Developing information fluency in introductory biology students in the context of an investigative laboratory

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100 students suggest that increases occurred, some statistically significant, in the number of students using various library-related resources, in the numbers and confidence level of students using various technologies, and in the numbers and confidence levels of students involved in various activities related to the scientific method. Following this course, students should be better prepared for more advanced and independent study.     

An information theory of the genetic code

An information theory of the genetic code is given, which deals with the process by which template codes (nucleotides or codons) choose substrate codes (nucleotides or anti-codons) in accordance with the base-pairing rules in the chain elongation phase of polynucleotide or polypeptide synthesis. A definite period of recognition time (τ) required for a template code to discriminate a substrate code is proposed, and an experimental method for determining the time is suggested. A substrate word is defined to be the sequence of substrate codes which have appeared at a recognition site in turn before a substrate code complementary to a template code first appears, and the mean length of substrate words (F) is derived from the mole fractions of template codes and substrate codes. The chain elongation rate is greatest when the mole fractions of template codes is proportional to the square of those of substrate codes to minimize the mean recognition time per word (Fτ). The uncertainty of a template (G) and the uncertainty of a medium (M) respectively are derived from the minimum of the function F. The amount of genetic information contained in a template is measured by the function G. The unit of the amount of genetic information is termed “cit”. The function M, the ratio of the number of all binary collisions to the number of homogeneous binary collisions in a mixture of different molecules, may be the new other “entropy” which represents informational properties of the mixture not represented by thermodynamic entropy of mixing. Both functions (G and M) have maxima when all random variables are equal and they are multiplicative in nature in contrast to entropy which is additive. The multiplicativity of the function G may contribute to the enormous informational capacity of genes.     

An evolutionary computational theory of prefrontal executive function in decision-making

The prefrontal cortex subserves executive control and decision-making, that is, the coordination and selection of thoughts and actions in the service of adaptive behaviour. We present here a computational theory describing the evolution of the prefrontal cortex from rodents to humans as gradually adding new inferential Bayesian capabilities for dealing with a computationally intractable decision problem: exploring and learning new behavioural strategies versus exploiting and adjusting previously learned ones through reinforcement learning (RL). We provide a principled account identifying three inferential steps optimizing this arbitration through the emergence of (i) factual reactive inferences in paralimbic prefrontal regions in rodents; (ii) factual proactive inferences in lateral prefrontal regions in primates and (iii) counterfactual reactive and proactive inferences in human frontopolar regions. The theory clarifies the integration of model-free and model-based RL through the notion of strategy creation. The theory also shows that counterfactual inferences in humans yield to the notion of hypothesis testing, a critical reasoning ability for approximating optimal adaptive processes and presumably endowing humans with a qualitative evolutionary advantage in adaptive behaviour.     

Visual neuroscience: computational brain dynamics of face processing

A recent study of how the brain processes emotionally expressive faces has revealed how task-relevant information is first gathered from the region around the eyes and then integrated downwards until categorization is achieved.     

SenseLab: new developments in disseminating neuroscience information

This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab's unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources.     

Intercalation of cationic dyes in the DNA double helix: introductory theory

The effect of salt on the intercalation of acridine dyes and DNA is rather well explained by the Gouy-Chapman double-layer theory as applied to a cylinder model of the DNA–dye complex. The free energy of transfer of a dye ion from the bulk solution to the complex is divided into several parts, one of which, ΔF₀, accounts for the short-range, nonelectrostatic interactions. The assumption that ΔF₀ should not depend on the amount of dye in the complex leads to an internal dielectric constant of the cylinder of about D_i = 7. The scatter in ΔF₀ values, as calculated from individual experimental points, is of order 0.5 kT per dye ion. This scatter is large enough to mask possible effects of heterogeneity in DNA sequences. The calculations are made for a long cylinder with radius 10 Å, with the DNA phosphate charges smeared uniformly at the surface, a uniform spacing of dye charges at the cylinder axis, and a length of b = 3.37 Å per base pair. Each intercalated dye ion also adds a length b to the total length of the cylinder. The salt-dependent part of the electric free energy of intercalation, ΔF₁, is tabulated for complexes with r = 0–0.24 dye ions per DNA phosphate in 0.002–0.2M monovalent salt and dye solutions.     

An introductory ecological biogeography of the Australo-Pacific Meliphagidae

Abstract

The Meliphagidae, that can readily be defined on tongue characteristics, are a monophyletic group centred in the Australo-Pacific region, but with one African genus (Promerops). The classification of Salomonsen (1967) allows 38 genera and 170 species in the former region, and one genus with two species in the latter. Australia and New Guinea jointly have 23 genera and 108 species, and constitute the centre of diversity of the group. Endemic genera are concentrated in Australia and New Guinea, and around the periphery of the Pacific part of the range (Sulawesi, Bonins, Marianas, Hawaii, New Zealand). The meliphagids are diversified in body size and bill form. They are basically nectarivores and insectivores, with most species combining the two roles to varying degrees. There is a good general correlation between bill form and way of life. A few species feed on trunks and aerial flycatching is well developed in many. Morphological modification is only minor in these instances and the meliphagids as a group remain rather generalised in bodily proportions. A long period of coevolution with Australian plant elements is shown by meliphagids being the major pollinators of several tree and shrub genera.

The group combines monotypic genera with restricted ranges and wide-ranging genera with many species. Of the latter; Myzomela, Lichema, and Philemon are centred in the tropics, and Meliphaga and Phylidonyris in Australia. Most of these co-occur over a wide area, this being favoured by differences in body size and bill morphology.

Comparison of three kinds of meliphagid communities, two typical continental ones, two of isolated forest outlyers in Australia, and six insular Pacific ones, shows the first to be rich (10 and 11 genera, 21 and 17 species), and the second impoverished (6 and 7 genera, 9 and 12 species). Individual Pacific island groups, however, have only 2–5 genera, and 3–6 species. Genus to species ratios are 0.55–0.64 in the major continental communities, but are 1.0 in New Zealand and Samoa.

Morphological distance between species, measured as the percent difference in size between successive members along a size gradient is 5.4 and 5.5% for wing length and 4.9 and 9.3% for bill length in the two continental communities. It increases to 7.8–14.9, and 11.3–12.7%, respectively, in the isolated forest outlyers of Tasmania and southwestern Australia. The figures are 23.0 and 35.0% for wing and bill length in New Zealand, and 41.0 and 51.0% in Fijian forms. This accords with current theory that in impoverished insular environments, size separation of co-occurring species must be greater.

The marked success of the Meliphagidae in the Australo-Pacific region can be attributed to their versatility and adaptibility, and dual role of insectivore and nectarivore in an area exceptionally rich in nectar-producing trees and shrubs.     

An application of information theory to biological evolution

An evolving population of two alleles which generates another new allele is investigated within the framework of information theory. A communication system model of self-reproducing organisms which reproduce the genetic information by the self-reproduction is proposed and the concept of distortion when the genetic information is reproduced is introduced. What genetic information should be transmitted to the next generation? This question may be answered by so called rate distortion theory. The theory is applied to our model and the exact solution is obtained. Numerical results show that in low distortion region, new allele cannot survive, hence no evolution occurs; in intermediate distortion region, all alleles coexist; and in high distortion region, minor allele cannot survive. Moreover, diversity of the progeny takes its maximum value in the intermediate distortion region. This suggests that there may exist an optimal distortion for a population to evolve.     

Ecological boundaries in the context of hierarchy theory

Ecological boundaries have been described as being multiscalar or hierarchical entities. However, the concept of the ecological boundary has not been explicitly examined in the context of hierarchy theory. We explore how ecological boundaries might be envisioned as constituents of scalar hierarchical systems. Boundaries may be represented by the surfaces of constituents or as constituents themselves. Where surfaces would correspond to abrupt transition zones, boundary systems might be quite varied depending on hierarchical context. We conclude that hierarchy theory is compatible with a functional vision of ecological boundaries where functions can be largely represented as the processing or filtering of ecological signals. Furthermore, we postulate that emergent ecological boundaries that arise on a new hierarchical level may contribute to the overconnectedness of mature ecosystems. Nevertheless, a thermodynamic approach to the emergence and development of boundary systems does indicate that in many situations, ecological boundaries would persist in time by contributing to the energy production of higher hierarchical levels.     

Adaptive aging in the context of evolutionary theory

Compelling evidence for an adaptive origin of aging has clashed with traditional evolutionary theory based on exclusively individual selection. The consensus view has been to try to understand aging in the context of a narrow, restrictive evolutionary paradigm, called the Modern Synthesis, or neo-Darwinism. But neo-Darwinism has shown itself to be inadequate in other ways, failing to account for stable ecosystems, for the evolution of sex and the maintenance of diversity and the architecture of the genome, which appears to be optimized for evolvability. Thus aging is not the only reason to consider overhauling the standard theoretical framework. Selection for stable ecosystems is rapid and efficient, and so it is the easiest modification of the neo-Darwinian paradigm to understand and to model. Aging may be understood in this context. More profound and more mysterious are the ways in which the process of evolution itself has been transformed in a bootstrapping process of selection for evolvability. Evolving organisms have learned to channel their variation in ways that are likely to enhance their long-term prospects. This is an expanded notion of fitness. Only in this context can the full spectrum of sophisticated adaptations be understood, including aging, sex, diversity, ecological interdependence, and the structure of the genome.     

Quasispecies theory in the context of population genetics

Background  

A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory.