Category Archives: Science

Harnessing Light to Drive Nanomachines

A team led by researchers has shown that the force of light indeed can be harnessed to drive machines – when the process is scaled to nano-proportions. Their work opens the door to a new class of semiconductor devices that are operated by the force of light. They envision a future where this process powers quantum information processing and sensing devices, as well as telecommunications that run at ultra-high speed and consume little power.

The energy of light has been harnessed and used in many ways. The “force” of light is different — it is a push or a pull action that causes something to move. “While the force of light is far too weak for us to feel in everyday life, we have found that it can be harnessed and used at the nanoscale,” said team leader Hong Tang, assistant professor at Yale. “Our work demonstrates the advantage of using nano-objects as ‘targets’ for the force of light – using devices that are a billion-billion times smaller than a space sail, and that match the size of today’s typical transistors.”

Full Press release

2,000 Species New to Science from One Island

photo of squat lobster

Photograph by Dr Tin-Yam Chan, University of Keelung

153 scientists from 20 countries fanned out across the remote South Pacific island of Espiritu Santo, examining mountains, forests, caves, reefs, and water for all living organisms. In five months, they collected 10,000 species. Some 2,000 of these may be new to science.

This squat lobster, found in waters 150 meters (492 feet) deep, is one of the new species. Eighty percent of the world’s species remain to be discovered, notes French scientist Philippe Bouchet, one of the expedition’s leaders.

A World of Crabs from One Tiny Island

About 600 of these were crab species. The two-horn box crab is able to crack and peel open snails’ shells using a sharp “tooth” on its right claw to cut open shells and long, slender “fingers” on the left claw to yank out its prey.

HHMI on Science 2.0: Information Revolution

The Howard Hughes Medical Institute does great things for science and for open science. They have an excellent article in their HHMI Bulletin – Science 2.0: You Say You Want a Revolution?

Cross-pollination among research disciplines is in fact at the core of many other popular science blogs. Michael Eisen, an HHMI investigator at the University of California, Berkeley, is an avid blog reader who particularly enjoys John Hawks’ site on paleoanthropology, genetics, and evolution. A recent post there discussed a new sequencing of Neanderthal mitochondrial DNA. “It’s like a conduit into another whole world,” says Eisen.
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The current extreme of collaboration via Science 2.0 is OpenWetWare.org. Begun in 2003 by Austin Che, who was then a computer science and biology graduate student at MIT, this biological-engineering Website uses the wiki model to showcase protocols and lab books: everything is open and can be edited by any of its 4,000 members.
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“Most publishers wish open access would go away,” says Brown. It won’t. Major research-funding organizations, including NIH, HHMI, and the Wellcome Trust, now require their grantees to post their findings on openaccess Websites such as PLoS or PubMed Central within 12 months of publication in traditional journals. Publishers are pushing back, however, and in September, the House Judiciary Committee began holding hearings on whether the federal government should be allowed to require grantees to submit accepted papers to a free archive.

How Large Quantities of Information Change Everything

Scale: How Large Quantities of Information Change Everything

There’s another important downside to scale. When we look at large quantities of information, what we’re really doing is searching for patterns. And being the kind of creatures that we are, and given the nature of the laws of probability, we are going to find patterns. Distinguishing between a real legitimate pattern, and something random that just happens to look like a pattern can be somewhere between difficult and impossible. Using things like Bayesian methods to screen out the false positives can help, but scale means that scientists need to learn new methods – both the new ways of doing things that they couldn’t do before, and the new ways of recognizing when they’ve screwed up.

There’s the nature of scale. Tasks that were once simple have become hard or even impossible, because they can’t be done at scale. Tasks that were once impossible have become easy because scale makes them possible. Scale changes everything.

I discussed related ideas on my Curious Cat Management Improvement blog recently: Does the Data Deluge Make the Scientific Method Obsolete?

The Science of Gardening

Photo of a bee by Justin Hunter

The Science of Gardening

Linda Chalker-Scott, an associate professor at Washington State University, is the author of The Informed Gardener and producer of the column “Horticultural Myths.” In The Truth About Garden Remedies: What Works, What Doesn’t, and Why, Jeff Gillman, associate professor at the University of Minnesota, is just as rational and informative
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Do go ahead and dig in soil improvements, Chalker-Scott advises, for vegetable gardens or annual flowerbeds, in which nutrients need replacing yearly. But there’s really no need to dig organic amendments—manure and peat moss, etc.—into landscapes that are permanent. Treat those plantings of trees and shrubs as if they were forest ecosystems, not agricultural fields—wood chips and decaying leaves on top, no tilling-in of fertilizer.
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It must drive both authors nuts to hear people say, “I’m an organic gardener. I never use chemicals.” Everything on earth is composed of chemicals.

The last line calls to mind the recent Royal Society of Chemistry attempt to reclaim the word chemical from the advertising and marketing industries: Â£1,000,000 for 100% chemical free material. A good example for our scientific literacy posts.

Photo by Justin Hunter.

How Cells Age

A new study by Harvard Medical School researchers reveals that the biochemical mechanism that makes yeast grow old has a surprising parallel in mice, suggesting it may be a universal cause of aging in all organisms.
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In young organisms, SIRT1 effectively doubles as a gene-expression regulator and a DNA repairer. But when DNA damage accumulates—as it does with age—SIRT1 becomes too busy fixing broken DNA to keep the expression of hundreds of genes in check. This process is so similar to what happens in aging yeast that its discoverers believe it may represent a universal mechanism of aging.

Harvard researchers gain new insight into aging

Aging may be a case of neglect — an absentee landlord at the cellular level that allows gene activity to go awry, according to a study published today.

Scientists have long known that aging causes gene expression to change, and DNA damage to accumulate. But now, research led by Harvard Medical School scientists explains the connection between the two processes in mammals.

The paper, published in the journal Cell, found that a multi-tasking protein called SIRT1 that normally acts as guardian of the genome gets dragged away to DNA fix-it jobs. When the protein abandons its normal post to work as a genetic handyman, order unravels elsewhere in the cell. Genes that are normally under its careful watch begin to flip on.

“What this paper actually implies is that aspects of aging may be reversible,” said David Sinclair, a Harvard Medical School biologist who led the research. “It sounds crazy, but in principle it should be possible to restore the youthful set of genes, the patterns that are on and off.”

The study is just the latest to draw yet more attention to sirtuins, proteins involved in the aging process

Aging is fascinating. By and large people just accept it. We see it happen to those all around us, without exception. But what causes biological aging? It is an interesting area of research.

Rate of Cancer Detected and Death Rates Declines

Declines in Cancer Incidence and Death Rates in report from the National Cancer Institute and CDC:

“The drop in incidence seen in this year’s Annual Report is something we’ve been waiting to see for a long time,” said Otis W. Brawley, M.D., chief medical officer of the American Cancer Society (ACS). “However, we have to be somewhat cautious about how we interpret it, because changes in incidence can be caused not only by reductions in risk factors for cancer, but also by changes in screening practices. Regardless, the continuing drop in mortality is evidence once again of real progress made against cancer, reflecting real gains in prevention, early detection, and treatment.”
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According to a U.S. Surgeon General’s report, cigarette smoking accounts for approximately 30 percent of all cancer deaths, with lung cancer accounting for 80 percent of the smoking-attributable cancer deaths. Other cancers caused by smoking include cancers of the oral cavity, pharynx, larynx, esophagus, stomach, bladder, pancreas, liver, kidney, and uterine cervix and myeloid leukemia.

Diagnoses Of Cancer Decline

The analysis found that the overall incidence of cancer began inching down in 1999, but not until the data for 2005 were analyzed was it clear that a long-term decline was underway. “The take-home message is that many of the things we’ve been telling people to do to be healthy have finally reached the point where we can say that they are working,” Brawley said. “These things are really starting to pay off.”

Brawley and others cautioned, however, that part of the reduction could be the result of fewer people getting screened for prostate and breast cancers. In addition, the rates at which many other types of cancer are being diagnosed are still increasing
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Some experts said the drop was not surprising, noting that it was primarily the result of a fall in lung cancer because of declines in smoking that occurred decades ago. They criticized the ongoing focus on detecting and treating cancer and called for more focus on prevention.

“The whole cancer establishment has been focused on treatment, which has not been terribly productive,” said John C. Bailar III, who studies cancer trends at the National Academy of Sciences. “I think what people should conclude from this is we ought to be putting most of our resources where we know there has been progress, almost in spite of what we’ve done, and stop this single-minded focus on treatment.”

Rat Brain Cells, in a Dish, Flying a Plane

[the video was removed]

Adaptive Flight Control With Living Neuronal Networks on Microelectrode Arrays [broken link was removed] (open access paper) by Thomas B. DeMarse and Karl P. Dockendorf Department of Biomedical Engineering, University of Florida

investigating the ability of living neurons to act as a set of neuronal weights which were used to control the flight of a simulated aircraft. These weights were manipulated via high frequency stimulation inputs to produce a system in which a living neuronal network would “learn” to control an aircraft for straight and level flight.

A system was created in which a network of living rat cortical neurons were slowly adapted to control an aircraft’s flight trajectory. This was accomplished by using high frequency stimulation pulses delivered to two independent channels, one for pitch, and one for roll. This relatively simple system was able to control the pitch and roll of a simulated aircraft.

When Dr. Thomas DeMarse[broken link was removed] first puts the neurons in the dish, they look like little more than grains of sand sprinkled in water. However, individual neurons soon begin to extend microscopic lines toward each other, making connections that represent neural processes. “You see one extend a process, pull it back, extend it out — and it may do that a couple of times, just sampling who’s next to it, until over time the connectivity starts to establish itself,” he said. “(The brain is) getting its network to the point where it’s a live computation device.”

To control the simulated aircraft, the neurons first receive information from the computer about flight conditions: whether the plane is flying straight and level or is tilted to the left or to the right. The neurons then analyze the data and respond by sending signals to the plane’s controls. Those signals alter the flight path and new information is sent to the neurons, creating a feedback system.

“Initially when we hook up this brain to a flight simulator, it doesn’t know how to control the aircraft,” DeMarse said. “So you hook it up and the aircraft simply drifts randomly. And as the data come in, it slowly modifies the (neural) network so over time, the network gradually learns to fly the aircraft.”

Although the brain currently is able to control the pitch and roll of the simulated aircraft in weather conditions ranging from blue skies to stormy, hurricane-force winds, the underlying goal is a more fundamental understanding of how neurons interact as a network, DeMarse said.

Related: Neural & Hybrid Computing Laboratory @ University of Florida [broken link was removed] – UF Scientist: “Brain” In A Dish Acts As Autopilot, Living Computer [broken link was removed] – Roachbot: Cockroach Controlled Robot – New Neurons in Old Brains – posts on brain research – Viruses and What is Life – Great Self Portrait of Astronaut Engineer

Dealth of Artic Plankton a Warning on Warming

Death bloom of plankton a warning on warming by David Perlman

Vanishing Arctic sea ice brought on by climate change is causing the crucially important microscopic marine plants called phytoplankton to bloom explosively and die away as never before, a phenomenon that is likely to create havoc among migratory creatures that rely on the ocean for food, Stanford scientists have found.
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Phytoplankton throughout the world’s oceans is the crucial nutrient at the base of the food web on which all marine life depends; when it’s plentiful, life thrives and when it’s gone, marine life is impossible.
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“It’s a complex system,” Arrigo said in an interview, “but as the changes in ice cover throw the timing of phytoplankton abundance off, then the birds and animals whose brains have long been programmed to migrate north at specific times of the year will have missed the boat if there’s no nourishment for them when they get there.”

Every spring and summer, phytoplankton in the Arctic blooms richly in explosive pulses, nourished by nitrogen and phosphorous in the seawater, and when those chemicals are consumed, the blooms end, Arrigo said.

Save the Microbes, Save the World

The panel starts speaking at about minute 14. The technical presentation of the video could be better (likely will be as we develop good, easy ways to capture speaking events for web delivery) but their is some interesting content.