University of California, Berkeley

An ecologist notes that important details are missing from climate-change models.

Unmitigated climate change will gravely reduce Earth's biodiversity. How much this will happen is calculated by combining data on how the species richness of different habitats varies with their area and projections of how much various habitat types will shrink as the planet warms.

But such grand analyses are blunt instruments; they miss numerous local processes. I have seen, for example, rosy finches and ptarmigans feeding on the contracting ring of vegetation that surrounds melting snow patches on Alpine slopes. Would these creatures survive the summer if the snow patches melted in late spring rather than late summer? Formed in existing mountainside hollows, snowbeds will not march uphill as the climate warms.

This question was recently answered by Robert Björk and Ulf Molau, then both at the University of Gothenburg in Sweden. They reviewed how the release of water and nutrients from the contracting edge of lingering snow patches sustains alpine life in midsummer by providing nourishing vegetation (R. Bjork and U. Molau Arctic Antarctic Alpine Res. 39, 34–43; 2007). The duo propose that bryophytes, grasses, sedges and rushes will be worst hit by the patches' earlier annual disappearance, and that these easy-to-graze species will be replaced by shrubs and trees, hitting Alpine herbivores hard.

This is just one example of the many impacts on biodiversity that fall through the cracks of current, coarse projections. Life and climate intersect on fine spatial and temporal scales — in the microclimates provided by terrestrial 'nurse plants' and in rock pools that form fleetingly in bedrock depressions. The disruption of these delicate intersections may add up to even more damage to biodiversity than the large-scale models predict. This deserves more study.

Posted on August 29, 2008 08:15 PM | Permalink | Comments (0) | TrackBacks (0)

Howard Hughes Medical Institute, Cornell University, Ithaca, New York

A biophysicist marvels at the idea of grabbing microscopic particles with light by tweaking its phase.

Light carries energy and momentum. Have you ever gazed at a comet on a hot summer night? The dust tail seen streaming out from a comet is caused by sunlight bombarding dust particles from its surface and pushing them away from the Sun. The same radiation pressure can be used to 'trap', or hold, microscopic particles. And if an item of interest — for example, a biological molecule — is attached to a particle subject to trapping, it can then be manipulated as the trap is moved.

So how does one generate optical traps? Conventionally, a laser beam is directed through the objective lens of a microscope and focused to a small spot very close to the specimen. The trapping force relies on the gradient of the laser's intensity — the tighter the focus, the greater the intensity change within the focused beam, and the greater the trapping force.

For a long time, this has been the only type of trap available. But not any more! David Grier and his colleagues have created a new type of trap that relies on the gradient of the 'phase' of a laser's light as well as its intensity (Y. Roichman et al. Phys. Rev. Lett. 100, 013602; 2008). Light waves, like ocean waves, have crests and troughs. The phase of a light wave specifies what position within the wave, from crest to trough, the light is in at a given moment. By tweaking the phase of the laser in the trap, the researchers are able not only to hold a particle steady, but also to move it in a line or spin it around in a circle. It is now possible to design optical traps that are more flexible and versatile, and that can generate as much trapping force as before, but with less light.

I would not be surprised if these traps soon become one of the must-have tools in single-molecule biophysics, cell biology and colloidal physics.

Posted on August 29, 2008 08:11 PM | Permalink | Comments (0) | TrackBacks (0)

Ecole Normale Supérieure, Lyon, France

A geochemist wonders about the Solar System's true age.

Scientists have long looked at the constituent elements of meteorites to find out how old the Sun and its planets are. The most perfect example of the oldest meteorites — those that formed at the same time as the planets — broke up and fell as a large shower near Pueblito de Allende in Mexico in 1969. This was named the Allende chondrite, and was recently the subject of a study by Jim Connelly of the University of Texas at Austin and his colleagues.

Meteorites are often dated by measuring how much aluminium-26 they contain. This isotope decays at a rate that allows researchers to tell when one meteorite is older than another, but too fast to work out these rocks' absolute ages. For the relative ages to be accurate, however, aluminium-26 must have been spread evenly among the protoplanetary debris from which meteorites were born. If it was not, this isotope would reflect where they formed as well as when they formed, and meteorite chronologies would be higgledy piggledy.

But true ages can be calculated from lead isotopes. Until recently, lead had not been measured in both of two common parts of the oldest meteorites — chrondules and calcium–aluminium-rich inclusions — for any one rock, and there was no way of telling whether different rocks formed in the same bit of the nascent Solar System. But the lead isotopes in both chrondules and calcium–aluminium-rich inclusions can be counted in Allende.

Connelly and his team have confirmed an age difference between the chondrules and calcium–aluminium-rich inclusions that had been inferred from aluminium-26 measurements. This means that the relative meteorite chronologies are correct, and that aluminium-26 was indeed evenly distributed when the Sun ignited (J. N. Connelly et al. Astrophys. J. 675, L121–L124; 2008). If this is right, then the Solar System must be 4,567.5 million years old.

Posted on August 14, 2008 02:06 PM | Permalink | Comments (0) | TrackBacks (0)

University of Texas at Austin

A chemical engineer notes that not all membrane pores are made equal; some are more equal than others.

Few cheap, man-made membranes have holes of uniform size. This makes them either inefficient or unreliable sieves of particles such as viruses. But membranes are also one of the least energy-intensive separation devices. As fuel costs rise, many of the billion or so people without access to safe drinking water find it harder to sanitize what water they have. This is why I view the low-cost manufacture of isoporous membranes as a holy grail in the field.

Recently, some scientists in Germany unearthed a path to this chalice by tinkering with a technique known as 'phase inversion'. This is often used to make synthetic membranes: a polymer solution is immersed in a liquid, often water, which diffuses into the solution and causes a thin, porous membrane of hydrophobic polymer to form. The solid polymer is a twisted, irregular matrix, full of odd-shaped pores.

Klaus-Viktor Peinemann and his co-workers started with a polymer in which the chain-like molecules have a hydrophobic and a hydrophilic end, and allowed the solvent solution to evaporate. As this happened, they think that the polymer assembled into connected cylinders, with the hydrophobic and hydrophilic parts of different molecules coming together. The researchers then plunged this nascent membrane into water, which moved through the hydrophilic cylinders, opening them up and thus creating identical and aligned pores (K.-V. Peinemann et al. Nature Mater. 6, 992–996; 2007).

The pores were all about 10 nanometres wide — roughly the right size to separate hepatitis B virus from water. Picking other polymers with hydrophobic and hydrophilic parts should allow the development of membranes with uniform-diameter pores of various sizes. That could be a boon for industry as well as public health.

Posted on August 14, 2008 02:02 PM | Permalink | Comments (0) | TrackBacks (0)

The University of Alabama, Tuscaloosa; Queen's University Belfast, Northern Ireland

A chemist believes that an ionic liquid is the place for a noxious gas.

As a 'green chemist', I worry about the potential dangers of moving toxic and flammable gases around. Most nasty gases are transported in pressurized canisters to save space, posing the risk of hazardous compounds being expressed over people and pleasant greenery on the rare occasions that a container breaks.

Recently, some scientists at Air Products and Chemicals, a chemicals supplier in Allentown, Pennsylvania, found a way to store phosphine (PH3) and boron trifluoride (BF3) — both toxic gases — in ionic liquids, and then recover the gases without introducing impurities (D. J. Tempel et al. J. Am. Chem. Soc. 130, 400–401; 2008).

The advantage of transporting gases in ionic liquids is that many such liquids have no measurable vapour pressure. So were a container to burst, the gases inside it would remain as chemical complexes in a liquid state, making them much easier to mop up. Furthermore, ionic liquids can be recycled in subsequent shipments.

Dan Tempel and his team used a computer model to consider two ionic liquids — the cation 1-butyl-3-methylimidazolium paired with either Al2Cl-7 and Cu2Cl-3 — for phosphine transport. They then tested the latter in the lab; the positively charged copper atoms bound the lone electron pair on phosphine. Similarly, the electron-deficient boron atom in boron trifluoride facilitated the formation of a covalent bond with a fluorine atom in another ionic liquid, in which the same cation is paired with BF-4.

In both cases, more than 90% of the ionic liquid's reactive sites formed complexes at room temperatures. This means that relatively small volumes of ionic liquids could move a lot of toxic gas around. I think this could revolutionize the industry.

Posted on August 4, 2008 03:24 PM | Permalink | Comments (0) | TrackBacks (0)

University of Massachusetts, Worcester

A biologist despairs over the difficulty of demonstrating heritability of chromatin states.

Chromatin, the packaged bundles of protein and DNA that make up eukaryotic genomes, is widely believed to be a carrier of 'epigenetic' inheritance — that is, heritable information not encoded by DNA. In multicellular organisms, the chromatin of mother and daughter cells is generally of similar shape, exposing similar regions of DNA for expression. And chromatin regulators often seem to be required for epigenetic states to be inherited. But there is a problem. It is possible that some other information carrier is inherited, and then directs chromatin regulators to re-establish a functional state.

One purported example of chromatin inheritance comes from yeast, which seem to 'remember' prior growth conditions. Galactose-naive yeast induce genes for Gal enzymes slowly; those whose recent ancestors experienced galactose induce them much faster. Because this 'memory' requires certain chromatin regulators, it has been suggested that it provided evidence for a heritable chromatin state.

Zacharioudakis et al. investigate this idea using heterokaryons, fused pairs of yeast cells that have mixed cytoplasmic contents but maintain separate nuclei. By inducing memory in one yeast and seeing speedy GAL1 expression in the other, they show that memory of galactose is transferable through cytoplasm (I. Zacharioudakis et al. Curr. Biol. 17, 2041–2046; 2007). Thus, the chromatin state around the GAL1 gene cannot be the heritable factor, and the authors further identify the probable inheritance factor as a soluble enzyme.

These results demonstrate the difficulty of proving that any example of epigenetic inheritance is due to inheritance of chromatin state per se. One wonders whether any chromatin state will ever be proved to be heritable, given the difficulty of proving the absence of another information carrier.

Posted on August 4, 2008 03:17 PM | Permalink | Comments (0) | TrackBacks (0)

University of California, Los Angeles

A physicist links magnetism, force and fatigue.

If a metal bar is repeatedly stretched and released it becomes fatigued and, eventually, ruptures. The latter can occur suddenly and unexpectedly: sometimes materials scientists can find no obvious thermodynamic hint that a steel rod is about to break. I am interested in fatigue because it parallels other phenomena that concentrate energy density, such as triboluminescence, whereby diffuse stress makes a crystal glow.

In both triboluminescence and fatigue, applied forces cause molecular rearrangements. But fatigue also involves nanometre-sized defects that accumulate during the useful life of a piece of metal and organize themselves into a soft spot. Recently, Sidney Guralnick and his colleagues at the Illinois Institute of Technology in Chicago measured how much work is needed to complete each 'stretch and release' cycle in rods of AISI 1018 steel, a common low-carbon steel that is used in vehicle parts such as gears (S. A. Guralnick et al. J. Phys. D Appl. Phys. 41, 115006; 2008). This allowed them to follow changes in the material's response to force as it fatigued.

A shift occurred at merely 12.3% of the time to rupture. What is happening inside the steel at this point is mysterious, but the number holds true even when the useful life of identically manufactured rods varies by a factor of 200.

Further clues will no doubt come from steel's piezomagnetism — the fact that its magnetism varies with the degree of stretch it experiences. This relationship is complex: even when the metal is so slightly strained that it goes back to its original shape on release, its magnetic field does not return to the pre-stretched state. One day investigations into this property may uncover the organizing principle of the nanometre-sized defects that underlie metal rupture.

Posted on July 22, 2008 04:15 PM | Permalink | Comments (1) | TrackBacks (0)

Semmelweis University, Budapest, Hungary

A network scientist highlights active sites of enzymes, cells, brains and society.

For proteins, chemical binding is a tricky business. Special signals must be sent across a sea of water molecules to the desired partner, and complex mutual structural adjustments (a fluctuation fit) must be completed before each successful binding event.

I have long taught that a protein at its lowest-energy conformation still has regions of higher energy. But I've always been intrigued: how is the extra energy of the active sites preserved? And why do we need such big enzymes when their active sites occupy only a tiny region?

Piazza and Sanejouand found part of the answer by identifying special energy-preserving segments of proteins (F. Piazza and Y.-H. Sanejouand Phys. Biol. 5, 026001; 2008). Taking into account the effect of the surrounding water, they modelled proteins with a computer program that arranges oscillating elements in the same pattern as amino acids in real proteins. In most of these proteins, they identified a few easily excitable segments that collected and harboured long-lived, localized vibrations. An analysis of 833 enzymes showed that these segments co-occur with the catalytic active sites; are located on the stiffest parts of the proteins; and have many connections but are surrounded by a less well-connected environment.

The generality of many network properties prompts me to ask: can we find 'active sites' of cells, brains, ecosystems and societies? Piazza and Sanejouand's segments correspond to Ronald Burt's "structural holes" in social networks — whereby areas of greatest economic potential are areas of low connectedness, where brokers can make new connections. Indeed, not only amino acids, but people may also act as brokers, mediators and catalysts. It may be worthwhile to think about creative, broker proteins as drug targets. One could even imagine creative sets of neurons.

Posted on July 4, 2008 11:43 AM | Permalink | Comments (3) | TrackBacks (0)