Deadly TB Strain is Spreading, WHO Warns

Posted on March 23, 2007  Comments (2)

Deadly TB strain is spreading, WHO warns:

Africa’s large AIDS population is at special risk from the particularly virulent strain, known as XDR-TB (extremely drug resistant), which had been documented in 35 countries worldwide, 16 of them in this year. “This is the most urgent thing I have seen in my 15 years of working on tuberculosis,” said Mario Raviglione, director of the STOP TB program at the World Health Organization. He introduced WHO’s TB report, which coincides with the 125th anniversary of the discovery of the microbe that causes TB.

Some 2 billion people worldwide live with TB, an airborne illness that is normally treatable through inexpensive medication. But if the disease is not diagnosed and treated, it can mutate into drug-resistant strains. In 2005, nearly 9 million people became infected with tuberculosis and 1.6 million died of it, about the same as the year before, which showed that containment efforts were working, Raviglione said. The epidemic is centered primarily in Asia and in Africa, which accounted for 84 percent of the total.

“The good news is that the global incidence may have peaked,” particularly in China, India, and Indonesia, he said. “The bad news is that although the incidence has declined [there] is resistance to most powerful first-line drugs and a form of TB that is resistant to second-line drugs.”

Related: TB infection rate may be on ‘threshold of decline’TB fight could take centuries without new tools: UN‘Virtually untreatable’ TB foundTB Pandemic Threat

Biologists Solve B-12 Vitamin Puzzle

Posted on March 22, 2007  Comments (0)

MIT biologists solve vitamin puzzle

B12, the most chemically complex of all vitamins, is essential for human health. Four Nobel Prizes have been awarded for research related to B12, but one fragment of the molecule remained an enigma–until now. The researchers report that a single enzyme synthesizes the fragment, and they outline a novel reaction mechanism that requires cannibalization of another vitamin.

Vitamin B12 is produced by soil microbes that live in symbiotic relationships with plant roots.

BluB catalyzes the formation of the B12 fragment known as DMB, which joins with another fragment, produced by a separate pathway, to form the vitamin. One of several possible reasons why it took so long to identify BluB is that some bacteria lacking the enzyme can form DMB through an alternate pathway, Walker said.

One of the most unusual aspects of BluB-catalyzed synthesis is its cannibalization of a cofactor derived from another vitamin, B2. During the reaction, the B2 cofactor is split into more than two fragments, one of which becomes DMB. Normally, the B2-derived cofactor would assist in a reaction by temporarily holding electrons and then giving them away. Such cofactors are not consumed in the reaction.

Antibiotics Too Often Prescribed for Sinus Woes

Posted on March 22, 2007  Comments (12)

This is not one of the more amazing articles, rather one more in the long line of those reporting on the overuse of anti-biotics: Antibiotics Too Often Prescribed for Sinus Woes:

But it’s hard to preach that wisdom to someone with a drippy, hurting sinus who wants immediate relief, Leopold acknowledged. Because more effective drugs are lacking, “patients are desperate, physicians are desperate, and it is not a happy situation,” he said.

I guess I am just out of touch but why do physicians think it is ok to practice bad medicine because people will whine if they try to practice sensible medicine? These stories often tell of doctors that can’t say no to patients even if it means going against what is the best medical advice. Is it any wonder that helath costs continue to escalate, now totaling 16% of GDP, with such practices accepted? How hard is it to say, yeah great you want x drug, that is not medically advisable and is only available by prescription because it is not advisable for people to decide they need it but rather physicians are suppose to make that decision.

And so the physician often makes the practical choice of giving what the patient wants, with a chance of relief, over the more abstract issue of antibiotic resistance, he said.

I understand this reality. I just find it very sad that that professionals sacrifice the future to today’s ignorance and short sightedness. I wish physicians would not reward those demanding they get what they want today since they are simultaneously condemning others to suffer the consequences of such decisions.

But I also want us to stop spending our grandchildren’s money today. Still the politicians act just like the physicians choosing to give the voters what they want today and let someone else deal with the consequences later. Current USA federal deficit: $8,841,291,672,873 (see live debt clock), $29,349 for every citizen of the USA. It seems pretty obvious the same willingness to sacrifice the future for an easier life today is at the root of the actions by both doctors and politicians. Thankfully some are trying to counter this behavior, by both parties, to varying success.

Related: CDC Urges Increased Effort to Reduce Drug-Resistant InfectionsAntibiotics related postsAntibiotic resistance: How do antibiotics kill bacteria?

Swiss dig world’s Longest Tunnel

Posted on March 21, 2007  Comments (0)

Swiss dig world’s longest tunnel:

As long ago as 1994, the Swiss voted in a nationwide referendum to put all freight crossing their country onto the railways. Naturally, such an ambitious plan was not going to happen overnight, but now the project dubbed the engineering feat of the 21st Century is slowly taking shape.

Deep beneath the Alps, the Swiss are building a high-speed rail link between Zurich and Milan. It will include, at 57 kilometres (35 miles), the world’s longest tunnel. A key feature of the project, which is new to alpine transport, is the fact that the entire railway line will stay at the same altitude of 500 metres (1,650ft) above sea level.

In fact the price tag for the entire rail link has soared from about $8bn (£4bn) to almost $15bn and final completion is unlikely to be before 2018.

Related: – Extreme EngineeringA ‘Chunnel’ for Spain and Morocco

Bdelloid Rotifers Abandoned Sex 100 Million Years Ago

Posted on March 21, 2007  Comments (7)

Who Needs Sex (or Males) Anyway? by Liza Gross:

If you own a birdbath, chances are you’re hosting one of evolutionary biology’s most puzzling enigmas: bdelloid rotifers. These microscopic invertebrates—widely distributed in mosses, creeks, ponds, and other freshwater repositories—abandoned sex perhaps 100 million years ago, yet have apparently diverged into nearly 400 species. Bdelloids (the “b” is silent) reproduce through parthenogenesis, which generates offspring with essentially the same genome as their mother from unfertilized eggs.

Scientists stumped by 100m years of chastity

Bdelloid rotifers are egg laying microscopic invertebrates — widely distributed in mosses, streams and ponds — which have managed to diverge into nearly 400 species without a scintilla of sex… Now a new study, published today in the journal PLoS biology, has confirmed the worst fears of scientists: the rotifers do indeed present a major challenge to the assumption that sex is necessary for organisms to diversify into species.

Rather than mixing up DNA, creatures like the bdelloid rotifers can evolve solely through the build-up of mutations that occur in the ‘cloning’ process when a new rotifer is born. The new study proves that these differences are not random and can help rotifers adapt to a different environment, such as the legs or chest of a water louse. Bdelloids can be found happily swimming around in a puddle in your garden, hot springs or in freezing ponds in the Antarctic.

Boeing CEO’s Speech to Engineering Students

Posted on March 21, 2007  Comments (0)

Boeing CEO offers UM students advice about careers, innovation:

He explained the reality, as it applies to the corporate world today, is that innovation is a team sport, not a solo sport. It (innovation) depends on a culture of technical sharing and openness to others not a reclusive environment, innovation can and should occur in all areas of the business, incremental doesn’t mean insignificant, eureka moments are rare, and in a business environment, creativity cannot exist without discipline.

“It takes people working together across different groups, disciplines, and organizational arms to make it happen,” Mr. McNerney said. “It also takes real leadership to charter the course and (inspire) people to reach for the highest level of performance supported by a never ending focus on integrity.”

According to McNerney business has become focused on measuring value practically, which causes engineering-based companies like Boeing to innovate more frequently than they invent all-new products.

Mechanical Hit Counter

Posted on March 20, 2007  Comments (0)

Mechanical Hit Counter:

I’ve always subscribed to the Rube Goldberg School of Engineering Design, the philosophy of which is “simple, elegant solutions are for the unimaginative”. These are words I can live by. Overengineered designs are where Art and Science meet, eye each other up a bit, sink a few pints, and head off to Science’s apartment to see his etchings. I tip my hat to Mr. Goldberg, using a machine that tips hats in 22 steps, starting with cracking an egg.

Here, then, is my humble contribution to the rich tradition of overengineering – the Mechanical Hit Counter. To operate it, open the webcam window

So, when you ping salem, you’re actually hitting my firewall, which redirects ICMP type 8 (Echo Request) so the board, whose internal address is BX decodes the ping request and asserts a TTL output high for 50ms. This turns on the transistor, which fires the relay, which cycles the power, which increments the counter. Then, the webcam takes a picture of it every 5 seconds and stores the image in the www directory. Voila!


Learning About the Human Genome

Posted on March 19, 2007  Comments (1)

You Don’t Miss Those 8,000 Genes, Do You? by Carl Zimmer:

Science moves forward by flow. One experiment leads to another. Observations accrue. What seem like side trips or even dead ends may bring a fuzzy picture further into focus. Yet science often seems as if it moves forward one bombshell at a time, marked by scientific papers and press conferences.

When Craig Venter and his colleagues published their rough draft of the human genome in 2001 they identified 26,588 human genes. They then broke those genes down by their functions. Some were involved in building DNA, some in relaying signals, and so on. Remarkably, though, they classified 12809 genes–almost half–as “molecular function unknown.” Last week I wanted to know if those numbers still hold.

They weren’t so easy to find. In 2003 some reports came out to the effect that the genome had shrunk down to 21,000 genes. But I couldn’t turn up much news in the past four years.

The pie shows that we’re now down to just 18,308 genes. That’s over 8,000 genes fewer than six years ago. Many sequences that once looked like full-fledged genes, capable of generating a protein, now don’t make the grade. Some genes turned out to be pseudogenes–vestiges of genes that once worked but have been since wrecked by mutations. In other cases, DNA segments that appeared to be parts of separate genes have turned out to be part of the same gene.

Today scientists still don’t know the function of 5898 genes in the human genome. In other words, over the past six years about 7,000 genes either have been figured out or have vanished into the land of nevermind.

Great post. Read it.

248-dimension Math Puzzle

Posted on March 19, 2007  Comments (0)

248-dimension maths puzzle solved:

What came out was a matrix of linked numbers, which together describe the structure of E8. It contains more than 60 times as much data as the human genome sequence.

Each of the 205,263,363,600 entries on the matrix is far more complicated than a straightforward number; some are complex equations. The team calculated that if all the numbers were written out in small type, they would cover an area the size of Manhattan.

In addition to facilitating further understanding of symmetry and related areas of mathematics, the team hopes its work will contribute to areas of physics, such as string theory, which involve structures possessing more than the conventional four dimensions of space and time.

Relationships Among Scientific Paradigms

Posted on March 18, 2007  Comments (0)

Relationships Among Scientific Paradigms

Links (curved black lines) were made between the paradigms that shared papers, then treated as rubber bands, holding similar paradigms nearer one another when a physical simulation forced every paradigm to repel every other; thus the layout derives directly from the data. Larger paradigms have more papers; node proximity and darker links indicate how many papers are shared between two paradigms. Flowing labels list common words unique to each paradigm, large labels general areas of scientific inquiry.

See the site for a interesting graphic display of the relationships.

Google Summer of Code 2007

Posted on March 18, 2007  Comments (4)

Google Summer of Code will pay about 800 students $4,500 to work on open source software development projects this summer at over 50 open source organizations including: Gaim, Drupal, EFF,,, Subversion and WordPress. Applications opened March 14th and are due by March 24th.

While the majority of past student participants were enrolled in university Computer Science and Computer Engineering programs, GSoCers come from a wide variety of educational backgrounds, from computational biology to mining engineering. Many of our past participants had never participated in an open-source project before GSoC; others used the GSoC stipend as an opportunity to concentrate fully on their existing open source coding activities over the summer.

See the site for many more details. Find internship opportunities via (a web site): engineering internshipsscience internships.

Related: Three summers of open sourceA Career in Computer Programmingscience and engineering career posts