Finding the roots and early branches of the tree of life.

A study published in PLoS Computational Biology maps the development of life-sustaining chemistry to the history of early life. Researchers Rogier Braakman and Eric Smith of the Santa Fe Institute traced the six methods of carbon fixation seen in modern life back to a single ancestral form.

Carbon fixation – life’s mechanism for making carbon dioxide biologically useful – forms the biggest bridge between Earth’s non-living chemistry and its biosphere. All organisms that fix carbon do so in one of six ways. These six mechanisms have overlaps, but it was previously unclear which of the six types came first, and how their development interweaved with environmental and biological changes.

The authors used a method that creates “trees” of evolutionary relatedness based on genetic sequences and metabolic traits. From this, they were able to reconstruct the complete early evolutionary history of biological carbon–fixation, relating all ways in which life today performs this function.

The earliest form of carbon fixation identified achieved a special kind of built-in robustness – not seen in modern cells – by layering multiple carbon-fixing mechanisms. This redundancy allowed early life to compensate for a lack of refined control over its internal chemistry, and formed a template for the later splits that created the earliest major branches in the tree of life. For example, the first major life-form split came with the earliest appearance of oxygen on Earth, causing the ancestors of blue–green algae and most other bacteria to separate from the branch that includes Archaea, which are outside of bacteria the other major early group of single-celled microorganisms.

“It seems likely that the earliest cells were rickety assemblies whose parts were constantly malfunctioning and breaking down,” explains Smith. “How can any metabolism be sustained with such shaky support? The key is concurrent and constant redundancy.”

Once early cells had more refined enzymes and membranes, giving greater control over metabolic chemistry, minimization of energy (ATP) used to create biomass, changes in oxygen levels and alkalinity directed life’s unfolding. In other words, the environment drove major divergences in predictable ways, in contrast to the common belief that chance dominated evolutionary innovation – and that rewinding and replaying the evolutionary tape would lead to an irreconcilably different tree of life.

“Mapping cell function onto genetic history gives us a clear picture of the physiology that led to the major foundational divergences of evolution,” explains Braakman. “This highlights the central role of basic chemistry and physics in driving early evolution.”

With the ancestral form uncovered, and evolutionary drivers pinned to branching points in the tree, the researchers now want to make the study more mathematically formal and further analyze the early evolution of metabolism.

Souce: Public Library of Science.







New monitoring system clarifies murky atmospheric questions.

A University of Colorado Boulder-led team has developed a new monitoring system to analyze and compare emissions from man-made fossil fuels and trace gases in the atmosphere, a technique that likely could be used to monitor the effectiveness of measures regulating greenhouse gases.


The research team looked at atmospheric gas measurements taken every two weeks from aircraft over a six-year period over the northeast United States to collect samples of CO2 and other environmentally important gases. Their method allowed them to separate CO2 derived from fossil fuels from CO2 being emitted by biological sources like plant respiration, said CU-Boulder Senior Research Associate Scott Lehman, who led the study with CU-Boulder Research Associate John Miller.

The separation was made possible by the fact that CO2 released from the burning of fossil fuels like coal, oil and gas has no carbon-14, since the half-life of that carbon radio isotope is about 5,700 years — far less than the age of fossil fuels, which are millions of years old. In contrast, CO2 emitted from biological sources on Earth like plants is relatively rich in carbon-14 and the difference can be pinpointed by atmospheric scientists, said Lehman of CU’s Institute of Arctic and Alpine Research.

The team also measured concentrations of 22 other atmospheric gases tied to human activities as part of the study, said Miller of the CU-headquartered Cooperative Institute for Research in Environmental Sciences. The diverse set of gases impact climate change, air quality and the recovery of the ozone layer, but their emissions are poorly understood. The authors used the ratio between the concentration level of each gas in the atmosphere and that of fossil fuel-derived CO2 to estimate the emission rates of the individual gases, said Miller.

In the long run, measuring carbon-14 in the atmosphere offers the possibility to directly measure country and state emissions of fossil fuel CO2, said Miller. The technique would be an improvement over traditional, “accounting-based” methods of estimating emission rates of CO2 and other gases, which generally rely on reports from particular countries or regions regarding the use of coal, oil and natural gas, he said.


“While the accounting-based approach is probably accurate at global scales, the uncertainties rise for smaller-scale regions,” said Miller, also a scientist at the National Oceanic and Atmospheric Administration’s Earth System Research Laboratory in Boulder. “And as CO2 emissions targets become more widespread, there may be a greater temptation to underreport. But we’ll be able to see through that.”

A paper on the subject was published in the April 19 issue of the Journal of Geophysical Research: Atmospheres, published by the American Geophysical Union. Co-authors include Stephen Montzka and Ed Dlugokencky of NOAA, Colm Sweeney, Benjamin Miller, Anna Karion, Jocelyn Turnbull and Pieter Tans of NOAA and CIRES, Chad Wolak of CU’s INSTAAR and John Southton of the University of California, Irvine.

One surprise in the study was that the researchers detected continued emissions of methyl chloroform and several other gases banned from production in the United States. Such observations emphasize the importance of independent monitoring, since the detection of such emissions could be overlooked by the widely used accounting-based estimation techniques, said Montzka.

The atmospheric air samples were taken every two weeks for six years by aircraft off the coastlines of Cape May, N.J., and Portsmouth, N.H.

Fossil fuel emissions have driven Earth’s atmospheric CO2 from concentrations of about 280 parts per million in the early 1800s to about 390 parts per million today, said Miller. The vast majority of climate scientists believe higher concentrations of the greenhouse gas CO2 in Earth’s atmosphere are directly leading to rising temperatures on the planet.

“We think the approach offered by this study can increase the accuracy of emissions detection and verification for fossil fuel combustion and a host of other man-made gases,” said Lehman. He said the approach of using carbon-14 has been supported by the National Academy of Sciences and could be an invaluable tool for monitoring greenhouse gases by federal agencies like NOAA.

Unfortunately, NOAA’s greenhouse gas monitoring program has been cut back by Congress in recent years, said Lehman. “Even if we lack the will to regulate emissions, the public has a right to know what is happening to our atmosphere. Sticking our heads in the sand is not a sound strategy,” he said.

Source: University of Colorado





Physical Activity in Advanced Age Associated with Lower Alzheimer’s Risk .

Daily physical activity is associated with reduced risk for Alzheimer disease among the elderly, according to a Neurology study.

Roughly 700 adults (average age, 82) free of dementia wore actigraphs on their wrists 24 hours a day for up to 10 days to measure their daily physical activity. Over a mean 3.5 years’ follow-up, 10% were diagnosed with Alzheimer disease.

Participants in the lowest decile of physical activity had more than twice the Alzheimer’s risk as those in the highest decile. The results remained significant after adjustment for self-reported physical, social, and cognitive activities. More physical activity on actigraphy was also associated with less cognitive decline.

Editorialists conclude: “In a world that is becoming progressively sedentary, and in the context of very limited success of the currently available medications to treat or delay AD, physical activity provides a promising, low-cost, easily accessible, and side-effect-free means to prevent AD.”

Source: Neurology




AHA Casts Doubt on Gum Disease as a Cardiovascular Risk Factor .

Periodontal disease, although often associated with atherosclerotic vascular disease, does not necessarily cause it, according to a statement from the American Heart Association published online in Circulation. (The Clinical Conversations podcast has a brief interview with the paper’s lead author.)

An AHA committee examined the published evidence associating the two conditions. They point to the many factors contributing to gum disease that are also seen in atherosclerosis: for example, smoking, diabetes, obesity, and the presence of inflammatory markers, such as C-reactive protein.

The committee concludes that high-level evidence for causation of atherosclerosis by periodontal disease does not exist. They add that claims implying that therapeutic periodontal interventions could lower risks or affect cardiovascular disease outcomes are “unwarranted.”

Source:AHA statement

Combined Ibuprofen/Famotidine Tablet Might Reduce Ulcers.

Patients receiving the combination tablet developed fewer upper gastrointestinal ulcers than those receiving ibuprofen alone.

Patients taking nonsteroidal anti-inflammatory drugs (NSAIDs) have an increased risk for upper gastrointestinal (GI) ulcers (gastric and duodenal ulcers). Acid reduction with a proton-pump inhibitor (PPI) has been shown to decrease this risk. However, many patients taking NSAIDs either do not receive a prescription for PPIs or do not take them.

To investigate the efficacy of a combination tablet of 800 mg ibuprofen and 26.6 mg famotidine to reduce development of upper GI ulcers in patients requiring NSAID therapy, researchers conducted two industry-sponsored, randomized, double-blinded trials (REDUCE-1 and REDUCE-2) in which patients received the combination tablet or an 800-mg ibuprofen tablet three times daily for 24 weeks. The endpoint for the studies was upper GI ulcers identified by endoscopy during the 24-week study period.

In the REDUCE-1 trial, incidence of gastric ulcers was lower in the combination-tablet group than in the ibuprofen group (12.7% vs. 22.9%; P=0.004). In REDUCE-2, results showed a nonsignificant trend toward lower incidence of upper GI ulcers with the combination-tablet group versus ibuprofen (13.0% and 20.5%; P=0.059). In a pooled analysis of results from both trials, the combination-tablet group had lower incidence of both gastric ulcers (12.5% vs. 20.7%) and duodenal ulcers (1.6% vs. 6.9%) than the ibuprofen group. After adjustment for other potential risk factors, the risk ratio for upper gastrointestinal ulcers with the combination therapy versus ibuprofen alone was 0.46 (95% confidence interval, 0.34–0.61).

Comment: Our ability to compare these findings with data on efficacy of acid reduction with proton-pump inhibitor cotherapy is limited because this study was based on endoscopic ulcers. There were not enough complicated ulcers in the study to allow for comparison of this outcome between the two treatment groups. While some studies suggest that endoscopic ulcers are a reasonable surrogate for clinically significant events, it is impossible for us to determine how combination therapy — with its improved acid-reduction compliance — compares with standard PPI cotherapy without a head-to-head trial based on clinical events.

Source: Journal Watch Gastroenterology

Ketamine Is Safe in Resource-Poor Settings.

Nurses independently administered sedation for 191 procedures in 118 patients with no serious adverse events.

Ketamine is unique among sedatives in that it does not cause respiratory depression. Serious adverse events are rare. Ketamine is used widely in resource-poor environments, but systematic studies of its safety in this setting are lacking. These authors reviewed a quality-assurance database from a rural Ugandan hospital to identify all cases of nurse-administered ketamine sedation during a 4-month period. The nurses underwent a brief training program in ketamine sedation.

Nurses administered ketamine sedation without physician supervision for 191 procedures in 118 patients. Procedures included abscess drainage (36%), orthopedic procedures (20%), and burn care (18%). Half the patients were younger than 18 years and 18% were younger than 2 years. Ketamine was administered intravenously in 90% of cases and intramuscularly in 10%. There were 39 minor adverse events in 35 patients. These included hypoxia without physiological consequences, vomiting, emergence phenomena, and hypersalivation. No serious adverse events occurred.

Comment: These findings are important to those charged with providing care in resource-poor environments. Ketamine is an extremely safe, effective agent for painful procedures, providing both analgesia and sedation without respiratory depression, unlike other agents or combinations of agents.

 Source: Journal watch of emergency medicine.

Physicists turn to Maxwell’s equations for self-bending light.

Can light self-bend into an arc? Can shape-preserving optical beams truly bend along a circular path? A confident answer emerged in this week’s Physical Review Letters. Researchers at Israel’s Technion reported their findings, saying that solutions to Maxwell’s equations suggest it is possible. They have found solutions to Maxwell’s equations— the equations governing electromagnetism–that precisely describe initial phases required for truly self-bending light.


Light travels in a straight line; light beams tend to propagate along a straight path. Under forced circumstances—with use of mirrors, lenses, and light guides–light can take a more circuitous path, What has interested some scientists is whether or not light beams can bend themselves along a curved path with no external cause.

What is more, the new report involves wave solutions to Maxwell’s equations that are nondiffracting and capable of following a tighter circular trajectory than was previously thought possible.


The authors said in the report that “We have found nonparaxial accelerating beams and nonparaxial periodically oscillating accelerating beams. These beams are the full vector solutions of Maxwell’s equation for shape-preserving accelerating beams. Moreover, in their scalar form, these beams are the exact solutions for nondispersive accelerating wave packets of the simple and most common wave equation describing time-harmonic waves.”


The study, titled “Nondiffracting Accelerating Wave Packets of Maxwell’s Equations,” by Ido Kaminer, Rivka Bekenstein, Jonathan Nemirovsky, and Mordechai Segev, joins a body of related light-bending research.

Reaching into the research background, ScienceNOW described some study markers, going back to the late 1970s, when physicists at the University of Bristol in the United Kingdom and State University of New York said that an Airy waveform, a wave describing how quantum particles move, can sometimes bend by a small amount. In 2007, physicists at the University of Central Florid generated optical versions of Airy waves by manipulating laser light, and found that the resultant beam curved slightly as it crossed a detector.


The Technion examination is unique in that the scientists claim they figured out how to make light self-bend through any angle, even through a complete circle. (The problem with the Airy function, said study coauthor Mordechai Segev, is that the shape of its oscillations specify the right phases only at small angles.)


Commenting on this week’s findings, Zhigang Chen, a physics professor at San Francisco State University, said in Physics that implications of their work are profound for other linear wave systems in nature, from sound and surface waves in fluids to many kinds of classical waves.”One would expect that the nonparaxial Bessel-like accelerating beams proposed in this study could be readily realized in experiment. Apart from many exciting opportunities for these beams in various applications, such as beams that self-bend around an obstacle one might expect one day light could really travel around a circle by itself, bringing the search for an ‘optical boomerang’ into reality.”


The study authors say that future work should examine the possibility of 3-D accelerating beams, including those with trajectories that do not lie in a single plane. “In practical terms, this work brings accelerating beam optics into the subwavelength regime, through the less-than-wavelength features of our solutions, facilitating higher resolution for particle manipulation.”


Source: Physics Viewpoint and ScienceNOW.