Boston University, USA

A physicist highlights a three-in-one deal for nonlinear science

As a student of nonlinear phenomena, I am continually amazed by new examples of deterministic chaos, solitary
waves and fractals.

A recent study (R. H. Goodman and R. Haberman Phys. Rev. Lett. 98, 104103; 2007) gave me the rare pleasure of seeing all three of these fundamental manifestations of nonlinearity woven together.

This paper addresses the collisions of solitary waves — localized nonlinear waves that propagate without changing shape and are found in systems ranging from solids to optical fibres.

In the 1980s, with several colleagues, I studied this problem numerically (see, for example, D. K. Campbell and M. Peyrard Physica D 18, 47–53; 1986). We discovered a surprising 'bounce' phenomenon, in which solitary waves would collide, remain trapped for a number (n) of bounces and then escape to infinity. This behaviour occurred only when the waves had specific relative velocities on colliding; these bounce windows were interspersed with regions in which the waves repelled each other immediately.

We developed a heuristic explanation for this behaviour, consistent with the waves behaving like elastic particles that can be deformed, but fell short of developing a full analytical explanation.
Journal club

Goodman and Haberman have now developed an analytical treatment of this effect and have shown, in their words, "that clusters of (n+1)-bounce windows accumulate at the edges of each n-bounce window, repeated at diminishing scales" in an effective fractal structure. This also means that the outcome of a collision is exquisitely sensitive to the initial velocity, a hallmark of deterministic chaos.

If all the above seems dry, take a look at the wonderful graphic (here) from the article, which represents the number of bounces as a function of the collision parameters. The image is certainly worth more than these few hundred words.

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Collegium Budapest, Hungary, and The Parmenides Foundation for the Study of Thinking, Munich, Germany

A theoretical biologist recommends thought-provoking reading on the origin of translation and the genetic code.

As Francis Crick and his co-workers once noted, "the origin of protein synthesis is a notoriously difficult problem". Our best hopes of resolving this problem begin, in my opinion, in an RNA world.

The RNA-world hypothesis holds that RNA emerged before DNA and proteins, neatly separating the origin of life from that of the genetic code and its translation. The question then becomes: how did RNA evolve to make proteins?

In a recent paper, Yuri Wolf and Eugene Koonin of the National Institutes of Health in Bethesda, Maryland, present one scenario (Biol. Direct 2, 14; 2007).

They rightly call attention to studies that suggest that protein-based aminoacyl-tRNA synthetases, which are involved in the first steps of assembling amino acids into proteins, are relatively late evolutionary inventions. This forces us to accept the idea that protein synthesis is older than such synthetases.

Before the evolution of synthetases, the only agents that could conceivably have marshalled amino acids are RNA enzymes, or ribozymes. Wolf and Koonin share my view that the recruitment of amino acids was driven by selection for enhanced catalytic activity, and that the ancestor of the large ribosomal RNA that catalyses protein synthesis in today's cells — a molecular 'fossil' — was a catalyst that linked only two amino acids.

I am less happy with these authors' suggestion of a relatively late switch from peptide-specific proto-ribosomes to those that could use an external template such as mRNA to synthesize peptides with arbitrary sequence — but they may well be right.

They lay out an evolutionary sequence that is more complete than the scenario I once proposed. I highly recommend this well-written, thought-provoking paper.

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University of British Columbia, Vancouver, Canada

A microbiologist wonders where diversity comes from.

Recent estimates indicate that the total number of bacteria in the biosphere approaches or exceeds 10 to the power 31. A major goal of microbiology is to understand what creates their diversity and how it is maintained.

Having trained as an organic chemist, I came to appreciate microbial diversity through the extravagance of small molecules that microbes produce. This reflects a diversity in microbial metabolism, which one might expect to have evolved as a result of the (organic) richness of the organisms' environments. But a couple of recent publications present findings that do not sit easily with this view.

Our first inkling of the huge diversity of the microbial world came from the use of ribosomal-RNA typing in the late 1980s. In the 1990s, this morphed into the expanding field of metagenomics, which is now providing catalogues of microbial communities from diverse terrestrial and marine environments.

One comparison of such catalogues showed that the seemingly bare and boring Arctic tundra exceeds fertile forest soils in phylogenetic content (J. D. Neufeld and W. W. Mohn Appl. Environ. Microbiol. 71, 5710–5718; 2005). A more recent study compared information from more than 100 different environments, finding that the microbial content of soils is generally less diverse than that of sediments and hypersaline environments (C. A. Lozupone and R. Knight Proc. Natl Acad. Sci. USA 104, 11436–11440; 2007).

I am looking forward to seeing what happens when the Human Microbiome Project gets under way. What variety of microbes is there to find living within us? What are they all doing? In what way will the population depend on diet? Given that we don't yet seem to understand the relationship between diversity and ecology, I am making no predictions.

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Massachusetts Institute of Technology, Cambridge, USA

A biological engineer searches for simplicity.

Several years ago, a good colleague suggested that I read about a discussion held in 1864 on nuts and bolts (J. Franklin Inst. 77, 344–351; 1864). The focus was a paper by one William Sellers that argued for the adoption of a uniform system of screw threads — 60° angles, squared off along the edges.

Machinists across the United States eventually started producing nuts and bolts according to Sellers' scheme. As a result, hardware stores now offer a wide selection of standardized parts that can be used in combination and behave as expected.

Inspired by this example and others, I have been studying how synthetic biological parts might be made as regular and easy to use as Sellers' nuts and bolts.

The starting complexity of nature has led some distinguished researchers to doubt such work is practical. But given that there has been little research on manufactured bio-simplicity, this seems premature.

And there are examples: a team at the California Institute of Technology in Pasadena recently developed a uniform system for engineering simple biological switches made from ribonucleic acids (M. N. Win and C. D. Smolke Proc. Natl Acad. Sci. USA doi:10.1073/pnas.0703961104; 2007).

The 'nuts and bolts' of the switches are RNA sensor and actuator domains. The method for combining any sensor domain to an actuator domain through a third communication domain provides the 'uniform screw threads'. Because such switches are produced by a standard process, many switches could be quickly programmed to control diverse cellular functions in response to myriad molecular inputs, from small molecules, to peptides, to nucleic acids.

I suspect that further efforts to engineer biological simplicity will have similarly powerful results.

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