MacDonald and Kreitman (1991) propose a test of the neutral mutationrandom drift (NM-RD) hypothesis, the central claim of the neutral theory of molecular evolution. The test involves generating predictions from the NM-RD hypothesis about patterns of molecular substitutions. Alternative selection hypotheses predict that the data will deviate from the predictions of the NM-RD hypothesis in specifiable ways. To conduct the test Mac- Donald and Kreitman examine the evolutionary dynamics of the alcohol dehydrogenase (Adh) gene (...) in three species of Drosophila. The test compares the number of DNA sequence changes between species and within species. The number of DNA differences is an indicator of the evolutionary rate of the Adh gene. Based on the test they conclude that there is strong evidence for adaptive protein evolution at particular sites in the gene. Understanding the test requires some basic knowledge about molecular terms and the predictions of neutral theory. The two important terms are fixed differences and polymorphisms. These are determined by comparing DNA sequences made up of thousands of individual nucleotide sites. A site that is unchanged within a species but different from a related species counts as a fixed difference. These are mutations that occur in some common ancestor of the lineage such that all descendants inherit the change. A site that differs within a species counts as a polymorphism. Determining the number of fixed differences and polymorphisms requires placing 1 each individual gene sequence onto a phylogenetic tree. A coalescent tree charts the ancestral relationships for a set of individual gene sequences. Sequences sampled from within a species form a within-species tree. The common ancestors of each within-species tree form a between-species tree. A detected difference counts as a polymorphism or a fixed difference depending on where it occurs in the phylogenetic tree (cf. Table 1). The test uses the numbers of polymorphisms and fixed differences as indicators of evolutionary rates.. (shrink)

This chapter contains section titled: The Neutral Theory of Molecular Evolution The Molecular Clock The Neutral Null Model Controversy in Molecular Evolution Acknowledgment References Further Reading.

Comparative studies of DNA sequences provide opportunities for testing the neutral and the selection theories of molecular evolution. In particular, the separate estimation of the numbers of synonymous and nonsynonymous substitutions is a powerful tool for detecting selection of the latter. The difference in the patterns of these two types of substitutions of mammalian genes turned out to be in accord with the slightly deleterious or nearly neutral mutation theory for nonsynonymous changes. Interaction systems at (...) the amino acid level were suggested to be responsible for such nearly neutral, or very weak, selection. Synonymous substitutions are not strictly neutral, but because of their minute effect, random drift predominates such that the rate of substitution is only slightly less than the completely neutral prediction. It was concluded that the strictly neutral theory has not held up as well as the nearly neutral theory, yet remains invaluable as a null hypothesis for detecting selection. On the other hand, the main difference between the nearly neutral and the traditional selection theories is that the former predicts rapid evolution in small populations, whereas the latter predicts rapid evolution in large populations. (shrink)

The neutral theory of molecular evolution has been instrumental in organizing our thinking about the nature of evolutionary forces shaping variation at the DNA level. More importantly, it has provided empiricists with a strong set of testable predictions and hence, a useful null hypothesis against which to test for the presence of selection. Evidence indicates that the neutral theory cannot explain key features of protein evolution nor patterns of biased codon usage in certain (...) species. Whereas we now have a reasonable model of selection acting on synonymous changes in Drosophila, protein evolution remains poorly understood. Despite limitations in the applicability of the neutral theory, it is likely to remain an integral part of the quest to understand molecular evolution. (shrink)

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. (...) A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory. (shrink)

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory, a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of (...) using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size. (shrink)

It is proposed that early in phylogeny a large proportion of amino acid substitutions were selectively neutral, but that bursts of adaptive substitutions during major radiations of life so increased selective constraints that most mutations in modern proteins are detrimental. Recent findings on DNA nucleotide sequences indicate that decreasing mutation rates further slowed the rate of molecular evolution in the lineage to humans.

Without directly addressing the Demarcation Problem for logic—the problem of distinguishing logical vocabulary from others—we focus on distinctive aspects of logical vocabulary in pursuit of a second goal in the philosophy of logic, namely, proposing criteria for the justification of logical rules. Our preferred approach has three components. Two of these are effectively Belnap’s, but with a twist. We agree with Belnap’s response to Prior’s challenge to inferentialist characterisations of the meanings of logical constants. Belnap argued that for a logical (...) constant to exist, its rules must be conservative over a previously given consequence relation and guarantee the uniqueness of the constant. The twist is that we require logical vocabulary to be provably conservative, not over a previously given formal consequence relation, but over a previously given meaningful vocabulary of a language. Uniqueness is also a feature defined in terms of provability: if two syntactically distinguished expressions are governed by the same rules, then formulas with them as main operators are interderivable. Belnap’s criteria are not only those for the existence of a logical constant, but more: they are what distinguishes logical vocabulary from all other expressions. It is the defining mark of a logical constant that it is provably conservative over the fragment of the language which excludes it and that its rules guarantee its uniqueness. The third component is the topic neutrality of logic. The provable conservativeness of logic over a previously given vocabulary of a language is motivated, in part, by appeal to molecularism in the theory of meaning. Molecularity is a feature endorsed by the theory of meaning as a whole, so it does not distinguish logical constants from other expressions. The same is true for conservativeness. We argue that molecularity, and hence conservativeness, are implicit presuppositions of speakers’ use of language: the addition of new vocabulary to a language is presupposed to be conservative. But this presupposition is one that we should be able reflectively to endorse (such as when attempting a rational reconstruction of the use of the vocabulary). Thus, where conservativeness is found to fail, this defect should be remedied and the use of the vocabulary corrected (as in classical negation) or excised altogether (as in pejoratives). We go on to characterise a notion of topic neutrality, which we argue applies to logical vocabulary. We then note that reflective endorsement of the conservativeness of a topic neutral vocabulary requires a proof that the vocabulary is conservative relative to any base vocabulary. Thus we require that logical vocabulary be demonstrably conservative. Allying this requirement, distinctive of logic, to a general consideration about the commitments of assertion yields a mode of justification for logical constants akin to some conceptions of Harmony, i.e., to the idea that the consequences of assertion of a logical complex need to be warranted by the grounds and ought to be the strongest consequences warranted by the grounds. Intuitionistic logic acquires a somewhat familiar justification but emanating from a new motivation. (shrink)

Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic (...) and molecular structures or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

In the 1960s molecular population geneticists used Monte Carlo experiments to evaluate particular diffusion equation models. In this paper I examine the nature of this comparative evaluation and argue for three claims: first, Monte Carlo experiments are genuine experiments: second, Monte Carlo experiments can provide an important meansfor evaluating the adequacy of highly idealized theoretical models; and, third, the evaluation of the computational adequacy of a diffusion model with Monte Carlo experiments is significantlydifferent from the evaluation of the emperical (...) adequacy of the same diffusion model. (shrink)

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes (...) that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. (shrink)

How to reconcile the theory of evolution with existing religious beliefs has occupied minds since Darwin's time. The majority of the discourse on the subject is still focused on the Darwinian version of evolutionary theory, or at best, the mid-twentieth century version of the Modern Synthesis. However, evolutionary thought has moved forward since then with the insights provided by the advent of comparative genomics in recent decades having a particularly significant impact. A theology that successfully incorporates evolutionary (...) biology needs to take such developments into account, because range of truly viable options among the many versions of theistic evolution that have been proposed in the past may narrow down when this is done. Here I present these previously underappreciated strains of contemporary evolutionary thought and discuss their potential theological impact. (shrink)

Constructive Neutral Evolution theory provides selectively neutral explanations of the origin and maintenance of biological complexity. This essay provides an analysis of CNE as an explanatory strategy defined by a tripartite set of conditions, and shows how this applies to cases of the evolution of complexity at higher-levels of the biological hierarchy. CNE was initially deployed to help explain a variety of complex molecular structures and processes, including spliceosomal splicing, trypansomal pan-editing, scrambled genes in (...) ciliates, duplicate gene retention and fungal ATP synthetase structure. CNE has also been generalized to apply to phenomena at the cellular level, including protein-protein interaction network modularity, obligate microbial symbioses, eukaryogenesis and microbial unculturability. This essay further extends CNE to cases of complexity at levels of organization higher than the molecular and cellular. These are multicellular phenotypic complexity, multicellular ecological complexity and, some cases of cultural complexity. (shrink)

This article offers three contrasting cases of the use of neutrality and drift in molecular evolution. In the first, neutrality is assumed as a simplest case for modeling. In the second and third, concepts of drift and neutrality are developed within the context of population genetics testing and the development and application of the molecular clock.

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both (...) the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

In 1968, Motoo Kimura submitted a note to Nature entitled “Evolutionary Rate at the Molecular Level,” in which he proposed what has since become known as the neutral theory of molecular evolution. This is the view that the majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral or nearly neutral alleles. Kimura was not proposing that random drift explains all evolutionary change. He does not challenge (...) the view that natural selection explains adaptive evolution, or, that the vertebrate eye or the tetrapod limb are products of natural selection. Rather, his objection is to “panselectionism’s intrusion into the realm of molecular evolutionary studies”. According to Kimura, most changes at the molecular level from one generation to the next do not affect the fitness of organisms possessing them. King and Jukes (1969) published an article defending the same view in Science, with the radical title, “Non- Darwinian Evolution,” at which point, “the fat was in the fire” (Crow, 1985b). The neutral theory was one of the most controversial theories in biology in the late twentieth century. This chapter will review the debate over the netural theory subsequent to Kimura. (shrink)

This paper supplements an earlier one (Wassermann 1978b). Its views aim to reinforce those of Lewontin and other prominent evolutionists, but differ significantly from the opinions of some philosophers of science, notably Popper (1957) and Olding (1978). A basic distinction is made between 'laws' and 'theories of mechanisms'. The 'Theory of Evolution' is not characterized by laws, but is viewed here as a hypertheory which explains classifiable evolutionary phenomena in terms of subordinate classifiable theories of 'evolution-specific mechanisms' (...) (ESMs), each of which could apply to a host of species. Adaptations could result from ESMs that are rooted in molecular complementarities. The status of optimization theories that aim to predict best adapted states of organisms or populations is also discussed. (shrink)

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular (...) constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes. (shrink)

The paper delves into the evolution of language in French and English, focusing on the feminization and neutralization of job titles in legal and professional settings. It explores how these linguistic changes are intertwined with the broader implications of language in shaping moral and ethical standards, advocating for gender equality, and challenging gender biases. The study highlights the slow but impactful progress in linguistic reform within legal contexts, suggesting strategies to align legal language with contemporary principles of gender equality.

The genetic equidistance result shows that different species are approximately equidistant to a simpler outgroup in protein sequence similarity, as first reported by Margoliash in 1963. This result, together with those of Zuckerkandl and Pauling in 1962 inspired the molecular clock and in turn the neutral theory of evolution. Here it is shown that the clock/neutral theory had from the beginning overlooked another characteristic of the equidistance result, the overlap feature, which shows a large (...) number of overlapped mutant amino acid positions where any pair of any three species is different provided that the species concerned differ from one another in complexity as a result of macroevolution. In contrast, when simple organisms of similar complexity and short evolutionary divergence are compared, there are only a small number of overlaps largely consistent with chance or the neutral theory. The full reality of the equidistance result strongly supports the Maximum Genetic Diversity hypothesis, a more complete account of hereditary changes. (shrink)

The concepts of hierarchical organization, genetic determinism and biological specificity have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled “reductionist”. However, the concepts have been marginalized or rejected in some of the research that in the late 1960s (...) began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that ‘molecular reductionism’ has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular ‘reductionism’, in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology. (shrink)

The concepts of hierarchical organization, genetic determinism and biological specificity have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled “reductionist”. However, the concepts have been marginalized or rejected in some of the research that in the late 1960s (...) began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that ‘molecular reductionism’ has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular ‘reductionism’, in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology. (shrink)

Despite considerable interest in viral evolution, at least among virologists, viruses are rarely considered from the same evolutionary vantage point as other organisms. Early work of necessity emphasized phenotype and phenotypic variation (and therefore arguably was more oriented towards the broader biological and ecological perspectives). More recent work (essentially since the development of molecular evolution in the 1960's but beginning earlier) has concentrated on genotypic variation, with less clarity about the significance of such variations. Other aspects of (...) evolutionary theory, especially considerations of natural selection and of evolutionary constraints, have not widely been applied to viruses, and an evolutionary framework for virology has long been lacking. This becomes apparent in considering 'emerging' viruses, which have often been treated on an ad hoc basis. It was often felt that, because previously unrecognized viruses are involved, mechanisms of viral emergence must mirror the unpredictability of mutations in the viral genome. However, most examples of viral emergence are independent of mutation, at least initially, and are often pre-existing viruses in changed circumstances ('viral traffic'). This conclusion also readily follows from ordinary Darwinian premises, which would require that, like other living species, 'new' organisms are descended only from existing species. In this respect, from a Darwinian perspective, viruses would appear to resemble other organisms. (shrink)

Since Darwin, the idea of psychological continuity between humans and other animals has dominated theory and research in investigating the minds of other species. Indeed, the field of comparative psychology was founded on two assumptions. First, it was assumed that introspection could provide humans with reliable knowledge about the causal connection between specific mental states and specific behaviors. Second, it was assumed that in those cases in which other species exhibited behaviors similar to our own, similar psychological causes were (...) at work. In this paper. we show how this argument by analogy is flowed with respect to the case of second-order mental states. As a test case, we focus on the question of how other species conceive of visual attention, and in particular whether chimpanzees interpret seeing as a mentalistic event involving internal states of perception, attention, and belief. We conclude that chimpanzees do not reason about seeing in this manner, and indeed, there is considerable reason to suppose that they do not harbor representations of mental states in general. We propose a reinterpretation model in which the majority of the rich social behaviors that humans and other primates share in common emerged long before the human lineage evolved the psychological means of interpreting those behaviors in mentalistic terms. Although humans, chimpanzees, and most other species may be said to possess mental states, humans alone may have evolved a cognitive specialization for reasoning about such states. (shrink)

The article offers an analysis of the concept of the Absolute in Fichte’s philosophy. Despite the difficulty of the definition, this concept receives a rich and creative rethinking in Fichte and will further influence the philosophical systems of thought. Gradually introducing this concept into his philosophical project of Wissenschaftslehre Fichte often changes its interpretation. So, starting with a somewhat vague understanding of the concept of the "absolute I" through Schelling's criticism of the Absolute, he develops the theory of the (...) manifestation of the Absolute, each time choosing new metaphors to denote it, and sometimes filling it with religious content, when the Absolute becomes a substitute for the concept of God. On the one hand, it’s important not to reduce the Absolute to a simple object of thought because this would indicate the limitation of the Absolute. On the other hand, it would be wrong to consider the Absolute as an empty or neutral concept or something completely enclosed in itself. Then, its existence will be doubtful. Fichte is careful about a clear definition of the Absolute. He solves this dilemma through the idea of the manifestation of the Absolute. Manifestation is the exit of the Absolute beyond itself while remaining unchanged. The ability to manifest itself is a prerequisite that the Absolute can be recognized and thought. This is how the Absolute manifests itself in the form of knowledge. Fichte emphasizes that the Absolute is not a projection of our mind, it may not depend on our thinking, however with such peculiarity that truth and knowledge have their basis in it. Thereby, with the theory of the Absolute, Fichte develops the idea of the foundation that is outside of ourselves, has transcendental character, and thus allows knowledge or truth not to be trapped in subjective tenets. Analyzing step by step the process of evolution of this concept, we will be able to see how in the last years of his life, Fichte states the importance of two realities: the “I” and the “Absolute” and how he explains the connection between them. (shrink)

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to ‘overselectionism’. Here I contend, that in its extended form, it has major conceptual problems, can (...) not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and – if seen as a major evolutionary mechanism for all organisms – could stifle further thought regarding the evolution of highly complex biological processes. (shrink)

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, viewing molecular (...) biology as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development. (shrink)

In 1809--the year of Charles Darwin's birth--Jean-Baptiste Lamarck published Philosophie zoologique, the first comprehensive and systematic theory of biological evolution. The Lamarckian approach emphasizes the generation of developmental variations; Darwinism stresses selection. Lamarck's ideas were eventually eclipsed by Darwinian concepts, especially after the emergence of the Modern Synthesis in the twentieth century. The different approaches--which can be seen as complementary rather than mutually exclusive--have important implications for the kinds of questions biologists ask and for the type of research (...) they conduct. Lamarckism has been evolving--or, in Lamarckian terminology, transforming--since Philosophie zoologique's description of biological processes mediated by "subtle fluids." Essays in this book focus on new developments in biology that make Lamarck's ideas relevant not only to modern empirical and theoretical research but also to problems in the philosophy of biology. Contributors discuss the historical transformations of Lamarckism from the 1820s to the 1940s, and the different understandings of Lamarck and Lamarckism; the Modern Synthesis and its emphasis on Mendelian genetics; theoretical and experimental research on such "Lamarckian" topics as plasticity, soft (epigenetic) inheritance, and individuality; and the importance of a developmental approach to evolution in the philosophy of biology. The book shows the advantages of a "Lamarckian" perspective on evolution. Indeed, the development-oriented approach it presents is becoming central to current evolutionary studies--as can be seen in the burgeoning field of Evo-Devo. Transformations of Lamarckism makes a unique contribution to this research. (shrink)

This paper traces the principal thematic developments in Aristotle’s conception of chemical substance as they bear on the evolution of the notion into modern times. A line of speculation is indicated about the interpretation of elemental proportions clearly raised by Aristotle’s discussion but not pursued in his extant writings. Apart from its historical interest, Aristotle’s discussion of substance and mixture has been taken up in contemporary systematic philosophy (Fine 1995), where it is treated as at best only relevant to (...) ordinary, everyday views. This approach gains support from the contention that such views have been superseded by the molecular conception of chemical substance developed in 19th century science and extolled by advocates of the Kripke-Putnam conception of microessentialism (Kripke 1980, Putnam 1975). Duhem (1902), who well understood what would now be called the macroscopic theory of thermodynamics and its relevance to chemistry, had a different view, and the present discussion is much influenced by him. Certainly, Aristotle’s view stands in need of modification in the light of the understanding of mixtures provided by Gibbs’ phase rule (Gibbs 1948). But with a certain weakening, a central Aristotelian claim about mixtures still has some bearing. (shrink)

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays (...) an important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

SummaryThe meaning of prebiotic evolution is first considered and analysed. The conclusion reached is that the phenomenon is both universal and predetermined, bringing interstellar molecules to the stage of proteins and DNA.Two important properties of living beings, evolution and senescence, are also discussed in depth from a new viewpoint.From this, dialectically, it is suggested that the first of the two phenomena corresponds to a progressive increase in the molecular weight of DNA, whereas the second is dependent on (...) a decrease in this.The theory on which the present research is based is in contradiction to that of the neo‐Darwinists. (shrink)

" The best way to predict the future is to invent it. —Alan Kay _1_ It is obvious that there are patterns of cultural change—evolution in the neutral sense—and any theory of cultural change worth more than a moment's consideration will have to be Darwinian in the minimal sense of being consistent with the theory of evolution by natural selection of Homo sapiens. —Daniel Dennett _2_ The future is here. It's just not widely distributed yet. (...) —William Gibson _3_ It is the magician's wand, by means of which he may summon into life whatever form and mould he pleases. —Charles Darwin commenting on the power of artificial selection _4_ " This article introduces an applied Theory of Evolution of Artificial Systems, called Directed Evolution. The theory is grounded in fifty years of research on Inventive Engineering known as TRIZ, which started in the former Soviet Union by G. Altshuller and continues today. The theory has generated a set of Patterns and Lines of Evolution that represent a compilation of trends that document strong, historically recurring tendencies in the development of manmade systems in general and technological systems in particular. Directed Evolution is the systematic applied-oriented process for “predicting” future generations of a system by inventing them along these evolutionary patterns. The current article introduces the theory, reflects on its basic underlying logic, and provides a broad historical context and intellectual justification for such an effort. It shows that the quest of DE theory and practice falls well within the boundaries of past pursuits to identify evolutionary patterns of complex systems and to use these patterns to control and manipulate possible futures of artificial systems. (shrink)

Darwinism is defined here as an evolving research tradition based upon the concepts of natural selection acting upon heritable variation articulated via background assumptions about systems dynamics. Darwin’s theory of evolution was developed within a context of the background assumptions of Newtonian systems dynamics. The Modern Evolutionary Synthesis, or neo-Darwinism, successfully joined Darwinian selection and Mendelian genetics by developing population genetics informed by background assumptions of Boltzmannian systems dynamics. Currently the Darwinian Research Tradition is changing as it incorporates (...) new information and ideas from molecular biology, paleontology, developmental biology, and systems ecology. This putative expanded and extended synthesis is most perspicuously deployed using background assumptions from complex systems dynamics. Such attempts seek to not only broaden the range of phenomena encompassed by the Darwinian Research Tradition, such as neutral molecular evolution, punctuated equilibrium, as well as developmental biology, and systems ecology more generally, but to also address issues of the emergence of evolutionary novelties as well as of life itself. (shrink)

Philosophical studies of complex scientific concepts are predominantly “adaptationist,” arguing that conceptual complexity serves important purposes. This is a historical artifact. Having had to defend their views against a monist presumption favoring simpler concepts, pluralists and patchwork theorists felt compelled to show that complexity can be beneficial. This neglects an alternative possibility: Conceptual complexity is largely neutral, persisting simply because it does little harm. This article defends the neutral theory of conceptual complexity in two forms: (a) as (...) a plausible theory in its own right and (b) as a useful foil for adaptationist arguments. (shrink)

List of figures -- Acknowledgements -- Preface -- Foreward by David Lamb -- Introduction -- The trials and tribulations of induction -- The perils of disproving theories -- Science as a daring enterprise: Choosing by convention -- Dogmatism in science: Kuhn and scientific revolutions -- Feyerabend and scientific anarchy -- One last plea for "rationality": Rationality and the growth of science -- Evolution and science -- Evolutionary relativism -- Alternative ways of perceiving the universe -- Appendix: The fate of (...) inductive logic -- Index. (shrink)

Molecular Weismannism is the claim that: “In the development of an individual, DNA causes the production both of DNA (genetic material) and of protein (somatic material). The reverse process never occurs. Protein is never a cause of DNA”. This principle underpins both the idea that genes are the objects upon which natural selection operates and the idea that traits can be divided into those that are genetic and those that are not. Recent work in developmental biology and in philosophy (...) of biology argues that an acceptance of Molecular Weismannism requires the tacit assumption that genetic causes are different in kind from other developmental causes. They argue that if this assumption proves to be unwarranted then we should abandon, not just gene selectionism and gene centred functional solutions to the units of selection problem, but also the very notion that there is any such thing as a “genetic trait”. A group of possible causal distinctions (proximity, ultimacy and specificity) are explored and found wanting. It is argued that an extended version of information theory, while not strong enough to support Molecular Weismannism, will support both the claim that traits can be divided into those that are genetic and those that are not as well as the claim that there is good reason to privilege genetic causes within evolutionary and developmental explanations. The outcome of this for the units of selection debate is explored. (shrink)

In his theory of evolution, Darwin recognized that the conditions of life play a role in the generation of hereditary variations, as well as in their selection. However, as evolutionary theory was developed further, heredity became identified with genetics, and variation was seen in terms of combinations of randomly generated gene mutations. We argue that this view is now changing, because it is clear that a notion of hereditary variation that is based solely on randomly varying genes (...) that are unaffected by developmental conditions is an inadequate basis for evolutionary theories. Such a view not only fails to provide satisfying explanations of many evolutionary phenomena, it also makes assumptions that are not consistent with the data that are emerging from disciplines ranging from molecular biology to cultural studies. These data show that the genome is far more responsive to the environment than previously thought, and that not all transmissible variation is underlain by genetic differences. In Evolution in Four Dimensions (2005) we identify four types of inheritance (genetic, epigenetic, behavioral, and symbol-based), each of which can provide variations on which natural selection will act. Some of these variations arise in response to developmental conditions, so there are Lamarckian aspects to evolution. We argue that a better insight into evolutionary processes will result from recognizing that transmitted variations that are not based on DNA differences have played a role. This is particularly true for understanding the evolution of human behavior, where all four dimensions of heredity have been important. (shrink)

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic, behavioral, and symbolic. (...) These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution.After discussing each of the four inheritance systems in detail, Jablonka and Lamb "put Humpty Dumpty together again" by showing how all of these systems interact. They consider how each may have originated and guided evolutionary history and they discuss the social and philosophical implications of the four-dimensional view of evolution. Each chapter ends with a dialogue in which the authors engage the contrarieties of the fictional "I.M.," or Ifcha Mistabra -- Aramaic for "the opposite conjecture" -- refining their arguments against I.M.'s vigorous counterarguments. The lucid and accessible text is accompanied by artist-physician Anna Zeligowski's lively drawings, which humorously and effectively illustrate the authors' points. (shrink)

The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size (“ecological drift”), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent (...) studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non‐neutral modes of speciation, such as adaptive radiations. (shrink)

Teilhard de Chardin's ideas about the mechanisms of biological evolution are revised and their connections with contemporary theories are reported. Teilhard de Chardin's main contribution is the proposal of a new scientific discipline, geobiology—the science of the biosphere evolving as a whole. The main fields of interest of geobiology are reported, and its relationships with contemporary hypotheses, such as Lovelock's Gaia, are discussed. The consequences of this kind of approach are the parallel evolution described as orthogenesis and the (...) presence of canalization phenomena. These Teilhardian hypotheses are discussed in relation to those of the process structuralists and to the novelties of the molecular evolution of the genome. Conclusions are that the mechanisms discussed by Teilhard are presently taken into consideration by contemporary evolutionists in order to construct a new theory of biological evolution. (shrink)

When I was an undergraduate student in biology, about twenty years ago, developmental biology was relatively absent in my curriculum. There were some elements of developmental biology in the zoology and botany courses, but one had to take two elective courses, Embryology and Molecular Biology of Development, in order to learn more. Fortunately, curricula have changed nowadays and for good reasons. The study of developmental processes is crucial for our understanding of life, perhaps more than ever. For example, it (...) is now important to consider development alongside the study of evolution and genetics. Evolutionary developmental biology is a very active field of research, which focuses on how changes in development affect evolution as well as on how developmental processes evolve. It is not only mutations that produce variation for evolution; development matters too. Similarly, research in genetics and genomics reveals numerous intra- and inter-cellular interactions that affect phenotypi .. (shrink)

The appearance of consciousness in the universe remains one of the major mysteries unsolved by science or philosophy. Absent an agreed-upon definition of consciousness or even a convenient system to test theories of consciousness, a confusing heterogeneity of theories proliferate. In pursuit of clarifying this complicated discourse, we here interpret various frameworks for the scientific and philosophical study of consciousness through the lens of social insect evolutionary biology. To do so, we first discuss the notion of a forward test versus (...) a reverse test, analogous to the normal and revolutionary phases of the scientific process. Contemporary theories of consciousness are forward tests for consciousness, in that they strive to become a means to classify the level of consciousness of arbitrary states and systems. Yet no such theory of consciousness has earned sufficient confidence such that it might be actually used as a forward test in ambiguous settings. What is needed now is thus a legitimate reverse test for theories of consciousness, to provide internal and external calibration of different frameworks. A reverse test for consciousness would ideally look like a method for referencing theories of consciousness to a tractable model system. We introduce the Ant Colony Test as a rigorous reverse test for consciousness. We show that social insect colonies, though disaggregated collectives, fulfill many of the prerequisites for conscious awareness met by humans and honey bee workers. A long lineage of philosophically-neutral neurobehavioral, evolutionary, and ecological studies on social insect colonies can thus be redeployed for the study of consciousness in general. We suggest that the ACT can provide insight into the nature of consciousness, and highlight the ant colony as a model system for ethically performing clarifying experiments about consciousness. (shrink)

Darwin proposed that evolutionary novelties are environmentally induced in organisms “constitutionally” sensitive to environmental change, with selection effective owing to the inheritance of constitutional responses. A molecular theory of inheritance, pangenesis , explained the cross‐generational transmission of environmentally induced traits, as required for evolution by natural selection. The twentieth‐century evolutionary synthesis featured mutation as the source of novelty, neglecting the role of environmental induction. But current knowledge of environmentally sensitive gene expression, combined with the idea of genetic (...) accommodation of mutationally and environmentally induced change, supports a revival of Darwin's original theory that is consistent with modern molecular and population genetics. †To contact the author, please write to: Smithsonian Tropical Research Institute, c/o Escuela de Biología, Universidad de Costa Rica, Costa Rica; e‐mail: [email protected]. (shrink)