March 2006 – Page 5 – David Bradley

Divine Trigonometry

Picture math class without those confusing sines, cosines, and tangents. Picture an architect working out the surface area of various building structures without having to work through a range of degrees. In short, how much simpler trigonometry would be if we could remove the complicated bits and distil it down to crystal clear calculations.

University of New South Wales mathematician Norman Wildberger has done just that and espouses the theory that a rational, algebraic approach to trigonometry could open the way to a universal geometry. His is a revolutionary text, essentially overwriting centuries of tedium with a crisp new approach that is bound to raise hackles among conventionalists. However, Wildberger is not discarding the foundations of mathematics, instead he is constructing an architecturally sound new geometry that unites number theory and algebra and simplifies many geometrical problems.

In “Divine Proportions”, Wildberger (an alumnus of Toronto and Yale) clearly lays out the required definitions and theorems and illustrates tehm with useful formulae, diagrams and exercises.

If you’re a professional mathematicia, scientist, engineer, or a student who wants a different take on their studies, this book could change your understanding of mathematics.

Killer Coral Compound

Jerry Pelletier of McGill University, in Quebec, Canada, and colleagues have discovered a small molecule (which means it could be easy to make) in coral that can inhibit the replication of certain viruses. The research shows that the natural product, known as hippuristanol, blocks the protein-production machinery in cells that is hijacked by viruses and so halts a viral invasion in its tracks.

Hippuristanol is produced by the coral Isis hippuris, hence the compound’s name and seemingly prevents the viral protein, eIF4A, from binding to messenger RNA, mRNA. mRNA carries the code to make proteins from DNA to specific sites of protein synthesis in the cell. By binding to the mRNA, eIF4A initiates the translation of the protein code. Hippuristanol prevents replication by inhibiting this process.

Viruses, such as poliovirus hijack this protein machinery and so can be blocked by hippuristanol, at least that’s the theory. Hippuristanol could soon join the growing arsenal of antiviral compounds although it is still a long way off from being added to the GPs prescription books.

You can find the complete paper in Nature Chemical Biology: http://dx.doi.org/10.1038/nchembio776

Herbal Hogwash

Why is it that in a centre of scientific and medical excellence, namely Cambridge, do the city’s powers that be think it’s a good idea to let a herbalist pedal their wares in a prominent city centre shop?

At best, the products on sale are pseudoscientific hogwash for which any positive effects are likely to be mere placebo in origin. At worst, the apothecary’s shelves are laden with unregulated, untested, and potentially toxic materials that dupe those with any of a vast range of diseases into believing in a panacea for their ills that simply does not exist.

If these products worked, wouldn’t it be an obvious sector of the market for the pharma industry to move into? Surely, that would have happened already, if these products worked…

Natural Chemicals

Here’s a thought “natural” is not all good and we really couldn’t live our lives as we do without “synthetic” chemicals. It’s a theme that is rarely acknowledged by the mainstream media, but a UK organisation known as “Sense about Science” is hoping to persuade British journalists, at least, of the truth of the matter. Earlier this year SaS published a neat little booklet, aimed primarily at writers and editors on so-called lifestyle magazines, that highlights the top misconceptions about chemicals. You can now download the booklet pdf here.

In it, the organisation corrects six notions, affirming that you cannot lead a “chemical-free” life, synthetic chemicals are not inherently dangerous, synthetic chemicals are not the main cause of cancer and disease, exposure to chemicals is not a ticking time-bomb, it is not always beneficial to avoid synthetic chemicals, and we are not subjects of an unregulated, uncontrolled experiment.

Visit the SaS site, or download their booklet for the full skinny.

I spoke to the organisation’s Chris Tyler this week and he explains how combating chemophobia involves constantly repeating the message that the lifestyle media has been so keen to disparage. It seems, however, that the organisation and their booklet is having some success. “We seem to be making some headway with the lifestyle sector,” Tyler told me, “comments like ‘but we all
know that detox socks don’t really work’ and ‘of course not all synthetic chemicals are bad’ are appearing more often, in the magazines.” So, maybe the tide is turning, perhaps the message really is getting through…

Trackback this posting to help spread the word beyond the shores of fair Blighty.

Lazarus Rats

Mammalian paleobiologists must be a cynical lot. How else to explain their presumably ironic use of the term Lazarus Effect in piecing together the very evidence for evolution that must by its nature preclude much of what is discussed in the same context as Lazarus? Moreover, this particular piece of evidence is one that plugs a gap in the fossil record and helps bring continuity to the theory of evolution, something that is often considered a fatal flaw by those who’d dispossess it. You could say they’ve brought it back to life…

Anyway, a new type of rodent discovered last year in Laos is a survivor of a group believed to
have been extinct for 11 million years, according to a new study published today in Science. Mary Dawson and colleagues compared skeletal remains of the squirrel-like animal with those of a little understood extinct group of Southeast Asian rodents and confirmed that it is actually a living member of this long-gone family. When the new species was discovered in early 2005, it drew wide acclaim because it was thought to be a member of an entirely new family of living mammals. Instead, according to the researchers, the rodent represents a striking example of the ‘Lazarus effect’ in which an organism suddenly reappears after a long gap in its fossil record. That such a phenomenon has only rarely been documented among mammals and other vertebrates shows that Southeast Asia’s prehistoric ‘zoo’ can offer invaluable insights regarding past and present
biodiversity, the researchers write.

Bursting the Fusion Bubble

Fresh questions surrounding Rusi Taleyarkhan’s work on bubble fusion, are raised today in an exclusive news report online in the journal Nature.

Purdue University nuclear engineer Taleyarkhan, came to prominence in
2002 when he claimed to have achieved table-top nuclear fusion in collapsing bubbles. If the effect were real, and could be harnessed, it could provide us with effectively unlimited energy at very little cost.

However, several of Taleyarkhan’s colleagues at Purdue have revealed to the journal that their confidence in his work and results has been seriously dented since he arrived in their department in 2004. Faculty members Lefteri Tsoukalas and Tatjana Jevremovic, along with several others who do not wish to be named, say that since Taleyarkhan began working at Purdue, he has removed the equipment with which they were trying to replicate his work, claimed as ‘positive’, experimental runs for which they never saw the raw data, and opposed the publication of their own negative results.

Moreover, UCLA’s Brian Naranjo is submitting a paper to Physical Review Letters that provides an analysis of Taleyarkhan’s recently published data. The conclusions strongly suggests that Taleyarkhan did not detect fusion, but a standard lab source of radioactivity. This latest episode seems certain to burst the bubble, but Nature leaves a caveat in their press release on this subject:

“Bubble fusion is theoretically possible,” the journal says, “but do these latest findings spell the end for this particular line of enquiry?”

Well, perhaps it isn’t their place to actual wield the needle, but on the basis of Naranjo’s study it certainly looks like the bubble has gone pear-shaped to say the least.

Detecting Unknown Viruses

A Norwegian graduate student reckons his new antivirus program which can detect unknown viruses is thirty times faster than rival systems developed by the team at Massachusetts Institute of Technology. Tom Lysemose’s software can also effectively detect attacks by unknown computer viruses. The press release from the Research Council of Norway claims that no previous software can detect unknown viruses, but I’m pretty sure that’s not the case. The antivirus companies have been using heuristic algorithms to spot virus characteristics in suspect files for years, albeit with nowhere near 100% accuracy.

Nevertheless, Lysemose hopes to address the rather embarrassing situation in which many software vendors have found themselves – namely that common programming errors lead to so-called buffer overflow, which can be exploited transparently by a virus.

Lysemose points out that such programming mistakes are common for all programrs who write in C, one of the world’s most common programming languages. The web browser Internet Explorer, the VOIP telephony system Skype and the database software from Microsoft SQL Server are all affected, even antivirus software itself, such as that proferred by Symantec, is susceptible to this problem.

The effects can be devastating. In 2003, the Slammer virus took control of a huge number of database servers, spreading itself rapidly. The virus was not especially destructive, it spread so widely that it slowed down the entire Internet. Systems over the entire world were affected, and even some banks’ automated teller machines were shut down, says Lysemose.

To understand Lysemose’s software, one needs a quick introduction to how Buffer Overflow is a unfortunate programming error. Within a computer’s internal memory are a series of containers called buffers. When running a program that communicates over the Internet, such as a web browser, the technology functions so that the contents in the buffers of the network server are transferred to the buffers in the computer.

One example is when a password is entered on a web page. The password is stored in its own buffer on the local computer. Consider, for example, that this buffer could only have enough space for eight characters. If the programr forgets to check the buffer size, the buffer runs over if someone enters more than eight characters.

Unfortunately, not all programrs are aware of this. If those who write software have not included a routine that checks if enough room exists in the buffer, the areas that are physically next to the buffer will be overwritten. This is extremely regrettable. The computer gives no warning and continues to run as if nothing has happened.

Unfortunately, the overwritten areas can hold important instructions for the software that’s running, such as “Please provide an overview of all my documents”.

This is exactly the type of weakness that virus creators exploit. They can make a virus that sends a larger data packet than the computer’s buffer capacity. If the hacker discovers exactly where the most important instructions are located, the virus can be programd so that it overwrites these instructions with completely different commands, such as “Delete all of my documents now”. And then the user is out of luck.

Which is where Lysemose’s innovation comes in to its own. His system, ProMon, cannot prevent an unknown virus from attacking a buffer and the areas around it, but ProMon monitors programs to ensure that they do not do things that they are not programd to do. This means that ProMon will stop a program if it suddenly begins to do another thing.

This solution is a new way of thinking about virus prevention. ProMon works within a program, such as the web browser Internet Explorer, in order to monitor the interaction between the program’s modules. As long as the program performs legitimate transactions between its modules, ProMon does nothing. But if an illegal transaction occurs, ProMon decides a virus has attacked and promptly stops the program, Lysemose explains. As such, ProMon can monitor any program. The product will be introduced to the large anti-virus companies later this month.

In the meantime, check out the sciencebase spyware, trojans and worms page

Regional Blood Groups

A sciencebase visitor emailed today, asking whether blood types really do correlate to different areas of the world and disease resistance in those particular areas. She suggested that maybe we should be living in those areas to give us protection. At least that’s what I think she was implying…

Well, there is no short answer, but I’m sure most people would rather not have where they live dictated by the disease protection status of their blood type. If I lived in a wealthy northern european city, but happened to have a blood type that protected me against malaria as is the case with carriers of the gene for sickle cell or thalassemia, I wouldn’t want to move to a place where malaria was rife, unless I had another good reason to go.

Anyway, the straight answer to the question is that yes, certain blood types have a different risk associated with specific diseases and that in terms of ancestry these blood types tend to be associated with particular regions. As I said, it seems that being a carrier of the sickle cell gene provides some protection against malaria and the same too for thalassemia. On a related note, other “diseases” are associated with reduced risk of specific infection. Carriers of the cystic fibrosis gene (not a blood type, obviously), for instance, have a lower chance of suffering from typhoid and cholera.

Sciencebase readers might be able to shed a little more light on the relationship between blood type and disease risk.

Ionic Liquids Lose their Green Stripes

Despite being heralded as the green alternative to noxious, toxic, inflammable volatile organic compounds, room temperature ionic liquids are slowly losing their green stripes. In a paper published in the journal Green Chemistry (2006, 8, 238-240), Italian researchers report the acute toxicity of these compounds to zebra fish.

Luigi Intorre of the University of Pisa and colleagues, explain that although interest in ionic liquids because of claimed environmental safety is on the increase, these very good non-volatile solvents, could have harmful effects on certain ecosystems nevertheless.

The team has assessed the acute toxicity towards zebrafish of several ionic liquids with different anions and cations and found that toxic effects depended on the specific structure of the ionic liquid. However, the overall effect is potentially fatal harm to the fish’s gills.

This publication comes in the wake of earlier revelations that ionic liquids, although purportedly non-volatile, can indeed be distilled, according to a C&EN report.

Having said all that, ionic liquids still present a potentially “greener” alternative, if handled and disposed of safely, than many of the volatile organic solvents used in industry.

Pretti, C., Chiappe, C., Pieraccini, D., Gregori, M., Abramo, F., Monni, G., & Intorre, L. (2006). Acute toxicity of ionic liquids to the zebrafish (Danio rerio) Green Chemistry, 8 (3) DOI: 10.1039/b511554j

Black Eyed Peas – Big Hit in Nanotech

Researchers at the John Innes Centre in Norwich have grown particles of a mosaic virus that infects black-eyed peas and dressed them up with a redox-active organometallic compound* to convert the particles into nanoscopic molecular capacitors.

The virus, which is only harmful to black-eyed, or cowpea plants, has a unique structure making it the perfect scaffold for chemical modification, allowing the team to tailor its chemical and physical properties to particular applications.

‘This is an exciting discovery in bionanotechnology using plant viruses to produce electronically active nanoparticles of defined size’ says graduate student Nicole Steinmetz, who is working on the EU-funded project with project leader David Evans and George Lomonossoff of the Department of Biological Chemistry. ‘Future applications may be in, for example, biosensors, nanoelectronic devices, and electrocatalytic processes,’ she adds.

The project is still in the very early stages, by the JIC considered it newsworthy enough to publish a press release today and capitalise on the popularity of young people’s popular music beat combo the Black-eyed Peas, and never one to miss out on an opportunity for catching a few new readers, particularly among the youth of today, Sciencebase is getting down with it, to give it a mention too.

The work was published in detail in the journal ‘Small’ and is, the press release says, the first piece of nanotechnology from the John Innes Centre.

Meanwhile, if you want more on the business of nanotech, you might wish to subscribe to Small Times, which you can get for free for a year through this special Sciencebase link. Grab it while you can, as these magazines sometimes drop off the roster.

*240 units of a ferrocenecarboxylate, in fact.