David Bradley – Page 293

Toxic scaremongering

The Independent on Sunday today reports that a UK researcher is claiming that fizzy drinks which contain sodium benzoate preservative (E211) could be harmful to mitochondrial DNA in our cells. Apparently, Sheffield University molecular biologist Peter Piper tested the compound on yeast cells (one of the organisms the preservative is added to drinks to eliminate in the first place). More to the point, the levels at which he assaulted the yeast was the equivalent of a person drinking ten gallons of soda in one go.

This new scare story follows closely on the tail of the benzene in soda debacle Sciencebase reported last year and the almost historical tale of benzene contamination of mineral water scare of the early 1990s. Intriguingly, The Independent article does not seem to mention the words “dose” or “concentration” once.

Perhaps there are individuals who drink large volumes of soda every day without realising there are other harmful effects of such drinks, like the concentrated sugar intake, or the relatively high levels of caffeine stimulant. But, even high-speed Digger users only claim to drink a couple of litres of Mountain Dew each day, not the ten gallons equivalent of the experiments. Perhaps experiments will push the safety threshold well below 10 gallons (please excuse the mixed units), maybe even to 1 gallon, but that’s still an awful lot of soda for anyone, even for a hardened Digger, to be drinking every day, surely?

There are many reasons to not drink soda, so instead choose tap water, choose life…

No, wait a minute, fish do their four essential biological “F’s” in water – Feeding, Fighting, Fleeing…Fu Mating. Best stick to beer.

Credit where credit is due

A fellow blogger, who regularly comments on this site, once asked me about the re-use of images on his blog. He’d published a logo or something similar from an organisation that does not grant re-use permission for such materials. So I advised him to remove it from his blog before they sent in the suits.

In the world of journalism, as opposed to the blogosphere, minor copyright infringement, such as the mistaken re-use of an image accompanying an article often results in a standard copyright infringement notice, removal of the offending image, and a notice of apology. Obviously, in print it is slightly different, but yesterday’s news is today’s fish and chips wrapper anyway (at least it was until they banned the use of old newspapers in chip shops).

Blogs fall into a slightly different camp. Not quite amateur, if they are getting big numbers of visitors and running ads, for instance, but certainly not in the same journalistic league as the NYT or the BBC news sites.

Anyway, a quick legal refresher: Unless it states somewhere that you can use an image without limitations, you must assume that the publisher and/or the authors reserve all rights, this means you usually cannot re-publish an image without express permission of the copyright holder, regardless of the benefits wider dissemination of the image and its associated context might bring.

The exception is a press release, unless it says you must seek permission. Usually the whole of a press release is intended for free publication with or without editorial attention at the discretion of the editor. Of course, press releases do not always include images, so an intrepid journalist or blogger must look elsewhere for illustrations.

There are exceptions to the copyright rules that might be used in this regard. Images produced by the US government or its employees are copyright free. So anything from NASA, for instance. Other public domain images, and images with a creative commons or other openaccess or copyleft statement are essentially free for use with credit and conditions as outlined in their respective terms and licensing document.

To search flickr for creative commons images you can use this link – http://www.flickr.com/search/?l=commderiv&w=all&q=photo&m=text – substitute the word “photo” in the link for an appropriate keyword, but be sure to check the CC license of the flickr’er in question.

Indeed, don’t take my word for any of this. You need to check each specific image and if in doubt, request permission for re-use, whether you are a blogger, journalist or publisher. There are other exceptions, but usually those who create images or other intellectual property want, at the very least, credit for their efforts. That, of course, includes images from other publications that have added value to an author’s image.

The current interpretation of copyright law is aimed at protecting those who produce creative works, but this often seems to be to the detriment of the individual when publishers have adopted the copyright. Publishers, however, it can be argued, do add significant value to the material they publish. I have seen it from the inside. They do so, not only from the point of view of validating the information to be published, but also to the point of rendering the words and pictures in a form that is intelligible to the target readership. Whether or not the author or reader should pay for that added value is a different matter. Publishing is currently in a state of flux in that regard with new experimental business models in place that seek to invert the traditional approach of reader pays.

Regardless, with the copyright law as it currently stands: assume you cannot, unless you know you can, and if you are unsure, seek permission, add a credit, and carry on blogging.

Youtube for science

Athenaweb moving picture science On June 27, AthenaWeb, the science and science communication portal funded by the European Commission, will morph into an online TV channel for European science.

The development of AthenaWeb V2 is headed by Lab To Media’s Kathleen Van Damme who says that this is “Europe’s big chance to take a leading position in science film streaming, reconciling scientific programmes on TV with content accessible at any time.” It all sounds very interesting, but will it cut the PUS* and become a major PEST** site?

Van Damme is not revealing too much at this stage, you will have to wait till launch day to find out what the new vortal will be offering. But, in a very unvegetarian press release it is stated that the revedelopment “will beef up its services to current communities and extend its scope to provide direct on-line placement of ‘non-broadcast’ videos made by researchers, teachers and professors.”

Inevitably, the new site will have a new look and feel, you would be rather disappointed if they had not updated and refreshed the site. It will also have a special domain for broadcasters, podcasts, blog spots, and high-quality full-screen viewing. Critically, and perhaps allowing the site to stake a claim on the Web 2.0 ethic, it will also present a greater emphasis on community shaping and hopes to become the leading site for sharing scientific imagery, films, and news. Most importantly of all though, AthenaWeb V2, will, the press release claims remain free of charge.

On a much smaller scale Sciencebase readers are invited to join our science TV channel on Searchles, which currently has a mere handful of videos, including a tribute to DNA pioneer Rosalind Franklyn, mentioned in my philosophy of science essay and how to demonstrate Newton’s laws of motion with Lego models. Those probably amount to about 30 minutes of footage, compared with AthenaWeb’s more than 750 science videos, stacking up to 100 hours.

*PUS – public understanding of science
**PEST – public engagement with science and technology

Balancing your gut bugs

Mouse Could those so-called “bio” yogurts and milk-type drinks with Scandinavian sounding names actually do you any good? Possibly.

According to a study published in the journal Molecular Systems Biology this week, microbial flora in the gut can profoundly affect how you absorb nutritients from your food and your overall health. Jeremy Nicholson and colleagues at Imperial College London suggest that keeping a balanced gut flora may prove important to prevent some human metabolic diseases. Those active yogurts and one-day milk substitutes containing live microbes could play a role in helping you maintain the balance.

Our guts are an internal ecosystem all their own. Quite bizarrely, the microbial community living in our intestines has 100 times as many genes as the whole of the human genome. It is almost as if those living inside you outrank you yourself. However, we rely on these microbes for the normal processes of digestion and waste disposal just as much as the microbes themselves need the lining of our intestine as their stamping ground. We, and all other mammals, are not so much individuals as “superorganisms”, a collective, a symbiotic biological system.

Nicholson and his team used metabolic profiling techniques to monitor changes in bile acid composition and lipid (fatty molecule) metabolism in mice whose gut flora had been replaced by human bacterial flora. Perhaps not surprisingly, the mice showed alteration in the composition of their bile acids and circulating lipoprotein levels, and displayed symptoms such as lipid accumulation in the liver that would eventually lead to disease. Closer inspection of the mouse gut, revealed that the human gut microbes could not form a strong and stable ecosystem.

Nicholson’s findings demonstrate that gut microbes control the absorption and storage of nutrients from our food and help us harvest its energy. They also show that the wrong type of microbes can lead to disease by affecting the chemical and metabolic balance of the gut and liver.

So, should you drink those liquid bio yogurts? If you can pronounce them easily then there is probably no harm in asking for them at your healthfood store, but the message is clear: steer well away from mice.

Chemists Pull Rank

The RSC recently published a league table showing the top-ranking, living chemists. The league is based on the so-called h-index. This parameter was devised by Jorge Hirsch in 2005 in order to measure the impact of an individual chemist’s research. Put simply, the h-index is equal to the highest number of papers that chemist has published which have gained at least that number of citations from other authors. According to the Chemistry World Blog today, thirty more chemists have been added to the league. Hirsch argued that the h-index avoids bias by combining total published papers with a citation parameter it does not reward the prolific but mediocre. The original league was created by Henry Schaefer and colleagues manually by trawling ISI citation data, but I am sure an intrepid chemical web student could create a suitable script to do the job automatically.

Windows cause pollution

Windows Cause
Pollution This is not another terrible advertisement for an alternative computer operating system to the eponymous installation mentioned in the title, but an environmental analysis that reveals how dirty windows are a major contributor to urban pollution.

A Scent for
Explosives A new type of biosensor based on yeast, jellyfish
proteins, and a rat’s sense of smell could sniff out explosives, landmines, and agents, such as sarin gas, according to researchers at Temple University.

The Long and the
Short of It A new composite material that acts as a catalyst to
speed up chemical reactions has been developed to create arrays of the
world’s longest carbon nanotubes.

Meeting of Molecular Movie Stars A clandestine meeting between molecules, a chemical handshake, and an exchange of energy have all been recorded on camera by scientists in the UK and Germany.

Read the full stories in Reactive Reports, the chemistry webzine from David Bradley Science Writer and ACD/Labs. Next month, we have a profile of Berkeley nuclear chemist and Sciencebase regular commentator Mitch Garcia.

Join the Mile High Club, Cure Jet Lag

Viagra could be the cure mile-high clubbers have been waiting for. Apparently, not only can the drug help men keep up appearances at any altitude, new research could lead to its extension to other areas of medicine, such as the treatment of jet lag.

Apparently, researchers in Brazil simulated jet lag in hamsters by exposing them to light out of phase with their natural body clock, giving the little beasts the feeling of having flown from Paris to New York on the red-eye day after day. The result was that the hamsters’ circadian cycle got so skewed that they would mount their wheels and run 14 hours before they should each night.

However, Diego Golombek and colleagues from the Quilmes National University in Buenos Aires, figured that a quick shot of Viagra (sildenafil citrate, sildenafil without its counter ion is shown) might work wonders for the hardy little creatures. In fact a 70 mg dose of the ED drug, reduced the jet lag recover period for the animals to just over a week, compared with the two weeks it took the Viagra-free hamsters to recover. What a relief.

Circadian clocks regulate the timing of biological functions in almost all higher organisms, say Cornell University and Dartmouth College researchers writing independently in the journal Science, this week. Anyone who has flown through several time zones knows the jet lag that can result when this timing is disrupted, they say.

Now, the Cornell and Dartmouth scientists believe they can explain the biological mechanism behind how circadian clocks sense light through a process that transfers energy from light to chemical reactions in cells. Whether or not this research tells us if you should keep your eyes closed during or after entry into the mile-high club or how to disguise why you are not suffering jet lag after a long trip is a different matter.

InChI=1/C22H30N6O4S/c1-5-7-17-19-20(27(4)25-17)22(29)24-21(23-19)16-14-15(8-9-18(16)32-6-2)33(30,31)28-12-10-26(3)11-13-28/h8-9,14H,5-7,10-13H2,1-4H3,(H,23,24,29)/f/h23H

Nanotechnology Used to Enter Plant Cells

US scientists are using nanotechnology to penetrate plant cell walls and deliver a gene and a chemical triggers with great precision. The work could lead to a powerful new tool for targeted delivery into plant cells.

The research is highlighted in the May issue of Nature Nanotechnology. Kan Wang of Iowa State University and his colleagues point out that introducing a gene into a plant cell is possible but chemical activation usuall involves an imprecise and separate process that may be toxic to the plant.

“With the mesoporous nanoparticles, we can deliver two biogenic species at the same time,” Wang said. “We can bring in a gene and induce it in a controlled manner at the same time and at the same location. That’s never been done before.”

The controlled release will improve the ability to study gene function in plants. And in the future, scientists could use the new technology to deliver imaging agents or chemicals inside cell walls. This would provide plant biologists with a window into intracellular events.

Lin’s porous, silica nanosphere system has arrays of independent porous channels, which form a honeycomb-like structure that can be filled with chemicals. “One gram of this kind of material can have a total surface area of a football field, making it possible to carry a large payload,” Trewyn said.

Organic Lectures Reach Drexel Island

Jean-Claude Bradley at Drexel University has taken his second life persona to his professional bosom and is now providing organic chemistry students not only with obelisks on the dragon-shaped island of Drexel (Drexopia, perhaps?), but they can now see organic chemistry lectures there too. It is an incredibly innovative use of SL, but I wonder whether students are going to feel like they are being monitored not only in the real world of university lecture rooms and study areas, but in the escapist virtual spaces of SL too. Scary thought.

Heavy metal plants in the spectral news

Over on SpectroscopNOW.com David Bradley reports on the usual eclectic mix of science news with a hint of the spectral. This week:

Heavy metal plants – Herbal medicine is a global phenomenon, a multibillion dollar industry, and its raw materials phytochemicals are widely used as the precursors for regulated pharmaceutical products. One problematic area on both sides is in product purity, with contamination by toxic heavy metals one of the most common complaints. Now, researchers in Argentina have developed a way to “digest” herbal medicines to improve the detection limits of heavy metal contaminants, such as lead and cadmium, for quality control of these products.

Tubeless and hyphenated – Slightly more esoteric, but equally important for analytical science is the development of a new software algorithm for getting the most out nuclear magnetic resonance (NMR) experiments. According the Gary Martin of Schering-Plough, the software developed with ACD/Labs collaboration, means that even if a sample of product has been lost, the spectroscopist can retrieve latent information from the initial NMR runs without having to find a new sample and spend a week record experimental spectra. Martin confesses that this new approach to sophisticated NMR is not without its critics. He gave an ENC invited lecture on the subject of this new technique, known as Unsymmetrical Indirect Covariance, and told me that his talk raised a few eyebrows, to say the least.

Super plat cats – A new form of platinum, 24-facet nanocrystals, have been produced by an international collaboration. The novel tetrahexahedral particles are four times as effective a catalyst as the industrially important commercial platinum available for oxidising formic acid and ethanol. The work could lead to a more efficient process of catalytic oxidation for the production of hydrogen for fuel cells. “If we are going to have a hydrogen economy, we will need better catalysts,” says Zhong Lin Wang of the Georgia Institute of Technology, “This new shape for platinum catalyst nanoparticles greatly improves their activity.” Discussion continues elsewhere on Sciencebase regarding the putative folly of a hydrogen economy. Hopefully, if such an approach to alternative energy does not come to pass, Wang will find numerous other industrial applications for these super plat cats.

Consolidated database – US researchers have exploited a new technique to identify almost all the chemical changes nature makes by adding phosphate groups to human proteins. They have now hooked up this data to the publicly accessible PhosphoMotif Finder system in an effort to stimulate further biomedical research into the vital process of phosphorylation.