Episodic memory and common sense: how far apart?

Research has revealed facts about human memory in general and episodic memory in particular that deviate from both common sense and previously accepted ideas. This paper discusses some of these deviations in light of the proceedings of The Royal Society's Discussion Meeting on episodic memory. Retrieval processes play a more critical role in memory than commonly assumed; people can remember events that never happened; and conscious thoughts about one's personal past can take two distinct forms-'autonoetic' remembering and 'noetic' knowing. The serial-dependent-independent (SPI) model of the relations among episodic, semantic and perceptual memory systems accounts for a number of puzzling phenomena, such as some amnesic patients' preserved recognition memory and their ability to learn new semantic facts, and holds that episodic remembering of perceptual information can occur only by virtue of its mediation through semantic memory. Although common sense endows many animals with the ability to remember their past experiences, as yet there is no evidence that humanlike episodic memory-defined in terms of subjective time, self, and autonoetic awareness-is present in any other species.     

Ethics and practice: two worlds? The example of genetic counselling

The aim of this paper is to work out the relationship between ethics and practice with reference to genetic counselling. First, the most important principles with respect to genetic counselling and to counsellor-client-interaction, are explained briefly. Then, we discuss what these principles might mean, when applied to the practice of counselling. To do so, we also look at some empirical data. Finally, we draw some conclusions.     

Epistatic interactions: how strong in disease and evolution?

When the chimpanzee genome sequence was released, human deleterious alleles associated with simple mendelian diseases were observed as wild-type alleles in six genes (AIRE, MKKS, MLH1, MYOC, OTC and PRSS1). The absence of recognizable phenotypic effects in chimpanzee, contrary to the clinical effect observed in humans, is attributed to epistatic interactions (compensation) between potentially deleterious and compensatory alleles. In this report we investigate the possible evolutionary histories by which substitution of alternative variants in these six genes either ameliorates or avoids pathological consequences.     

Endo-α-1,4-polygalactosaminidases and their homologs: Structure and evolution

Endo-α-1,4-polygalactosaminidase is a rare enzyme. Its catalytic domain belongs to the GH114 family of glycoside hydrolases. It is shown by phylogenetic analysis that the evolution of the corresponding genes involved duplications, elimination, and horizontal transfer. The domain and secondary structures of endo-α-1,4-polygalactosaminidases are discussed. A hypothesis is put forward as to the structure of the active center of the enzyme. Iterative screening of a protein database reveals evolutionary relationships of the GH114 family with the GH13, GH18, GH20, GH27, GH29, GH31, GH35, GH36, and GH66 families of glycoside hydrolases and with the COG1306, COG1649, COG2342, GHL3, and GHL4 families of proteins with unknown enzymatic functions. Unclassified homologs are grouped into 13 new families of hypothetical glycoside hydrolases: GHL5-GHL15, GH36J, and GH36K.     

Drugs and parasites: global experiments in life history evolution?

Recent work has shown that the evolution of Drosophila melanogaster resistance to attack by the parasitoid Asobara tabida is constrained by a trade-off with larval competitive ability. However, there are two very important questions that need to be answered. First, is this a general cost, or is it parasitoid specific? Second, does a selected increase in immune response against one parasitoid species result in a correlated change in resistance to other parasitoid species? The answers to both questions will influence the coevolutionary dynamics of these species, and also may have a previously unconsidered, yet important, influence on community structure.     

Cell biology and evolution: molecular modules link it all?

Classical studies comparing developing embryos have suggested the importance of modified cell biological processes in the evolution of new phenotypes. Here, I revisit this connection focusing on embryonic development, in particular nematode embryogenesis. I compare phenotypic differences in nematode embryogenesis in two basic cell biological processes, the cell cycle and the localization of the first division axis. The analysis of these and other processes shows that, at the cell biological level, exhaustive variation is found that does not necessarily translate into morphological differences. Modern molecular analyses have led to a view in which molecular complexes, made up of groups of proteins, or modules, that are working together, are responsible for the proper execution of cell biological programs. I discuss how this modular architecture could facilitate the phenotypic changes observed in cell biological processes. Ultimately, understanding the connection between cellular behavior and phenotypic outcome will further elucidate the mechanisms responsible for phenotypic evolution.     

How can quantum mechanics of material evolution be possible?: Symmetry and symmetry-breaking in protobiological evolution

Material self-assembly as a self-organizing process is always accompanied by symmetry-breaking in the material configuration. Self-sequencing of amino acids during their thermal polymerization has lost a certain property of permutation symmetry that was observed in the mixture of free amino acids. The evolutionary precursor state is more symmetrical about its internal material configuration and more degenerate due to the multitude of the indistinguishable individuals. The evolution proceeds in the direction along which the degeneracy in the internal states dissolves owing to the symmetry-breaking originating in material flow equilibrium of open material aggregates. Protobiological information is latent in the material system which is highly symmetrical and highly degenerate in its internal states. Evolution of matter is an endogenous process in which the earlier symmetric property is lost and less degenerate states are approached. Quantum-mechanically, the generation of protobiological information is due to the symmetry-breaking of the Hamiltonian originating in the interaction with the exterior through material flow, in contrast to the Schrödinger equation which preserves a symmetry and the associated invariants.     

Cultural evolution and the social sciences: a case of unification?

This paper addresses the question of how to understand the relationship between Cultural Evolutionary Science (CES) and the social sciences, given that they coexist and both study cultural change. I argue that CES is best understood as having a unificatory or integrative role between evolutionary biology and the social sciences, and that it is best characterized as a bridge field; I describe the concept of a bridge field and how it relates to other non-reductionist accounts of unification or integration used in the philosophy of science literature.     

Nutrient enrichment and food chains: can evolution buffer top-down control?

We show how evolutionary dynamics can alter the predictions of classical models of the effects of nutrient enrichment on food webs. We compare an ecological nutrient-plant-herbivore food-chain model without evolution with the same model, including herbivore evolution, plant evolution, or both. When only herbivores are allowed to evolve, the predictions are similar to those of the ecological model without evolution, i.e., plant biomass does not change with nutrient addition. When only plants evolve, nutrient enrichment leads to an increase in the biomass of all compartments. In contrast, when plants and herbivores are allowed to coevolve, although these two classical patterns are common, a wide variety of other responses is possible. The form of the trade-offs that constrain evolution of the two protagonists is then critical. This stresses the need for experimental data on phenotypic traits, their costs and their influence on the interactions between organisms and the rest of the community.     

Genomics and chloroplast evolution: what did cyanobacteria do for plants?

The complete genome sequences of cyanobacteria and of the higher plant Arabidopsis thaliana leave no doubt that the plant chloroplast originated, through endosymbiosis, from a cyanobacterium. But the genomic legacy of cyanobacterial ancestry extends far beyond the chloroplast itself, and persists in organisms that have lost chloroplasts completely.     

Oxidative damage, ageing, and life-history evolution: where now?

The idea that resources are limited and animals can maximise fitness by trading costly activities off against one another forms the basis of life-history theory. Although investment in reproduction or growth negatively affects survival, the mechanisms underlying such trade-offs remain obscure. One plausible mechanism is oxidative damage to proteins, lipids, and nucleic acids caused by reactive oxygen species (ROS). Here, we critically evaluate the premise that ROS-induced oxidative damage shapes life history, focussing on birds and mammals, and highlight the importance of ecological studies examining free-living animals within this experimental framework. We conclude by emphasising the value of using multiple assays to determine oxidative protection and damage. We also highlight the importance of using standardised and appropriate protocols, and discuss future research directions.     

Is evolution Darwinian or/and Lamarckian?

Background  

The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject.