Liverpool John Moores University, UK

An ecologist enjoys a smelly experiment on a neglected link in the food web.

I have long been fascinated by an idea from the 1970s about rotting food. Daniel Janzen, now at the University of Pennsylvania in Philadelphia, suggested then that many of the noxious chemicals secreted by microbes in decaying food are produced to fend off large animals, allowing the microbes to keep the resource for themselves.

It's an intuitively appealing hypothesis. Our own experience is to be repulsed by putrid food, and several studies have shown that birds prefer fresh over rotted fruit. Most recently, a careful study in the seas off the southeasten United States provided further support for Janzen's idea (D. E. Burkepile et al. Ecology 87, 2821–2831; 2006).

In what must have been a gloriously smelly experiment, the researchers baited crab traps with dead fish, either rotten or fresh. The microbe-laden carrion was four times less likely to be consumed by scavengers than the fresh fish.

This provides clear evidence that microbes compete for food with larger animals, something that has been largely overlooked in the huge ecological literature on food webs and feeding relationships. But it doesn't tell us how the chemicals evolved.

Last year, I published with colleagues a theoretical analysis of the evolutionary implications of Janzen's idea (T. N. Sherratt et al. Ecol. Modell. 192, 618–626; 2006). Our model suggested that the chemicals cannot have evolved solely to protect against large animals, because the temptation for microbes to 'cheat' by free-riding on toxin production by others undermines the system.

The experiments done by Burkepile et al. show that the effect is real, but perhaps these chemicals first evolved for other reasons, such as inter-microbe competition?

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Princeton University, New Jersey, USA

A chemical engineer is struck by the strange properties of 'patchy' colloids.

A recent paper about the behaviour of colloids makes an intriguing prediction — suggesting that they can adopt an 'empty' liquid state.

I study disordered states of matter, such as liquids and glasses. I find colloids interesting because they make phenomena such as crystal nucleation and the glass transition amenable to direct observation. Nanometre- or micrometre-sized particles suspended in liquids are wonderful model atoms. They arrange themselves in the same way that atoms and simple molecules do into solids, liquids or gases.

But controlling the interactions between colloidal particles provides a window into structural and thermodynamic behaviour beyond that found in atomic systems, as this recent theoretical paper shows (E. Bianchi et al. Phys. Rev. Lett. 97, 168301; 2006).

It maps the phase diagrams of 'patchy' colloids. The particles in such colloids are decorated with sticky spots, which tend to bond them together. As the number of bonded neighbours per particle is reduced towards two, the phase diagrams predict liquid states with a vanishing packing fraction. This means the colloidal particles occupy a tiny fraction of the available space — but they still behave as a liquid that is distinct from the gas-like phase of still lower packing fraction.

The low-temperature behaviour of such 'empty' liquids is especially interesting. The calculations suggest that cooling the colloid can freeze in place the empty configuration to give a glassy state of arbitrarily low density.

These predictions have not been tested experimentally. But chemists have already developed techniques for making patchy particles, so the work of Bianchi et al. could guide experimentalists in their exploration of this fascinating form of matter.

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Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts

A geneticist rebuts criticism of cancer genome projects.

What do you learn if you sequence 13,000 genes in 11 breast and 11 colorectal cancer samples? The question taps into an intense debate about how best to identify genes relevant to human cancer.

Last year, researchers reported the results of a survey such as the one described (T. Sjöblom et al. Science 314, 268–274; 2006). They found that each tumour contains, on average, 90 mutant genes — an unexpectedly high number. They also defined mutation spectra that were specific to colon and breast tumours, including the intriguing observation that the DNA letter sequence CG was swapped for GC at high frequency in breast tumours. This could be due to an uncharacterized DNA repair defect or differential carcinogen exposure.

I consider this report a step towards answering key questions in cancer biology, such as how many genes are mutated in cancer, how many mutations are required for cancer, and whether accumulation of genetic alterations in cancer cells drives tumour progression.

But others disagree. Many labs see large-scale sequencing of cancer genomes as unfocused and expensive fishing experiments. I have been doing genomics experiments since the dawn of this era, and have often faced this criticism.

But just this one study has identified more genes mutated in human cancer than thousands of investigators have found over past decades. And another recent, large-scale sequencing project pinpointed close to 120 mutant kinase enzymes that may have a role in human cancers (C. Greenman et al. Nature 446, 153–158; 2007).

Both cases show that the outcome of unbiased, genome-wide studies may not be what we expect, which is exactly why they're worth doing.

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Stanford University, California

A palaeoceanographer worries not about corals, but about coral reefs.

To understand what the consequences of human-induced CO2 increases might be, I study how atmospheric CO2 concentrations fluctuated in the past.

One outcome of high atmospheric CO2 that is inevitable is ocean acidification. Atmospheric CO2 dissolves in sea water, lowering the pH of the ocean's surface layer.

We expect this to create problems for marine creatures that precipitate their skeletons from calcium carbonate, because the mineral dissolves in acid. Some researchers have suggested that scleractinian corals might even be driven to extinction.

But what does the geological record tell us? Corals' reef-building fossils have appeared and disappeared over the past 200 million years and despite periods of elevated atmospheric CO2, the organisms did not go extinct.

A recent experiment (M. Fine & D. Tchernov Science 315, 1811; 2007) resolves this apparent paradox. The team grew scleractinian corals for a year in sea water with a lower-than-normal pH. They found that the corals reproduced and grew happily in this acidic environment — albeit without their hard skeletons. The corals adjusted their skeleton-forming physiology in response to the different growing conditions.

So corals seem to be quite adaptable. But I would like to know whether other calcifying organisms have such physiological versatility.

Moreover, we have to remember that although corals may survive in an ocean with a lower pH as sea-anemone-like organisms, they are currently major contributors to the intricate physical structure of coral reefs. What will be the future of these ecosystems if their calcium-carbonate scaffolding disappears? Will our grandchildren enjoy the spectacular beauty of these 'rainforests' of the ocean?

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