Tag Archives: Science

Beautiful Basics of Science

Natalie Angier’s recent book, The Canon, is a great overview of the world of science. The book gets a bit too carried away with being cute (A top-of-the-line radar can pinpoint the whereabouts of a housefly two kilometers away, although clearly this is a radar with far too much time on its hands), but overall is excellent. Such lines are find, in moderation, but this book has too many by a factor of 10 or 100. Some gems from the book:

page 19: Science is not a rigid body of facts. It is a dynamic process of discovery.

page 47: true happenstance bears a distinctive stamp, and until you are familiar with its pattern, you are likely to think it messier, more haphazard, than it is… it often makes people uncomfortable by not looking random enough.

page 92: while the different atoms are all about the same size – a tenth of a billionth of a meter across – they diverge in their mass, in the number of protons and neutrons with which their nucleus is crammed.

page 99: If you drag a comb through your dry hair, the comb will strip off millions of electrons from the outermost shells of the atoms of you coiffure.

The details are great (about a trillion electrons are involved when you get a small static electricity shock) and it is an excellent book for those interested in an overview of science that does not require in depth science education to follow. And yet with a good background in science the material presented is still plenty interesting.

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

Adaptive Flight Control With Living Neuronal Networks on Microelectrode Arrays (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 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.

New Supercomputer for Science Research

“Jaguar is one of science’s newest and most formidable tools for advancement in science and engineering,” said Dr. Raymond L. Orbach, DOE.s Under Secretary for Science. The new capability will be added to resources available to science and engineering researchers in the USA.

80 percent of the Leadership Computing Facility resources are allocated through the United States Department of Energy’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, a competitively selected, peer reviewed process open to researchers from universities, industry, government and non-profit organizations. Scientists and engineers at DOE’s Oak Ridge National Laboratory are finding an increasing variety of uses for the Cray XT system. A recent report identified 10 breakthroughs in U.S. computational science during the past year. Six of the breakthroughs involved research conducted with the Jaguar supercomputer, including a first-of-its-kind simulation of combustion processes that will be used to design more efficient automobile engines. Read the computational science report. Read full press release.

ORNL’s Jaguar fastest computer for science research

Jaguar will be used for studies of global climate change, as well as development of alternative energy sources and other types of scientific problem-solving that previously could not be attempted.

Zacharia said ORNL’s Jaguar was upgraded by adding 200 Cray XT5 cabinets – loaded with AMD quadcore processors and Cray SeaStar interconnects – to the computer’s existing 84 Cray XT4 cabinets. The combined machine resulted in the new standard for computational science.

The peak operating speed is apparently just below that of Los Alamos National Laboratory’s IBM Roadrunner system, which is designed for 1.7 petaflops. But the Jaguar reportedly has triple the memory of Roadrunner and much broader research potential.
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Because the Jaguar has come online sooner than expected, Zacharia said an alert was sent to top U.S. scientists inviting them to apply for early access to the Oak Ridge computer. Their scientific proposals will be reviewed on an accelerated timetable, he said.

The peak capability of 1.64 petaflops is attributed to 1.384 petaflops from the new Cray XT5, combined with 0.266 petaflops from the existing Cray XT4 system, Zacharia said.

How fast is a quadrillion calculations per second? “One way to understand the speed is by analogy,” Zacharia said recently. “It would take the entire population of the Earth (more than 6 billion people), each of us working a handheld calculator at the rate of one second per calculation, more than 460 years to do what Jaguar at a quadrillion can do in one day.”

Static Stretching Decreases Muscle Strength

Stretching: The Truth

Researchers now believe that some of the more entrenched elements of many athletes’ warm-up regimens are not only a waste of time but actually bad for you. The old presumption that holding a stretch for 20 to 30 seconds – known as static stretching – primes muscles for a workout is dead wrong. It actually weakens them.
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A well-designed warm-up starts by increasing body heat and blood flow.
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To raise the body’s temperature, a warm-up must begin with aerobic activity, usually light jogging. Most coaches and athletes have known this for years.
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Athletes who need to move rapidly in different directions, like soccer, tennis or basketball players, should do dynamic stretches that involve many parts of the body. “Spider-Man” is a particularly good drill: drop onto all fours and crawl the width of the court, as if you were climbing a wall.

Toward a More Open Scientific Culture

Michael Nielsen wrote a great post, The Future of Science, which is also the topic of a book he is writing. He discusses how scientific advancement has often been delayed as those making discoveries did not share them openly. And how 300 years ago scientific journals and reward systems created ways for scientists to be rewarded for publication. And he continues with the need for the process to again change and promote more open sharing of scientific knowledge, which I agree with and have written about previously: Publishers Continue to Fight Open Access to Science, Science Journal Publishers Stay Stupid, The Future of Scholarly Publication, etc..

Why were Hooke, Newton, and their contemporaries so secretive? In fact, up until this time discoveries were routinely kept secret.
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This cultural transition was just beginning in the time of Hooke and Newton, but a little over a century later the great physicist Michael Faraday could advise a younger colleague to “Work. Finish. Publish.” The culture of science had changed so that a discovery not published in a scientific journal was not truly complete. Today, when a scientist applies for a job, the most important part of the application is their published scientific papers.

This has been a great advance. Now we need to continue that advance to use the internet to make that publication open and increase the advantage of shared knowledge to society.

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.
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This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services. Such extreme openness is the ultimate expression of the idea that others may build upon and extend the work of individual scientists in ways they themselves would never have conceived.
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To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: (1) build superb online tools; and (2) cause the cultural changes necessary for those tools to be accepted.

I agree we need to take advantage of the new possibilities to advance the practice of science. His full post is well worth reading.

Atlantic Hurricane Season 2008

photo of hurricane evacuation sign

Here is a nice post on weather and understanding data – Atlantic Hurricane Season 2008

A well-accepted metric which convolves storm frequency, intensity, and duration is called accumulate cyclone energy (ACE) and is calculated very simply: take the maximum sustained winds reported by the NHC every 6-hours for all storms (> 34 knots), square this value, and sum over the entire lifetime, then divide by 10,000. In 2007, even though there were also 15 storms, the ACE was only 72 compared to 132 for 2008 with the same number of named storms. This is partially because the storms in 2008 were much longer lived especially Bertha.
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When encapsulated in the recent active period in North Atlantic activity (1995-2007), 2008 experienced normal or expected activity as measured by ACE. In terms of a long-term climatology, either the last 30 or 65 years, 2008 is clearly an above average year.

Data can’t lie but mistaken assumptions can lead you to form mistaken impressions. If you believe the number of named storms = hurricane activity and then are surprised that in fact there was many more days of hurricane activity it is not because the data lied but because you didn’t understand what the data represented.

76 Nobel Laureates in Science Endorse Obama

76 Nobel Laureates in Science Endorse Obama!. This is the largest number of Nobel laureates to endorse anything according to that post. Letter:

An Open Letter to the American People

This year’s presidential election is among the most significant in our nation’s history. The country urgently needs a visionary leader who can ensure the future of our traditional strengths in science and technology and who can harness those strengths to address many of our greatest problems: energy, disease, climate change, security, and economic competitiveness.

We are convinced that Senator Barack Obama is such a leader, and we urge you to join us in supporting him.

During the administration of George W. Bush, vital parts of our country’s scientific enterprise have been
damaged by stagnant or declining federal support. The government’s scientific advisory process has been distorted by political considerations. As a result, our once dominant position in the scientific world has been shaken and our prosperity has been placed at risk. We have lost time critical for the development of new ways to provide energy, treat disease, reverse climate change, strengthen our security, and improve our economy.

We have watched Senator Obama’s approach to these issues with admiration. We especially applaud his emphasis during the campaign on the power of science and technology to enhance our nation’s
competitiveness. In particular, we support the measures he plans to take – through new initiatives in
education and training, expanded research funding, an unbiased process for obtaining scientific advice, and an appropriate balance of basic and applied research – to meet the nation’s and the world’s most urgent needs.

Senator Obama understands that Presidential leadership and federal investments in science and technology are crucial elements in successful governance of the world’s leading country. We hope you will join us as we work together to ensure his election in November.

Signed,

Alexei Arikosov, Physics, 2003
Peter Agre, Chemistry, 2003
Sidney Altman, Chemistry, 1989
Philip W. Anderson, Physics, 1977
Richard Axel, Medicine, 2004
David Baltimore, Medicine, 1975
Baruj Benacerraf, Medicine, 1980
Paul Berg, Chemistry, 1980
J. Michael Bishop, Medicine, 1989
N. Bloembergen, Physics, 1981
Michael S. Brown, Medicine, 1985
Linda B. Buck, Medicine, 2004 Continue reading →

The Rush to Save Timbuktu’s Crumbling Manuscripts

Fabled Timbuktu, once the site of the world’s southernmost Islamic university, harbors thousands upon thousands of long-forgotten manuscripts. A dozen academic instutions from around the world are now working frantically to save and evaluate the crumbling documents.
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The Ahmed Baba Library alone contains more than 20,000 manuscripts, including works on herbal medicine and mathematics, yellowed volumes of poetry, music and Islamic law. Some are adorned with gilded letters, while others are written in the language of the Tuareg tribes. The contents remain a mystery.

Manuscript hunters are now scouring the environs of Timbuktu, descending into dark, clay basements and climbing up into attics. Twenty-four family-owned collections have already been discovered in the area. Most of the works stem from the late Middle Ages, when Timbuktu was an important crossroads for caravans.
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Archaeologists have shown that an incredible system of underground canals up to 20,000 kilometers (12,422 miles) long once existed at Wadi al-Hayat in Libya. Thanks to such hydraulic marvels, the desert blossomed and crops sprouted in the fields of the Tuareg.

Science Postercasts

I wrote about SciVee, over a year ago, saying I thought they could become a valuable resource. It has been taking longer to really get going than I thought it would but this new feature, Postercasts, is great. I am glad to see SciVee living up to my high expectation. Keep up the great work SciVee. The experience can still use improvement but this is a great start.

They have provided a tutorial on: How to Synchronize my Poster to my Video. I hope some of our readers try this out.

via: Interactive Virtual Posters

Related: Engineering TV – Science Webcasts – Magnetic Movie