David Bradley – Page 313

CiteXplore

What is it with software and websites and scientific tools that they all have to have these mixed case acronyms, abbreviations, and odd spelling?

Anyway, today sees the launch of another odd spelling from the European Molecular Biology Laboratory’s European Bioinformatics Institute – CiteXplore. This is a freely accessible literature resource service that melds data from the peer-reviewed scientific literature with key biological data such as DNA and protein sequences, functions and structures of molecules and microarray data.

The tool essentially searches Medline abstracts, patent abstracts, and Chinese Biological Abstracts and links to publisher websites. But, the crucial difference between this and any other literature search tool is that it cross-links to EMBL-EBI’s biological databases.

‘When you are reading an abstract describing a specific gene or protein, typically you want more information on it, for example its sequence or its function, as well as easy access to the full paper,’ says Peter Stoehr, who coordinates CiteXplore. Built-in text-mining tools allow “touch of a button” or more aptly, “click-of-a-(lab)-mouse” access to the specific record for a molecule of interest.

This is just the kind of system that chemists Peter Murray-Rust and Henry Rzepa have been aiming for the chemical sciences. Once again, the bio guys seem to have stolen a march on chemistry.

Santa Claus Address

Santa Claus Address Now that Thanksgiving, Black Friday, the Holiday Weekend, and Cyber Monday are over for another year, it’s time to start writing your letter to Santa Claus…

Of course, to make sure it reaches him, you’ll want to know his proper address, not just one of those scammy spammy addresses that say “North Pole”. As you probably know there are actually two North Poles and they never sit still. There’s the geographical North Pole, which is the point at the top of the world through which the earth’s axis passes, then there is the magnetic North Pole, which is quite variable and at several times in history has actually been at the South Pole.

Thankfully, NASA has done some satellite tracking and a little remote imaging to try and trace Santa Claus’ address and have come up with the goods. Check out their images and learn how to pronounce Santa’s zip code here. But, for our recent anonymous visitor who cannot click a link I’ll spell it out:

Mr S Claus

North Pole

H0H OH 0

The Internet is a series of tubes…

…no, sorry…wrong story. Tubes, carbon nanotubes are the new material of choice for a wide range of experimental technological applications. Now, US researchers hope that they will be used to make implantable biomedical devices that could act as artificial nerve cells, control severe pain, or maybe one day move paralyzed muscles.

Nicholas Kotov of the University of Michigan and colleagues at Oklahoma State University and the University of Texas Medical Branch have used carbon nanotubes to connect an integrated electronic circuit to living nerve cells. The new technology offers the possibility of building cyborg type interfaces between biology and electronics only dreamed of in science fiction stories until now.

Read on…

Ayurvedic analysis

I, like many with a chemistry training, have on occasion dismissed the more mystical-seeming strands of non-western medicine. The origins of homeopathy, for instance, relied on literal Bible bashing of glass phials to ensure the infinitely dilute remedies would work. Which of course western medicine says is ludicrous. Herbal medicine on the other hand needed the industrial age to extract its active ingredients and bring us the likes of aspirin from the sap of the cricket bat willow and asthma inhalers from ephedra plants.

One area of non-western science that many western medics and scientists say is nothing more than pseudoscientific claptrap is Ayurvedic medicine. This is a holistic healing system that emerged in ancient India. It talks of the mind-body balance and the kind of “energy” and humours that modern science claims not to exist, yet there may be a grain of truth in some aspects of this system for which modern science has not given due credit.

Consider the western approach to the common problem of anaemia in pregnancy. The treatment of choice, according to western medicine, is simply to ingest iron sulfate. In this form, iron can be readily absorbed by the body, assimilated into new red blood cells, and anaemia solved.

Unfortunately, many pregnant women cannot tolerate iron sulfate and regurgitate it so they don’t get to ingest the iron and the anaemia remains.

Now consider the Ayurvedic approach. The sage assesses the pregnant woman, finds she has an imbalance in her energies, humours, whatever, and prepares a herbal infusion aimed at shifting the balance towards a more healthy state. It works, there’s no vomiting, the morning sickness subsides, and that anaemic look is replaced by the flush of pregnancy once more.

So, what is going on? How can a bunch of herbs cure anaemia so readily?

AP de Silva of the Queen’s University Belfast, whom I recently interviewed for Reactive Reports, was once equally as sceptical of the possibilities of Ayurvedic medicin. He told me that, as a fledgling chemist, he challenged an Ayurvedic practitioner to answer the question of validity. The practitioner, however, was entirely confident of his position and turned the tables on AP suggesting that he take away the herbal infusion and analyse it in his lab, which he did.

The result? A standard elemental analysis revealed the infusion to contain a stabilised concentration of iron(II) ions. Natural chelating agents in one of the herbs provide a suitable chemical environment to maintain iron in the II state, as opposed to its more common (III) state. This allows it to be ingested, absorbed, and to cure the anaemia without the sickness of raw iron sulfate.

This is, of course, circumstantial evidence, and does not provide the support of full double-blind placebo-controlled clinical trials. However, the chemical analysis provides one possible rational explanation of the efficacy of this remedy beyond a placebo effect.

Perhaps it is time modern science took a closer look at the multitude of alternative remedies that sit under the Ayurvedic umbrella. Ancient herbal remedies evolved from folk knowledge and a huge proportion of modern drugs are based on such remedies, 40% of them, or thereabouts. Instead of instantly assuming isolation of an active ingredient is the optimal approach, perhaps science should consider the holistic approach to drug discovery with a view to coping with the side effects and improving efficacy overall.

Science journalist in the news

UPDATE: October 2023 I heard from UCL chemist Andrea Sella, who had attended a Poliakoff lecture, that Martyn still gives me a shoutout when discussing SCFs, which is great to hear!

It’s not often that I’m on the receiving end of journalism, but today Jenny Gristock gave me a taste of celebrity in a Guardian media article about the role played by science journalism in science.

I’d tipped her off about one of the biggest success stories, from the perspective of academic research becoming an industrial commercial reality, that had emerged from the pages of New Scientist in recent years. This is how she put it:

“In 1994 freelance science journalist, David Bradley, wrote an article about the work of the Nottingham University chemist, Professor Martyn Poliakoff (Yes, brother of…). Poliakoff was conducting experiments with supercritical carbon dioxide, a highly compressed gas that can dissolve all manner of chemicals. “It acts like a solvent, but has none of the environmental problems of traditional ones,” says Poliakoff.

Bradley’s article captured Poliakoff’s vision of his research. After it appeared in New Scientist, Poliakoff’s world changed completely. “I was happily working away as an academic, and then the article was published,” says Poliakoff. “Thomas Swan, an industrialist, read it and phoned me. He said we ought to collaborate.”

The result, says Poliakoff, is one of New Scientist’s greatest success stories. In 2002, Poliakoff and Thomas Swan & Co built the world’s first full-scale, multi-reaction supercritical carbon dioxide plant.”

You can read Gristock’s full article here, although you’ll need to register with the Grauniad site to do so. Alternatively, Gristock has posted the full text on her blog.

I’m just waiting for the paparazzi to arrive, and the full profile in Hello magazine, and maybe even a chance to jump up and down on Oprah’s sofa!

Synthesizing a new breed of chemist

From the age of 13, Mark Leach has had a subscription to the popular-science magazine Scientific American, and more recently the journal Nature. His scientific interests include cosmology, high energy and nuclear physics, materials science (particularly carbon nanotubes), geophysics, molecular biology, evolution, information technology, the brain, defense technology, and scientific ethics. Professionally, Mark is a chemist interested in ‘chemistry, the-whole-thing’. I interviewed for my Reactive Profile column this month, find out about the origins of meta-synthesis.com, Dr Leach’s aspirations for his various sites, and how he believes chemistry education could be radically improved through a re-think of some fundamental principles.

The latest Reactive Profile is in Issue 60 of our chemistry magazine.

Geekish girls

The Cnet newsite has a rather politically incorrect item this week listing the Top Ten girl geeks. I’m not entirely sure how they’re defining geek but among those listed are Marie Curie, Ada Byron (Lovelace), Rosalind Franklin (after whom my wife wanted to name our daughter), and…Paris Hilton (don’t ask).

So, where’s crystallography pioneer Dorothy Crowfoot Hodgkin? And, what about Judith Howard, first female Professor of Chemistry in the UK? Then there’s Helen Sharman first British woman in space (also a chemist), finally what about Margaret Thatcher (she trained as a chemist too and then spent her time in office effectively dismantling UK science, can’t get more geekish than that!

Alexander Litvinenko Dead

Former Russian spy, defector, and activist-writer Alexander Litvinenko has died in a London hospital of suspected poisoning with radioactive thallium. [Subsequently, found to have been polonium]

Litvinenko’s friend Alexander Goldfarb read a statement prepared by the former spy on his deathbed just two days before he passed away. In that statement, Litvinenko lays the blame for his poisoning firmly at the feet of Russian President Vladimir Putin and says: “You may succeed in silencing me, but that silence comes at a price,” according to news reports, “You have shown yourself to be as barbaric and ruthless as your most hostile critics claim.

The Russian government has declared the claims as preposterous and suggests that infighting among Russians living in London is more likely to have led to Litvinenko’s death.

Preliminary post-mortem results suggest that a radioactive material – possibly a large dose of radioactive polonium-210 – may have been associated with his death. In our earlier report, it was suggested that thallium, then radioactive thallium, may have been implicated. Whether or not Litvinenko ingested this material was exposed to it in the environment is not yet known raising serious public safety concerns.

A UK press conference held this afternoon provided more information.

Science Experiments More Test-tube than Youtube

Science experiments video Ever wanted to observe the dissection of fruitfly ovaries but were too squeamish? What about monitoring actin disassembly with time-lapse microscopy, not sure how it’s done? Maybe you have been wondering how to freeze human embryonic stem cells but were afraid to ask…

Don’t worry the online Journal of Visualized Experiments has come to the rescue of cash-strapped demonstrators with little spare time who can now call on a video of a growing number of biological experiments that can show how a particular procedure should best be carried out.

The journal’s site, MyJove.com, has a rather different modus operandi to Youtube, but nevertheless provides almost instant access to a searchable database of scientific “how-to” videos as well as allowing research assistants and others to submit their own (No Brainiacs please!). In truth, that’s where the similarity with Youtube ends, JOVE has a fully fledged editorial board and presumably reviewers to carry out the peer review process required of almost every academic journal, online or not.

The site’s raison d’etre is spelled out in its About page – “As every practicing biology researcher knows, it takes days, weeks or sometimes months and years to learn and apply new experimental techniques. It is especially difficult to reproduce newly published studies describing the most advanced state-of-the-art techniques. Thus, a major part of the PhD and post-doctoral training in life sciences is devoted to learning laboratory techniques and procedures.”

“Video-based visualization of biological techniques and procedures provide an effective solution to the problem described.”

And, for those of us not training in a biological research lab, we get to see what these guys spend their time on. Embed code, allows other sites to more effectively link to specific videos.

Be warned, though some of these videos are long and will buffer only slowly on a narrow bandwidth internet connection.

As part of the Learn with Sciencebase project, I’ve added a Top Ten Science Videos page to the site.

Genetic Variation on a Theme

What does it mean to be human? We thought that the Human Genome Project had set the limites on the genetic make-up of our species. But, according to Steve Connor, writing in the Independent today, much of the genetic variation between individuals can best be explained by the presence of multiple copies of certain key genes rather than variations in the genome sequence.

The research suggests that whereas previously we thought all people shared 99.9% of their DNA, it could be that two individuals can differ by ten times that. The research has important implications for our understanding of inherited traits and genetic disease.

The findings appear in three simultaneous papers in three leading science journals, including Nature and were reported by teams from thirteen different research centres in the UK and the US.