Thursday, July 31, 2008

Mother Earth Naked: A Modern Masterpiece

Have you ever wondered what our world would look like stripped bare of all plants, soils, water and man-made structures? Well wonder no longer; images of the Earth as never seen before have been unveiled in what is the world’s biggest geological mapping project ever.

Earth and computer scientists from 79 nations are working together on a global project called OneGeology to produce the first digital geological map of the world. This project is doing the same for the rocks beneath our feet that Google does for maps of the Earth’s surface. These scientists have achieved their goal in just over one year after initiating this global project. For a science that usually counts time in millions of years, this is no mean feat!

OneGeology is supported by UNESCO and six other international umbrella bodies and is the flagship project for UN International Year of Planet Earth 2008. The key results of this project are:

  1. Geological maps from around the globe are accessible on the World Wide Web;
  2. A new web language has been written for geology which allows nations to share data with each other and the public;
  3. The know-how to do this is being exchanged so that all nations across the world, regardless of their development status, can take part and benefit.

Explaining the significance of this project, Ian Jackson, Chief of Operations at the British Geological Survey, who is coordinating OneGeology explained: “Geological maps are essential tools in finding natural resources e.g. water, hydrocarbons and minerals, and when planning to mitigate geohazards e.g. earthquakes, volcanoes and radon. Natural resources are a crucial source of wealth for all nations, especially those that need to develop and build their economies. Identifying geohazards is often a matter of life or death. Other challenges facing all nations in the 21st century include rising sea levels, management of waste (nuclear or domestic) and storage of carbon. Knowledge of the rocks that we all live on has become increasingly important and sharing that knowledge at a time of global environmental change is crucial”.

François Robida, Deputy Head of Division, Information Systems and Technologies at the Bureau de Recherches Géologiques et Minières, France, explained; “Today you can go to the OneGeology website and get geological maps from across the globe — from an overview of our entire planet, to larger scale maps of the rocks of individual nations. You also have the ability to hop from this web site to higher resolution applied maps and data on linked national web sites. Participating nations are contributing to a legacy for humankind; by acting locally they are thinking globally”.

Unfortunately information about the Earth’s rocks isn’t always up-to-date, joined-up, and in some parts of the world is not available at all! This was the challenge that OneGeology project set out to tackle and these scientists will be unveiling the the result of their work at the 33rd International Geological Congress in Oslo, Norway on 6 August 2008.

Life In A Bubble: Mathematicians Explain How Insects Breathe Underwater

Hundreds of insect species spend much of their time underwater, where food may be more plentiful. MIT mathematicians have now figured out exactly how those insects breathe underwater.

By virtue of their rough, water-repellent coat, when submerged these insects trap a thin layer of air on their bodies. These bubbles not only serve as a finite oxygen store, but also allow the insects to absorb oxygen from the surrounding water.

"Some insects have adapted to life underwater by using this bubble as an external lung," said John Bush, associate professor of applied mathematics, a co-author of the recent study.

Thanks to those air bubbles, insects can stay below the surface indefinitely and dive as deep as about 30 meters, according to the study co-authored by Bush and Morris Flynn, former applied mathematics instructor. Some species, such as Neoplea striola, which are native to New England, hibernate underwater all winter long.

This phenomenon was first observed many years ago, but the MIT researchers are the first to calculate the maximum dive depths and describe how the bubbles stay intact as insects dive deeper underwater, where pressure threatens to burst them.

The new study, which appears in the Aug. 10 issue of the Journal of Fluid Mechanics, shows that there is a delicate balance between the stability of the bubble and the respiratory needs of the insect.

The air bubble's stability is maintained by hairs on the insects' abdomen, which help repel water from the surface. The hairs, along with a waxy surface coating, prevent water from flooding the spiracles—tiny breathing holes on the abdomen.

The spacing of these hairs is critically important: The closer together the hairs, the greater the mechanical stability and the more pressure the bubble can withstand before collapsing.

However, mechanical stability comes at a cost. If the hairs are too close together, there is not enough surface area through which to breathe.

"Because the bubble acts as an external lung, its surface area must be sufficiently large to facilitate the exchange of gases," said Flynn, who is now an assistant professor of mechanical engineering at the University of Alberta.

The researchers developed a mathematical model that takes these factors into account and allows them to predict the range of possible dive depths. They found that there is not only a maximum depth beyond which the bubble collapses, but a minimum depth above which the bubble cannot meet the insect's respiratory needs.

Though the researchers found that the insects can go as deep as 30 meters below the surface, they rarely venture deeper than several meters, due to environmental factors such as amount of sunlight, availability of prey and the presence of predators.

The researchers first took an interest in the external lung phenomenon when they accidentally captured one of the underwater breathers while looking for water striders. A few years ago, Bush and colleagues figured out how the striders use surface tension to glide across the water's surface.

Other researchers have explored systems that could replicate the external lung on a larger scale, for possible use by diving humans. A team at Nottingham Trent University showed that a porous cavity surrounded by water-repellent material is supplied with oxygen by the thin air layer on its surface. The surface area required to support human respiration is impractically large, in excess of 100 square meters; however, other avenues for technological application exist. For example, such a device could supply the oxygen needed by fuel cells to power small autonomous underwater vehicles.

New Yeast Trick For Eating Favorite Food

It is well known that yeast, the humble ingredient that goes into our breads and beers, prefer to eat some sugars more than others. Glucose, their favorite food, provides more energy than any other sugar, and yeast has evolved a complex genetic network to ensure that they consume as much glucose as possible whenever it is available. UC San Diego bioengineers have recently identified a previously unknown mechanism that allows yeast to shut down the metabolism of another sugar, galactose, when they sense glucose in the environment.

The findings will be published online by the journal Nature on 30 July 2008.

This research marks the first discovery of post-transcriptional gene regulation in a key model for gene regulation in higher organisms: the galactose genetic system in the yeast Saccharomyces cerevisiae.

Molecular biologists have long thought that the primary mechanism for regulating genes is through proteins called transcription factors, which can either increase or decrease the activity of a gene by binding directly to the DNA. However, a paradigm shift has occurred in recent years as researchers have shown that the control of genes frequently occurs at the intermediated stages between transcription and the formation of functional proteins. This "post-transcriptional" regulation provides cells with an additional level of control over phenotypic expression.

The UCSD team demonstrated that the glucose network actively shuts down the galactose network by degrading messenger RNA that would otherwise go on to form the enzymes needed to metabolize galactose.

"To find something new in the well-known galactose network after predicting it is extremely exciting," said Matthew Bennett, the first author on the Nature paper and a postdoctoral researcher in the Systems Biodynamics Lab in UC San Diego's bioengineering department.

A better understanding of the yeast galactose network could lead to new insights in human cell behavior, human physiology and metabolic diseases such as diabetes. "The more we know about gene networks, the more we learn about how they can fail," said Bennett.

Feeding Yeast the Microfluidic Way

The work also highlights the kinds of important biological insights that scientists can gain by studying how gene networks operate in dynamic, life-like environments, rather than in steady-state environments. The bioengineers built yeast growth chambers in which food is delivered by microfluidic tubes. The design allowed for the raising and lowering of glucose levels with great control, while keeping galactose levels steady.

"Much of gene regulation appears to deal with changes in the environment. Our new work demonstrates that you can modify the environment in a highly controlled way and then monitor single cells in order to see how specific gene networks respond to the environmental changes," explained bioengineering professor Jeff Hasty, the senior author on the Nature paper.

The researchers found that yeast are much better at adapting to changes in available food sources than the prevailing models predicted.

"We didn't expect that yeast would respond so quickly to changes in glucose levels until we did these experiments," said Bennett

By controlling the exact growth conditions with microfluidic technology, the engineers determined that the canonical models for the yeast metabolic network underestimated how quickly and nimbly yeast can switch from galactose to glucose.

"The experimental system was much better than the computational models predicted. The model started filtering out the glucose pulses too soon," said Hasty, who stressed the utility of their tried-and-true engineering approach. "We drove our system with a sine wave in typical engineering fashion, and sure enough, we learned something interesting."

The undulating sine wave represents pulses of glucose delivered to the yeast cells while galactose levels remained constant.

When the glucose pulses started coming faster and faster, the model underestimates the ability of the yeast to react to the glucose pulse by shutting down the galactose metabolic network.

This discrepancy between the experimental results and the model predictions got the bioengineers thinking about what could be happening that is not captured in the current model. A combination of computational modeling and experimental work led the researchers to a new post-transcriptional control mechanism in which jumps in glucose increase the degradation rate of messenger RNA that are crucial for the functioning of the galactose metabolic network.

Antikythera Mechanism: Scientists Crack Secrets Of 2,000-year-old Astronomical Computer

Cardiff University experts have led an international team in unravelling the secrets of a 2,000-year-old computer which could transform the way we think about the ancient world.

Professor Mike Edmunds of the School of Physics and Astronomy and mathematician Dr Tony Freeth first heard of the Antikythera Mechanism, a clock-like astronomical calculator dating from the second century BC, several years ago. Now they believe they have cracked the centuries-old mystery of how it actually works.

Remnants of a broken wooden and bronze case containing more than 30 gears was found by divers exploring a shipwreck off the island of Antikythera at the turn of the 20th century. Scientists have been trying to reconstruct it ever since. The new research suggests it is more sophisticated than anyone previously thought.

Detailed work on the gears in the mechanism showed it was able to track astronomical movements with remarkable precision. The calculator was able to follow the movements of the moon and the sun through the Zodiac, predict eclipses and even recreate the irregular orbit of the moon. The team believe it may also have predicted the positions of the planets.

The findings suggest that Greek technology was far more advanced than previously thought. No other civilisation is known to have created anything as complicated for another thousand years.

Professor Edmunds said: "This device is just extraordinary, the only thing of its kind. The design is beautiful, the astronomy is exactly right. The way the mechanics are designed just makes your jaw drop. Whoever has done this has done it extremely carefully."

The team was made up of researchers from Cardiff, the National Archeological Museum of Athens and the Universities of Athens and Thessaloniki, supported by a substantial grant from the Leverhulme Trust. The researchers were greatly aided by Hertfordshire firm X-Tek, who developed powerful X-Ray computer technology to help with the study of corroded fragments of the machine. Computer giant Hewlett-Packard provided imaging technology to enhance the surface details of the machine.

The mechanism is in 70 pieces and stored in precisely controlled conditions in Athens where it cannot be touched. Recreating its workings was a difficult, painstaking process, involving astronomers, mathematicians, computer experts, script analysts and conservation experts.

After unveiling their full findings at a two-day international conference in Athens and in the journal Nature, the researchers are now hoping to create a computer model of how the machine worked, and, in time, a full working replica. It is still uncertain what the ancient Greeks used the mechanism for, or how widespread this technology was.

Professor Edmunds said: "It does raise the question what else were they making at the time. In term of historic and scarcity value, I have to regard this mechanism as being more valuable than the Mona Lisa."