Month: December 2006

Carl Sagan Blog

Carl Sagan BlogCarl Sagan was one of my childhood heroes, watching the Cosmos unfold on his seminal TV show was almost a weekly religious experience.

On 20th December, Sagan fans and bloggers will launch a worldwide blog-a-thon to commemorate the life and legacy of Carl Sagan on the tenth anniversary of his death.

The event has been organized by New York City Sagan fan Joel Schlosberg, and encourages bloggers of all stripes to discuss the influence of outspoken astronomer, science communicator and creator of Contact. Schlosberg plans to compile a blog of blogs.

Make contact on December 20.

All the Little Birdies Go Tweet, Tweet, Tweet

Reuters this week reported that poultry farmers should make sure to prevent sparrows, starlings, and pigeons from entering chicken houses because they could potentially infect poultry with the H5N1 bird flu virus.

I suppose that does make sense, but sounds rather impractical. Small birds have an amazing ability to worm (is that a suitable word?) their way into even the smallest of openings. Chimneys and vents are absolutely no problem for sparrows. It’s only a couple of months ago that I had to dismantle our heating system to release a trapped bird from the flu and there’s a tiny gap (half an inch?) between two roof tiles on our neighbour’s property into which starlings wantonly fly in and out on a daily basis.

Now, picture a chicken farm – I assume they’re referring to battery chickens rather than free range. Every chicken farm I’ve ever seen, and there are quite a few in this locale, has dodgy roof tiles, vents, ducts, openings, doors, even. And, dozens upon dozens of chickens feeding on all kinds of tasty grains and pellets. The temptation for any small bird is just too much and they flock in and out as often as they can get away with.

Admittedly, the article is referring mainly to small chicken coops, that are perhaps a little more manageable. But, that said, a poverty stricken keeper of a few domestic chickens may not have the means to repair one of those dodgy roofs even if it is small.

Regardless of what we do to protect poultry from H5N1 it is not likely that this viral strain specifically will be the culprit when a global pandemic gets underway. There are other strains, there are other viruses, the strain that will be P2P transmissable may already have jumped to another host, such as a pig on a Vietnamese smallholding or a cat in a Hong Kong market cage. It may even have made the leap to humans, in which case it is only a matter of time before it emerges into the wild.

No amount of fixing up chicken coops and keeping the starlings at bay is going to prevent that from happening.

YAFSE – train your beady eye on EB-eye

The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) this week launched its new website. Apparently, the web interface has been streamlined on the basis of user feedback. Nothing too exciting in that, except they have also upgraded their search engine and describe it as being at the centre of the site and exhaustive in its breadth.

Underpinning the new site is “EB-eye”, a trendy-sounding and powerful search engine allowing instant searches of all the EBI’s databases from a single query. “If you can use Google you can use this,” explains associate directory Graham Cameron, latching on to the “proper-verb” of the day.

Seriously though, the new site architecture should allow much swifter navigation between databases, so that you can get from genomes to genes, proteins to structures and biological functions from a single, simple interface.

Intriguingly for an organisation that goes by the monicker of EMBL-EBI acronyms (and jargo, allegedly) have been banished from the site wherever possible. You’re unlikely to hear scientists say, “I’ve just EB-eye’d it,” just yet. But, it might make more sense for specialists to do just that rather than “Googling” for their information needs.

Squaring the fish eye

Square fish eyeThe classic fish-eye lens gives photographers the visual equivalent of surround sound, capturing an all-encompassing view. But, while the results are dramatic the subject is considerably distorted to fit within the bounds of the circular image formed. This renders such lens ineffective as an all-seeing-eye in a security setting or for providing robots with better navigation.

South Korean researchers have now designed and built an inexpensive optical lens that collects light from a large area and produces an almost distortion-free wide-angle image with the more familiar rectangular shape.

The complete story is available in the latest edition of the Intute Spotlight column.

Buying Nano This Holiday

According to the Nanotech Project, more than twenty years of research, has begun to yield the first commercial applications for nanotechnology in consumer products. They explain that nanoscale materials can now be found in electronics, cosmetics, automotive parts, and medical products. Apparently, there are about 350 such products.

But, while the British media is running scared at the idea of nanotechnology turning the world to grey goo (and we’re not talking Second Life here), The Register reports on a Nature Nanotechnology paper that claims almost three quarters of Americans have heard little or nothing about nanotechnology. Nano, of course, refers only to the scale of any particular particle or component of any technology.

Nano, meaning nothing more than a billionth, so a nanometre is a billionth of a metre. Funnily enough, most of the so-called nanoscale products actually have dimensions of several hundred nanometres, so in truth such objects could be called microscale (or in more familiar parlance microscopic). Micro meaning a millionth. A micrometre is therefore a millionth of a metre. Something that’s 500 nanometres might just as readily be described as half a micrometre.

The author of the Nature Nanotechnology paper warns that public ignorance in the US of nanotechnology means that legislation may be passed without informed debate. Fair point, but it can be pushed to the opposite extreme with precautionary attitudes predominating and stifling research and development that might benefit us all, as has happened in the UK with respect to genetically modified organisms (GMOs and GM food).

Do you agree?

Emerging environmental contaminants

Lake ContaminationMore than forty research papers highlight the effects of emerging contaminants on human health and the environment in the December 2006 issue of the journal Environmental Science & Technology, among their number are reports on nanoparticles, pharmaceuticals, disinfectant by-products, and fluorochemicals.

“It might be tempting to define emerging contaminants as one thing or following certain criteria but it’s not that simple,” says the journal’s guest editor Jennifer Field of Oregon State University. The following Spotlight editorial reveals some of the issues and diversity of materials studied as well as highlighting a significant technology that might allow decontamination for certain materials to be carried out. An audio summary from the journal’s editors is available as an mp3 download courtesy of ES&T.

Read the full article under Intute’s Spotlight

Phishing for spam

The New York Times this week reported that spam levels have doubled in the last six months. I’m pretty sure there was a lull towards the end of the summer, but we’ll take their word for it. The paper reports on figures released by one of the myriad spam-filtering companies, Ironport, and claims that 90 percent of the 50 billion e-mails sent across the internet (as opposed to internal company emails, which are a different matter) every day is a spam or a phishing mail.

Everyone assumes that the vast majority of the spam sent is offering pictures and videos of people in various states of undress for the one-handed surfers out there. However, the spam figures don’t quite stack up like that. The “London” Times published figures that reveal half of all spam is for health products, a third of all spam is for money and stocks advice and tips, and a mere 3 out of every 100 is adult-only content, as it were. That’s still 1.5b adult spams a day.

Moreover, the London Times’ report suggests more worryingly that spam mail has increased by 300% in the last four months, not merely doubling as the NYT has it.

The anti-spam companies claim they can trap 95% of the spam, but that leaves 2.5b spams getting through every day. The vast majority of those seem to arrive in my inbox, and I daren’t take a holiday for fear of missing that false positive when the spam trap clears the filters each week.

What do you think? Is spam affecting your work? What can we do to stem the tide?

A sweet little fairy story

The fairies at the bottom of my garden have been digging up the pot of gold at the end of the rainbow. A spokesdog for the Society of Wolves tells me that Canis Lupus is no longer dining on geriatric homeowners nor juvenile females in crimson headgear. Oh, and there is no link between sugar in the diet and diabetes.

The first two statements may seem a little far-fetched but that last one, surely it’s a fairy story…

Well, apparently not. In a press release posted on AlphaGalileo by the UK’s Sugar Bureau, new evidence from researchers at the Royal Victoria Hospital and Queen’s University Belfast suggests that receiving a quarter of daily calories from sucrose (sugar) as part of a balanced, weight-maintaining diet does not result in any difference in insulin resistance compared to getting 10% of the same number of calories from sucrose.

The press release states, that “It has long been suspected that a high sugar diet over a long term period may lead to an increased risk of developing diabetes. But there has been little or no evidence to support this idea, with studies on the role of any aspect of the diet in the development of diabetes difficult to conduct.”

So, is this the evidence we’ve all been waiting for?

The research, published by Steven Hunter and colleagues in the journal Diabetes points to sugar’s innocence. “Sugar has traditionally been linked to the development of diabetes,” he says, “These findings challenge that thinking, and show that intakes of more than double that currently recommended do not appear to have an adverse effect on markers of diabetes risk.”

But, let’s take a closer look at this little story from the Sugar Bureau. The trial studied the effects of different amounts of sucrose in the diets of 13 healthy men without diabetes over a period of six weeks.

Thirteen volunteers? Six weeks?

How can they draw any serious conclusions from such a tiny sample tested over such an incredibly short period? Where is the data on sucrose intake for hundreds if not thousands of people over several years of sucrose abuse? While there is evidence that saturated fat intake and obesity are closely linked to diabetes risk, this single very small study cannot seriously claim that sugar intake has no effect on diabetes risk. How can they tell in a month and a half with just 6 or 7 men being fed a larger amount of sugar in their diet?

I don’t doubt the researchers’ integrity, but this news, coming as it does from the Sugar Bureau, does smack of sickly sweet spin to my cynical eye. It doesn’t tell us anything about the long-term effect of repeated blood sugar spikes caused by excessive intake nor about the effects of aging on sucrose processing and the harmful cross-links it can form with body proteins.

It’s a story that will have the tooth fairy rubbing its hands in glee as well as giving anyone with a penchant for two desserts the impression that they can get away with a large amount of sugar in their diet without having to worry about diabetes. I find it hard to imagine a happy ever after for this story.

What do you think? Should organisations or companies that promote a particular product be allowed to fund scientific research into the benefits or otherwise of that product?

Too much protein increases cancer risk

Earlier this week scientists reported a strong correlation between obesity and the risk of common cancers, such as cancer of the colon and breast cancer. Today, initial findings from a US study suggest that eating less protein could be a way to protect some people from cancers that are not directly associated with obesity.

The research is published in the December issue of the American Journal of Clinical Nutrition (2006, 84, 1456), shows that lean people on a long-term, low-protein, low-calorie diet or participating in regular endurance exercise training have lower levels of plasma growth factors and certain hormones linked to cancer risk. “However, people on a low-protein, low-calorie diet had considerably lower levels of a particular plasma growth factor called IGF-1 than equally lean endurance runners,” says Luigi Fontana of Washington University, “That suggests to us that a diet lower in protein may have a greater protective effect against cancer than endurance exercise, independently of body fat mass.”

“Our findings show that in normal weight people IGF-1 levels are related to protein intake, independent of body weight and fat mass,” Fontana says. “I believe our findings suggest that protein intake may be very important in regulating cancer risk.”

Fontana says most of us don’t eat nearly enough fruits and vegetables or enough whole-grains, cereals or beans. “Many people are eating too many animal products – such as meat, cheese, eggs and butter – as well as refined grains and free sugars,” he says. “Our intake of vegetables and fruits is low, and beans are vastly underconsumed in the U.S. and Europe these days.”

He believes diets would be healthier if we ate more whole grains, beans, fruits and vegetables and far fewer animal products. He recommends mostly fish, low-fat dairy products and, occasionally, some red meat. Such a diet would both cut total calories and reduce the amount of protein we consume to healthier levels.

“Eating too many calories increases our risk of developing obesity, diabetes, cardiovascular disease and of certain types of cancer related to obesity,” Fontana adds, “We hope to further clarify what happens to cancer risk when we are chronically eating more protein than we need.”

AIDS in Libya

Previously we reported on the case of six medical workers in Libya who face the death sentence having been charged with deliberately contaminating more than 400 children with HIV in 1998. The evidence in their defence has now reached the molecular level and is published today online in Nature.

Oliver Pybus and colleagues in an international research team has used the genetic sequences of the viruses isolated from the patients to reconstruct the exact history, or “family tree” of the outbreak. They assessed accumulated mutations and have demonstrated unequivocally that the HIV subtype involved in this case was already infecting patients well before the medical workers had even set foot in Libya.

The trial ended on November 4 and the verdict is expected for December 19. However, a growing body of scientific evidence already suggested that the outbreak was caused by poor hospital hygiene rather than deliberate action.

Thomas Leitner of Los Alamos National Laboratory has provided forensic HIV evidence in more than thirty such cases over the past fifteen years. He describes the Nature paper as “compelling evidence that the outbreak had started before the accused could have started it.”

Do you agree? What else should we as outsiders be doing if anything?