Category Archives: Science

The Science Behind Spore

Spore is the hugely anticipated game from Wil Wright (the creator of Sims). In this webcast he discusses the science behind Spore. The creature creator was released this week and the full game will be released soon. Spore has been doing a great job marketing the product and they continue to do so with lots of material on You Tube including the Spore Ultimate Dance Contest.

The idea of the game is to design creatures that then go out into the world and interact and evolution takes it course. It looks very cool.

Lancelet Genome Provides Answers on Evolution

Lancelet genome shows how genes quadrupled during vertebrate evolution by Robert Sanders

“If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements.”
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Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine “housekeeping” genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that, Putnam said, make us different from all other creatures.

“These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal,” he said. “The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them.”

“The most exciting thing that the amphioxus genome does is provide excellent evidence for the idea that Ono proposed in 1970, that the human genome had undergone two rounds of whole-genome duplication with subsequent losses,”

A great example of the scientific method in action. It often isn’t a matter of developing a theory one day, testing it the next and learning the outcome the next. The process can take decades for complex matters.

How Humans Evolved Allergies

Ancient antibody molecule offers clues to how humans evolved allergies

The chicken molecule, an antibody called IgY, looks remarkably similar to the human antibody IgE. IgE is known to be involved in allergic reactions and humans also have a counterpart antibody called IgG that helps to destroy invading viruses and bacteria. Scientists know that both IgE and IgG were present in mammals around 160 million years ago because the corresponding genes are found in the recently published platypus genome. However, in chickens there is no equivalent to IgG and so IgY performs both functions.

Lead researcher, Dr. Rosy Calvert said: “Although these antibodies all started from a common ancestor, for some reason humans have ended up with two rather specialised antibodies, whereas chickens only have one that has a much more general function.
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Professor Brian Sutton, head of the laboratory where the work was done said: “It might be that there was a nasty bug or parasite around at the time that meant that humans needed a really dramatic immune response and so there was pressure to evolve a tight binding antibody like IgE. The problem is that now we’ve ended up with an antibody that can tend to be a little over enthusiastic and causes us problems with apparently innocuous substances like pollen and peanuts, which can cause life-threatening allergic conditions.”

Mathematicians Critique Journal Rankings

Three international math groups joined forces to issue a report last week decrying the use of citation statistics to evaluate scientific journals, research institutions and individual scientists. These statistics, sometimes called “bibliometrics,” measure how frequently a given journal’s articles are cited by other journals.

Read the report on Citation Statistics. This concern is justified. I do have some interest in some of these (and related) statistics but one must always remember their limitations.

TX Active Cement

TX active cement graphic

Industry scrambles to find a ‘greener’ concrete

While Italcemente’s smog-eating cement has been used in Europe for several years, it was released in the United States only in 2007 under the name TX Active. It contains titanium dioxide, which, in the presence of sunlight, acts as a photocatalyer, hastening the decomposition of such pollutants as nitrogen oxides, sulfur oxides, and ozone. TX Active also keeps a building shiny white – a quality admired by architects – by preventing the buildup of pollutants on the surface.

Research suggests that if 15 percent of the surface area of Milan, Italy, were covered in TX Active, air pollutants there could be reduced by 50 percent.

When weighing the environmental effects of concrete, some other benefits need to be included, says Rick Bohan of the Portland Cement Association (PCA), a nonprofit trade group based in Skokie, Ill. For example, the insulation provided by concrete walls combats greenhouse-gas emissions by reducing the energy needed for heating and cooling a building by up to 40 percent compared with wood- and steel-frame structures, according to PCA research.

TXActive Cement graphic from HeidelbergCement

Cloak of Silence

Experts unveil ‘cloak of silence’

“The mathematics behind cloaking has been known for several years,” said Professor John Pendry of Imperial College London, UK, an expert in cloaking. “What hasn’t been available for sound is the sort of materials you need to build a cloak out of.”
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The Spanish team who conducted the new work believe the key to a practical device are so-called “sonic crystals”. These artificial composites – also known as “meta-materials” – can be engineered to produce specific acoustical effects.
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The research builds on work by scientists from Duke University in North Carolina, US, and the Hong Kong University of Science and Technology. Earlier this year, independent teams from the two institutions demonstrated the mathematics necessary to create an acoustic cloak. Other scientists have shown that objects can be cloaked from electromagnetic radiation, such as microwaves.

Shaw Laureates 2008

Image of the Shaw Prize Medal

The Shaw Prize awards $1 million in each of 3 areas: Astronomy; Life Science and Medicine; and Mathematical Sciences. The award was established in 2002 by Run Run Shaw who was born in China and made his money in the movie industry. The prize is administered in Hong Kong and awards those “who have achieved significant breakthrough in academic and scientific research or application and whose work has resulted in a positive and profound impact on mankind.” The 2008 Shaw Laureates have been selected.

Astronomy
Professor Reinhard Genzel, Managing Director of the Max Planck Institute for Extraterrestrial Physics, in recognition of his outstanding contribution in demonstrating that the Milky Way contains a supermassive black hole at its centre.

In 1969, Donald Lynden-Bell and Martin Rees suggested that the Milky Way might contain a supermassive black hole. But evidence for such an object was lacking at the time because the centre of the Milky Way is obscured by interstellar dust, and was detected only as a relatively faint radio source. Reinhard Genzel obtained compelling evidence for this conjecture by developing state-of-the-art astronomical instruments and carrying out a persistent programme of observing our Galactic Centre for many years, which ultimately led to the discovery of a black hole with a mass a few million times that of the Sun, in the centre of the Milky Way.

Supermassive black holes are now recognized to account for the luminous sources seen at the nuclei of galaxies and to play a fundamental role in the formation of galaxies.

Mathematical Sciences
Vladimir Arnold, together with Andrei Kolmogorov and Jurgen Moser, made fundamental contributions to the study of stability in dynamical systems, exemplified by the motion of the planets round the sun. This work laid the foundation for all subsequent developments right up to the present time.

Arnold also produced extremely fruitful ideas, relating classical mechanics to questions of topology. This includes the famous Arnold Conjecture which was only recently solved.

In classical hydrodynamics the basic equations of an ideal fluid were derived by Euler in 1757 and major steps towards understanding them were taken by Helmholtz in 1858, and Kelvin in 1869. The next significant breakthrough was made by Arnold a century later and this has provided the basis for more recent work.

Ludwig Faddeev has made many important contributions to quantum physics. Together with Boris Popov he showed the right way to quantize the famous non-Abelian theory which underlies all contemporary work on sub-atomic physics. This led in particular to the work of ”²t Hooft and Veltman which was recognized by the Nobel Prize for Physics of 1999.
Continue reading →

Plastic Balls for the Resevoir

photo of Los Angeles resevoir

This photo looks like a April fools joke but I think it is real. Los Angeles Drops 400,000 Balls in Reservoir to Fight Suspected Carcinogen

So why deploy these balls — which are typically used by airports to prevent bird congregation on runways — in particular? Some of the other alternatives, such as a large tarp or metal cover, were considered too costly or impractical. The balls, on the other hand, are (relatively) cheap — costing 40 cents each — and are safe for drinking water; black is also the only color able to deflect UV rays.

The DWP has ordered 6.5 million of these balls, 3 million of which it plans on using to blanket the Ivanhoe and Elysian reservoirs. So, yeah, this probably isn’t the best solution for the city’s water woes but, given the circumstances, maybe the only “realistic” option in the short-term.

Los Angeles Department of Water and Power drops 400,000 balls onto Ivanhoe Reservoir:

The water needs to be shaded because when sunlight mixes with the bromide and chlorine in Ivanhoe’s water, the carcinogen bromate forms, said Pankaj Parekh, DWP’s director for water quality compliance. Bromide is naturally present in groundwater and chlorine is used to kill bacteria, he said, but sunlight is the final ingredient in the potentially harmful mix.

Photo by (Irfan Khan / Los Angeles Times)

Call me a bit skeptical. Adding a huge number of plastic balls to a water supply in order to try and prevent a chemical reaction caused by added chemicals and sunlight seems a bit crazy to me. But who know maybe it is a good idea.

Bacteria Evolutionary Shift Seen in the Lab

Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait. And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.
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sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.
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The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

Big Drug Research and Development on Campus

Big Drug R&D on Campus

Merck and Harvard just signed an agreement to develop treatments for the bone disease osteoporosis. On Apr. 25 rival Pfizer (PFE) invested $14 million in an alliance with four universities to study diabetes and obesity.

Drugmakers are counting on these deals to solve a persistent problem: underperforming product pipelines. Merck, Pfizer, and others have been losing sales of one blockbuster drug after another as patents expire and competitors charge in with generics. Big drug companies have fought back by spending more on research, yet the number of new medicines approved each year is falling. In the last week of April alone, the U.S. Food & Drug Administration rejected two of Merck’s experimental drugs, prompting the company to lay off 1,200 salespeople.
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Past deals between industry and academia have been hampered by patent disputes and tussles over publication rights, as companies tried to thwart academics who want to share their discoveries with colleagues around the world. So now the companies have devised policies allowing their Ivory Tower partners to patent and publish their discoveries, even as they draw the professors more deeply into corporate affairs.

Funding university activities this way can lead to conflicts and problems but realistically huge amounts of funding are entangled with possible conflicts of interest. The biggest concern I is that universities will bow to the almighty dollar instead of their missions. And inadequate oversight can damage their credibility (not one failure, most likely, but if a pattern emerges). For example: Researchers Fail to Reveal Full Drug Pay (“The Harvard group’s consulting arrangements with drug makers were already controversial because of the researchers’ advocacy of unapproved uses of psychiatric medicines in children.”). Then find out the companies were paying them well, the professors failed to disclose that and the advocacy is rightfully questioned.