Category Archives: Science

Science Commons: Making Scientific Research Re-useful

Science Commons is a project of Creative Commons. Like other organizations trying to support the advancement of science with open access they deserve to be supported (PLoS and arXiv.org are other great organizations supporting science).

Science Commons has three interlocking initiatives designed to accelerate the research cycle – the continuous production and reuse of knowledge that is at the heart of the scientific method. Together, they form the building blocks of a new collaborative infrastructure to make scientific discovery easier by design.

Making scientific research re-useful, help people and organizations open and mark their research and data for reuse. Learn more.

Enabling one-click access to research materials, streamline the materials-transfer process so researchers can easily replicate, verify and extend research. Learn more.

Integrating fragmented information sources, help researchers find, analyze and use data from disparate sources by marking and integrating the information with a common, computer-readable language. Learn more.

NeuroCommons, is their proof-of-concept project within the field of neuroscience. The NeuroCommons is a beta open source knowledge management system for biomedical research that anyone can use, and anyone can build on.

Fast Fitness Forecast is False, it Takes Time

Fitness Isn’t an Overnight Sensation

“To make a change in how you look, you are talking about a significant period of training,” Dr. Kraemer said. “In our studies it takes six months to a year.” And, he added, that is with regular strength-training workouts, using the appropriate weights and with a carefully designed individualized program. “That is what the reality is,” he said.

And genetic differences among individuals mean some people respond much better to exercise than others
…
Now, said Mr. Antane, who runs with a group in Princeton on Thursday nights, “everything changed — my outlook on life, who I hung out with, how I felt about myself.”

Our bodies evolved under conditions with much more exercise than we currently get if we sit in an office all day. And we had less food. It is no surprise with more food and less exercise that we gain weight. And given that the benefit of fat was to help us survive when we had little food out bodies don’t change overnight. If they did then our ancestors would have had much more difficulty surviving – the whole point was to provide a resource to tap in bad times. If that resource dissipated quickly it would not have helped much.

New Family of Antibacterial Agents Discovered

Bacteria continue to gain resistance to commonly used antibiotics. In this week’s JBC, one potential new antibotic has been found in the tiny freshwater animal Hydra.

The protein identified by Joachim GrÃ¶tzinger, Thomas Bosch and colleagues at the University of Kiel (Germany), hydramacin-1, is unusual (and also clinically valuable) as it shares virtually no similarity with any other known antibacterial proteins except for two antimicrobials found in another ancient animal, the leech.

Hydramacin proved to be extremely effective though; in a series of laboratory experiments, this protein could kill a wide range of both Gram-positive and Gram-negative bacteria, including clinically-isolated drug-resistant strains like Klebsiella oxytoca (a common cause of nosocomial infections). Hydramacin works by sticking to the bacterial surface, promoting the clumping of nearby bacteria, then disrupting the bacterial membrane.

GrÃ¶tzinger and his team also determined the 3-D shape of hydramacin-1, which revealed that it most closely resembled a superfamily of proteins found in scorpion venom; within this large group, they propose that hydramacin and the two leech proteins are members of a newly designated family called the macins.

Source: American Society for Biochemistry and Molecular Biology

Evolution, Methane, Jobs, Food and More

Photo from May 2005 by NASA’s Mars Exploration Rover Spirit as the Sun sank below the rim of Gusev crater on Mars.

Science Friday is a great National Public Radio show. The week was a great show covering Antimicrobial Copper, Top Jobs for Math and Science, Human-Driven Evolution, Methane On Mars, Fish with Mercury and more. This show, in particular did a great job of showing the scientific inquiry process in action.

“Fishing regulations often prescribe the taking of larger fish, and the same often applies to hunting regulations,” said Chris Darimont, one of the authors of the study. “Hunters are instructed not to take smaller animals or those with smaller horns. This is counter to patterns of natural predation, and now we’re seeing the consequences of this management.” Darimont and colleagues found that human predation accelerated the rate of observable trait changes in a species by 300 percent above the pace observed within purely natural systems, and 50 percent above that of systems subject to other human influences, such as pollution

Very interesting stuff, listen for more details. A part of what happens is those individuals that chose to focus on reproducing early (instead of investing in growing larger, to reproduce later) are those that are favored (they gain advantage) by the conditions of human activity. I am amazed how quickly the scientists says the changes in populations are taking place.

And Methane On Mars is another potentially amazing discovery. While it is far from providing proof of live on Mars it is possibly evidence of life on Mars. Which would then be looked back on as one of the most important scientific discoveries ever. And in any even the podcast is a great overview of scientists in action.

This week astronomers reported finding an unexpected gas — methane — in the Martian atmosphere. On Earth, a major source of methane is biological activity. However, planetary scientists aren’t ready to say that life on Mars is to blame for the presence of the gas there, as geochemical processes could also account for the finding. The find is intriguing especially because the researchers say they have detected seasonal variations of methane emissions over specific locations on the planet.

Martian Methane Reveals the Red Planet is not a Dead Planet
The Mars Methane Mystery: Aliens At Last?

Soil Mineral Degrades the Nearly Indestructible Prion

Warped pathogens that lack both DNA and RNA, prions are believed to cause such fatal brain ailments as chronic wasting disease (CWD) in deer and moose, mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans. In addition to being perhaps the weirdest infectious agent know to science, the prion is also the most durable. It resists almost every method of destruction from fire and ionizing radiation to chemical disinfectants and autoclaving, which reduce prion infectivity but fail to completely eliminate it.

Other studies have shown that prions can survive in the soil for at least three years, and that soil is a plausible route of transmission for some animals, says Joel Pedersen, a UW-Madison environmental chemist. “We know that environmental contamination occurs in deer and sheep at least,” he notes.

Prion reservoirs in the soil, Pedersen explains, are likely critical links in the chain of infection because the agent does not appear to depend on vectors — intermediate organisms like mosquitoes or ticks — to spread from animal to animal.

That the birnessite family of minerals possessed the capacity to degrade prions was a surprise, Pedersen says. Manganese oxides like birnessite are commonly used in such things as batteries and are among the most potent oxidants occurring naturally in soils, capable of chemically transforming a substance by adding oxygen atoms and stripping away electrons. The mineral is most abundant in soils that are seasonally waterlogged or poorly drained.

full press release

Moth Jams Bat Sonar

Superloud moth jams bat sonar

A gray moth with orange highlights called Bertholdia trigona “goes berserk,” making lots of noise above the range of human hearing when a hunting bat approaches, says William Conner of Wake Forest University in Winston-Salem, N.C. Bats rely on their natural sonar to locate flying moths in the dark, but in a lab setup, the bats rarely managed to nab a loud moth.

When researchers disabled the moth’s noisemaking organs, though, bats caught the moths in midair with ease, Conner reported at the annual meeting of the Society for Integrative and Comparative Biology.

Conner says the work is “the first example of any prey item that jams biological sonar.” Conference attendee David Yager of the University of Maryland in College Park says Conner’s experimental paradigm is “very strong, and I do think he has documented jamming by a species of moth.”

Insect-hunting bats and their moth prey have become a classic in the study of evolutionary arms races, Conner says. “This is warfare … The first counter-adaptation is that the insects developed ears.”
…
Jamming isn’t the only possible explanation for moth noises, he said. An explosive clicking sound coming back out of the night might startle a bat just a split-second long enough for the moth to get away.

Providing Computer to Remote Students in Nepal

photo of students using computers in Nepal

Pupils conquer fear of computers

“I was really scared when I saw the computer,” he says. “I didn’t go near it. I was worried it might explode and kill me. “It was only when the teacher called me saying it was harmless that I went into the room, but I still hesitated.” Things have changed now, he adds.

“I’m feeling much better. The E-library has helped with my studies. “We can see the periodic table of science, and also maps and other geography things in a pictorial way that is easy to understand. It’s not only that – we can also play games and have fun.”

Kamal says his parents were very excited when he told them about the computer and came to watch the very next day. It was not only Kamal. His computer teacher, Shankar Prajapati, says all the pupils were afraid. “They all worried they would catch some virus and fall ill or even die. But now they are familiar with computers,” he says.

“Even we teachers are gaining knowledge from the E-library. It’s really helpful for us, too. “The students can see science experiments carried out on screen and search for whatever they want in the encyclopaedia.
…
This is a free and open-source (accessible to everyone) package which connects one powerful central server in the school, using the Linux operating system, to a number of diskless low-end computers. When linked to the server, each computer receives a full Linux desktop.

Read more about the Help Nepal Network’s eLibrary program. Photos from this web site shows students in Nepal using computers.

In the face of rapidly changing technological advancement and the exorbitant cost of proprietary hardware and software solutions, which had stymied Nepal in attempting to participate in ICT for development, the use for Free and Open Source Software (FOSS) is emerging as a solution.
…
Linux Terminal Server Project (LTSP) can be a low cost solution for deprived communities who cannot afford a bigger volume financial expense.
…
LTSP, a system that works with only one central high end server and other diskless low-end thin client computers, allows to run Linux on a server, and then use thin clients (almost any computer will do) to connect to the server and receive a full-blown Linux desktop.

I believe strongly in the ability of kids to learn if they are just provided some tools that help them do so. See a great post on Hole in the Wall computers.

Does the Earth Have Two Cores?

Did Earth’s Twin Cores Spark Plate Tectonics?

a new theory aims to rewrite it all by proposing the seemingly impossible: Earth has not one but two inner cores.

The idea stems from an ancient, cataclysmic collision that scientists believe occurred when a Mars-sized object hit Earth about 4.45 billion years ago. The young Earth was still so hot that it was mostly molten, and debris flung from the impact is thought to have formed the moon.

Haluk Cetin and Fugen Ozkirim of Murray State University think the core of the Mars-sized object may have been left behind inside Earth, and that it sank down near the original inner core. There the two may still remain, either separate or as conjoined twins, locked in a tight orbit.

Their case is largely circumstantial and speculative, Cetin admitted. “We have no solid evidence yet, and we’re not saying 100 percent that it still exists,” he said. “The interior of Earth is a very hard place to study.”

The ancient collision is a widely accepted phenomenon. But most scientists believe the incredible pressure at the center of the planet would’ve long since pushed the two cores into each other.

I must say two cores seems very far-fetched to me. But it is another great example of the scientific discovery process and an interesting idea.

A Microscopic Layer of Diamonds Beneath the Surface of North America

Diamonds show comet struck North America, scientists say

A discovery of microscopic diamonds a few feet beneath the surface of North America reveals that a comet caused a cataclysm of fire, flood and devastation nearly 13,000 years ago that extinguished mammoths and mastodons and dealt a blow to early civilization, scientists said Friday.

The nanodiamonds, so small that they are barely visible in an electron microscope, are thought to be remnants of that comet, which would have hit about 65 million years after the much larger collision that wiped out the dinosaurs.
…
Battered by fire and ice, as many as 35 species of mammals, including American camels, the short-faced bear, the giant beaver, the dire wolf and the American lion, either immediately vanished or were so depleted in number that humans hunted them to extinction.

The humans, a Paleo-Indian grouping known as the Clovis culture for the distinctive spear points they employed, suffered a major population drop, disappearing in many areas for hundreds of years.
…
gems can only be created under the extreme temperatures and pressures of a massive explosion, such as a comet striking the Earth’s surface.

“There’s no other way we can interpret the presence of these diamonds other than an extraterrestrial impact,” said James Kennett, a paleooceanographer.

Such an impact would be the most likely source of nanodiamonds, critics agreed. But many argued that the one-page paper in Science did not provide enough evidence to support the authors’ claim.

“Nanodiamonds could be a good indicator of an impact event . . . but after reading the paper, I wasn’t convinced they found diamonds,” said physicist Tyrone Daulton of Washington University in St. Louis. “Maybe they found diamonds and maybe they didn’t.”

Swarm of Yellowstone Quakes Baffles Scientists

photo of Yellowstone's Old Faithful by John Hunter

Photo of Old Faithful geyser in Yellowstone National Park by John Hunter

Swarm of Yellowstone Quakes Baffles Scientists

Swarms of small earthquakes happen frequently in Yellowstone, but it’s very unusual for so many earthquakes to happen over several days, said Robert Smith, a professor of geophysics at the University of Utah. “They’re certainly not normal,” Smith said. “We haven’t had earthquakes in this energy or extent in many years.”
…
“There doesn’t seem to be anything to be alarmed about,” Vallie said. Smith said it’s difficult to say what might be causing the tremors. He pointed out that Yellowstone is the caldera of a volcano that last erupted 70,000 years ago.
…
Yellowstone has had significant earthquakes as well as minor ones in recent decades. In 1959, a magnitude 7.5 quake near Hebgen Lake just west of the park triggered a landslide that killed 28 people.

So far the most powerful quake over the last few days has been one at 3.8 on the Richter scale. An earthquake of 4.0-4.9 “Noticeable shaking of indoor items, rattling noises. Significant damage unlikely.” The Richter scale is a logarithmic scale, meaning a measure of 4.0 is 10 times as powerful as 3.0 quake, and 5.0 is 100 times more powerful than a 3.o quake.