Genetic, epigenetic and exogenetic information

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. We then consider the evolutionary significance of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Nontrivial quantum effects in biology: A skeptical physicists' view

Invited contribution to "Quantum Aspects of Life", D. Abbott Ed. (World Scientific, Singapore, 2007).Comment: 15 pages, minor typographical errors correcte

"Life" shaped by genes that depend on their surrounds

Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization of genes requires molecular environments, in particular pertinent to the cytoplasm of the unfertilized egg. Individuality of an organism therefore is not only determined by its genome, but is shaped through developmental processes (it needs time!). Organisms can only exist through mutual interplays with their respective (molecular and cellular) environments at all levels of organization. Thus, life can be conceived of as endless networks of communication, e.g. as a mutual continuum, connecting all individuals, all species and all generations within their given environments. Evolutionarily, nature does not select fitting genes, but rather viable traits. The presented concepts render it unlikely that it was genes that founded our living world, but rather that distinct environments shaped “genes” (of whatever chemical nature) which proved to be “life-suitable”

A Model for the Generation and Transmission of Variations in Evolution

The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it does not prescribe, per se, the mechanisms by which this is operated. The mechanisms of inheritance are not, however, unconstrained, since they are themselves subject to natural selection. We introduce a general, analytically solvable mathematical model to compare the adaptive value of different schemes of inheritance. Our model allows for variations to be inherited, randomly produced, or environmentally induced, and, irrespectively, to be either transmitted or not during reproduction. The adaptation of the different schemes for processing variations is quantified for a range of fluctuating environments, following an approach that links quantitative genetics with stochastic control theory

The Algorithmic Origins of Life

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems. Here we propose that the origin of life may correspond to a physical transition associated with a shift in causal structure, where information gains direct, and context-dependent causal efficacy over the matter it is instantiated in. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some potential novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.Comment: 13 pages, 1 tabl

An extra-memetic empirical methodology to accompany theoretical memetics

Abstract Purpose: The paper describes the difficulties encountered by researchers who are looking to operationalise theoretical memetics and provides a methodological avenue for studies that can test meme theory. Design/Methodology/Approach: The application of evolutionary theory to organisations is reviewed by critically reflecting on the validity of its truth claims. To focus the discussion a number of applications of meme theory are reviewed to raise specific issues which ought to be the subject of empirical investigation. Subsequently, the empirical studies conducted to date are assessed in terms of the progress made and conclusions for further work are drawn. Findings: The paper finds that the key questions posed by memetic theory have yet to be addressed empirically and that a recurring weakness is the practice of assuming the existence of a replicating unit of culture which has, however, yet to be demonstrated as a valid concept. Therefore, an 'extra-memetic' methodology is deemed to be necessary for the development of memetics as a scientific endeavour. Narrative analysis is abducted as an appropriate avenue for the operationalisation of extra-memetic empirical research. Originality/Value: The paper highlights inconsistencies, embedded in much of the memetic literature, which have not previously been recognised and the colloquial nature of the discipline is challenged from a positive but critical perspective. Consequently, the paper develops a rationale for the adoption of a widely recognised social science methodology for memetics which has been absent to date. In proposing narrative orientated research, knowledge concerning memes' validity can be facilitated whilst avoiding the current circularity in memetic truth claims. Key Words: Meme, Memetics, Narrative, Complexity, Evolution Classification: Conceptual Pape

On Modern Science, Human Cognition, and Cultural Diversity

The development of modern science has depended strongly on specific features of the cultures involved; however, its results are widely and trans-culturally accepted and applied. The science and technology of electricity provides a particularly interesting example. It emerged as a specific product of post-Renaissance Europe, rooted in the Greek philosophical tradition that encourages explanations of nature in theoretical terms. It did not evolve in China presumably because such encouragement was missing. The trans-cultural acceptance of modern science and technology is postulated to be due, in part, to the common biological dispositions underlying human cognition, with generalizable capabilities of abstract, symbolic and strategic thought. These faculties of the human mind are main prerequisites for dynamic cultural development and differentiation. They appear to have evolved up to a stage of hunters and gatherers perhaps some 100 000 years ago. However, the extent of the correspondence between some constructions of the human mind and the order of nature, as revealed by science, is a late insight of the last centuries. Quantum physics and relativity are particularly impressive examples