Recently in Biophysics Category

guardian.co.uk: Tyrannosaurus rex was an athletic, warm-blooded animal that jogged rather than lumbered around its territory, according to a new study.

Researchers led by Herman Pontzer at Washington University in St Louis examined the anatomical details of 14 dinosaurs of different sizes to work out how much energy the animals might have needed to move around.

He found that, for dinosaurs weighing from a few kilograms to tons, the power their muscles needed was far too high for the animals to have been cold-blooded.

Related Link
Biomechanics of running indicates endothermy in bipedal dinosaurs

Wired.com: A cell in the eye may be worth two in the beak, at least when it comes to a migratory bird's magnetic compass.

In European robins (right image), a visual center in the brain and light-sensing cells in the eye—not magnetic sensing cells in the beak—allow the songbirds to sense which direction is north and migrate correctly, a new study finds. The study published in Nature, may improve conservation efforts for migratory birds.

Related Link
Visual but not trigeminal mediation of magnetic compass information in a migratory bird

The Daily Telegraph: The mantis shrimps, found on the Great Barrier Reef in Australia, have the most complex vision systems known to science, researchers at Bristol University have found.

The shrimps can see in 12 colors—humans see in only three—and can distinguish between different forms of light to give a sophisticated and vivid 3D image.

Related Update
A mantis shrimp's extraordinary eyes

Related Link
A biological quarter-wave retarder with excellent achromaticity in the visible wavelength region Nature Photonics

NYTimes.com: Two cases involving CT scans are under scrutiny in California—one involving a large, well-known Los Angeles hospital, the other a tiny hospital in the northern part of the state—underscoring the risks that powerful CT scans pose when used incorrectly.

Raven Knickerbocker, then an X-ray technologist at Mad River Community Hospital in Arcata, activated a CT scan 151 times on the same area of the head of 2 ½-year-old Jacoby Roth, investigators concluded.

A week ago, Cedars-Sinai Medical Center in Los Angeles disclosed that it had mistakenly administered up to eight times the normal radiation dose to 206 possible stroke victims over an 18-month period during a procedure intended to get clearer images of the brain.

Although CT scans are useful in determining internal injuries, there are major risks associated to patients because of the intensity of the X-rays used in the device, either through human error, or through too frequent exposure to X-rays.

In 2000-2001, CT scans constituted 7% of all radiologic examinations, but contributed 47% of the total collective dose from medical X-ray examinations.

Nature News: A new generation of light sources—the newly completed Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory in Menlo Park, California, one under construction in Japan and the European X-Ray Free-Electron Laser (XFEL) being built at at DESY in Germany—are getting set not only to put atoms and molecules under the spotlight, but also to illuminate their dynamics.

The devices, called X-ray free-electron lasers, produce flashes of X-ray light with angstrom-level wavelengths—small and coherent enough to image individual atoms. The flashes are also more intense than any created before—stuffed with enough photons to create and study extreme states of matter such as plasma.

But perhaps most importantly, the bursts of light are short—just hundreds of femtoseconds long, the time it takes for light to cross a human hair. Pulses as brief as this can record functions, not just forms: the folding of a protein, the action of a catalyst, the splitting of a chemical bond.

Physics Today: The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2009 jointly to

Venkatraman Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge,United Kingdom
Thomas A. Steitz, Yale University, New Haven, CT, USA
Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel

"for studies of the structure and function of the ribosome."

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant, or a bacterium looks and functions.

The DNA is transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make the chemistry of life: proteins, such as oxygen-transporting hemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar.

There are tens of thousands of proteins in the body and they all have different forms and functions.

Ramakrishnan, Steitz, and Yonath discovered what the ribosome looks like and how it functions at the atomic level.

All three used X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome and created 3D models that show how different antibiotics bind to the ribosome. X-ray crystallography is a fundamental research tool in biophysics and chemistry, and has resulted in a number of Nobel Prizes.

"Today's award is one of the great stories in biophysics," says Jason Bardi, a spokesperson for the American Institute of Physics (which publishes Physics Today). "People worked for years to get these structures, and for a long time, many in the field doubted whether it could even be done."

The ribosome is a massive protein, weighing in at 2.5 million atomic mass units (amu) and has a complicated structure.

Ribosomes are so big that they can often be spotted under electron microscopes but attempts to look at their structures using diffracted light of much shorter X-wavelengths proved to be challenging.

When the hi-resolution images of ribosomes came out a decade ago by the three laureates, it was held as a significant breakthrough. "Frankly I was stunned," says Bardi. "The ribosomal structure most familiar to me previous to that was the one that adorned my "GENES IV" textbook in graduate school. It was a big purple blob—a molecular Barney. Now suddenly, I could see a thousand interwoven protein helices and finger-like sheets and an impossibly complicated tangle of RNA. It was a truly stunning image."

Paul Guinnessy

Related Physics Today Resources
A three-dimensional x-ray image of a single pair of human chromosomes, Charles Day, February 2009
Time-resolved macromolecular crystallography, Eric A. Galburt and Barry L. Stoddard, July 2001
Nobel Prize in Chemistry to Hauptman and Karle, Bruce Schechter, December 1985
Aaron Klug wins Nobel Prize in Chemistry, Bertram M. Schwarzschild, January 1983

Related Resources
Protein factory reveals Its secrets Chemical & Engineering News, February 2007
Venkatraman Ramakrishnan
Thomas A. Steitz
Ada E. Yonath

Related News Stories
Ribosome map makers win chemistry Nobel NPR
Cambridge chemist wins Nobel prize for showing how proteins are made in cells The Guardian
Three share Nobel Prize in Chemistry Associated Press
Three win Nobel for ribosome research New York Times

NYTimes.com: Researchers have discovered that the topography of a desert locust’s wings and the way they twist when flapping are important for the insect’s efficiency as a flier. Compared with flat, stiff wings, they produce about 30 percent more lift for the same effort.

IEEE Spectrum: The human eye is a perceptual powerhouse. It can see millions of colors, adjust easily to shifting light conditions, and transmit information to the brain at a rate exceeding that of a high-speed Internet connection.

But why stop there?

In the Terminator movies, Arnold Schwarzenegger's character sees the world with data superimposed on his visual field--virtual captions that enhance the cyborg's scan of a scene. In Rainbows End by the science fiction author Vernor Vinge, characters rely on electronic contact lenses, rather than smartphones or brain implants, for seamless access to information that appears right before their eyes.

"These visions might seem far-fetched, but a contact lens with simple built-in electronics is already within reach," says Babak A. Parviz.

"In fact, my students and I are already producing such devices in small numbers in my laboratory at the University of Washington, in Seattle. These lenses don't give us the vision of an eagle or the benefit of running subtitles on our surroundings yet. But we have built a lens with one LED, which we've powered wirelessly with RF. What we've done so far barely hints at what will soon be possible with this technology."

Physics Today: Last year, Derek Briggs, director of Yale's Peabody Museum of Natural History, and colleagues discovered that tiny fossilized structures usually 1-2 μm long, which were previously believed to be the remains of bacteria on fossilized feathers, were in fact carbon deposits called melanosomes that could produce black and white strips on the ancient feathers.

Briggs's team published new research in the journal Biology Letters, based on 40-million-year-old fossilized feathers obtained from deposits in Messel, Germany. Using scanning electron microscopy, the team proved that shining some light on the melanosomes can create a diffraction pattern whose iridescence, or color sheen, is similar to that seen on modern bird feathers.

"Discovery of a color-producing nanostructure in a fossil feather opens up the possibility that we someday be able to determine such colors in fossil birds, as well as in feathered dinosaurs," said H. Richard Lane, a paleontologist and program director in NSF's Division of Earth Sciences.

"The feathers produced a black background with a metallic greenish, bluish or coppery color at certain angles—much like the colors we see in starlings and grackles today," said Richard Prum, one of the paper's authors.

Related Links
Structural coloration in a fossil feather
The colour of fossil feathers

WSJ.com: In a paradox of creation, new evidence suggests that devastating avalanches of cosmic debris may have fostered life on Earth, not annihilated it. If so, life on our planet may be older than scientists previously thought—and more persistent.

Nature: The Cambrian period, roughly 500 million years ago, was marked by a seeming explosion of diverse multicellular organisms. For the past 10–15 years, the carbon-isotope signature in Precambrian limestone has been studied for clues to what prompted this burst of life.

Wild fluctuations in carbon-isotope values during the late Precambrian were interpreted as sudden, drastic changes in the global carbon cycle, such as methane releases or glaciations that could have altered ocean conditions to such extremes that an evolutionary burst was plausible. But new analysis suggests that photosynthetic organisms spread over land earlier than previously thought, and the subsequent rise in atmospheric oxygen was what triggered the Cambrian explosion

Related Link
The late Precambrian greening of the Earth.

2009 AIP Industrial Physics Forum: Pancreatic cancer strikes less than 2% of the population, yet this brutal disease has one of the highest mortality rates among patients, with a mean survival time of only four to six months after diagnosis.

Scientists hope that early detection will be the key to increasing patient survival rates, and Kimberly Kelly from the University of Virginia believes that within the year her team will be able to go to clinical trials with new biomarkers to target early indicators of the cancer, as well as stem cells left over after removal.

2009 AIP Industrial Physics Forum: It took scientists more than twenty years after the first DNA sequencing technology was discovered to sequence the entire human genome; yet our own cells complete this task every time our bodies produces a daughter cell.

So to achieve the goal of real time DNA sequencing, Pacific Biosciences had the idea to spy on Mother Nature as she goes to work copying DNA. Now, the company's commercial device planned to be on the market in 2010, promises to be 20,000 times faster than current second generation technology, with turn around time of about ten minutes rather than ten days.

Chief Technology Officer Steve Turner says in four to five years, new technologies promise to rocket this technology forward even further, making it will possible to sequence an entire human genome in fifteen minutes, on a chip that costs less than 100 dollars

Los Angeles Times: The first comprehensive effort to identify and catalog every species in the world's oceans, from microbes to blue whales, is a year from completion. But early discoveries have profoundly altered understanding of life beneath the sea.

New tracking tools, for example, show that some bluefin tuna migrate between Los Angeles and Yokohama, Japan; one tagged tuna crossed the Pacific three times in a year. White sharks forage even farther for food, commuting between Australia and South Africa.

Since the $650-million, decade-long project began in May 2000, researchers have used deep-sea robots, laser-based radar and super-sensitive sonar that can track fish 90 miles away.

Census teams also embarked on about 400 shipboard expeditions. They discovered life forms faster than they could verify and name—more than 5,600 suspected new species so far, many from the hottest, coldest, saltiest and deepest parts of the oceans.

Science News: A macromolecule that was accidentally discovered when scientists left stuff sitting on a lab bench seems to soak up atmospheric carbon dioxide.

The original find was made by a research team led by chemists at the University of Southampton in England. They were trying to design and create molecules that could capture negatively charged ions, such as chlorides and phosphates, on the surfaces of bioengineered cells.

In one experiment, the researchers set aside an alkaline solution of various organic substances to evaporate, says geochemist John A. Tossell, author of the new study. When analyzing the crystals that formed, the team found that the organic macromolecule that made up the crystal unexpectedly contained carbonates, which form in solutions containing carbon dioxide.

Related Link
Catching CO2 in a Bowl

msnbc.com: Bats use sonar to navigate and hunt. Many have been killed by wind turbines, however, which their sonar doesn't seem to recognize as a danger. Surprisingly, radar signals could help keep bats away from wind turbines.

New York Times: A tiny glass telescope, the size of a pea, has been successfully implanted in the eyes of people with severely damaged retinas, helping them to read, watch television and better see familiar faces.

The telescope implant is only 4mm long and contains two wide angle glass microlenses.

The new device is for people with an irreversible, advanced form of macular degeneration in which a blind spot develops in the central vision of both eyes.

In a brief, outpatient procedure, a corneal specialist implants the mini-telescope in one eye in place of its natural lens. The telescope magnifies images on the retina, extending them so they fall on healthy cells outside the damaged macula, said Allen W. Hill, chief executive of VisionCare Ophthalmic Technologies in Saratoga, California, the implant's maker.

Various: Lawrence Berkeley National Laboratory’s Bevatron, built by the Atomic Energy Commission—the forerunner of the Department of Energy—in the early 1950s, is slowly being demolished thanks to $74 million of stimulus funding. Soon, by 2011, all traces of it will be gone reports Wired magazine.

LBNL has a flicker photo galley of the Bevatron, some of which are posted below.

The 10,000 ton Bevatron is a weak focusing synchrotron that was closely watched by Physics Today, both during construction and for the scientific results it produced.

Paul Dirac had predicted the existence of antimatter in the 1930s and the Bevatron's mission—as the most powerful accelerator in the world—was to discover the antiproton (which it did) and explore the fundamental physics behind hadrons using beams of 6.2-GeV protons.

The Bevatron had a number of upgrades during its lifetime in an attempt to regain its status as one of the most powerful synchrotrons in the world, and to continue to do interesting science.

In 1960 the Bevatron had a three-year upgrade which cost more than the initial construction ($9.6 million) and increased the intensity of the proton beam by a factor of four. In 1967, metal fatigue shut the Bevatron down for three months while repairs were made. In the early 1970s the accelerator switched to nitrogen ions, which were more energetic than the protons initially used in the accelerator, and made the Bevatron more attractive to the biological sciences.

By linking parts of the Bevatron with other equipment at LBNL— the SuperHILAC serving as the injector and the Bevatron as an accelerator—the Bevalac accelerator was created in 1974 which led to a completely new field of research: relativistic heavy-ion reactions. This time carbon-12 ions were injected into the ring (reaching 2.1 GeV), which regained LBNL's reputation of having the most powerful heavy-ion accelerator in the world.

Improvements to the Bevalac continued well into the 1980s. In 1982 new upgrades, which included a new vacuum system for the Bevatron, allowed the Bevalac to accelerate uranium ions.

In science, research at the Bevatron led to at least four Nobel Prizes, one for the discovery of the antiproton by Emilio Segré and Owen Chamberlain.

The Bevatron's beam was finally turned off in 1993 by one of the people who built it: Edward Lofgren.

Related Physics Today articles
Bevatron Launched (1954)
During the next three years (1961)
The Bevatron Reactivated (1963)
Bevatron Shut Down 3 Months: Metal Fatigue in Alternator (1967)
Long-lived kaon shows no 2-muon decay (1971)
Two accelerators switch to nitrogen ions (1971)
Conflicting evidence for K-meson decay (1972)
Bevalac makes a successful debut (1974)
Bevalac accelerates uranium (1982)
Probing Dense Nuclear Matter in the Laboratory (1993)

New York Times: David Lentink, with Michael H. Dickinson of the California Institute of Technology and colleagues, reports in Science that the wings of a maple seed generate a leading edge vortex—a spinning horizontal tunnel of air along the wing—as they descend. This vortex is stable, Dr. Lentink said, because it has a low-pressure core that reduces the air pressure over the wing, causing the wing to be sucked up. “It really increases the lift,” he said.

Related Link
Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds

Explanations for the electro stun weapon's apparent ability to stiffen the whole of the human body without (usually) causing any physiological damage remain unclear, inconsistent and contradictory, and it might be that psychological factors play a more important role in its effect than previously thought.

These were the conclusions of researchers at the Bundeswehr Medical Centre, who presented their research at the 5th Symposium on Non Lethal Weapons in Ettlingen, Germany earlier last month.

Associated Press: A mass extinction some 260 million years ago may have been caused by volcanic eruptions in what is now China, new research suggests.

[Image credit: Re-evaluating vertical motion preceding the Emeishan continental flood basalt province, SW China]

The so-called Guadalupian Mass Extinction, devastating marine life around the world, was preceded by massive eruptions in the Emeishan geological province of Southwest China, says Paul Wignall of the University of Leeds and colleagues in Science.

Related Link
Volcanism, Mass Extinction, and Carbon Isotope Fluctuations in the Middle Permian of China

Within 100 million years of being formed, the young Earth was hit by a rogue planet, the debris from which ultimately formed the Moon, melting the Earth's surface. For the next 600 million years the planet was bombarded by debris and meteors that heated up both land and oceans. Few, if any, rocks remain from before the end of this era, with the oldest currently known being from 4.03 Gyr ago.

The earliest know isotopic evidence for life is at 3.8 Gyr, although its findings remain controversial.

For years geological models suggested that the oceans, where life is thought to have originally formed were sterilized during this period.

This left two uncomfortable conclusions—that life originated more than once, or that life started elsewhere in the solar system.

This story began to change with the discovery of zircons that pre-date the late bombardment. Zircons are telltale mineral inclusions in ancient rocks, and the evidence from them supported the idea that between 4.38–3.85 Gyr the Earth had liquid water, crustal recycling, a granitoid crust and low-temperature processes occurring at the boundaries of tectonic plates.

Abramov and Mojzsis's research now suggests that the conditions were never severe enough to sterilize Earth, eliminating the need for more esoteric solutions for how life survived on the early Earth.

Related article
Microbial habitability of the Hadean Earth during the late heavy bombardment

The technique, which relies of frequencies close to 1 MHz, has an effective raduis of 20-meters, and is ideal for clearing algae blooms in lakes and ponds. However, because of the loud-nature of the sound (more than 35 dB over government safety standards) the researchers warn that caution should be taken if there are aquatic or semi-aquatic animals present.

Related Links
How to avoid contaminating planetary neighbors NPR

"I see a whale, I see a six-to-12-volt electric generator that is able to pump 1,000 liters per pulse through more than 108 miles of veins and arteries," he said. The intricate wiring of the whale's heart is being studied as a model for a device called a nanoscale atrioventricular bridge, which will undergo animal testing next year and could replace pacemakers for the millions of people whose diseased hearts need help to beat steadily.

Water samples collected around an island in the eastern Pacific over the past eight years showed seawater had acidified more than 20 times faster than scientists expected. The effect could be devastating for shellfish and other crustaceans, because acidic waters dissolve calcium carbonate used by the organisms to make their protective shells.

Various: The FBI has released details about its case against accused researcher Bruce Ivins, who killed himself last week after being told he would be prosecuted as the prime suspect in the 2001 anthrax attacks. A number of websites have provided some analysis of the FBI's case. The Smoking Gun has collated the highlights to the prosecution's case. Meryl Nass, a noted anthrax researcher, writes on her blog Anthrax Vaccine that “What came out today was another pastiche of innuendo and circumstantial evidence, with an awful lot of holes.”

Nass raises the following main questions:

1. Ivins had just been immunized against anthrax. He was required to have yearly immunizations, and some anthrax scientists have chosen to be vaccinated every six months for safety, since the vaccine’s efficacy is weak — and Ivins had proven its weakness in several animal models. In his career he had probably received about 33 separate anthrax vaccinations.

2. Earlier in the week, anonymous officials at the FBI leaked to the press that the envelopes came from the specific post office he frequented. Today the affidavit states it is "reasonable to conclude" they were purchased in Maryland or Virginia.

3. Choosing a strain that would direct suspicion at Ivins. The perpetrator(s) were tremendously careful to leave no clues vis a vis the envelopes. For example, block lettering was used, which is the hardest to identify with handwriting analysis. Second, stamped envelopes were chosen to avoid using saliva. Third, there were no fingerprints on anything.

Why would the person(s) who took such care select an anthrax strain that would focus suspicion on himself? In 2001, strain analysis was possible. It had been discussed many times as a forensic tool for biowarfare, including in a paper Nass wrote in 1992, which Ivins had read, and in which Nass thanked him for his contributions.

4. Ivins was the “sole custodian” of the strain. But the strain was grown in 1997, and more than 100 people had access to it over that four year period. Having received a sample, or obtained it surreptitiously, they would be “custodians” of it too.

Nass also points out that the FBI report does not explain how the anthrax was weaponized, nor can explain how Ivins created it. The FBI also cannot explain how the letters were mailed from Princeton. "Either Ivins had an alibi or he didn't.... If Ivins cannot be placed in New Jersey on those dates, he is not the attacker, or he did not act alone," says Nass.

Update: 8/19/2008. The FBI release some of the evidence related to their investigation. NPR's David Kestenbaum provides some details of the case, along with New York Times reporters Eric Lichtblau and Nicholas Wade. Although some of the techniques have been reviewed, the research has yet to be independently verified by experts not associated to the case. Richard O. Spertzel, a retired microbiologist who led the United Nations’ biological weapons inspections of Iraq, told the New York Times that he remained skeptical of the bureau’s argument despite the new evidence. “It’s a pretty tenuous argument,” Spertzel said, adding that he questioned the bureau’s claim that the powder was less than military grade. Nass adds some more questions to the coverage

Washington Post: Colleagues and friends of Bruce E. Ivins, the vaccine specialist who committed suicide earlier this week after the FBI indicated they were going to indict him for the 2001 anthrax attacks remained convinced that Ivins was innocent: They contended that he had neither the motive nor the means to create the fine, lethal powder that was sent by mail to news outlets and congressional offices in the late summer and fall of 2001. Mindful of previous FBI mistakes in fingering others in the case, many are deeply skeptical that the bureau has gotten it right this time.

Update: 8/4/2008. The New York Times Scott Shane writes that most of the evidence against Ivins is circumstantial, and that the FBI was several weeks away from indicting the scientist. While genetic analysis had linked the anthrax letters to a supply of the deadly bacterium in Dr. Ivins’s laboratory at Fort Detrick, Md., at least 10 people had access to the flask containing that anthrax, said the source, who spoke on condition of anonymity because he was not authorized to discuss the investigation publicly.

“What has bothered me is the unscientific, bumbling approach of our investigators,” said Rep Rush D. Holt (D-NJ),a physicist whose New Jersey district includes the contaminated Princeton mailbox.

Mr. Holt said in a recent interview that his first doubts came after anthrax was found in his Congressional office in October 2001 but investigators never returned to conduct systematic testing to trace the path of the anthrax spores.

After that, he said, when contamination at a New Jersey postal processing center indicated that the letters had been mailed on one of a limited number of routes, it took investigators seven months to test several hundred mailboxes and identify the source.

“Within two days they could have dispatched 50 people to wipe all those mailboxes,” Holt said. He wrote to Robert S. Mueller III, the F.B.I. director, on Friday to ask that he testify to Congress about the investigation as soon as it is closed.

Meryl Nass, a doctor with some background in anthrax, queries whether Ivins could have produced the dry form of anthrax used in the attacks.