Mathematical Models of Plasma in Morozov’s Projects

Plasma Physics Reports - Mathematical models and simulations of plasma processes in scientific and technological projects proposed and, to a large extent, implemented by A.I. Morozov are reviewed....     

The Evolutionary Biology of Musical Rhythm: Was Darwin Wrong?

In The Descent of Man, Darwin speculated that our capacity for musical rhythm reflects basic aspects of brain function broadly shared among animals. Although this remains an appealing idea, it is being challenged by modern cross-species research. This research hints that our capacity to synchronize to a beat, i.e., to move in time with a perceived pulse in a manner that is predictive and flexible across a broad range of tempi, may be shared by only a few other species. Is this really the case? If so, it would have important implications for our understanding of the evolution of human musicality.     

The Practical Mode—A Distinct Mode of Performance in Biology

Linnaeus' timely work was a major contribution to botany and is of interest to students of botany at all levels. This is a brief biographical outline with a version of his Flora's Clock which some might like to try.     

Role of Concentration-dependent Unloading in Mathematical Models of Münch Transport

It has been erroneously claimed (Goeschl et al. [1976] Plant Physiol. 58: 556-562) that concentration-dependent unloading is required for a correct mathematical solution for Münch phloem transport. Although it may prove to be physiologically correct, concentration-dependent unloading is not a mathematical necessity. Furthermore, its use in a mathematical model may not be desirable, because there is an infinite family of solutions for any given unloading distribution, irrespective of whether concentration-dependent unloading is assumed. Some illustrative numerical results are presented.     

Not Just a Sum? Identifying Different Types of Interplay between Constituents in Combined Interventions

Motivation

Experiments in which the effect of combined manipulations is compared with the effects of their pure constituents have received a great deal of attention. Examples include the study of combination therapies and the comparison of double and single knockout model organisms. Often the effect of the combined manipulation is not a mere addition of the effects of its constituents, with quite different forms of interplay between the constituents being possible. Yet, a well-formalized taxonomy of possible forms of interplay is lacking, let alone a statistical methodology to test for their presence in empirical data.

Results

Starting from a taxonomy of a broad range of forms of interplay between constituents of a combined manipulation, we propose a sound statistical hypothesis testing framework to test for the presence of each particular form of interplay. We illustrate the framework with analyses of public gene expression data on the combined treatment of dendritic cells with curdlan and GM-CSF and show that these lead to valuable insights into the mode of action of the constituent treatments and their combination.

Availability and Implementation

R code implementing the statistical testing procedure for microarray gene expression data is available as supplementary material. The data are available from the Gene Expression Omnibus with accession number GSE32986.     

A-Level ‘Questions’ in Biology—The Nature of the Influence

The purpose of keeping animals in schools and the main problems encountered in their maintenance are summarised. Many teachers prefer animals which are kept typically in research laboratories over animals which can be collected from the student's environment. However, small animals of economic importance can combine some of the advantages of both of these groups of animals. Chickens, bees, plant pests and their natural enemies have been tried out in the Agriculture as Environmental Science Curriculum Project and can be used for observation and measurement as well as to stress the aspect of relevance to real life problems. In their maintenance, standard equipment and methods can often be used and help the teacher to solve some of the main problems of keeping animals.

Two curriculum units, on a fruit fly and on honey bees, are described. Reasons for a widespread negative image of rural studies are discussed, and positive, effective outcomes, reported in the evaluation of an environmental science course, are used to substantiate the advantages of keeping animals of economic importance in schools.     

The Genetic Code—More Than Just a Table

The standard codon table is a primary tool for basic understanding of molecular biology. In the minds of many, the table’s orderly arrangement of bases and amino acids is synonymous with the true genetic code, i.e., the biological coding principle itself. However, developments in the field reveal a much more complex and interesting picture. In this article, we review the traditional codon table and its limitations in light of the true complexity of the genetic code. We suggest the codon table be brought up to date and, as a step, we present a novel superposition of the BLOSUM62 matrix and an allowed point mutation matrix. This superposition depicts an important aspect of the true genetic code—its ability to tolerate mutations and mistranslations.     

Sympatric Speciation in the Post “Modern Synthesis” Era of Evolutionary Biology

Sympatric speciation is among the most controversial and challenging concepts in evolution. There are a multitude of definitions of speciation alone, and when combined with the biogeographic concept of sympatric range overlap, consensus on what sympatric speciation is, whether it happens, and its importance, is even more difficult to achieve. Providing the basis upon which to define and judge sympatric speciation, the Modern Evolutionary Synthesis (Huxley in Evolution: the modern synthesis. MIT Press, Cambridge, 1942) led to the conclusion that sympatric speciation is an inconsequential process in the generation of species diversity. In the post Modern Synthesis era of evolutionary biology, the PCR revolution and associated accumulation of DNA sequence data from natural populations has led to a resurgence of interest in sympatric speciation, and more importantly, the role of natural selection in lineage diversification. Much effort is currently being devoted to elucidating the processes by which the constituents of an initially panmictic population can become reproductively isolated and evolve some level of reproductive incompatibility without the complete cessation of gene flow due to geographic barriers. The evolution of reproductive isolation solely due to natural selection is perhaps the most controversial manner by which sympatric speciation occurs, and it is that which we focus upon in this review. Mathematical model simulations indicate that even strict definitions of sympatric speciation are possible to satisfy, empirical data consistent with sympatric divergence are accumulating, but irrefutable evidence of sympatric speciation in natural populations remains elusive. Genomic investigations are advancing our ability to identify genetic patterns caused by natural selection, thereby advancing our understanding of the power of natural selection relative to gene flow. Overall, sympatric lineage divergence, especially at the sub-species level, may have led to a substantial portion of biodiversity.     

A Phylogenetic Study of Late Growth Events in a Mammalian Evolutionary Radiation—The Cranial Sutures of Terrestrial Artiodactyl Mammals

We recorded the relative timing of fusion of 29 ectocranial sutures in 480 skulls belonging to 35 extant and four fossil species from all major clades of terrestrial artiodactyls. The resulting data were studied in a phylogenetic context, using mapping of event-pairing of suture fusion events and Parsimov. As phylogenetic framework we generated a compound phylogeny from several previously published analyses. Overall suture closure per species ranged from five to all 29 sutures in Hexaprotodon. All living non-ruminants (suids, camelids, and hippopotamids) fuse more than 50% of the studied sutures (most over 75%), whereas in almost all ruminants less than 50% of the sutures fuse completely. Phylogenetic regression found a significant correlation between suture closure and body mass. In all species we observed an early fusion of the sutures surrounding the foramen magnum (Exoccipital-Supraoccipital, Exoccipital-Basioccipital), a consistent scheme also among other mammals. Scaling the number of changes to the number of sutures in each of the usually recognized skull modules reveals relatively equal numbers of changes in the cranial vault, the zygomatic-sphenoid region, the orbit, and the anterior oral-nasal region. Only the basicranium shows a much smaller number in terms of absolute and relative amount of suture fusion change. Some species show a unique pattern of suture fusion, such as the early fusion of many sutures in the palatal region in Pecari or that of premaxillary sutures in †Cainotherium, perhaps related to feeding mode. A strategy to strengthen the skull by obliterating the sutures could explain the pattern of increased sutural fusion in ruminant species with large cranial appendages.     

The avoidance of superparasitism in four species of parasitic wasp—Mathematical models and experimental results

Experimental results, and interpretation, are presented which relate to oviposition behaviour in four species of parasitic wasp (Hymenoptera: Chalcidoidea). All lay their eggs in pupae of the common house fly (Musca domestica) and of other flies associated with man. Probability models suggested byD. J. Daley for describing the avoidance of superparasitism are used to analyse the data. Certain of the models considered by previous authors appear as specieal cases. A satisfactory fit was obtained either by assuming a fixed probability of oviposition in an already parasitised pupa, or by using a model motivated by supposing that a female will tolerate without oviposition some fixed number of visits to already parasitised pupae. A third model was considered which makes the probability depend on the number of previous ovipositions in the pupae now visited. In all four species the presence of other females (with parasite: host ratio unchanged) increased the probability of oviposition upon encountering an already parasitised pupa. In the presence of other females Spalangia endius laid an increased number of eggs, whereas the other three species laid fewer eggs.     

From Here to Eternity—The Theory and Practice of a Really Long Experiment

In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.     

(Too Many) Mathematical Models of Circadian Clocks (?)

Many mathematical models derived from the principles obtained from empirical observations in chronobiology have been proposed and explored. They cover several organisms and phenomena, and utilize quite different formal approaches. These models can be divided into the ones that intend to describe pacemaker core function, such the Goodwin-oscillator family, non-genetic approaches or purely mathematical (i.e., without clear biochemical correlations) models, and the ones that represent events depending on pacemaker activity, i.e., photoperiodic phenomena. We aim to illustrate the diversity of mathematical and methodological approaches to describe circadian systems and related matters.     

Evolutionary Psychology��s Place in Evolutionary Studies: a Tale of Promise and Challenge

The Evolutionary Studies (EvoS) Consortium and the academic programs born from its creation have been wildly successful in their initial ventures. These achievements are marked by feedback from across the EvoS campuses, the resultant scholarly work produced by participating students, and faculty collaborations spurred by exposure to the organization. The success of EvoS is probably best marked by the recent National Science Foundation grant (CCLI Award #0817337), awarded jointly to SUNY New Paltz and Binghamton University, with the purpose of expanding EvoS beyond the bounds of these two institutions. A particularly noteworthy element of many EvoS programs is the role of Evolutionary Psychology (EP), a perspective in the behavioral sciences that addresses questions of human behavior from the perspective of evolution. In light of several forms of data, including analyses of a variety of disciplines drawn on from evolutionary psychologists in their work, we argue that evolutionary psychologists may well be the most naturally interdisciplinary scholars within the behavioral sciences, making them highly appropriate for inclusion in EvoS. But our research shows not only promise regarding the relationship between EP and EvoS—challenges are raised as well. We present additional data showing that EP is currently represented disproportionately within the EvoS world—a fact that clearly shows that there are currently limitations to the potential impact of EvoS in modern academia. Scholars from other disciplines, particularly within the humanities and social sciences, seem to be missing the evolution revolution. Implications regarding how EvoS can broaden its scope to be even more powerful in its integrative scope are discussed.