Author: David Bradley

Let’s Get Physical, Right Now

The latest issue of the monthly Spotlight column over on the physical sciences section of Intute is now online, this time featuring research from the earth sciences, the greening of chemistry in the developing world, and humans acquitted over Neanderthal extinction.

Cassava by David MonniauxChemists go veggie

Chemists working on tight budgets in developing countries may be able to swap flasks of laboratory reagents for extracts of celery and potatoes, or cassava and carrots and other inexpensive, …

Neanderthals more than severely put out by bad weather

Climate change saw off the last of the Neanderthals from their final stronghold on the Iberian peninsula thousands of years ago, according to …

Slumbering Yellowstone snores

Beneath the beautiful Yellowstone National Park in Wyoming lies a slumbering giant, a supervolcano who wakes every few hundred thousand years and wreaks havoc across hundreds of …

Viruses Do Not Eat Spaghetti

BacteriophagesThe faint glow from a single molecule combined with a stretch from “magnetic tweezers” could help scientists get a grip on how viruses that infect bacteria, so-called bacteriophages pack up their DNA. The research could lead to a resurgence of interest in the West for a potent treatment for infection that uses bacteriophages instead of antibiotics to attack disease-causing bacteria. The treatment side-steps the problem of bacteria evolving resistance to antibiotics because the agent of bacterial death can evolve just as quickly to cope with any defences put up by the bacteria.

In the face of deadly emergent bacteria such as Escherichia coli O157, multiple-resistance Staphylococcus aureus (MRSA) and Clostridium difficile, there is renewed interest in this alternative to antibiotics. The same study might also lead to new insights into how to combat viruses that infect people too, including herpes and adenoma viruses.

Many viruses use a self-assembly stage in which a powerful molecular motor packs their genetic code into the viruses’ preformed protein shell, its capsid. Now, Carlos Bustamente and colleagues at the University of California, Berkeley, have demonstrated that the genetic code is not coiled up like so much spaghetti on a fork but is packed using a concertina type approach. You can find out more about the details of this work in the current news round-up on SpectroscopyNOW.com

People caught pubic lice from gorillas

GorillaNo, it’s not some kind of deviant gorillas in the mist story, apparently, millions of years ago our ancestors picked up pubic lice (crabs) either by sleeping in gorilla nests (without the gorilla) or through eating our silver-backed cousins. David Reed and colleagues at the University of Florida publish details of their findings today in BMC Biology journal.

Reed is quick to point out that there was no monkey business between gorillas and humans. Of course gorillas are apes not monkeys, but this would be a perfect story for Ricky Gervais podcast star Karl Pilkington. “It certainly wouldn’t have to be what many people are going to immediately assume it might have been, and that is sexual intercourse occurring between humans and gorillas,” Reed says, “Instead of something sordid, it could easily have stemmed from an activity that was considerably more tame.”

Reed suggests that 3.3 million years ago, gorilla lice took up residence in the pubic region in our ancestors, this was probably around the same time that evolution took us from a fully hirsute state to our current nakedness. With no hair on our bodies other than the head and pubic regions, the lice would have been hard pushed to linger anywhere else.

Chemical Wedding Gifts

FullereneMost people are well aware of the traditional materials offered to married couples to celebrate their wedding anniversary. You know the kinds of thing I mean – ruby for instance is the gem of choice for a 40th anniversary, although why a chunk of chromium infested aluminium oxide should have been chosen for this year in particular I don’t know. The noble elements silver and gold are 25th and 50th respectively, while the hardest allotrope of carbon, represents the 60th celebration (diamond, that is). If you want the complete list check out our traditional wedding anniversary gifts page, but if you want something a little different, a reference for Kevlar, zeolites, buckyballs, or PVC say, take a look at our chymical wedding round-up.

Acid test research project

This probably is not a project you could do for your school science project, unless you are really, really keen. Chemists at Queen’s University Belfast have developed a molecular system that acts like an ion-selective electrode across a pH range of 9. Prasanna de Silva and his colleagues, who featured in a special issue of Intute Spotlight recently, explain that their device has the advantage of operating on the nanoscale and so could be incorporated into microelectromechanical systems, or so-called lab-on-a-chip devices. The team used a set of four sensor molecules in relay to act as the quantitative version of universal indicator paper. One sensor does the hard work of sensitively responding to pH across approximately 2 pH units and then hands on the baton to the next, which in turn works hard over the next 2 pH units and so on covering 9.5 units on the pH scale. de Silva says that the molecular devices show an almost linear intensity-pH profile that is reminiscent of the response of a conventional glass pH electrode but a thousand times smaller than even micrometer-scale intracellular pH electrodes.

“Our research shows a simple and predictive way of greatly extending the sensing range of molecular sensors,” de Silva told Sciencebase, “We do it by using a set of four sensors to act somewhat like a 4×100 m relay team. One sensor does the hard work of sensitively responding to pH across approximately 2 pH units and then hands over the task to the next one, which in turn works hard over the next 2 pH units (approximately) and then hands over the task to the next one etc. In this way we get a range of 9.5 pH units whereas the normal range of a molecular sensors is only 2 (as you learn in high school science).”

Scientists have thought about this problem before (resulting in the famous universal indicator), there was no quantitative version of a molecular universal indicator until now. The nearly linear intensity-pH profile is reminiscent of the glass pH electrode’s response, even though the electrode is obviously a lot bigger in size (the smallest ones are micrometer-sized and used for intracellular pH measurements), de Silva told me.

You can get the full experimental details in their JACS paper on this: Analog Parallel Processing of Molecular Sensory Information

Levitation for Real

Magnetic levitationThis isn’t exactly your average high school science fair project, in fact please don’t try this for yourself without proper supervision, as you’ll need a magnet, a chunk of high temperature superconductor and a flask of liquid nitrogen, oh and a pot that won’t crack when you pour in the liquid nitrogen. (Standard cyro lab safety equipment is recommended) When this video first hit the streets, lots of people said it was a fake, but what it is, is a classic demonstration from modern physics of non-classical behaviour in materials cooled below a certain critical temperature. The effect in question is well-known to scientists working with superconductors and is known as the Meissner-Ochsenfeld effect, or more commonly the Meissner effect. Poor old Ochsenfeld rarely gets a name check. It was discovered by the pair in 1933, so it’s nothing new to physics, relatively speaking.

So, what’s going on? How does the high temperature superconductor levitate the magnet and if it’s high temperature why does it have to be cooled with liquid nitrogen to near 77 Kelvin, that’s almost minus 200 Celsius). Well, we’ll answer the last question first, it’s the easiest. The High is relative! Low temperature superconductors only work at close to absolute zero, minus 273 K, so anything at the almost balmy temperature of liquid nitrogen is positively smoking!

Now to the hard bit. Superconductors are unusual ceramic materials. They have lots of weird properties not least the fact that they superconduct, which means they can carry an electric current with zero resistance. So, picture the magnetic field around the magnet, if you bring the magnet close to the ceramic when it’s at room temperature, the magnetic field lines pass straight through. But, when the ceramic is chilled below its critical temperature to make it a superconductor, those magnetic field lines can no longer penetrate the ceramic. But, that doesn’t really answer the question, it just begs another – why can the magnetic field not penetrate the superconductor?

The final answer lies in the fact that the magnet induces tiny electrical currents in the superconductor as it is lowered towards the superconductor (remember, a moving magnetic field induces a current in a conductor, it’s the basis of the dynamo and electrical generation). However, this is no ordinary conductor, it’s a superconductor and so those electrical currents keep flowing round and round in infinite circles within the superconductor. Now, conversely to a moving magnetic field producing a current in a conductor, an electrical field will induce a magnetic field and because of Fleming’s right-hand rule, that induced magnetic field matches the pole to which the superconductor is exposed by the placing of the magnet in the first place.

The resulting repulsion is counteracted by the downward force of gravity and the magnet hovers neatly above the superconductor, at least until it warms to above its critical temperature.

Just for completeness, I should also point out that the magnet is effectively pinned in position by an effect known as flux pinning, which is caused by magnetic field lines getting snarled up by impurities in the superconductor. But, if you set the magnet spinning it will spin without friction (well not in this demo because there is air friction). Incidentally, this levitation effect has a serious application in some types of Mag-lev train.

A semantic chemist – fixed

RSC ProspectI recently interviewed Robert Parker, the new Managing Director of RSC Publishing, you can read his interview in the February issue of chemistry news magazine Reactive Reports in which he discusses a new approach to the publication of scientific papers, RSC Prospect, and how it will benefit readers and the scientific community at large. It would be interesting to know what users think to the RSC’s new approach to meta data and a semantic chemical web.

“We needed a meaningful way of identifying compounds uniquely and one that’s machine readable – InChI fits the bill. Similarly, CML offers us a way of structuring lots of the science within a paper to both preserve the original science and do interesting things with it, and by demonstrating some of these applications, we hope to encourage wider adoption,” Parker told me, among other things. Check out the interview for his take on Web 2.0 for chemists, blogs and wikis, and more.

Also, featuring in Issue 62 of Reactive Reports:

Mass debate on stem cell research

Embryonic stem cellsJust £300,000 (about $600k) is being plugged into a national public debate by the UK government on stem cell research. According to Science and Innovation Minister Malcolm Wicks the UK’s two major public funders of stem cell research will use the cash to run a national public discussion about this cutting-edge area of science.

The Biotechnology and Biological Sciences Research Council (BBSRC) and the Medical Research Council (MRC) will receive the funding as part of the government’s ScienceWise initiative. The aim will be to find out what are the public’s concerns, views and attitudes to this face-most moving area of science. It will also provide a forum for revealing the challenges that researchers face and the potential benefits of stem cell science.

At today’s launch Wicks said: “The Government believes that stem cell research offers enormous potential to deliver new treatments for many devastating diseases where there is currently no effective cure. Huge numbers of people are affected by these diseases and Britain is a world-leader in stem cell research. But there must be a proper dialogue with the wider public on the future of stem cell research. We need to raise public awareness about the potential opportunities
and challenges in this area.”

One key element of the initiative is to raise awareness of the world-class stem cell
research being carried out in the UK, at centres such as Newcastle University, and the progress being made towards practical treatments.

BBSRC’s Julia Goodfellow added, “It is essential that scientists working in areas such as stem cell research engage in a real dialogue with the public. The new programme will give scientists, funders and the government up-to-date information on what the public really think about stem cell research while giving people the chance to voice their views and concerns.” So, basically repeating what Wicks said. The MRC’s chief Colin Blakemore, had a slightly different slant. “Scientists who work
on stem cells want to ensure they maintain the trust and support of the public for their research,” he said. “But to achieve this, we need to explain what work is being carried out and why it’s being done.”

So, is £300,000 enough to do the job? Compare this with the ludicrous amounts of money available to anti-science type lobby groups which amount to millions and it really does look like a pittance. Half of that amount could easily be eaten up by an independent designer putting together a corporate logo for the project and the other half will have gone on snacks and wine for the launch party buffet, or am I being far, far too cynical? You tell me.

New radiation warning sign

Ionizing radiation warning signThe sixtieth issue of the “new” Alchemist is now online over on Sciencebase partner site ChemWeb.com. As you might expect having reached this tender age, we’ve put on a little weight, as of this issue there will be more chemistry matters.

In this week’s issue, new symbolism in the world of ionizing radiation, a rubber band theory that requires no stretch of the imagination to work, and an atomic approach to murder. Also in this week’s issue, new catalysts could make use of wasted natural gas that is simply vented and flared at oil wells and archaeological evidence that Christopher Columbus’ fellow travelers struggled to find enough silver. Finally, crumpling hydrogels could give chemists a taste for plastic origami. Also in this issue our new awards/announcements section – this week fueling fuel cell research to the tune of $1.5million.

Check out the ChemWeb Alchemist every fortnight.

Chemistry aside though, what do Sciencebase readers think of the new radiation sign the IAEA wants to make standard? To me it looks far more cluttered and confusing than the original trefoil. the IAEA says that lots of people don’t know what the trefoil represents, but surely if you come across a huge lead box with a big red triangle on it and a symbol that looks like something out of a science fiction movie you’re not going to break it open to see what’s inside…or maybe some people would. The IAEA says there are too many needless deaths and serious injuries from accidental exposure to large radioactive sources and that tests have shown that the meaning of this new symbol for category 1, 2, and 3 radiation sources is far more obvious than the old trefoil. It will mean a whole new redesign for those movie sets though.

Shadowy face recognition

Shadowy faceFace recognition is the most obvious approach to identification but it suffers from a major drawback – shadows and bad lighting. If there is inconsistent lighting in a room or on a face then it becomes difficult to produce reproducible digital image of the face for face recognition algorithms to work with. Now, researchers in China have turned to near infra-red to help computers cope with variable lighting conditions and so recognize even the most shadowy of faces.

Face recognition is a key function of the human brain…let me put it another way, from a very, very early age we can all recognize faces, from the familiar view from mother’s knee to spotting a friend in a crowd. Computers too can process a digital image and compare it with a database entry to carry out simple face recognition. But only if the light is right. Throw in a few shadows, sunlight through a window, or a flickering overhead fluorescent light, and the computer usually cannot spot the difference between John Doe and Joe Bloggs. Stan Li believes the answer lies in the near infra red, you can find out more tomorrow in the latest issue of spectroscopynow.com or get an advance view here.