Author: David Bradley

Molecular wolfram demonstrations

Buckyball mathematicaThe Wolfram Demonstrations Project launched this week and represents what the developers describe as “a major new resource for research and education”. Well, that’s as maybe, but what is it? The project was first conceived by Stephen Wolfram creator of the Mathematica software that as its name suggests allows computers to produce visualisations of mathematical concepts.

The project sits under the umbrella of open-code and uses dynamic computation to bring Mathematica’s prowess to bear on a range of endeavours in science, technology, mathematics, art, finance and more. You do not actually need Mathematica to try out the site, but interactivity comes into its own if you have the program on your system.

The Demonstrations site presents a good gallery of examples of what’s possible in Mathematica 6, although it is not yet complete in the sense that users and others can provide input and help it develop still further. “The Demonstrations are contributed by a mix of Wolfram employees and Mathematica enthusiasts,” site Manager Joe Bolte told us, “so some topics are better represented than others.” He adds that, “Now that the site development is largely complete, we should be able to use Mathematica’s strength’s to quickly help chemistry
catch up to our better represented topics.”

Which brings me to my first search. I did the obvious one for a chemist visiting the site and typed “molecules” into the search box. Just three demonstrations with that keyword came up – Insulin molecule, Lotus effect, cluster of 120 spheres. The insulin shows a mutant protein based on data from the Brookhaven Protein Data Bank and allows you to rotate the molecule in 3D, to hide and reveal various atoms, and to zoom in. Everything that chemists are used to doing with Chime or JMol.

Lotus is a little more gratifying. This demo places spheres on a larger sphere, copies this assembly and places the duplicates on a still larger sphere. It heads towards a fractal structure and so can mimic the surface morphology of lotus leaves, which have incredible self-cleaning and water repellent properties. You can see an artificial lotus leaf surface in action in our video section.

The Lotus demo allows you to vary the size and spacing of the virtual balls and so allows you to emulate molecular and atomic clusters and viruses. There are other specialist tools for doing such manipulations with more accurate models of such entities, but the demonstration does indeed produce some very or ornamental images.

The final demonstration that showed up in my search also simulates molecular structure in a novel way. In this producing 3D models that resemble the shape, but not quite, of the [60]fullerene molecule, better known as the buckyball. Although such a representation may not be accurate in terms of the chemistry, playing with these structures could inspire new ideas with regard to what might be possible experimentally in terms of geometry. After all, Kroto, Smalley and colleagues figured out the buckyball structure when they realized it might resemble a soccerball.

Searching for the word “chemistry” itself threw up quite a few more demonstrations related to the field, including generalized Arrhenius function, a buckyball of buckyballs, discrete reaction and diffusion, and one on carbon dating. All provide a unique view of various physical phenomena.

Mathematica is a powerful tool and the demonstrations provide a superb showcase of the kinds of graphics it can produce.

I asked Bolte more about the technical extension of the site. “Mathematica’s high-level language makes it easy to quickly display data and prototype algorithms in a way that no other software package can match,” he explains, “And new in version 6, it has built-in access to databases of relevant data that are available with a single line of code.”

The system is backed up with a range of data sources, including chemical data and element data sources. Closely related is the Periodic Table by co-founder and chemist Theodore Gray.

Local fluff is no gas

Local fluffSending astronauts up to our nearest star to reignite the Sun, the premise of sci-fi movie Sunshine, is truly the least of our problems when we are currently faced with global climate change, global terrorism, and global economic collapse. Nevertheless, astronomers are concerned about recent findings regarding the hot gas surrounding our star and its stellar neighbours. Put simply they cannot find them.

A team led by Martin Barstow of Leicester University, England, has used data from the Far Ultraviolet Spectroscopic Explorer (FUSE) satellite to map the space in between the stars within a sphere of radius 300 light years. He reported details of the observations to the Royal Astronomical Society National Astronomy Meeting in Preston in April, explaining how the FUSE results show a distinct lack of oxygen. Received astronomical wisdom has it that local interstellar medium including the whole Solar system is embedded in a wispy diffuse cloud of hot gas, the so-called Local Fluff.

The findings, or lack of finding oxygen, suggests that an ancient stellar explosion, a supernova, blew away the gas from within the local interstellar medium leaving us with a less than fluffy cloud. More in this week’s SN.

Raman and the usual substrates

My latest round up of science news over on SpectroscopyNOW.com is now online. This week, I discuss how a lot of protein research looks only at molecules at rest, but could be enriched so much more by observing how these biological molecules change step by step as they interact with each other and their usual substrates. Researchers at the European Synchrotron Radiation Facility (ESRF) and the Structural Biology Institute (IBS) have exploited the power of Raman spectroscopy to help them lock in on protein intermediates states that can then be snapped using X-rays from the synchrotron. The team can then piece together a stop-motion movie, in the style of Ray Harryhausen or Wallace and Gromit without the sword-wielding skeletons or sardonic dog.

Also in this week’s issue, dental researchers in London have demonstrated that the antibacterial solutions containing sodium hypochlorite (household bleach) and the calcium-sponge EDTA commonly used to clean up after root canal work, can actually destroy the organic content of the tooth’s dentine. I spoke to team leader, Kishor Gulabivala of the Eastman Dental Institute at University College London who pointed out that his team’s results have only so far been presented at a conference. Nevertheless, the research represents the first quantitative study of the effects of the antibacterial solutions on teeth, and suggest a need to reconsider their use in dental surgery.

Initially, I was concerned that it was their use in artificial teeth whitening that was the major issue, but Gulabivala assures me it is not. Despite this, I found several websites (amateur and otherwise) that suggest hypochlorite can be used as a bleaching agent for the teeth. Personally, I’d rather stick with yellow, stained teeth (if I happened to have them) rather than risking a mouthful of bleach.

A surgical robot that uses its own MRI scanner to pinpoint targets with microscopic precision also caught my eye for news on the SpectroscopyNOW MRI channel this week.

Ten years of online chemical community

Joao Aires de Sousa emailed me a while back to tell me that the excellent ORGLIST email discussion group was coming up to its tenth anniversary. I remember it was essential reading for bored staff in the editorial offices where I worked, providing light relief and a loose connection with the real world of chemistry happening beyond our admin system and manuscripts.

Trouble is, I got waylaid with other matters on the Sciencebase blog and overlooked Joao’s original post until last week, when I discovered that the tenth anniversary had been and gone. The first post was made on March 15, 1997 to announce the formation of the list and said simply “ORGLIST is a new mailing list dedicated to Organic Chemistry” and giving details on how to subscribe. Joao in this inaugural missive also asked everyone who received it to forward the email to potentially interested parties. Such was the extent of viral marketing in those days at a time when Youtube, Web 2.0, wikis, and blogs simply didn’t exist in the current sense.

The first “real” post was in French and asked about where to find information on the Blue Bottle experiment and the Ammonia Fountain, perennial high school science lab fodder, I believe.

A celebratory ORGLIST symposium entitled “Computers at the frontiers of Organic Chemistry” will be held this July 17 in parallel with the 7th National Meeting of Organic Chemistry of the Portuguese Chemical Society.

“Thousands of chemists from all over the world have gathered on ORGLIST to discuss Organic Chemistry,” Joao says.

I asked Joao about the longevity of the list. “Its success resides in email,” he says, “Email has a unique combination of features that make it extremely convenient. It is probably the Internet tool most integrated into the information processing routines of chemists.” He points out that checking email is pretty much a daily routine for almost everyone in science. “I think that makes email a great channel for building virtual networks of scientists,” he adds, “probably more than ever before!” Reaches the daily lives of hundreds of subscribers. “This allows quick, useful answers to posts and makes users feel part of a community,” Joao says, “That and ten years of online history.”

How colourful language can improve your image

Color gamutColourful language usually refers euphemistically to the kind of expletives and oaths you hear in a barrack room brawl. But, in the context of technology it could be the next big thing in colour printing.

Colour and natural language experts at Xerox have been working on what sounds like an entirely new way to get the best out of your digital photos. Their research could allow you to talk to your printer and tell it to “make the green a ‘mossy’ green” or “make the sky more sky blue”. More technically, you might one day be able to do all the kinds of colour and contrast corrections that are usually the preserve of programs like Photoshop, with simple phrases sent to the printer itself.

The approach speed up the workflow for graphic artists, printers, photographers and other image professionals and their assistants who could save time side-stepping the on-screen fine tuning process of printouts.

“You shouldn’t have to be a colour expert to make the sky a deeper blue or add a bit of yellow to a sunset,” research leader Geoff Wolfe says. The software is still in the development stages, but works by translating human descriptions of colour – “emerald green”, “brick red”, “sky-blue pink” – into the precise numerical codes printers use to control the amount of each primary colour they deposit at a single point in the printed image.

“Today, especially in the office environment, there are many non-experts who know how they would like colour to appear but have no idea how to manipulate the color to get what they want,” Woolfe adds. Moreover, the vast majority of computer screens in “non-expert” offices are setup incorrectly for screen to print comparisons and so cause the whole gamut of problems when a document that looks okay on screen is printed. Simple commands to rectify such issues avoid the problem of having to know how to set up the screen and ambient lighting.

Woolfe’s discovery could mean that colour adjustments can be made on devices like office printers and commercial presses without having to deal with the mathematics. For instance, cardinal red on a printer or monitor is really expressed by a set of mathematical coordinates that identify a specific region in a three-dimensional space, which is the gamut of all the colours that the device can display or print. To make that colour less orange, the colour expert distorts (morphs) that region to a new region in the gamut.

The ability to use common words to do this gamut morphing and adjust colour would have far-reaching implications for non-experts as well as graphic artists, printers, photographers and other professionals who spend a significant amount of time fine tuning the colours in documents.

“In the end it’s all about usability,” Woolfe adds, “Colour is so prevalent today, you shouldn’t have to be an expert to handle it.”

Nanotech threat to your safety

Nanotechnology cartoon - Scott Dougherty, LLNLDoes nanotechnology pose a threat to humanity on a par with the threat we face from genetically modified (GM) foods? That is the question asked by various lobbying groups from the verdant greens to the confused consumers. But, governments, academics and commercial bodies see the issue from an entirely different perspective and are asking, will the nanotechnology industry face the same outpouring of hostility as that caused by genetically modified (GM) foods? The kind of outpouring that stymies and often destroys research that could benefit us all.

Nanotechnology, the application of objects and structures that are very small, usually less than 100 nm in diameter is growing rapidly. But aside from the bizarre imaginings of those who originally pioneered the term, this new science is really not much different from what chemists, materials, scientists, and physicists have always done and that is to work with particles, molecules, and other species that just happen to be individually very small. The advent of scanning microscopy techniques has given us a closer look at the structure of atomic clusters, supermolecules and nanomaterials, and new techniques for handling materials at the very small scale or creating species that have novel functionality at this level are emerging all the time. However, the nano, meaning a billionth (in this case a billionth of a metre) is really nothing new, it simply defines the size limits.

Much of the nano that hits the press is nothing of the sort, remember those little cogs and pistons etched in silicon? And, what about the tiny bots that would defur arteries? They are a thousand times bigger than truly nanoscopic objects and the likes of liposomes, which the cosmetic industry briefly marketed as nanotechnology are really nothing of the sort, they are simply supramolecular chemistry given a trendy name.

According to a Leicester University press release this week touting a talk to be
given in May by new media expert Rachel Gibson is studying the nature of the growing online nanotech debate and will present her latest findings to the annual meeting of the International Communication Association in May 2007. The release says that, “at such scales, the ordinary rules of physics and chemistry no longer apply.” This is baloney! The normal rules of physics and chemistry very much apply, at almost every scale. In fact it is at the nanoscale that we can see the beauty of the normal rules of physics and chemistry in action – the quantum effects, such as tunnelling, the formation of electrostatic, non-covalent bonds, the non-linear behaviour that continually astounds but never breaks those laws. These are the normal rules of the physical sciences. There is no mystery about nanotechnology.

That said, the promise of nanotechnology is as big as the grants researchers are receiving should they happen to splash a few “nanos” into the application forms. Novel materials and composites indeed do have huge potential medicine, engineering, communications, transport, even the home.

But, the inevitable questions from environmental groups and ethicists are repeatedly raised. The outpourings of certain British Royals concerning “grey goo” and other garbage do not lend themselves to a sensible debate either. And, yes, there should be a debate if we are finding such unique physical behaviour on this scale that it represents some kind of threat. But, the idea of self-replicating nanobots that chomp their way across the planet, is quite literally, a Michael Crichton plot, I believe, rather than a serious prediction about where nano is heading.

Gibson, however, hopes to examine the efforts of the scientific community to engage with the various social concerns and to assess the extent to which the GM lessons are being learned as nanotechnology (more realistically at the moment mere nanoscience) diffuses into the public consciousness.

She is working with colleagues from the Australian National University, to develop software to study the structure, evolution and implications of the online hyperlinking activities of political and social organisations. The Virtual Observatory for the Study of Online Networks (VOSON) (http://voson.anu.edu.au) thus provides social scientists with the means to study the success of opposition of groups. Watching the evolution of the debate online offers a new way of studying this question, she says, particularly as many of the groups active on the issue are enthusiastic users of the Web.

“This project demonstrates the growing interest among social scientists in applying online technologies, and particularly cyber-mapping tools, to address important social science questions,” she says, “The research allows us to examine the development and expansion of issue networks in a wholly new three dimensional space that means we can track the formation of alliances between groups over time and across countries.”

One cannot help but wonder whether all the money being spent on such endeavours, the cash ploughed into lobbying, and the cost of endlessly debating non-issues, could not be better spent by the nanoscientists themselves to investigate with even greater precision the properties and safety aspects of their discoveries. Surely, the money could assist the maturation of nano, rather than us having to see scientists fending off lobbyists and rebuilding labs, as opposed to GM crops, trashed by extremists.

Build a better mousetrap, they say, and the world will beat a path to your door. While, nano is not really anything but a question of scale, it really could be the better mousetrap we have been looking for, figuratively speaking. Advocates have to hope that those beating at their door are as keen to see the technology mature safely as they are.

Should you worry about HRT and cancer?

Menopausal womanA female friend of a friend started on hormone replacement therapy (to treat quite severe early postmenopausal symptoms, and on the advice of her GP to reduce the risk of osteoporosis). The symptoms have all but been relieved (although it’s difficult to separate out the effects of the HRT hormones themselves from the phytoestrogens she imbibes from soy milk and other related foods).

Either way, the recent Lancet paper, which received lots of media attention, got her all hot and bothered. She’s an earlier finisher, and is likely to be on HRT for ten years or so, is that going to mean she will get ovarian cancer. The tabloid hype surrounding the paper would seem to suggest so, but as with all statistical health studies that get pounced on by the media it’s worth taking a closer look.

Interpreting the results and scaling up to whole number women, as opposed to fractional women, over 5 years, ovarian cancer incidence for those who have never used HRT was 26 per 10,000. It was 30 per 10,000 for HRT users.

The researchers conclude that, “Women who use HRT are at an increased risk of ovarian cancer. Since 1991, use of previous has resulted in 72 additional cancers per year and 55 additional deaths in the UK.” Their results are based on the million women study, in which 500,000 were HRT and 500,000 were not.

Of course, ovarian cancer is the fourth most common cancer in women in the UK, with some 6700 developing the malignancy and 4600 dying from it every year. The high incidence of deaths is presumably down to the hidden nature of this form of cancer, which is often not detected until it has reached a lethal stage. 72 additional cancers and 55 additional deaths is a significant but not an enormous increase.

The researchers also add that, “In total, ovarian, endometrial, and breast cancer account for 39% of all cancers registered in women in the UK.1 and 2 The total incidence of these three cancers in the study population is 63% higher in current users of HRT than in never users (31 vs 19 per 1000 over 5 years, figure 6). Thus, when ovarian, endometrial, and breast cancer are taken together, use of HRT results in a material increase in the incidence of these common cancers.”

But, these are risk factors and there is simply no way of making any kind of prediction, with current medical knowledge, of whether or not a particular woman on HRT will suffer any form of cancer because of the HRT drugs she is taking. The researchers mention that as HRT use has declined in the US (partly because of the negative publicity it receives), we are also now seeing falling breast cancer rates there.

According to the author of the paper, Valerie Beral of Cancer Research UK, “It is a small but significant risk. It’s more an issue for women to think about how much they want to take HRT to relieve their symptoms against the known risks.”

However, it’s not all about hot sweats and sexual libido, as life expectancy rises in general and the aspirations of older people for a happy and active retirement rises concomitantly, it will be interesting to see whether a few less cancers will be offset by a rise in osteoporosis incidence and the other “side-effects” of the menopause (particularly early onset menopause).

An elderly neighbour of mine has been in and out of hospital with bone density issues and fractures repeatedly and at one point suffered a potentially lethal hospital-acquired MRSA (multiple-resistant Staphylococcus aureus) infection as a result. To my mind, she would most likely not have suffered in this way had she taken HRT during the early menopause. But, equally there is also the thought that had she died of cancer sooner than the osteoporosis kicked in, she would not have suffered bone density problems later in life either.

For every statistic, a counter statistic can be found and when the overall risks are very small it is difficult for the public, the media, and even the medical scientists to know for sure which way to push the agenda.

Spiderman v Geckoman

Forget Spiderman, Geckoman is where it’s at, at least so suggests research due to be published in the Journal of Physics: Condensed Matter. According to Nicola Pugno at the Polytechnic University of Turin, Italy, the secret of making a sticky, but non-stick, material could lie in creating a “hierarchical structure” of branching bristles from ever finer carbon nanotubes. Such a bristly material would mimic the physical properties of gecko feet that allow them to hang effortlessly by a single pad from even the smoothest of surfaces.

Pugno’s calculations suggest that the hierarchical approach could lead to a stiff, non-tangling material with tips flexible enough for temporary adhesion. Previously, the research team has suggested that carbon nanotubes might allow us to build a space elevator, which was blogged about at length in the summer of 2006.

According to a report in New Scientist, Stefano Mezzasalma of the University of Trieste in Italy says the approach definitely could work, “The first prototype of a Spiderman suit might be ready in a decade or so.” But, like I say, move over Spiderman, it’s Geckoman we want to see!

Welcome to Earth 2.0 (beta)

Earth 2.0No, before you switch off, this is not a Second Life clone, or anything to do with global wikis and blogs. This is the first astronomical post on Sciencebase for quite some time, but because it is not your usual run of the mill supernova announcement, or dark energy revelations, we thought it worthy of a slot. Okay, so what’s all the fuss?

Well, astronomers have finally discovered an Earth-like planet beyond the Solar System and it is bigger by half than earth. Most importantly, the exoplanet, spotted with the ESO 3.6 m telescope, by a team of Swiss, French and Portuguese scientists is capable of having liquid water. Could this Earth 2.0 offer human kind a planetary upgrade?

Well, it might be inhabitable, but the beta version has a few technical problems that might be difficult to overcome. First, aside from being 50% bigger than earth and therefore offering a lot of storage space, it also has a mass about five times that of the Earth, which means even the leanest among us will tip the scales. But, perhaps more importantly it orbits a red dwarf rather than a nice life-supporting star like the Sun. Of interest, but not necessarily a problem this planet has a couple of near neighbours, a Neptune-mass planet, and at least one more planet of about eight times the mass of the Earth.

More worrying, though the planet’s clock speed, or “year” is just 13 days and it is 14 times closer to the red dwarf than Earth is to the Sun. But, the exoplanet lies, nevertheless, in the life support zone in which water could be liquid.

“We have estimated that the mean temperature of this super-Earth lies between 0 and 40 degrees Celsius, and water would thus be liquid,” explains Stéphane Udry, from the Geneva Observatory, “Moreover, its radius should be only 1.5 times the Earth’s radius, and models predict that the planet should be either rocky — like our Earth — or covered with oceans,” he says.

Team member Xavier Delfosse from Grenoble University, France, has already marked this planet on his treasure map of the Universe, with an X. Of course, any pioneers hoping to boot up a new human race on exoplanet X, will have rather a long upload time, the host red dwarf, Gliese 581, is close to the Earth, lying at 20.5 light years in the constellation Libra. So, it will be a very long time before we have even the vaguest opportunity to get a closer look at Earth 2.0.

Chemical blogs, wikis, and quanta

I recently interviewed quantum chemist Steve Bachrach of Trinity University and asked him his thoughts on the web 2.0 revolution and whether or not chemists might benefit realistically from blogs and wikis.

“Well, this is really an issue of culture. My personal hesitancy to adopt Web 2.0 technologies is that I don’t have the time to read random thoughts by random individuals. I barely have time to keep up with the old-school (i.e., traditional journals) literature in my field. The blogosphere just seemed to me to be filled with the rantings of people who have nothing better to do with their time. Peter Murray-Rust’s blog was the first to demonstrate to me that real chemistry content could be had, that interesting and novel ideas could be found and shared and discussed.”

You can read the complete interview in the latest issue of Reactive Reports together with my regular round up of chemical science news for the site.

 Proteins’ Web of Intrigue  The latent strength of Miss Muffet’s arachnoid friend may have been in sexual allegory, but the image of a spider’s web as somehow weak, a glistening, gossamer netting for trapping only flies could not be further from the truth.

 Stem to Sperm  Stem cells from human bone marrow can be converted into early-stage sperm, according to a research team based at the North-east England Stem Cell Institute (NESCI), Newcastle.

 Dino Remains  We have not quite entered Jurassic Park, but researchers have successfully extracted protein from a 68 million year old Tyrannosaurus rex bone.