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July 26, 2007

Jon Kleinberg

Cornell University, Ithaca, New York

A computer scientist wonders how much information is really good for us.

I am interested in understanding how groups of people or computer systems work together to solve complex problems. This is relevant in real-life situations that demand collective problem-solving, ranging from scientific research to military operations, so we hope to learn about the underlying mechanisms through experiment.

Stanley Milgram's famous 'six degrees of separation' studies form one such set of experiments. In these, participants were asked to help send a letter to a far-away stranger by forwarding it to a friend they thought might know the target. That this strategy often succeeded hints at how people lacking a global picture of the social network they inhabit can still jointly solve a difficult search problem.

One of the interesting questions here is how a group's ability to solve a problem is affected by the amount of information available. I expected that if people had a global view of the system, rather than just a local one, their effectiveness at solving the problem would increase.

A fascinating experiment (M. Kearns et al. Science 313, 824–827; 2006) shows that this isn't always so. The researchers posed a task in which they deliberately varied how much information was revealed to participants about what others in their group were doing.

For certain settings of the problem, giving participants a global view significantly slowed down progress. People faced with too much information in a time-pressured setting became 'overloaded', and this impaired the group's function.

As we consider designing tools to help people work together effectively, we should remember that increasing everyone's situational awareness might not always lead to improved performance.

July 18, 2007

Colin Prentice

QUEST, University of Bristol, UK

A theoretical biologist suggests that evolution makes plants more predictable.

The debate over how forests respond to rising levels of carbon dioxide has brought home to me how much spin even a dry journal article can contain.

In the mid-1990s, when the forest Free Air Carbon dioxide Enrichment (FACE) experiments began, I thought that we were poised to learn how trees really respond to carbon dioxide. In these experiments, carbon dioxide is pumped over forests to simulate future conditions.

Unfortunately, years of data collection and scores of papers later, we still haven't reached agreement. Using the same data, researchers conclude that carbon dioxide either fertilizes forests or it doesn't (or the effect is small, or it goes away, or will soon go away...)

The situation would be helped if we had better theories of how trees might be expected to react to changes in their resources. It was refreshing, therefore, to encounter an elegant analysis of plant behaviour (O. Franklin New Phytol. doi:10.1111/j.1469-8137.2007.02063.x; 2007).

Plants, subject to selective pressure, have to optimize what they can. This is a basic principle of evolutionary biology, too often disregarded in experimental contexts.

Theoreticians have long known that an individual leaf in high carbon dioxide will maximize the amount of carbon it fixes — a measure of its growth success — if it lowers its nitrogen content to optimize the balance between photosynthesis and respiration.

Franklin extends this nitrogen optimization principle to the whole plant, a significantly more complex problem. His model predicts 83% of the variation in plant growth enhancement seen across FACE studies, explains the observed relationship between plant growth and canopy nitrogen content, and does much else besides. It is a welcome step forwards.

July 11, 2007

Michael A. Marletta

University of California, Berkeley, USA

A biochemist marvels at a molecule that shares his love of playing with fire.

I like to capture my students' attention by recounting how my early fascination with fire inspired my interest in the stability of sugars.

Glucose will 'burn' to carbon dioxide and water, liberating lots of energy. But it is stable enough that you can stamp on it without triggering the reaction — the energy barrier to the reaction is too high.

In my research, I am interested in how biology harnesses and controls oxygen reactivity. Most reactions, such as burning glucose, are held back by an energy barrier to getting things started. Enzymes can bypass this, finding a lower energy route through some reaction intermediate, to carry out a 'controlled burn'. Their control is not perfect, sometimes causing damage to both themselves and surrounding molecules, but by and large it works.

Typically, these enzymes have metal or organic components, which drive the oxidation. I often tell students that enzymes need their metal and organic cofactors because the 20 naturally occurring amino acids cannot carry out all the chemistry. Two recent papers shake that belief.

The surprise comes from the enzyme DpgC, which is involved in the biosynthesis of the antibiotic vancomycin. The first paper (C. C. Tseng et al. Chem. Biol. 11, 1195–1203; 2004) reports that DpgC uses oxygen in a complex dioxygenase reaction with no bound metal or organic cofactor.

More recently, researchers reported the structure of DpgC and confirmed that it has no cofactor (P. F. Widboom et al. Nature 447, 342–345; 2007). They find that the enzyme has a structure known as an oxyanion hole, which helps to stabilize the reaction intermediate.

I am still amazed that DpgC does oxygen chemistry with no help — and my students should be too.

July 04, 2007

Allan Balmain

University of California, San Francisco, USA

A cancer geneticist delves into family matters.

A mystery lies at the heart of a small family of growth signalling enzymes (K-Ras, H-Ras and N-Ras), which are widely mutated in human cancers. In culture, all three enzymes have similar functions, but different ras genes are associated with cancers in different tissues.

My laboratory, for instance, noted more than 25 years ago that skin cancers show activation of H-ras. Others have demonstrated that lung, colon and pancreatic cancers show activation of K-ras, whereas N-ras is the oncogene of choice in melanomas and some leukaemias.

What determines this intriguing specificity? Are the enzymes' functions somehow modified in certain tissues in vivo? Or is it regulation of the genes, affecting where and when they are expressed, that matters?

We may get some answers by following the lead of an elegant study (N. Potenza et al. EMBO Rep. 6, 432–437; 2005). In this work, the authors knocked out K-ras in mice, but simultaneously replaced the gene with its close relative H-ras, doctored to have the regulatory elements of K-ras. Mice can survive without the H-ras or N-ras genes (or even both of them) but usually die if K-ras is deleted. These mice, despite lacking K-ras, were viable and lived to a ripe old age.

This important observation provides novel opportunities to probe the mechanisms of cancer initiation. Are the mice lacking K-ras now resistant to the lung and pancreatic cancers that are normally linked to K-ras? If yes, this would indicate a true requirement for the K-Ras protein in lung-cancer development; if not, the focus would switch to regulation.

A straw poll of Ras cognoscenti suggests that opinion is for now divided, but my group and others are working on this mouse model, and hope to have answers soon.