The origins and physical roots of life’s dual – metabolic and genetic – nature

This review paper aims at a better understanding of the origin and physical foundation of life’s dual – metabolic and genetic – nature. First, I give a concise ‘top-down’ survey of the origin of life, i.e., backwards in time from extant DNA/RNA/protein-based life over the RNA world to the earliest, pre-RNA stages of life’s origin, with special emphasis on the metabolism-first versus gene/replicator-first controversy. Secondly, I critically assess the role of minerals in the earliest origins of bothmetabolism and genetics. And thirdly, relying on the work of Erwin Schrödinger, Carl Woese and Stuart Kauffman, I sketch and reframe the origin of metabolism and genetics from a physics, i.e., thermodynamics, perspective. I conclude that life’s dual nature runs all the way back to the very dawn and physical constitution of life on Earth. Relying on the current state of research, I argue that life’s origin stems from the congregation of two kinds of sources of negentropy – thermodynamic and statistical negentropy. While thermodynamic negentropy (which could have been provided by solar radiation and/or geochemical and thermochemical sources), led to life’s combustive and/or metabolic aspect, the abundant presence of mineral surfaces on the prebiotic Earth – with their selectively adsorbing and catalysing (thus ‘organizing’) micro-crystalline structure or order – arguably provided for statistical negentropy for life to originate, eventually leading to life’s crystalline and/or genetic aspect. However, the transition from a prebiotic world of relatively simple chemical compounds including periodically structured mineral surfaces towards the complex aperiodic and/or informational structure, specificity and organization of biopolymers and biochemical reaction sequences remains a ‘hard problem’ to solve

The modern versus extended evolutionary synthesis : sketch of an intra-genomic gene's eye view for the evolutionary-genetic underpinning of epigenetic and developmental evolution

Studying the phenotypic evolution of organisms in terms of populations of genes and genotypes, the Modern Synthesis (MS) conceptualizes biological evolution in terms of 'inter-organismal' interactions among genes sitting in the different individual organisms that constitute a population. It 'black-boxes' the complex 'intra-organismic' molecular and developmental epigenetics mediating between genotypes and phenotypes. To conceptually integrate epigenetics and evo-devo into evolutionary theory, advocates of an Extended Evolutionary Synthesis (EES) argue that the MS's reductive gene-centrism should be abandoned in favor of a more inclusive organism-centered approach. To push the debate to a new level of understanding, we introduce the evolutionary biology of 'intra-genomic conflict' (IGC) to the controversy. This strategy is based on a twofold rationale. First, the field of IGC is both ‘gene-centered’ and 'intra-organismic' and, as such, could build a bridge between the gene-centered MS and the intra-organismic fields of epigenetics and evo-devo. And second, it is increasingly revealed that IGC plays a significant causal role in epigenetic and developmental evolution and even in speciation. Hence, to deal with the ‘discrepancy’ between the ‘gene-centered’ MS and the ‘intra-organismic’ fields of epigenetics and evo-devo, we sketch a conceptual solution in terms of ‘intra-genomic conflict and compromise’ – an ‘intra-genomic gene’s eye view’ that thinks in terms of intra-genomic ‘evolutionarily stable strategies’ (ESSs) among numerous and various DNA regions and elements – to evolutionary-genetically underwrite both epigenetic and developmental evolution, as such questioning the ‘gene-de-centered’ stance put forward by EES-advocates

Linguistic reference in science : problems and progress

The crucial role that mathematical notation systems have played in the success of the hard or mathematical sciences is well known and richly documented: the origin of the history of these sophisticated notation systems more or less coincides with the birth of modern science. The role of our linguistic notation systems (as applied to, or used in, the scientific study of nature), by contrast, is hardly documented at all, at least not in a systematic way. We distinguish between (metaphorical and non-metaphorical) meta-scientific terms and scientific terms and, as far as the latter is concerned, between methodology and content terms. It is the latter sort of terms that interest us here. Five different dysfunctions in the relationship between scientific linguistic tokens and their referents will be presented and illustrated: scientific terms or phrases can not only be imprecise, they can also be meaningless, indiscriminate, inapt and ambiguous. By correcting or alleviating such dysfunctions, our linguistic notation systems have, in the course of the past four centuries, become more refined and functional scientific tools. This simple, illustrated taxonomy is not only historically relevant, it may also help contemporaneous scientists to identify and avoid possible pitfalls, associated with the use of language in science

From animal signals to art : manipulative animal signaling and the evolutionary foundations of aesthetic behavior and art production

As humans are evolved animals, we propose a nonanthropocentric framework based on animal signaling theory to understand the evolutionary foundations of human art, instead of a classical anthropocentric approach based on sociocultural anthropology that may incorporate evolutionary thinking but does not start with it. First, we provide a concise review of the basics of the evolutionary theory of animal communication or signaling. Second, we apply this theory to specifically human aesthetic behavior and art and provide four empirical arguments or factors that reduce the conceptual gap between nonhuman animal signaling and human aesthetic-artistic behavior (two from the nonhuman and two from the human side) and that, as such, grant an implementation of human aesthetic behavior and art production within animal signaling theory. And, third, we explore the theory’s explanatory power and value when applied to aesthetic behavior and art production through proposing four valuable insights or hypotheses that it may contribute or generate: on art’s operation within multiple functionally adaptive signaling contexts; on the basic evolutionary economics of art or what art is (for); on why art is functionally adaptive rather than a nonfunctional byproduct; and on how art is functionally rooted in competitive-manipulative animal signaling and—unlike language—only to a lesser extent in cooperative-informative signaling. Overall, animal signaling theory offers a potentially integrating account of the arts because humans and their signaling behaviors are conceptually situated within a broader, transhuman field that also comprises nonhuman species and their behaviors, thus allowing for an identification of deeper commonalities (homologs, analogs) as well as unique differences. As such, we hope to increase insights into how acoustic, gestural/postural, visual, olfactory, and gustatory animal signaling evolved into music, dance, visual art, perfumery, and gastronomy, respectively

Interpreting the history of evolutionary biology through a Kuhnian prism : sense or nonsense?

Traditionally, Thomas S. Kuhn’s The Structure of Scientific Revolutions (1962) is largely identified with his analysis of the structure of scientific revolutions. Here, we contribute to a minority tradition in the Kuhn literature by interpreting the history of evolutionary biology through the prism of the entire historical developmental model of sciences that he elaborates in The Structure. This research not only reveals a certain match between this model and the history of evolutionary biology but, more importantly, also sheds new light on several episodes in that history, and particularly on the publication of Charles Darwin’s On the Origin of Species (1859), the construction of the modern evolutionary synthesis, the chronic discontent with it, and the latest expression of that discontent, called the extended evolutionary synthesis. Lastly, we also explain why this kind of analysis hasn’t been done before

From DNA- to NA-centrism and the conditions for gene-centrism revisited

First the 'Weismann barrier' and later on Francis Crick's 'central dogma' of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a 'central source' from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic. Here, we first explore the causal implications of the following two central dogma-related issues: (1) widespread reverse transcription-arguing for an extension from 'DNA-genome' to RNA-encompassing 'NA-genome' and, thus, from traditional DNA-centrism to a broader 'NA-centrism'; and (2) the absence of a mechanism of reverse translation-arguing for the 'structural primacy' of NA-sequence over protein in cellular biochemistry. Secondly, we explore whether this latter conclusion can be extended to a 'functional primacy' of NA-sequence over protein in cellular biochemistry, which would imply a limited kind of 'gene/NA-centrism' confined to the subcellular level of NA/protein-based biochemistry. Finally, we explore the conditions-and their (non)fulfilment-for a more generalised form of gene-centrism extendable to higher levels of biological organisation. We conclude that the higher we go in the biological hierarchy, the more dubious gene-centric claims become

Life's dual nature: a way out of the impasse of the gene-centred 'versus' complex systems controversy on life

Living cells and organisms are complex physical systems. Does their organization or complexity primarily rely on the intra-molecular crystalline structure of genetic nucleic acid sequences? Or is it, as critics of the ‘gene-centred’ perspective claim, predominantly a result of the inter- and supra-molecular – thus ‘holistic’ – network dynamics of genetic and various extra-genetic factors? The twentieth-century successes in several branches of genetics caused intensive focus on the causal role of genes in the biochemistry, development and evolution of living organisms, resulting in a relative abstraction or even neglect of life’s complex systems dynamics. Today, however, partly due to the success of systems biology, a number of authors defend life’s systems complexity while criticizing the gene-centred approach. Here, we offer a way out of the impasse of the gene-centred ‘versus’ complex systems perspective to arrive at a more balanced and complete understanding of life’s multifaceted nature. After sketching the conceptual and historical background of the controversy, we show how the present state of knowledge in biology vindicates both the holistically complex and gene-centred nature of life on Earth, but decisively falsifies extreme genetic ‘determinism’ and ‘reductionism’ as well as extreme ‘gene-de-centrism’. Contrary to what is often claimed, the fact that genes are one among many extra-genetic causal factors contributing to the biochemistry and development of cells and organisms, only undermines or falsifies genetic determinism and reductionism but not necessarily gene-centrism. Some implications for evolutionary theory, i.e., for the controversy between the Modern Synthesis and an ‘Extended Synthesis’, are outlined

What’s Wrong with the Modern Evolutionary Synthesis? A Critical Reply to Welch (2017)

Welch (2017) has recently proposed two possible explanations for why the field of evolutionary biology is plagued by a steady stream of claims that it needs urgent reform. It is either seriously deficient and incapable of incorporating ideas that are new, relevant and plausible or it is not seriously deficient at all but is prone to attracting discontent and to the championing of ideas that are not very relevant, plausible and/or not really new. He argues for the second explanation. This paper presents a twofold critique of his analysis: firstly, the main calls for reform do not concern the field of evolutionary biology in general but rather, or more specifically, the modern evolutionary synthesis. Secondly, and most importantly, these calls are not only inspired by the factors, enumerated by Welch, but are also, and even primarily, motivated by four problematic characteristics of the modern synthesis. This point is illustrated through a short analysis of the latest reform challenge to the modern synthesis, the so-called extended evolutionary synthesis. We conclude with the suggestion that the modern synthesis should be amended, rather than replaced