Author: David Bradley

Cultural evolution in the lab

Adding a little culture to the chemical laboratory could help chemists find structures much faster than before. According to UK chemists, Samantha Chong and Maryjane Tremayne, of the University of Birmingham, combining the principles of social and biological evolution with a little fashion sense to make a new Cultural Differential Evolution algorithm allowed them to half the time it took to solve the structure of a molecule from its powder diffraction data.

Their research could have widespread application in solving a variety of global optimization problems in chemistry, nanoscience and bioinformatics.

The use of evolutionary algorithms is a relatively new approach to solving problems based on mimicking the principles of “natural selection” and “survival of the fittest”. The Birmingham team reasoned that the much more rapid social evolution experienced by humans, essentially fashion sense, could be merged into an evolutionary algorithm to help reduce the number of likely candidates for a particular structure much more quickly. They have now demonstrated how this works on two compounds, a previously unsolved structure and baicalein, the active ingredient in the Asian herbal medicine “Sho-saiko-to”.

Read on…

Not fade away

sn14a N st petersNo one of whatever religious persuasion who visits the Sistine Chapel in Rome can fail to be impressed by the results of a 20-year restoration project that has brought Michelangelo’s frescoes back to their original level of artistry. Most notable is the brilliance of the sky blue that almost illuminates the Last Judgement on the altar wall of the chapel. But, recent NMR analysis of the ultramarine pigment used to produce this stunning blue suggests its tendency to fade could see the Last Judgement and other works ultimately perish.

Alexej Jerschow of New York University, Eleonora Del Federico of the Pratt Institute, and their colleagues have now discovered why the blue pigment fades. Their findings could provide art conservationists with vital information on how to protect works of art.

You can read the full story in the latest news round up from DB in SpectroscopyNOW.com

Parkinson symptoms

The common perception of Parkinson’s disease is of a disorder that leads to problems with movement, tremors, involuntary spasms, and a shuffling gait. However, functional MRI has now confirmed that the disease can also cause widespread abnormalities in the sense of touch and vision for sufferers. An international team from the US and China presented their findings at the Society for Neuroscience meeting in Atlanta on October 17.

Research into Parkinson’s disease has previously focused mainly on the brain’s motor and premotor cortex, sidestepping the somatosensory and the visual cortex because the most prominent symptoms are associated with movement and not the senses. However, neurologist Krish Sathian of Emory University and colleagues discovered through tests of tactile ability, that PD patients also have sensory problems with touch. The researchers recently designed a study using fMRI to investigate this earlier finding and to ascertain whether or not changes in the brain underly these sensory abnormalities.

Read on…

It’s not easy being green

News just in from Imperial College London suggests that climate change in Europe is worsening the impact of a deadly disease which is wiping out vast numbers of amphibians. IC’s Matthew Fisher and colleagues working with colleagues in Madrid have found a correlation between significant warming of the local climate in Spain between 1976 and 2002 and the emergence of the fungal disease Batrachochytrium dendrobatidis (BD) in the area and its effects on midwife toads.

The fungus infects amphibians’ skin and is believed to cause disease by interfering with the skin’s ability to absorb water. As a result of BD, the common midwife toad is now virtually extinct in the area of Spain studied by the researchers, the Penalara Natural Park, where it once thrived.

The researchers believe various factors are at play in increasing the impact of BD on toad mortality. Amphibians are cold-blooded, so their body temperature is linked to the surrounding environment, for instance. meaning that changes in external temperature may affect their bodies’ ability to ward off disease. BD is also thought to be better suited to a warmer climate.

More details can be found in today’s issue of the journal Proceedings of the Royal Society B.

Chemical reactions

The current update of Reactive Reports is now online featuring:

An interview with molecular logician AP de Silva, the Nobel Prize in Chemistry, how a biologically compatible gel could revolutionize surgery and save lives in the emergency room, and a dietary response to Alzheimer’s disease that puts red wine, spicy food and a mediterranean salad squarely on the preventative menu.

Check our latest reactions here.

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.