Category Archives: Research

Google Lunar X Prize

seeks to create a global private race to the Moon that excites and involves people around the world and, accelerates space exploration for the benefit of all humanity. The use of space has dramatically enhanced the quality of life and may ultimately lead to solutions to some of the most pressing environmental problems that we face on earth – energy independence and climate change.
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we hope to usher in an era of commercial exploration and development, in which small companies, groups of individuals and universities can build, launch and explore the Moon and beyond.

Sergey Brin: “So now, we are here today embarking upon this great adventure of having a nongovernmental, commercial organization return to the Moon and explore. And I’m very excited that Google can play a part in it.”

Clues to Prion Infectivity

Structural Studies Reveal New Clues to Prion Infectivity

One of the unexplained questions facing prion researchers is how a single prion can apparently assume different conformations — with each conformation having different disease or phenotypic properties. Previous structural studies of prions had not yielded a clear understanding of the basis of strains because the prion protein is large and complex. Due to the size and complexity of prions, studies utilizing x-ray crystallography, a technique commonly used to determine the structure of proteins and other molecules, have been limited to short peptide fragments of the prion protein.

“There have been a number of fairly low-resolution pictures of prions that more or less proved that these different strains were in different conformations; but they really hadn’t established the nature of the different conformations,” Weissman said. “It was really a big black box. We basically didn’t have the conformation of any single prion, let alone the two prion protein strains in two different conformations.”
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““In our minds, our findings brought to a certain level of closure the understanding of the structural differences underlying strains,” said Weissman. “Now we understand the structural differences. We also have an idea how those differences lead to the differences in physical properties, and, in turn, how these differences in the physical properties lead to the phenotypic differences. We are starting to go all the way from the structural understanding of the different strains up to in vivo understanding of why they cause different behaviors inside the cell.”

Weissman noted that the findings offer a broader lesson to researchers studying prions and other proteins whose misfolding can cause disease. “Certainly, a bottom line from this study is that the rules of protein folding and the rules of protein misfolding are fundamentally different,” he said. “In many ways, we have to relearn basic principles of how proteins misfold. We have to forget many of the rules we learned from textbooks about protein folding because they are not necessarily applicable.”

Prions are very interesting. Related posts: Scientists Knock-out Prion Gene in Cows – Gene Study Finds Cannibal Pattern – Open Access Education Materials on Protein Folding

Nanotechnology Breakthroughs for Computer Chips

Nano On Off Switch

Photo: Actual scanning tunneling microscopy images of the naphthalocyanine molecule in the “on” and the “off” state. More images

IBM Unveils Two Major Nanotechnology Breakthroughs as Building Blocks for Atomic Structures and Devices

IBM scientists have made major progress in probing a property called magnetic anisotropy in individual atoms. This fundamental measurement has important technological consequences because it determines an atom’s ability to store information. Previously, nobody had been able to measure the magnetic anisotropy of a single atom.

With further work it may be possible to build structures consisting of small clusters of atoms, or even individual atoms, that could reliably store magnetic information. Such a storage capability would enable nearly 30,000 feature length movies or the entire contents of YouTube – millions of videos estimated to be more than 1,000 trillion bits of data – to fit in a device the size of an iPod. Perhaps more importantly, the breakthrough could lead to new kinds of structures and devices that are so small they could be applied to entire new fields and disciplines beyond traditional computing.

In the second report, IBM researchers unveiled the first single-molecule switch that can operate flawlessly without disrupting the molecule’s outer frame — a significant step toward building computing elements at the molecular scale that are vastly smaller, faster and use less energy than today’s computer chips and memory devices.

In addition to switching within a single molecule, the researchers also demonstrated that atoms inside one molecule can be used to switch atoms in an adjacent molecule, representing a rudimentary logic element. This is made possible partly because the molecular framework is not disturbed.

One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

Continue reading →

Science Journal Publishers Stay Stupid

Science publishers get even stupider by Andrew Leonard:

The American Association of Publishers and everyone associated with it should be ashamed of trying to protect their profit margins by slandering the open access movement as government intervention and censorship. Research paid for with government funds should be freely accessible to the general public.

I wish it was amazing that these people have so little grasp of what has been going on in the world the last 5 years (but I must say such failure to adapt seems to be a common trait in too many organizations). Previously I have posted on the importance of continuing the scientific tradition of open debate and open access. In the past there have been distribution complexities that made paid journals an acceptable compromise. That people working at journals don’t see that the internet changes that is going to lead to their rapid irrelevance. They had to figure this out a couple of years ago. Given they still haven’t, I must say that they really don’t seem to have much understanding of science or modern communication methods. Given their industry that is sad. It is time for the scientific community to give up on these journals and start looking to move to work with new organizations that will encourage scientific communication and advancement (PLoS – arXiv.org – Open Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.

“It is not necessary to change. Survival is not mandatory.” Dr. W. Edwards Deming

I do object to scientific knowledge being kept out of the scientific and public community. The ability to use the internet to more effectively communicate new knowledge should not be sacrificed to protect the old model journals had for sustaining themselves. They should find a way to fund themselves and make their material available for free on the internet (I think some delay for free public access would be fine – the shorter the delay the better). Or they should be replaced by others that do so.

Studying Martian Soil for Evidence of Microbial Life

Study: Martian soil may contain life

The search for life on Mars appeared to hit a dead end in 1976 when Viking landers touched down on the red planet and failed to detect biological activity. But Joop Houtkooper of the University of Giessen, Germany, said on Friday the spacecraft may in fact have found signs of a weird life form based on hydrogen peroxide on the subfreezing, arid Martian surface.

His analysis of one of the experiments carried out by the Viking spacecraft suggests that 0.1 percent of the Martian soil could be of biological origin. That is roughly comparable to biomass levels found in some Antarctic permafrost, home to a range of hardy bacteria and lichen. “It is interesting because one part per thousand is not a small amount,” Houtkooper said in a telephone interview.

“We will have to find confirmatory evidence and see what kind of microbes these are and whether they are related to terrestrial microbes. It is a possibility that life has been transported from Earth to Mars or vice versa a long time ago.”

Interesting, certainly far from convincing evidence but still fun speculation. Claim of Martian Life Called ‘Bogus’:

Norman Pace, a microbiologist at the University of Colorado, is skeptical of the new claims. “It sounds bogus to me,” Pace told SPACE.com. “I don’t consider the chemical results to be particularly credible in light of the harsh conditions that Mars offers.”

Mining the Moon

Mining the Moon by Mark Williams:

At the 21st century’s start, few would have predicted that by 2007, a second race for the moon would be under way. Yet the signs are that this is now the case. Furthermore, in today’s moon race, unlike the one that took place between the United States and the U.S.S.R. in the 1960s, a full roster of 21st-century global powers, including China and India, are competing.

Even more surprising is that one reason for much of the interest appears to be plans to mine helium-3–purportedly an ideal fuel for fusion reactors but almost unavailable on Earth–from the moon’s surface
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But a serious critic has charged that in reality, He3-based fusion isn’t even a feasible option. In the August issue of Physics World, theoretical physicist Frank Close, at Oxford in the UK, has published an article called “Fears Over Factoids” in which, among other things, he summarizes some claims of the “helium aficionados,” then dismisses those claims as essentially fantasy.

As I stated in January in Helium-3 Fusion Reactor: “This sounds pretty incredible to me and I find the claims of using fuel from the Moon economically to power our needs on Earth. Still it is interesting and just because it sounds fantastic does not mean it can’t be true. But I am skeptical.”

Common Virus May Contribute to Obesity

Common virus may contribute to obesity

Infection with human adenovirus-36 (Ad-36) seems to direct adult stem cells from fat tissue to turn into fat cells, researchers have found in lab experiments. Stem cells not exposed to the virus, in contrast, were unchanged. More importantly, the researchers have identified the specific gene in the virus that appears to be involved in this obesity-promoting effect: E4Orfl.

The field of research investigating the role of viruses in obesity — dubbed “infectobesity” — is still relatively new and experimental. Researchers don’t believe that infection with one of these pathogens is the sole cause of obesity but they say some obesity cases may involve viral infections.

‘Looming Crisis’ from NIH Budget

‘Looming crisis’ from NIH budget by Ted Agres:

“Promising research is now being slowed or halted,” said Edward Miller, dean of Johns Hopkins Medicine. “We are seeing veteran scientists spending time not in labs but on the fundraising circuit. We are seeing young researchers quitting academic research in frustration, having concluded that their chances of having innovative research funded by NIH are slim to none,” Miller told a Capitol Hill news conference yesterday.

The scientists released a report prepared by 20 leading researchers from a consortium of nine academic institutions and universities, that outlines the benefits of increased NIH funding on biomedical innovations, and warns of the negative implications should the present budget be left unaddressed. The report cited threats from unexpected new diseases, such as SARS and pandemic influenza, as well as obesity, HIV, and bioterrorism.

While Congress and the White House doubled NIH’s budget from 1998 to 2003, funding has failed to keep pace with inflation. NIH’s budget has hovered at around $28 billion, but once inflation is factored in, its purchasing power has fallen 13% over the past four years. According to the report, an average of eight out of ten NIH grant applications currently go unfunded, while at the National Cancer Institute, only 11 percent of grants are funded. “This is a recipe for disaster,” Miller said. “The number of termination letters at Johns Hopkins is up three-fold.”

Peak Soil

An interesting article. Obvious the author has a biased viewpoint (that doesn’t mean the conclusions are wrong but it certainly can make one cautious – just as if a drug company shows results that their drug is effective or safe – you just have to pay a bit more attention…). I would be interested in others thoughts on this. My perception (though it is just an opinion based on limited facts) is that topsoil loss is a problem and that using corn for ethanol is more a federal government payoff to buy votes than a wise national policy. I am less inclined to accept some of the more extreme suggestions in the article. Peak Soil: Why cellulosic ethanol, biofuels are unsustainable and a threat to America

“The nation that destroys its soil destroys itself.” – President Franklin D. Roosevelt
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When you take out more nutrients and organic matter from the soil than you put back in, you are “mining” the topsoil. The organic matter is especially important, since that’s what prevents erosion, improves soil structure, health, water retention, and gives the next crop its nutrition. Modern agriculture only addresses the nutritional component by adding fossil-fuel based fertilizers, and because the soil is unhealthy from a lack of organic matter, copes with insects and disease with oil-based pesticides.

I believe it makes sense to research things like bio-fuels. However I am not convinced massive payments to the political well connected is a wise course of action.