively worsening greenhouse trend and dwindling fuel supplies, shouldn’t we be looking for sustainable energy resources that neither add to our carbon emissions nor require us to find complex routes to lock them down?

I guess the methane hydrate factory could be powered by wind turbines and solar cells, but that’s not the point is it?

Darwin online

charles-darwin

The world of online publishing continues to evolve and today marks a new landmark with the release on to the web of the complete works of one of history’s greatest scientists, Charles Darwin.

Every book, journal entry, and letter amounting to some 50,000 searchable pages and around 40,000 images from his original publications are now available to everyone with web access for free within a few mouseclicks.

Charles Darwin (1809-1882) revolutionized our understanding of life on earth and Darwin Online will revolutinize many people’s understanding of Darwin as well as bringing his findings to a much wider audience. The site represents the largest collection of his work ever assembled and allows users to search the complete text as well as view images of the original manuscripts in parallel. There are many documents that all but the keenest Darwin scholar will never have seen, including many previously unpublished transcriptions from his handwritten papers including the field notes from his seminal trip to the Galapagos islands.

Moss side analysis

Rhynchostegium riparioidesA bag of moss lying in an irrigation ditch in North East Italy does not conjure up a picturesque image nor the cutting edge of analytical science but nevertheless the special characteristics of the moss Rhynchostegium riparioides make it the ideal environmental monitor according to researchers at the University of Trieste and their colleagues at ARPAV.

Waterways are often intermittently polluted by metals from industrial outflows and other sources. Such waterways are often used in rural parts for agricultural irrigation. The phenomenon is frequent in the Veneto Region of Northeast Italy, according to biologists M. Cesa, F. Fumagalli, and Pier Nimis at Trieste and Alessandro Bizzotto and C. Ferraro of the Vicenza ARPAV Italy.

You can read the complete story in my SpectroscopyNOW news round-up this week.