David L. Goodstein

The Genome of the Western Clawed Frog Xenopus tropicalis

Frog Genome The African clawed frog Xenopus tropicalis is the first amphibian to have its genome sequenced. Hellsten et al. (p. 633, see the cover) present an analysis of a draft assembly of the genome. The genome of the frog, which is an important model system for developmental biology, encodes over 20,000 protein-coding genes, of which more than 1700 genes have identified human disease associations. Detailed comparison of the content of protein-coding genes with other tetrapods—human and chicken—reveals extensive shared synteny, occasionally spanning entire chromosomes. Assembly, annotation, and analysis of the frog genome compares gene content and synteny with the human and chicken genomes. The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

Criticality and superfluidity in liquid ^4He under nonequilibrium conditions

We review a striking array of recent experiments and their theoretical interpretations on the superfluid transition in ^4He in the presence of a heat flux Q. We define and evaluate a new set of critical point exponents. The statics and dynamics of the superfluid-normal interface are discussed, with special attention to the role of gravity. If Q is in the same direction as gravity, a self-organized state can arise, in which the entire sample has a uniform reduced temperature, on either the normal or superfluid side of the transition. Finally, we review recent theory and experiment regarding the heat capacity at constant Q. The excitement that surrounds this field arises from the fact that advanced thermometry and the future availability of a microgravity experimental platform aboard the International Space Station will soon open to experimental exploration decades of reduced temperature that were previously inaccessible.

Erratum: Genome sequence of the palaeopolyploid soybean (Nature (2010) 463 (178-183))

This corrects the article DOI: 10.1038/nature08670

Phonon focusing catastrophes

We present an elegant application of formal catastrophe theory to phonon focusing phenomena in crystals. The standard analysis of phonon focusing breaks down near singular directions known as caustics. The theory we present, in addition to being numerically accurate, provides a qualitative picture of caustic surfaces which yields important new insights into the results of phonon propagation experiments. Supporting experimental evidence is also presented.

Richard Feynman and the History of Superconductivity

Abstract. This paper deals with two topics. One is the history of superconductivity, and the other is what Richard Feynman had to do with it. The history of superconductivity can be traced back to Michael Faraday and the first liquefaction of a gas in 1823. It is a heroic tale of triumph over cold and resistance, and once the phenomenon was actually discovered in 1911, it would take almost 50 years more before a satisfactory explanation emerged. Although Richard Feynman only authored one published paper on the subject, he worked prodigiously on the problem through much of the 1950s, and his competitors, particularly Bardeen, Cooper, and Schrieffer, fully expected that he would be the one to crack the problem. It did not work out that way.

The science literacy gap: A Karplus lecture

The great American experiment in mass higher education has failed completely in the sciences, where we have a small educated elite and an illiterate general public. Our graduate education in science is the best in the world, and contrary to the belief of some, we do not face a future shortage of scientists. However, the rest of our educational system is bad enough to constitute a threat to the ideal of Jeffersonian democracy. “The Mechanical Universe,” a video series produced by Caltech and aimed at high school physics teachers, is described. Although that project has been very successful, much more must be done. The educational infrastructure must be strengthened to the point where science can be taught gradually, throughout the school years and beyond. Furthermore, those of us who are professional teachers of science must become better teachers, both by increasing our own mastery of our subjects and by better understanding the difficulties our students have in learning science.

Phase diagrams of multilayer adsorbed methane

We propose multilayer phase diagrams based on recent observations of methane adsorbed on graphite and gold (111). Methane wets graphite at all temperatures observed, but it fully wets gold only above the bulk triple point. Possible reasons for this difference in behavior are discussed. The methane-graphite phase diagram also includes layer by layer condensation with critical points leading to a predicted bulk roughening temperature, and an extension of the bulk melting curve into the multilayer film region where it closes at a triple point with a compressed incommensurate first layer solid phase. Experimental evidence for these features is presented and discussed.

Direct and thermal desorption of ^4He films

We have studied desorption from a ^4He film due to a hot but low-intensity beam of phonons incident from a sapphire substrate. Time of flight spectra of the desorbed atoms revealed two distinct peaks which we attribute to direct desorption by substrate phonons and to thermalization with subsequent desorption.

Phonon reflection at a sapphire-vacuum interface

Theoretical and experimental studies have been conducted of the transmission of phonons in sapphire and their reflection at a crystal-vacuum interface. The effects of crystal anisotropy on the reflection process are discussed in detail. The heat-pulse technique has been used to obtain high-resolution time-of-flight spectra as a function of the angle of incidence in accurately known crystallographic directions. The agreement with predictions from numerical calculations is excellent. The relevance of these observations to studies of the anomalous transmission of energy through a crystal-liquid helium interface is also discussed.

A note on the structure of positive ions in liquid 4He

Evidence that the positive ion in liquid 4He forms a solid core with a solid-liquid interface is examined in the light of new analytic solutions to the Navier-Stokes equations. It is found that the existing evidence does not decisively favor the picture that a solid core is formed.