March 2008 – Page 2 – David Bradley

French Fries, Wild Mushrooms and Ouzo

Alchemist ChemWeb A mixed bag this week in my Alchemist column on ChemWeb.com this week. First up, news that US$1 million is to be ploughed into biofuels research that could circumvent some of the serious environmental concerns associated with this renewable energy source.

In the world of pharmaceuticals we discover that there might be yet another string to the bow of aspirin-like drugs, this time in the fight against breast cancer. There’s good chemical news for those hoping to save Gulf Coast Wetlands from the rampages of the coypu with the discovery of a chemical lure, The Alchemist also hears of a novel system of surfactants and gelating agents that can form separate compartmentalized structures resembling the organelles in a living cell. You might care to have a drink with The Alchemist this week in celebration of a clearer understanding of why some drinks, such as ouzo, form cloudy emulsions with water. There’s more on the ouzo effect in my SpectroscopyNOW story on the subject where an independent team working in parallel have used NMR to take a look at these rare and peculiar emulsions.

Finally, a little kitchen chemistry could give your French fries a little je ne c’est quoi.

Edible wild mushrooms

Speaking of haute cuisine…also on this week’s SpectroscopyNOW, I report on how Portuguese scientists have identified a whole range of smelly molecules found in wild edible mushrooms. It’s pioneering work that will allow the food industry to ensure it is not being fobbed off with cheap mushrooms when a more expensive variety is what they ordered. The results could also be used by biotechnologists to engineer specific flavours into easily cultivatable varieties of mushroom. Two points arose as I was writing the item: The first is that overall mushrooms smell of nothing more complex than 1-octen-3-ol, which the researchers describe helpfully as having a mushroom-like odour. Secondly, the notion of cultivating wild things is at odds with the whole ethos of wild mushrooms, surely?

Either way, it’s hopefully an interesting read. Now, pass the ketchup for my mushrooms and fries, would ya?

Shedding Light on Optical Storage

HVD Roadmap (Sourced from HVD Forum) A review of the state-of-the-art in optical storage technology from Sony scientists caught my eye while I was data mining journal ToC feeds recently. The demise of the Toshiba HD DVD format and the emergence of Sony’s Blu-Ray as the winner has been this decade’s equivalent of the VHS-Betamax face-off of the 1980s.

While many commentators point out that other technologies, such as solid state storage are waiting in the wings white-out optical, the Sony team sees growth lying ahead and the development of a CD-sized holographic disk that can store several terabytes of data available to the consumer realm.

Writing in a forthcoming issue of the International Journal of Product Development (2008, 5, 447-454), Toshiharu Okanishi, Toru Takeda, and Mamoru Nishio of the Technology Strategy and Development Department, at Sony Corporation, in Tokyo, Japan, point out that the “pit-by-pit” optical recording and reading technology used initially in the CD, then the DVD and more recently with sharper blue-purple lasers will see continued growth in one form or another. However, there will be no significant jumps in the near future, they say. There will be some significant improvement with the emergence of so-called near-field recording and super-resolution near-field recording, which will push the boundaries of what is possible with pit-by-pit to data densities.

Data storage technology, whether IBM’s magnetic disks of the 1970s, which are still with us, or the 1980s optical technology pioneered by Philips, is an enormous market. Magnetic hard drives – the Winchester technology – have progressed from disks of a few megabytes to the multi-platter terabyte beasts of today, total annual market is estimated at US$25 billion. In contrast, optical represents a market of $10b, but with rewritable disks adding some $3b each year to that total.

The Sony team offers a cosy view of the Winchester and Optical partnership:

Both technologies and both businesses have been developed back-to-back for the last 25 years and they will go hand-in-hand into the future, too.

While R&D in magnetic disks has continued apace, the technology remains locked pretty much in the 1970s. That said, storage and reliability of grown enormously and disks got much smaller since the early days. Nevertheless, new ways to make optical disks, to code and decode them and to ensure error correction have pushed the partner technology forward rapidly too. The development of high-frequency semiconductor lasers was key to the progression from CD (several hundred megabytes) to Blu-Ray disks that can store 25 gigabytes on a single layer. And almost as an aside there is Ultra Density Optical (UDO) storage from Plasmon, which uses highly precise tracking to increase the data density and allows 120 and 240 Gb capacities.

The Sony team points out that the technology that makes optical storage possible – the semiconductor lasers that read-write the disks, encoding and decoding systems, and the error correction systems have pretty much converged. With such a state of affairs there is little room for a significant jump in bit-by-bit optical storage in the near future. They also assert that there is room in the market for a mere ten percent increase in volume sales. Both factors coupled with falling revenues will reduce R&D spending still further. A paradigm shift could be the only change that could drive the industry forward – holographic disks could represent just such a shift.

It’s a paradigm shift whose time is long overdue, however. The concept of holographic recording was proposed way back in the 1970s and such systems have been used for decades for high-level purposes on incredibly expensive systems for companies and organisations that need to store vast amounts of data.

It took a significant development in chemistry, the invention of photo-polymer recording materials, before researchers could foresee a practical way to implement holographic recording. Okanishi and colleagues emphasise that holographic recording is a totally different approach compared to other optical storage systems, but requires a shift in the costly precision technology currently available to bring it to the mainstream consumer.

First off, there are two types of hologram possible – thin film and volume. With a volume hologram device used for large data storage purposes it is possible to store different pieces of data on the same area of the data medium, that is at different depths instead of a single layer (as in a CD) within a cone-shaped volume. Indeed, prototype systems promise storage of 60000 bits per pulse in a single 3D pit on a disk the same size as a CD. “This means the total capacity of a package is basically proportional to the three-dimensional volume of the medium,” the researchers explain. The team points out that to make such a system work well requires coherent optimisation of different parts of the technology in parallel.

The Holographic Versatile Disc (HVD) format utilises two lasers – a red and a green which are piped into a single pulse of light. The green laser picks up data from interference patterns in a holographic layer, while the red acts as a control or reference beam. The potential is for a system with a capacity of almost 3.9 terabytes (39000 gigabytes), which is nearly 6000 times as much data as can be stored on a CD, hundreds of times a DVD. Costs will initially make HVD inaccessible to most consumers with drives costing tens of thousands of dollars and the disks themselves at least a couple of hundred dollars. As with most technology, prices will fall as the market matures. “I am not sure which (consumer or professional) market HVD is currently aiming,” Okanishi told Sciencebase, “But it is a good challenge to gather industrial eyes to this prospective technology.”

The other benefits of HVD over DVD will be data transfer rates, with speeds some six times faster. Such speeds will be quite useful if one is carrying out file transfers with the entire US Library of Congress (storable on just 6 HVDs), the whole of Google Earth data (2 disks) or 12000 hours of mpeg files (that’s a year’s continual viewing).

There are various companies working on HVD, including Optware (site offline), InPhase Technologies (also offline) and its patented Tapestry Media, Hitachi Maxell Ltd. Other companies and more information can be found on the HVD Forum

Copyright and CAS Numbers

There’s discussion all over the chemical blogosphere at the moment about copyright and CAS numbers Chemspider’s Tony Williams first broached the subject in his blog and has followed up here. Cameron neylon has touched on the issue here as too have PeterMR and Kurt Wegner. If I’ve missed any links, please leave a reference to your post in the comments.

Anyway, here’s a thought…

Thumbnails (i.e. reduced size) versions of photos, images, and other visual creative works were recently the subject of a court case in the US, I believe. The judge suggested that displaying a thumbnail of an image was not a breach of copyright.

CAS registry numbers, InChIs, DOI’s and other such “creative works” might, in some sense, be considered an analog of an image thumbnail, and therefore may fall outside of a copyright claim similarly. Has anyone got the legal prowess to test such a case.

However, in writing this comment it occurred to me that there may be a more fundamental factor that would preclude CAS numbers being copyrighted. Aren’t they generated sequentially and automatically? If so, then perhaps they don’t fall under the description of “creative works” and therefore may not be copyrightable at all.

Lemon Battery

The lemon battery, it’s a perennial kids science favourite and perfect for a rainy Saturday morning (if it’s not raining why aren’t you kids outside playing instead of surfing the Pipes on the InterWebs, huh?) Anyway, with a single lemon, a few bits of wire, a copper penny, and a zinc-galvanized nail you can generate electricity (just over one volt).

However, one lemon is not enough to light an LED or power a pocket calculator, for that you’ll need not only more voltage but a higher current, which means more power – Power (Watts) equals voltage (in Volts) multiplied by current in Amps. Four lemons produce enough power to make an LED glow dimly. But, that low current is probably not going to be enough to power your iPod, which is a higher current device. For that you will need what is called a lithium-ion battery and iPods (other mp3 players are available) usually come with such a battery built in, so there’s no need to worry about carrying a dozen lemons and a bag of nails with you for portable music.

The following video explains the ins and outs, quite literally, of making a lemon battery, it’s very methodical and shows you the precise steps needed even if the narration is a bit stiff.

More science videos from the same labs available here

Linked In Questions

Linked In Questions Recently, I did a little blogging experiment on the business networking site LinkedIn (inspired by a post on Copyblogger). I was writing a feature article for Sciencebase about risk and the public perception of trust in science and technology. As an alternative route into the opinions of lots of members of the community, I posted an open question asking rhetorically why the public no longer trusts science and told potential respondents to let me know if they didn’t mind being quoted in the article.

The question was worded very loosely with the aim of eliciting the strongest responses possible. It’s not something I would usually do, I’d simply approach independent experts and contacts and ask their opinions directly in a more traditional journalistic way. But, like I say, this was an experiment.

Replies poured in quite quickly. One respondent thought I was crazy for imagining that the public does not trust science. “People do trust science and scientists," he said, "Anyone who doesn’t, please stand up and be allowed to fall immediately victim to polio, the Black Death, measles, chronic sinus infection, prostate cancer, and on on and on.” Others were in a similar vein.

They were not the kind of responses I was expecting. As if by listing the various things that many people take for granted somehow measures their trust of science. In fact, one can make a similar list of the kinds of science-related topics that are alluded to in the research about which I was writing in the original post – GMOs, nuclear, cloning, mobile phone radiation, stem cells, cancer risk, adverse drug reactions, superbugs, vaccines, environment, pollution, chemical weapons, biological agents, military technology.

These are all science subjects, in some sense, and are considered seriously problematic in the eyes of the public. Of course, the solutions to all those problems also lies with science, but that doesn’t detract from the fact that the public commonly distrusts.

The article itself looked at how the public respond to such issues, specifically cancer clusters, and delved into how trust in such matters is actually coloured by the particular organisation or entity that is offering the information about the topic. Moreover, the study showed that the way people assess risk when faced with such information differs greatly depending on the source of the information. Their thinking seems to change in working on such a risk-benefit equation depending on the source, whether it’s come from an official organ or a pressure group, for instance.

Strangely, another respondent accused me of bias in my writing, as if somehow the placement of a deliberately provocative question in a public forum was somehow the writing itself rather than simply an enquiry.

I could not understand why he thought that my posing a question journalistically would preclude me from writing a neutral piece? It was his response to my initial broad question that has led me to write this post, however, so maybe I should thank him for the inspiration.

As I explained, I put the question with a deliberate and strong inflection in order to provoke the strongest response from the community. That’s pretty much a standard approach to getting useful opinions from people on both sides of an argument in journalism. If you don’t believe me listen to the way people like the BBC’s Jeremy Paxman and John Humphrys posture through their questioning in order to get the best response out of their interviewees. They often hint at a strong statement through their question one way or the other and people will either support what you say and offer their positive opinions or else argue against you.

It’s usually best to lean away from them (not only to avoid the blows but to inspire them to give the strongest argument for their case, and I’m not referring to Paxman or Humphrys here). Either way, you get useful comments on both sides that will provide the foundations for the actual writing and so allow you to produce a neutral article that reveals the pros and cons of an issue without personal bias.

Anyway, as an experiment, it didn’t work too well, initially. However, once the community had warmed to the question and I’d added a clarification some quite useful answers that weren’t simply an attack on the question itself began to emerge.

As it turns out, none of the responses really fit with what I wanted to report in the original post, which you can read in the Sciencebase blog under the title In What We Trust, by the way, and so I intend to write another post discussing the various points raised and namechecking those members of the LinkedIn community who were happy to be quoted.

Girly Games

My latest science news write-ups on the SpectroscopyNOW portal are now up for grabs. This week, I cover the apparent gender gap when it comes to computer games, how Japanese researchers are using near-infrared light to probe young women’s brains to find out if they can reduce stress and potentially acne with pleasant fragrances, and the discovery that cancer cells seem to be stuffed full of the dreaded trans fats. You can find my other spec news from this week linked in the Sciencebase Geeky Bits column.

Perfect skin However, I want to step back a little with respect to that video games research. The team used the apparently powerful technique of functional MRI (basically a brain scan that can spot changes and lights up active regions of the brain). The researchers devised a very simple computer game, a kind of cross between Tetris and Pong (without the bats). To win you had to gain territory. The researchers scanned the brains of males and females while they played this game. Their results showed that men and women got the game, but the men were sharper when it came to realising you had to use a particular strategy to gain the most territory.

What was most interesting to Allan Reiss and colleagues at Stanford University School of Medicine who carried out the research was that the region of the brain associated with rewarding feelings lit up the most in the males than in the females. This, the researchers say, suggests a possible explanation as to why males enjoy, and even become addicted to, video games more commonly than females. “These gender differences may help explain why males are more attracted to, and more likely to become ‘hooked’ on video games than females,” Reiss explains in the Journal of Psychiatric Research.

Now, I take issue with the fundamental assumption that Reiss and his colleagues make regarding video games. While historically video games have been aimed almost squarely at boys, the manufacturers over the last few years have recognised that they only corner half the potential market with such a biased aim. As such, they have developed dozens of new types of games that are not of the familiar war and killing fantasy type. They have also remodelled their hardware to offer colours and skins that will appeal to females, the pink and white Nintendos, for instance, generally appeal to the female market more than the blue.

More to the point though, my ten-year old daughter and dozens, if not all, of her friends have taken to Nintendos, Wiis, Playstations, Tamagotchi, just as addictively as their male counterparts, fighting for screen time on their various devices and computers. Admittedly, the games they play are more frequently of the SingStar, Petz, and Sims kind as opposed to Halo, World of Warcraft etc. They also network with each other online in various online games with small furry animals rather than three-eyed aliens with vast armaments. Like I say, though, they are just as addicted to these games as the boys.

So, while Reiss’s work is fascinating and does hint vaguely at latent aspects of how territorialism evolved in the male brain. One has to wonder whether if he and his colleagues created a different type of game, a more “feminine” type game, like a pet simulation, for instance, they would see those reward centres lighting up more brightly in the female brain. Perhaps if the experiment had had an intrinsic bias towards a feminine type of game and they’d seen such activity in their fMRI, they would have come to a very different conclusion about video game addiction.

Gingko Biloba Controversy

The structure of an active component of herbal remedy Gingko biloba is causing controversy among chemists apparently related to InChI strings and such matters.

Structural controversies may become a moot point given recent research that seems to suggest that one of the main benefits of taking this herbal remedy – memory improvement – is not valid.

A three-year study involving 118 people age 85 and older with no apparent memory problems was carried out by Hiroko Dodge and colleagues in the Department of Public Health and Center for Healthy Aging Research at Oregon State University in Corvallis. Half of the participants took Ginkgo biloba extract three times a day and half took a placebo. During the course of the study, 21 people developed mild memory problems, or questionable dementia: 14 of those took the placebo and seven took the ginkgo extract. Although there was a trend favoring ginkgo, the difference between those who took gingko versus the placebo was not statistically significant.

More on this from the American Academy of Neurology

Chemical MSDS Sheets

Material safety data sheets (MSDS) is a perennial search favourite on the Chemspy site. The site has its own MSDS section and a javascript widget you can even add to your own site to allow your visitors to search for chemical MSDS sheets (yes, I know it’s a tautology on two counts, chemical material safety data sheets sheets, but like PIN number and “ATM machine”, the phrase is in common parlance.

Anyway, follow the link to search for MSDS on ChemSpy and here if you’d like to add the MSDS search toolbox (feel free to edit the script once you’ve saved it to your server to fit your site’s requirements).

Meanwhile, an offsite resource that looks promising for Chemical MSDS sheets is the obviously named MSDS Search, which duplicates some of the ChemSpy resources but adds a few new ones too.

Rubbing Up the Gene Genie

Sciencebase is this week proud to play host to the Gene Genie Blog Carnival thanks to an offer from Bertalan “Berci” MeskÃ³ over on the excellent ScienceRoll. For those who don’t already know, a Blog Carnival doesn’t usually involve a lot of be-costumed revellers dancing through the streets to the sound of the samba band, but is a gathering of like-minded bloggers brought together through the power of the tubular Interwebs to share their latest posts on a given subject.

The Gene Genie carnival has an obvious theme. No, it’s not the songs of aging but outlandish popster David Bowie. No, it’s not the magical character of Arabian Nights entombed in a lamp, and no it’s nothing to do with quasi-sci-fi-retro-fit BBC cop show Ashes to Ashes. It’s about genes. See, I told you it was obvious.

Anyway, the carnival (from the Latin carnis, meaning meat, and levare, to put away) covers some of the hot topics in the world of genes, genetics, DNA and all things inherited.

So, here we go:

Gene Found for Ghosal Hematodiaphyseal Dysplasia Syndrome: A Rare Syndrome with Increased Bone Density (DNA And You)
Home DNA tests on the up, ‘safer’ clinic DNA tests on the down (Genetics and Health)
Gene Plays a Role in Hair Loss Identified (The Biotech Weblog)
Extinction Fears of the Red-Headed Homo Sapien (GNIF Brain Blogger)
Where are brown people short? and Shadows of the Past in Genes (Gene Expression)
Genetics Cause of Smell Perception (ArticleBiz.com)
Why do we have common risk variants for metabolic diseases? (Genetic Future)
Researchers Discuss MEGF10 Gene Assocation To Schizophrenia (Scientificblogging)
Differences of gene expression between human populations (Anthropology)
Brain scan reveals cultural differences (Sciencebase)
Scientists Link Gene That Promotes Long Lifespan to Cholesterol (Biosingularity)

In the realm of personalized genetics:

NY Times: Insurance Fears and DNA Testing (DNA Direct Talk)
Ann Turner on Personal Genomics Companies 23andMe vs deCODEme and deCODE Launches PrCa Prostate Cancer DNA Test (Eye on DNA)
One Fifth of GDP! (Gene Sherpas)
Why should you get a free 23andme test? (bbgm)
23andMe Adds Paternal Ancestry and an Updated Gene Journal (Genetic Genealogist)
New York Times: Genetics and insurance (Tracing the Tribe)
SNPwatch: One SNP Makes Your Brown Eyes Blue (Spittoon)
Global Awakening in Genetic Counseling (Scienceroll)
Your Future IS Your Genes: Diagnosing Bipolar Disorder from a Blood Sample (Living the Scientific Life)
The next edition of Gene Genie will be hosted by DNA Direct Talk, watch out for it! For more information about the Carnival here.