Reply to the Comment by S. Harvey on “Entropy,Energy, and Bending of DNA in Viral Capsids”

The comment by Stephen Harvey in this issue of the Biophysical Journal concludes with two statements regarding my recent letter about DNA packaging into viral capsids. Harvey agrees with my interpretation of the origin of the large confinement entropy predicted by the molecular-dynamics simulations of his group, and its sensitive dependence on the molecular parameters of their wormlike chain model of double-stranded DNA. On the other hand, he doubts my assertion that the confinement entropy is already included in the interstrand repulsion free energy derived from osmotic stress measurements, which constitutes the major contribution to the packaging free energy used in recent continuum theories of this process. Harvey suggests instead that the confinement entropy should be added to this free energy as a separate term (using, for instance, the method described in my letter). I will argue that this addition is redundant, and, in a brief discussion of continuum theories, will also discuss his comments as relates to the work of other researchers.     

Reply to “Commentary on Photosynthesis and Negative Entropy Production by Jennings and coworkers” by J. Lavergne

It is argued that the chemical potential analogy does not provide useful information on the thermodynamics of photosystems, as the thermodynamic efficiency of an absorbed quantum is not considered. Instead, the approach based on either entropy balance or entropy flux considerations does provide this information. At high thermodynamic efficiencies, primary photochemistry can, in principle, violate the Second Law of Thermodynamics.     

Taxonomic structure of phytoplankton assemblages in Crater Lake, Oregon, U.S.A.

SUMMARY. 1. A taxonomic analysis of 171 phytoplankton samples obtained from Crater Luke, Oregon, between 1985 and 1987 revealed 132 taxa in the upper 250 m of the water column. The greatest temporal variation in taxonomic structure occurred between 40 and 80 m below the water surface, a depth range which corresponded to the zone of maximum primary production.
2. Phytoplankton cell biovolume in the upper 20 m of the water column was relatively high during the summer months, a period when Nitzschia gracilis was dominant in the epilimnion. However, 72% or more of the cell biovolume between 0 and 200 m was distributed below 20 m and, during the winter and spring months, 61% was found below 80 m.
3. Cluster analysis identified a sparse, temporally ubiquitous flora which was modified to various degrees when environmental conditions became favourable for the growth of a few dominant taxa. These surges ot dominance by individual taxa accounted for 2 to 5-fold increases in cell biovolume and generated a pronounced taxonomic discontinuity between the floras in the epilimnion and hypolimnion.
4. While the taxonomic structure of the phytoplankton in the epilimnion corresponded closely with the structure found in a 1978–80 study, the flora below the metalimnion was more diverse and less predictable in species composition than the pattern reported in the earlier study.     

Comment on the Letter by A. Ben-Shaul: “Entropy,Energy, and Bending of DNA in Viral Capsids”

The conformational entropic penalty associated with packaging double-stranded DNA into viral capsids remains an issue of contention. So far, models based on a continuum approximation for DNA have either left the question unexamined, or they have assumed that the entropic penalty is negligible, following an early analysis by Riemer and Bloomfield. In contrast, molecular-dynamics (MD) simulations using bead-and-spring models consistently show a large penalty. A recent letter from Ben-Shaul attempts to reconcile the differences. While the letter makes some valid points, the issue of how to include conformational entropy in the continuum models remains unresolved. In this Comment, I show that the free energy decomposition from continuum models could be brought into line with the decomposition from the MD simulations with two adjustments. First, the entropy from Flory-Huggins theory should be replaced by the estimate of the entropic penalty given in Ben-Shaul’s letter, which corresponds closely to that from the MD simulations. Second, the DNA-DNA repulsions are well described by the empirical relationship given by the Cal Tech group, but the strength of these should be reduced by about half, using parameters based on the Rau-Parsegian experiments, rather than treating them as “fitting parameters (tuned) to fit the data from (single molecule pulling) experiments.”     

The world is not inhabited by schematic patterns: Reply to the article by Z.S. Kaufman

In this reply to Z.S. Kaufman’s article Some Problems of Regressive Evolution, sedentary and parasitic modes of life are regarded as evolutionary strategies requiring morphological and functional rearrangements of organs, systems of organs, and the structure of the body as a whole that are not regressive. First of all, this applies to adaptations to sedentary life. Regress and degradation of parasitic forms take place only at the last stages of evolution, in parasites living in body cavities and tissues.