Archive for the ‘Slimey stuff’ Category

Why spiders’ silk is so much stronger than silkworms’

Friday, February 27th, 2009


Spider silk and silkworm silk are almost identical in chemical composition and microscopic structure. And yet spider silk is far tougher. “One strand of pencil thick spider silk can stop a Boeing 747 in flight,” say Xiang Wu and colleagues at the National University of Singapore. Whereas a pencil thick strand of silkworm silk couldn’t. Why the difference?

Xiang and co say they’ve worked out why by successfully simulating the structure of both silks for the first time. Both spider silk and silkworm silk are made up of long chains of amino acids called polypeptides and are particularly rich in the amino acids alanine and glycine.

Various imaging techniques have shown that the sequences of amino acids differ slightly between spide and silkworm silk but this alone cannot explain the huge difference in strength, says Xiang.

Instead, the secret appears to lie in the way polypeptide chains fold into larger structures. Xiang’s model shows that a subtle difference exists between the silks in structures called beta sheets and beta crystallites. This insight has allowed the team to model for the first time the way in which both silks break.

That’s important because being able to predict the mechancial properties of an organic material simply by studying its structure is going to be increasingly useful. It may even allow us to take a better stab at making spider-like silk synthetically for the the first time.

Anybody with a 747 watch out.

Ref: Molecular Spring: From Spider Silk to Silkworm Silk

The coming of age of hadrontherapy

Tuesday, February 24th, 2009


There’s a problem with conventional radiotherapy for tumours: the body absorbs the radiation as it passes through. So zap a deep seated tumour with X-rays and the dose decreases exponentially with the depth of target. This means that both diseased and healthy tissue end up getting targeted.

In 1946, Robert Wilson, a physicist  at FermiLab near Chicago pointed out that protons with an energy of between 200 and 250 MeV and carbon ions with an energy of 3500 to 4500 MeV work in a different way. Inside the body, they tend to dump all their energy at the end of their range. Not only that, but because the particles are charged, they can be sharply focused. He said that makes these particles ideal for targeting tumours.

It’s taken 60 years, but there is now real interest in hadrontherapy. Several thousand patients have been treated at various particle physics labs around the world. and therein lies the problem: the only places that can produce protons or carbon ions with these energies are  specialised accelerators such as those at GSI in Germany and Chiba in Japan.

There is one facility dedicated to medical work at the Loma Linda University Medical Centre near Los Angeles but it has become clear to the medical and physics community that more are desperately needed.

So how do you build reliable, easy-t0-use, affordable particle accelerators for medical centres? Enter Ugo Amaldi and buddies from the TERA Foundation in Italy, who today propose a design that they think could revolutionise this kind of treatment. (Amaldi was a hot shot at the European particle physics lab CERN for many years before turning to medical therapy.)

The idea is to build a cyclotron (a circular accelerator) and bolt it to a linac (a linear accelerator) and to call the hybrid a Cyclinac. So protons or carbon ions are injected into the cyclotron which stores and accelerates them. They are then injected into a linac which accelerates them to the appropriate energies for medical applications. The result is a therapeutic beam ready for action.

This design can also produce synchrotron  x-rays for other  medical apps.
Of course, there several significant engineering challenges ahead, like increasing the repetition rate of these devices to practical levels, something that Cyclinacs are being designed to address.

The big question, of course, is not whether such a project will be funded (everyone seems to agree on that) but when. And then where to build it. Given the Terra Foundation’s location, what odds on Italy being host to the first of these devices in Europe?

Ref: Cyclinacs: Fast-Cycling Accelerators for Hadrontherapy

Glider guns created in chemical Game of Life

Thursday, February 5th, 2009


If you’ve ever played Conway’s Game of Life, you’ll be familiar with cellular automata and, more importantly,  glider guns. So get this:  a team of British chemists and computer scientists  have  created a chemical cocktail that behaves like a cellular automata and which  reproduces this behavior: chemical  guns firing chemical gliders across a chemical grid.

For those who haven’t played with it, Conway’s  Game of Life is a two dimensional grid known as a cellular automata in which each square can be black or white. The game starts in an initial state–a pattern of black and white squares–and its evolution is determined by a set of rules that specify what color a square should become depending on the color of its neighbors.

The game was devised by the British mathematician John Conway in 1970 and has been studied in detail by countless generations of computer scientists, mathematicians and students ever since, not least because of the extraordinary patterns and structures that the game can produce.

One of these is the glider gun: a structure that periodically “fires” projectiles across the landscape.

Now Ben de Lacy Costello and pals from the University of West of England in Bristol have created a chemical version of all this. Their model is based on the famous Belousov-Zhabotinsky reactions in which a specific cocktail of chemicals  can produce complex patterns of oscillating colors.

The team set up a grid in which each square could change colour via a BZ reaction and in which the reaction diffused across the boundaries of each square in way that mimics Conway’s Game of Life.

The oscillating patterns produced by BZ reaction have long been thought of as similar to cellular automata but this is the first time that the Game of Life has been reproduced in a chemical system.

That’s impressive but it looks as if the best is yet to come. It is well known that cellular automata can operate as universal Turing machines . The next step, says  Costello and buddies, is to build a similar chemical grid capable of  arithmetic.

Beyond that, the question is this: if we can do this in the lab, might evolution also have harnessed these reactions in a similar way. Let the search begin.

Ref: Implementation of Glider Guns in the Light-Sensitive Belousov-Zhabotinsky Medium

Fermi’s paradox solved?

Monday, February 2nd, 2009


We have little to guide us on the question of the existence intelligent life elsewhere in the universe. But the physicist Enrico Fermi came up with the most obvious question: if the universe is teeming with advanced civilizations, where are they?

The so-called Fermi Paradox has haunted SETI researchers ever since. Not least because the famous Drake equation, which attempts put a figure on the number intelligent civilisations out there now, implies that if the number of intelligent civilisations capable of communication in our galaxy is greater than 1, then we should eventually hear from them.

That overlooks one small factor, says Reginald Smith from the Bouchet-Franklin Institute in Rochester, New York state. He says that there is a limit to how far a signal from ET can travel before it becomes too faint to hear. And when you factor that in, everything changes.

Smith uses this idea to derive a minimum density of civilizations below which contact is improbable within a given volume of space. The calculation depends on factors such as the lifetime of a civilization and the distance that it might be possible to communicate over and it produces some interesting scenarios:

Assuming the average communicating civilization has a lifetime of 1,000 years, ten times longer than Earth has been broadcasting, and has a signal horizon of 1,000 light-years, you need a minimum of over 300 communicating civilization in the galactic neighborhood to reach a minimum density.

So if there are only 200 advanced civilizations in our galaxy, the chances are that they’ll never notice each other.

Of course, we’ve no way of knowing how many advanced civilizations are out there. But this kind of thinking could, for the first time, put a limit on the number that could be out there: less than 200 perhaps?

It also has significant implications for Fermi’s line of thinking.

Would it be too early to say the paradox has been solved?

Ref: Broadcasting But Not Receiving: Density Dependence Considerations for SETI Signals

Rippling in muscles caused by molecular motors detaching

Friday, January 30th, 2009


Muscle tissue is made of molecular engines called sarcomeres, which contract and expend when the muscle is flexed. In sarcomeres the business of contracting is carried out by molecular motors called myosins as they pull themselves along filaments of a protein called actin. When you flex your arm, it is these myosin molecular motors that are doing the work.

One curious phenomenon that can sometimes be observed in muscles is a wavelike oscillation of the tissue. What causes this infamous “rippling” of muscles has been somewhat of a mystery but today Stefan Gunther and Karsten Kruse from Saarland University in Germany throw some light on the matter.

They’ve modeled the rate at which molecular motors detach themselves from the actin filaments as the load they are under changes. It turns out that oscilllations occur naturally under certain loads, as the molecular motors attach and re-attach.

So when the next bodice ripper you read mentions rippling muscles, you’ll know exactly what this means.

Ref: Spontaneous Waves in Muscle Fibres

Is meditating good for the heart?

Thursday, January 29th, 2009


Let’s calm things down with some deep breaths: in…out…in…out. Relax. Feel your pulse rate slowing?

We’ve known for some time that there’s more to pulse rate than beats per minute. Heart rate variability–the change in intervals between beats–can be used to distinguish healthy hearts from diseased and damaged ones.

One sign of a healthy heart is slight, seemingly random variations in the intervals between beats. These variations seem to be governed by power laws which is somewhat of a puzzle in itself.

By contrast, a steady unchanging beat interval seems to be a sign of disease.

Now Nikitas Papasimakis and Fotini Pallikari at the University of Athens in Greece have studied the heart beat intervals in people who are meditating and found that the power law variations disappear.

That raises an interesting question: is meditating good for the heart or not? Papasimakis and Pallikari argue that the loss of power law correlations cannot be used as evidence of ill health because the correlations return as soon as the subject stops meditating. Fair enough.

But what does the ability to switch these correlations on and off mean for health? Nobody knows just yet but it’s  a fascinating area in which it’ll be interesting to see  where more data leads.


: Breakdown of Long-Range Correlations in Heart Rate Fluctuations During Meditation

Electronic nose spots anthrax bacteria by smell alone

Thursday, January 22nd, 2009


In the last ten years or so electronic noses have become commercially available, based on a detection device known as a Taguchi sensor. These are heated semiconductor oxide films that change their resistance when they absorb gases. The gases break down inside the film and the various molecular species gather at grain boundaries within the film changing its resistance.

Electronic noses consist of an array of Taguchi sensors designed to spot different molecular species. These are connected to a computer that analyses the pattern of signals they produce to identify the gases present in a mixture. These can work with fairly complex volatiles and some electronic noses are capable of evaluating various foods .

Now Hung-Chih Chang at Texas A&M University and a few pals say it is possible to use the tools to identify bacteria by their smell alone. (more…)

The waltz of the spherical algae

Friday, January 16th, 2009


“Long after he made his great contributions to microscopy and started a revolution in biology, Antony van Leeuwenhoek peered into a drop of pond water and discovered one of nature’s geometrical marvels,” say Ray Goldstein and pals at the University of Cambridge in the UK.

Val Leeuwenhoek had discovered Volvox, a spherical green algae that uses thousands of cells with flagellla to move around.

Because of its size, Volvox is relatively easy to study and Goldstein and co have been keeping a close eye on the organism, watching the way it moves and the flow of fluid around it as it does so.

They’ve also found some unusual behaviours. In certain circumstances, Volvox likes to team up with a partner and waltz through the water like they’d been watching Strictly Ballroom.

The team say that the forces responsible for bringing the partners together are “short-range lubrication forces”, whatever they are, and that the creatures have probably evolved to take advantage of the opportunity this affords for some hanky panky. That must be first in hydrodynamics research.

The team have put together a set of fascinating videos showing Volvox in action which is recommended viewing for all algae.


Dancing Volvox : Hydrodynamic Bound States of Swimming Algae

How to spot vegetation on Earth-like planets

Tuesday, January 13th, 2009


In December 1990, scientists analysing data from the Galileo spacecraft found compelling evidence for the existence of life in space.

The data famously came from the craft’s first fly by of Earth, a planet on which life seemed a definite possibility.  The exercise led to the establishment of a number of criteria that if found elsewhere, would point to the existence of life

Among the most persuasive of these criteria is the vegetation red edge–a sharp increase in the reflectance of light at a wavelength of around 700 nm.  This is the result of chlorophyll absorbing visible light but reflecting near infrared strongly which Galileo found strong evidence for.

Assuming alien plant life is similar to ours,  could we spot a vegetative red edge on an Earth-like planet orbiting a star several light years away, asks Luc Arnold at the Saint-Michel-l’Observatoire in France and amis.


First “movie” of fruitfly gene network aging

Tuesday, January 6th, 2009


One of the major goals in biology is to reconstruct the complex genetic networks that operate inside cells, and to “film” how these networks evolve during the course of an organism’s development.

Today, Eric Xing and buddies at Carnegie Mellon University in Pittsburgh claim to have worked out how the way patterns of gene expression change in fruitflies over the course of their entire development. That’s a world first and no mean feat to boot.