A Unified Model of Codon Reassignment in Alternative Genetic Codes

Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA for the reassigned codon, or the gain of function of an existing tRNA due to a mutation or a base modification. In the codon disappearance mechanism, the codon disappears from the genome during the period of reassignment. In the other mechanisms, the codon does not disappear. In the ambiguous intermediate mechanism, the gain precedes the loss; in the unassigned codon mechanism, the loss precedes the gain; and in the compensatory change mechanism, the loss and gain spread through the population simultaneously. We present simulations of the gain-loss model and demonstrate that all four mechanisms are possible. The frequencies of the different mechanisms are influenced by selection strengths, number of codons undergoing reassignment, directional mutation pressure and the possibility of selection for reduced genome size.Comment: Latex file, 11 pages including 5 ps figures; revised version; to appear in 'Genetics

Modelling coevolution in multispecies communities

We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary timescale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is then calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.Comment: 21 pages, 3 Postscript figures, uses psfig.sty Affiliations correcte

A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.Comment: 16 pages, 2 tables, 4 figures. Accepted for publication in Astrobiolog

The Influence of Predator-Prey Population Dynamics on the Long-term Evolution of Food Web Structure

We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are non-linear, and are based on ratio-dependent functional responses. The equations account for competition for resources between members of the same species, and between members of different species. Predators divide their total hunting/foraging effort between the available prey species according to an evolutionarily stable strategy (ESS). The ESS foraging behaviour does not correspond to the predictions of optimal foraging theory. We use the population dynamics equations in simulations of the Webworld model of evolving ecosystems. New species are added to an existing food web due to speciation events, whilst species become extinct due to coevolution and competition. We study the dynamics of species-diversity in Webworld on a macro-evolutionary timescale. Coevolutionary interactions are strong enough to cause continuous overturn of species, in contrast to our previous Webworld simulations with simpler population dynamics. Although there are significant fluctuations in species diversity because of speciation and extinction, very large scale extinction avalanches appear to be absent from the dynamics, and we find no evidence for self-organised criticality.Comment: 40 pages, preprint forma

A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code

<p>Abstract</p> <p>Background</p> <p>The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties. Hence, the effects of translational error are minimized with respect to randomly reshuffled codes. Further inspection reveals that it is amino acids in the same column of the code (i.e. same second base) that are similar, whereas those in the same row show no particular similarity. We propose a 'four-column' theory for the origin of the code that explains how the action of selection during the build-up of the code leads to a final code that has the observed properties.</p> <p>Results</p> <p>The theory makes the following propositions. (i) The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii) These amino acids are assigned to codons with G at first position. Therefore the first code may have used only these codons. (iii) The code rapidly developed into a four-column code where all codons in the same column coded for the same amino acid: NUN = Val, NCN = Ala, NAN = Asp and/or Glu, and NGN = Gly. (iv) Later amino acids were added sequentially to the code by a process of subdivision of codon blocks in which a subset of the codons assigned to an early amino acid were reassigned to a later amino acid. (v) Later amino acids were added into positions formerly occupied by amino acids with similar properties because this can occur with minimal disruption to the proteins already encoded by the earlier code. As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution.</p> <p>Conclusion</p> <p>The driving force during this process is not the minimization of translational error, but positive selection for the increased diversity and functionality of the proteins that can be made with a larger amino acid alphabet. Nevertheless, the code that results is one in which translational error is minimized. We define a cost function with which we can compare the fitness of codes with varying numbers of amino acids, and a barrier function, which measures the change in cost immediately after addition of a new amino acid. We show that the barrier is positive if an amino acid is added into a column with dissimilar properties, but negative if an amino acid is added into a column with similar physical properties. Thus, natural selection favours the assignment of amino acids to the positions that they occupy in the final code.</p> <p>Reviewers</p> <p>This article was reviewed by David Ardell, Eugene Koonin and Stephen Freeland (nominated by Laurence Hurst)</p

Aging, Embodiment, and the Somatic Turn

This article addresses contemporary representations of bodily aging by calling attention to the difference between “corporeality” and “embodiment.” Drawing on Haraway’s distinction between the body as social actant and the body as a site of social agency, we argue for the need to distinguish between aging as corporeality—treating the aging body as a social actant—and aging as embodiment—treating the aging body as co-constructor of its own identity. Embodiment, or embodied habitus, is realized through embodied identities and the embodied practices associated with past and present identities. This distinction is important in locating the new narratives and performances of later life emerging in the aftermath of the cultural revolution of the 1960s. The rise of somatic society, the growth of mass consumerism, and the new politics of identity initially targeted youth buthave since extended their infuence across the life course. These phenomena have helped realize variously embodied, valued identities through whose trajectories it has become possible to think the aging body differently.

Ageing, corporeality and social divisions in later life

This paper concerns the social divisions of later life. Although research in this field has focused on class, gender and, more recently, sexuality as sources of division in later life, the division between the fit and the frail has tended to be ignored or viewed as an outcome of these other divisions. This paper challenges this assumption, arguing that corporeality constitutes a major social division in later life. This in many ways prefigures a return to the 19th-century categorisation of those ‘impotent through age’, whose position was among the most abject in society. Their ‘impotence’ was framed by an inability to engage in paid labour. Improved living standards during and after working life saw age's impotence fade in significance and in the immediate post-war era, social concern turned towards the relative poverty of pensioners. Subsequent demographic ageing and the expanding cultures of the third age have undermined the homogeneity of retirement. Frailty has become a major source of social division, separating those who are merely older from those who are too old. This division excludes the ‘unsuccessfully’ aged from utilising the widening range of material and social goods that characterise the third age. It is this social divide rather than those of past occupation or income that is becoming a more salient line of fracture in later life

Technologies of Ascription: How Does a Dementia Diagnosis Acquire its Symbolic Power of Exclusion in Later Life?

Amidst the widespread stigma and exclusion attached to dementia in dominant narratives of successful ageing, this article addresses a gap in the scientific literature concerning our understanding of the medicalization of cognitive decline as a natural phenomenon. To this end, it explores how a dementia diagnosis acquires its symbolic power of exclusion in later life through an ethnography of cognitive rehabilitation therapy in two memory clinics in a southern European nation. It argues that this symbolic power of exclusion is locally produced through the meaning making practices of therapists and researchers administering regular cognitive training therapy and exercises to support autonomy. It shows how the different steps involved in rehabilitation play a role in dividing later life by defining and reifying a category of abnormal ageing during the cognitive assessment, and by applying a confrontational approach exposing decline. It shows how this approach generates the position of older adults who can be rehabilitated against those who cannot; the latter representing a “failed” ageing in the narrative of successful ageing. This article proposes the adoption of the concept of “technologies of ascription” to characterize this process of exclusion through reification and confrontation of “abnormal cognitive decline.” The paper argues that such practices are central to the local production of the symbolic power attached to a dementia diagnosis as well as its capacity to fragment later life. Finally, it argues for the utility of this concept in offering new opportunities for anthropology to characterize exclusion in later life through medicalization