Evolution of Natural Selection

Design for an Individual of the inputs). Specifically, we hypothesise that the conditions necessary to evolve a new level of individuality are described by the conditions necessary to learn nondecomposable functions of this type (or deep model induction) familiar in connectionist models of cognition and learning.

This document serves as a formal, global notification that the prevailing theoretical foundation of cultural evolutionary science has now been displaced. David R. Wood's Unified Framework of Evolution has revealed that the processes long assumed to govern cultural change-namely, cumulative imitation, passive transmission, and group-level adaptation-are not aligned with Darwinian logic, nor with the actual competitive dynamics of real-world systems. Instead, cultural evolution is more accurately explained as a second process of evolution: one driven by individual imaginative mutation and selected in artificial, competitive environments.

The Unified Framework for the Science of Evolution. This completes the quest that began with Aristotle, progressed by Darwin, and not finished by David R. Wood. The cultural evolutionary scientific community never thought to look to existing commerical and military best practices to find the conceptual patterns they needed to complete the second process of evolution - the process of artificial evolution by means of artificial selection. Now, a former infantry officer and ITIL Master has conclusively completed this quest for the ages. It required the paradigm shift Thomas Kuhn envisioned of a resurrected ancient Greco-Roman worldview possessed by a Philosopher-Warrior to make this historic and transformational scientific discovery.

biology in uncovering the world of anatomy, morphology and transformism that existed prior to Darwin, and more proximately, to the dominance of the Modern Synthesis and its emphasis on population dynamics and gene selectionism. Preceded by the publication, also by the University of Chicago, of the relevant writings of George Cuvier by Martin Rudwick (Rudwick 1997), the essays of Etienne Geoffroy St Hilaire by Hervé le Guyader (Le Guyader 2004), and now this text by Owen, these textual sources allow those interested in exploring the texture and the issues of the pre-Darwinian anatomical debates to do so with the original texts. This is a fine volume and I recommend it to anyone interested in these issues.

Niche construction theory concerns how organisms can change selection pressures by altering the feature–factor relationship between themselves and their environment. These alterations are standardly understood to be brought about through two kinds of organism–environment interaction: perturbative and relocational niche construction. We argue that a reconceptualization is needed on the grounds that if a niche is understood as the feature–factor relationship, then there are three fundamental ways in which organisms can engage in niche construction: constitutive, relational, and external niche construction. We further motivate our reconceptualization by showing some examples of organismic activities that fall outside of the current categorization of niche construction, but nonetheless should be included. We end by discussing two objections to niche construction and show how our reconceptualization helps to undercut these objections.

One contentious debate in the philosophy of biology is that between the statisticalists and causalists. The former understand core evolutionary concepts like fitness and selection to be mere statistical summaries of underlying causal processes. In this view, evolutionary changes cannot be causally explained by selection or fitness. The causalist side, on the other hand, holds that populations can change in response to selection-one can cite fitness differences or driftability in causal explanations of evolutionary change. But on the causal side, it is often not clear how, precisely, one should understand these causes. Thus, much more could be said about what sort of causes fitness and driftability are. In this paper, I borrow Dretske's distinction between structuring and triggering causes and suggest that fitness and driftability are structuring causes of evolution.

Fitness plays many roles throughout evolutionary theory, from a measure of populations in the wild to a central element in abstract theoretical presentations of natural selection. It has thus been the subject of an extensive philosophical literature, which has primarily centered on the way to understand the relationship between fitness values and reproductive outcomes. If fitness is a probabilistic or statistical quantity, how is it to be defined in general theoretical contexts? How can it be measured? Can a single conceptual model for fitness be offered that applies in all biological cases, or must fitness measures be case-specific? Philosophers have explored these questions over the last several decades, largely in the context of an influential definition of fitness proposed in the late 1970s: the propensity interpretation. This interpretation as first described undeniably suffers from significant difficulties, and debate regarding the tenability of amendments and alternatives to it remains unsettled.

A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organization (more than the parts) that largely conditions most higher-level properties, which are not reducible to the properties of the individual parts. Can the topological organization of these webs provide some insight into their evolutionary origins? Both biological and artificial networks share some common architectural traits. They are often heterogeneous and sparse, and most exhibit different types of correlations, such as nestedness, modularity or hierarchical patterns. These properties have often been attributed to the selection of functionally meaningful traits. However, a proper formulation of generative network models suggests a rather different picture. Against the standard selection–optimization argument, some networks reveal the inevitable generation of complex patterns resulting from reuse and can be modelled using duplication–re...

Greek mythology formed the basis of much of Greek philosophy, art and science. The Greeks conceptualised their universe as animated by forces and elements which they anthropomorphised as gods and other supernatural beings. However, only recently has there been increasing attention on Greek mythology as a source of advanced technological and biomedical concepts. The Greek myths are fascinating for their technological ideas pertaining to body/cognitive enhancement. This paper provides theoretical correlations between Greek mythological and socio-historic dimensions of human enhancement, and some of their current/future technological developments, hence, offering a cultural anthropological perspective.

In his personal copy of Owen's On the Nature of the Limbs, Darwin entered two interesting comments at different times inside the rear cover: I look at Owens Archetypus as more than ideal, as a real representation as far as the most consummate skill & loftiest generalization can represent the parent [present?] form of the Vertebrata.

New species and higher categories of biological organisms are actually formed by the insertion of DNA from radioactivity-generated viruses into cellular genomes of members of earlier species, according to a revolutionary new testable scientific hypothesis for the origin of species. With this hypothesis, new species are not produced by Darwin’s “natural selection” or “survival of the fittest” species evolutionary process, or its modern version called neo-darwinism. This virus-based DNA insertion produces a burst of genetic and morphogenetic change as some species members are transformed into a new species, which then remains essentially unchanged until it become extinct perhaps millions of years later. The outward result is similar to that of the hypothesis of punctuated equilibria for rapid species formation proposed by Eldredge and Gould in 19721 (to explain persistent gaps in the species fossil record that are not predicted by Darwinism). But in the new hypothesis, the rapid genetic changes that produce new species are “pre-planned”, according to Prabhat Ranjan Sarkar’s “great exceptions” species evolutionary hypothesis of 1979. According to P.R. Sarkar, atoms are composed of billions of subatomic living entities called microvita, first described in 1986. Microvita were emanated from a Cosmic Mind to produce our universe-forming Big Bang 13.8 billion years ago. Microvita carry pre-planned codes for DNA or RNA from the Cosmic Mind. These microvita first created the fundamental physical particles and then atoms. Microvita are later released from radioactive atoms and in a suitable chemical environment form DNA or RNA-carrying viruses that produce different species of living beings in the universe through the scientifically-accepted evolutionary process of descent with modification, but not by natural selection, which rarely if ever has been observed to cause species transformation. A biological experiment has been proposed to detect the existence of RNA- or DNA-virus-forming microvita in radioactive atoms that could help substantiate this proposed hypothesis for the origin of species.

biología. Para ello se reconstruye en primer término la argumentación de J.J.C. Smart en contra de su existencia y la discusión que de ella hacen M. Ruse y R. Munson. El examen de esta controversia pone de manifiesto que, a pesar de las diferencias existentes entre el primero de estos autores y los dos restantes en relación con el problema de las leyes en biologia, los tres comparten el supuesto según el cual en caso de haber leyes (en sentido estricto o fundamentales) en la genética, éstas deberían ser alguna de las llamadas "leyes de Mendel". En la presente comunicación, y a partir de una revisión del concepto metacientífico de ley fundamental, el anterior supuesto es cuestionado, proponiéndose un análisis alternativo, basado en una reconstrucción estructuralista de la teoría genética.

This review paper presents the role of ecological speciation in natural variations in animals, which is a fundamental process in the origin of biodiversity. The study focuses on the unique system of animal (lizard) adaptation to gypsum soil at White Sands National Park in New Mexico, USA, where multiple faunal species have evolved independently in response to this specific habitat.

There is a widespread philosophical interpretation of natural selection in evolutionary theory: natural selection, like mutation, migration, and drift are seen as forces that propel the evolution of populations. Natural selection is thus a population level causal process. This account has been challenged by the Statistics, claiming that natural selection is not a population level cause but rather a statistical feature of a population. This paper examines the nature of the aforementioned ontological debate and the nature of statistical explanations given by population genetics. I claim that the Modern Synthesis provides good explanations of the changes in trait structure of populations without appealing to detailed causal information about the individual trajectories of the members of a population.

En el presente artículo se realiza una reconstrucción de la bioquímica analizando la estructura de sus ejemplares. Hace justicia a la manera expositiva de los propios científicos, a la vez que a su práctica. Se trata de una versión modificada de la concepción estructuralista, en la que se prescinde de modelos matemáticos. Conserva, sin embargo, la distinción entre términos teóricos y no-teóricos, así como el rol de los ejemplares paradigmáticos en el uso de la teoría. Se pragmatiza la afirmación empírica de la bioquímica, introduciendo a "un bioquímico" como el sujeto epistémico que conoce las estructuras de la teoría, y la emplea localizando semejanzas estructurales entre ejemplares. En el análisis histórico del nacimiento de la bioquímica, se muestra que no sólo su uso, sino su génesis siguen la secuencia de pasos que prevé la reconstrucción. Se propone que esta manera de reconstruir una teoría es la más adecuada al conocimiento biológico y biomédico, aunque pudiera extenderse a teorías de otros campos, incluyendo el social o el físico. Palabras clave: Bioquímica; filosofía de la ciencia; reconstrucción de ejemplares; estructuralismo sin modelos matemáticos; ejemplar paradigmático de la bioquímica; semejanzas estructurales entre ejemplares.

biología. Para ello se reconstruye en primer término la argumentación de J.J.C. Smart en contra de su existencia y la discusión que de ella hacen M. Ruse y R. Munson. El examen de esta controversia pone de manifiesto que, a pesar de las diferencias existentes entre el primero de estos autores y los dos restantes en relación con el problema de las leyes en biologia, los tres comparten el supuesto según el cual en caso de haber leyes (en sentido estricto o fundamentales) en la genética, éstas deberían ser alguna de las llamadas "leyes de Mendel". En la presente comunicación, y a partir de una revisión del concepto metacientífico de ley fundamental, el anterior supuesto es cuestionado, proponiéndose un análisis alternativo, basado en una reconstrucción estructuralista de la teoría genética.

is both an historian and a philosopher of biology and has done research work that requires such a double ability. In this book, he forces us to look at biology as a whole-history, science, and epistemological models-and calls for a new equilibrium to be achieved by a revision of certain basic tenets that shaped neo-Darwinian biology in the 20th century. The subtitle of his book, Roots of Evo-Devo, and the title of the first section, ''Evo-devo as a new and old science'' shows that a synthetic model, encompassing evolutionary and developmental biology, is the key to such a new equilibrium and that the model is not a recent creation. Actually, it dates back before the neo-Darwinian synthesis. I think the historical framework Amundson has devised can have a part in this project and he has also designed an insightful philosophical plan of his own. A central question lies at the heart of this plan: how is it possible to recapture morphology, and bring it back into evolution? The answer is in the title of the book: embryology. Just as the adult form emerges by a gradual process of ontogenetic differentiation from a less differentiated embryo, a new species emerges from a gradual modification in the embryogenetic processes that are responsible for that form. Biology scholars must account for these processes, both at the genetic and population level. Thus, as a philosopher, Amundson has tied his historiographical work to the philosophical background of current scientific problems. Hopefully, his book may finally bring to an end the remaining reluctance of a few neo-Darwinists to accept developmental biology on a parity basis.

Processes of evolutionary transition (ET), becoming part of a new reproducing collective while losing the capacity of independent reproduction, seem difficult to track without circularity, since their features—units of selection, individuality, inheritance at multiple levels (MLS1, MLS2)—are products of one process. We describe ET in a non-circular way, noting kinds of interactions among community members necessary for such major transitions that are not instances of those same interactions within community members. Reproducing ‘systems’ tend to hybridize with environmental components, employing eco–devo scaffolding interactions forming communities. Communities are developmentally scaffolded systems of diverse members engaged in heterogeneous interactions. They may become individuals in their own right with the potential to evolve an inheritance system at the emergent community level. We argue for the explanatory benefits of treating ‘individuality’ as a special case of ‘collectivity’. We characterize an idealized sequence of collective processes—coordination, cooperation and collaboration (3Cs)—which scaffolds transitions to new forms of collective individuality: communities. Hominid evolution and learning draw attention to developmental interactions driving both dimensions of ET: new ‘levels of individuality’ and inherited ‘information systems’. Here, we outline a theoretical perspective that we suggest applies across a wide range of cases and scenarios.This article is part of the theme issue ‘Human socio-cultural evolution in light of evolutionary transitions’.

Using the evolution of the stickleback family of subarctic fish as a touchstone, we explore the effect of new discoveries about regulatory genetics, developmental plasticity, and epigenetic inheritance on the conceptual foundations of the Modern Evolutionary Synthesis. Identifying the creativity of natural selection as the hallmark of the Modern Synthesis, we show that since its inception its adherents have pursued a variety of research projects that at first seemed to conflict with its principles, but were accommodated. We situate challenges coming from developmental biology in a dialectic between innovation and tradition, suggesting on the basis of past episodes that even if developmental plasticity and epigenetic inheritance are aligned with its principles the Modern Synthesis (and its image in the public reception of evolution) will be significantly affected.

Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.

En lo que sigue, se reconstruye el dominio de teorías relativas a la herencia biológica, propuestas durante el periodo 1865-1902. Se trata de un episodio científico de mucha controversia y audaces especulaciones, libres de los constreñimientos de un paradigma establecido. En consecuencia, surgieron propuestas muy diversas, para las cuales no empata bien la categoría metateórica de red. De cualquier manera, los elementos teóricos detectados sí guardan vínculos entre sí, debido a que comparten ciertas estructuras, y esto permite introducir mediante un arreglo reticular la idea de dominio, donde la naturaleza de los vínculos no alude a especializaciones de leyes fundamentales sino a la secuencia en el armado de subestructuras. El trabajo explora esta posibilidad combinando el aparato del programa estructuralista con la técnica ordenadora denominada Análisis Formal de Conceptos (Formal Concept Analysis): en concreto se aplica dicho procedimiento a una muestra de veinte reconstrucciones,...

Over the past fifteen years there has been a considerable amount of debate concerning what theoretical population dynamic models tell us about the nature of natural selection and drift. On the causal interpretation, these models describe the causes of population change. On the statistical interpretation, the models of population dynamics models specify statistical parameters that explain, predict, and quantify changes in population structure, without identifying the causes of those changes. Selection and drift are part of a statistical description of population change; they are not discrete, apportionable causes. Our objective here is to provide a definitive statement of the statistical position, so as to allay some confusions in the current literature. We outline four commitments that are central to statisticalism. They are: 1. Natural Selection is a higher order effect; 2. Trait fitness is primitive; 3. Modern Synthesis (MS)-models are substrate neutral; 4. MS-selection and drift are model-relative.

A hitherto neglected form of explanation is explored, especially its role in population genetics. "Statistically abstractive explanation" (SA explanation) mandates the suppression of factors probabilistically relevant to an explanandum when these factors are extraneous to the theoretical project being pursued. When these factors are suppressed, the explanandum is rendered uncertain. But this uncertainty traces to the theoretically constrained character of SA explanation, not to any real indeterminacy. Random genetic drift is an artifact of such uncertainty, and it is therefore wrong to reify it as a cause of evolution or as a process in its own right.

Organisms are born; they die; they mate. These events change the make-up of organism-ensembles. Organisms enter an ensemble when they are born and exit when they die; by mating, organisms determine what kind of individual enters by a subsequent birth. This is how births, deaths and matings influence the make-up of organism-ensembles. Since evolution consists of changes to the make-up of organismensembles, let us call these events individual-level selection events or ILSEs. (The significance of the term 'selection' will become evident in a moment.) There are other kinds of ILSE-e.g., migration-but we need not worry about them here. Organism-ensembles also change. For instance, suppose that we have an ensemble of 100 organisms, evenly divided into two kinds, K and K′. An organism of kind K (call it Kris) is killed by a predator; in the meanwhile, an organism of kind K′ (call it Kristie) is born. If there are no other births or deaths, there are now 49 organisms of kind K, and 51 of kind K′. Kind K′ has proportionately increased relative to kind K. This change of ensemble-wide proportions is an ensemble-level selection event or ELSE. That is, it is a change involving an ensemble of individual organisms. What is the cause of this ELSE? Nothing other than that the predator killed Kris, and that Kristie became pregnant. That is: nothing other than ILSEs. After Kris's death and Kristie's birth-these events are both ILSEs-the ensemble-proportions change as a merely mathematical consequence. To put it in another way, the ensemble-level change is mere bookkeeping (cf. Walsh 2004); the causes of change are to be found at the individual level. It is because Kris's death and Kristie's birth result in changes in ensemble-level proportions that I call them individual-level selection events.

Over the past fifteen years there has been a considerable amount of debate concerning what theoretical population dynamic models tell us about the nature of natural selection and drift. On the causal interpretation, these models describe the causes of population change. On the statistical interpretation, the models of population dynamics models specify statistical parameters that explain, predict, and quantify changes in population structure, without identifying the causes of those changes. Selection and drift are part of a statistical description of population change; they are not discrete, apportionable causes. Our objective here is to provide a definitive statement of the statistical position, so as to allay some confusions in the current literature. We outline four commitments that are central to statisticalism. They are: 1. Natural Selection is a higher order effect; 2. Trait fitness is primitive; 3. Modern Synthesis (MS)-models are substrate neutral; 4. MS-selection and drift are model-relative.

De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the ...

La teoria darwiniana della selezione naturale presenta diverse criticità. La più importante riguarda proprio la nozione di "selezione", che Darwin ricava dalla selezione artificiale e applica al campo della natura. Quest'applicazione produce però una visione "umana troppo umana" del divenire naturale, in cui a risultare centrale è l'azione del negativo anzichè il proliferare positivo delle forme naturali.
Il saggio nasce da una discussione svoltasi presso il Laboratorio di Filosofia e Cultura "Mechrì" di Milano, che ha dedicato un anno di ricerche e seminari al tema dell'evoluzione, lavori poi confluiti nel volume "Evoluzione, progresso" da cui è tratto il testo.

De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture.

1. Introduction
1.1 Cause and effect
1.2 Prerequisites of selforganization
2. Phenomenological theory of selction
3. Stochastik approach to selection
4. Selforagnization based non complementary recognition: nucleic acids
5. selforganization via cyclic Catalysis: Proteins
6. Selfordering by enclosed catalytic function
7. Evolution experiments
8. Vonclusion
9. Deutsche Zusammenfassung
10. English summary (translated by Manfred Bundschuh

En lo que sigue, se reconstruye el dominio de teorías relativas a la herencia biológica, propuestas durante el periodo 1865-1902. Se trata de un episodio científico de mucha controversia y audaces especulaciones, libres de los constreñimientos de un paradigma establecido. En consecuencia, surgieron propuestas muy diversas, para las cuales no empata bien la categoría metateórica de red. De cualquier manera, los elementos teóricos detectados sí guardan vínculos entre sí, debido a que comparten ciertas estructuras, y esto permite introducir mediante un arreglo reticular la idea de dominio, donde la naturaleza de los vínculos no alude a especializaciones de leyes fundamentales sino a la secuencia en el armado de subestructuras. El trabajo explora esta posibilidad combinando el aparato del programa estructuralista con la técnica ordenadora denominada Análisis Formal de Conceptos (Formal Concept Analysis): en concreto se aplica dicho procedimiento a una muestra de veinte reconstrucciones,...

This essay attempts to combine some recent theoretical results in (bio)semiotics on arbitrariness, semiotic fitting, umwelt, choice, and extended theory of evolution into a more coherent whole. The proposed model describes a living being through its subjectivity and the ability to create meaning, which are often overlooked in models based on replicability The concept of the umwelt is divided into two – the synchronic umwelt and the distributed or diachronic umwelt. For the latter, a new term 'umweb' is introduced. A mechanism of evolution is described in which arbitrary relating followed by semiotic fitting is somewhat analogous to the neo-Darwinian mechanism of random mutations followed by natural selection. The paper proceeds to discuss the alternativity and coexistence of these two radically different ways of evolution and learning.

'For having, in the natural history of this earth, seen a succession of worlds, we may from this conclude that there is a system in nature; in like manner as, from seeing revolutions of the planets, it is concluded, that there is a system by which they are intended to continue those revolutions. But if the succession of worlds is established in the system of nature, it is in vain to look for anything higher in the origin of the earth. The result, therefore, of our present enquiry is, that we find no vestige of a beginning,-no prospect of an end.' James Hutton, Theory of the Earth, 1788. 'I think we may with much probability say that the consolidation cannot have taken place less than 20,000,000 years ago, or we should have more underground heat than we actually have, nor more than 400,000,000 years ago, or we should not have so much as the least observed underground increment of temperature.' Sir William Thomson (Lord Kelvin), On the Secular Cooling of the Earth, 1862. 'I do not presume to throw the slightest doubt upon the accuracy of any of the calculations made by such distinguished mathematicians as those who have made the suggestions I have cited. On the contrary, it is necessary to my argument to assume that they are all correct. But I desire to point out that this seems to be one of the many cases in which the admitted accuracy of mathematical processes is allowed to throw a wholly inadmissible appearance of authority over the results obtained by them. Mathematics may be compared to a mill of exquisite workmanship, which grinds you stuff of any degree of fineness; but, nevertheless, what you get out depends on what you put in; and as the grandest mill in the world will not extract wheat-flour from peascods, so pages of formulae will not get a definite result out of loose data.' Thomas Henry Huxley, Address to the Geological Society, 1869. 1 Early estimates Speculation on the age of the earth has existed for millennia. Many, like Aristotle have suggested that it is infinitely old, but most in early years have taken it to be finite and essentially unchanging albeit with variations in weather and with occasional volcanic eruptions and earthquakes superimposed.

A given explanatory theory T falls into circular reasoning if the only way to determine its explanandum is through the application of T. To find an (often previous) underlying theory T′ that determines T′s explanandum helps us save T from this accusation of circularity. We follow the structuralist view of theories in presenting and dealing with this issue, by applying it to particular theories. More specifically, we focus on the relationship between the Darwinian theory of common ancestry and the determination of homologies.

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, coul...

El artículo inicia subrayando la creciente importancia de los diagramas en filosofía de la ciencia, en particular se destaca su capacidad para la evocación heurística, su utilidad para la representación y el cálculo, y su poder de síntesis. A continuación, se presenta la importancia y buena recepción que diagramas de diferentes mecanismos causales en ciencia, han tenido dentro del nuevo mecanicismo lo que contrasta con el rechazo de esta escuela a los enfoques centrados en leyes y modelos. Finalmente se presenta una interpretación de las leyes y de las explicaciones mecanísticas que torna compatibles las ideas de mecanismo y de ley. Se utiliza el mecanismo de la síntesis de proteínas como caso ilustrativoThis paper starts with an emphasis on the increasing importance of diagrams in philosophy of science, highlighting their capacity for heuristic evocation, their usefulness for representation and calculus, and their power of synthesis. Next, we present how diagrams are important and ...

One of life's most striking characteristics is its purposeful (teleonomic) character, a character already evident at the simplest level of life-a bacterial cell. But how can a bacterial cell, effectively an aqueous solution of an assembly of biomolecules and molecular aggregates within a membrane (that is itself a macromolecular aggregate), act purposefully? In this review, we discuss this fundamental question by showing that the somewhat vague concept of purpose can be given precise physicochemical characterization, and can be shown to derive directly from the powerful kinetic character of the replication reaction. At the heart of our kinetic model is the idea that the stability that governs replicating systems is a dynamic kinetic stability, one that is distinctly different to the thermodynamic stability that dominates the inanimate world. Accordingly, living systems constitute a kinetic state of matter as opposed to the thermodynamic states that dominate the inanimate world. Thus, the model is able to unite animate and inanimate within a single conceptual framework, yet is able to account for life's unique characteristics, amongst them its purposeful character. As part of that unification, it is demonstrated that key Darwinian concepts are special examples of more general chemical concepts. Implications of the model with regard to the possible synthesis of living systems are discussed.

By using a panel of 603 commensal and pathogenic Escherichia coli and Shigella isolates, we showed that mutation rates of strains vary considerably among different ecotypes. Uropathogenic strains had the highest frequency of mutators, while strains from patients with bacteremia had the lowest mutation rates. No correlation between the mutation rates and antibiotic resistance was observed among the studied strains.

The interrelationships of 31 actinistian species (including Latimeria chalumnae) are analyzed based on a cladistic analysis of 75 osteological characters. Inference of evolutionary trends (e.g., modification of body shape and skull morphology) from the phylogenetic patterns demonstrates that the morphology of actinistians is less conservative than has been proposed previously. This empirical cladistic approach supports two distinct tempos of evolution during an evolutionary history of 380 million years. Along a phylogenetic pathway originating with a Devonian stem-species and ending with the living Latimeria chalumnae (including 101 morphological changes and 18 cladogenetic events), the first tempo occurred during the Devonian-Permian periods as a decreasing rate of morphological changes, which was followed by a stabilizing tempo during the Permian-Recent periods. The decreasing tempo is characterized by a sequence of gradual versus quantum temporal changes and low versus faster rates, whereas the stabilizing tempo primarily is gradual and low. In contrast to a common assumption, no significant correlation was found between the rates of morphological evolution and the temporal diversity of species.

Understanding the role mechanistic constraints play in shaping evolution can relieve the tension between the generally accepted intuition that there are no strict laws in biology and empirical findings showing that evolutionary processes are biased toward preferred outcomes. Mechanistic constraints explain why some evolutionary outcomes are more probable than others and allow for predictions in specific lineages. At the same time, mechanistic constraints are neither necessary nor universal in the way laws are traditionally characterized: they remain contingent on the past evolution of the biological mechanisms underpinning them and only constrain the future evolution of the organisms possessing them.

The Price equation was a piece of abstract mathematics. What kind of a connection could it possibly have had to George Price's personal life and biography? Here, I will argue that the initial impetus for Price's foray into mathematical population genetics stemmed from a preoccupation with the origins of family, one that was born following a divorce from his wife and the abandonment of their two young girls. What is special about the Price equation is the way in which it associates statistically between two groups, a ‘mother’ and ‘daughter’ population. The association need not mean genetic relatedness in the narrow sense of direct descent, and it allows us to see selection working at different levels simultaneously, a fact that was not lost on William Hamilton. Hamilton was one of the few friends who desperately tried to save Price from falling into the abyss of depression and homelessness in the period following the publication of ‘Selection and covariance’ (Price 1928 Natur...

An evolutionary transition in individuality is defined as the emergence of higher-level individuals from the interaction of lower-level ones during evolution. To occur, it requires both a process of natural selection at the higher (collective) level and heritability of traits at that level. Much of the literature on evolutionary transitions in individuality has focused on collective-level selection with some authors calling for a similar work to be carried out with respect to collective-level heritability. Starting from a model akin to Wilson's trait-group model I provide such an analysis. I show first that when a collective trait is a linear function of the lower (particle) level trait, collective-level heritability is a by-product of particle-level heritability. It is equal to particle-level heritability, whether the particles interact randomly or not to form collectives. Second, one effect of population structure is the reduction in variance of offspring collective-level char...

A high heritability estimate usually corresponds to a situation in which trait variation is largely caused by genetic variation. However, in some cases of gene-environment covariance, causal intuitions about the sources of trait difference can vary, leading experts to disagree as to how the heritability estimate should be interpreted. We argue that the source of contention for these cases is an inconsistency in the interpretation of the concepts ‘genotype’, ‘phenotype’, and ‘environment’. We propose an interpretation of these terms under which trait variance initially caused by genetic variance is subsumed into a heritability for all cases of gene-environment covariance.

Drift is often characterized in statistical terms. Yet such a purely statistical characterization is ambiguous for it can accept multiple physical interpretations. Because of this ambiguity it is important to distinguish what sorts of processes can lead to this statistical phenomenon. After presenting a physical interpretation of drift originating from the most popular interpretation of fitness, namely the propensity interpretation, I propose a different one starting from an analysis of the concept of drift made by Godfrey-Smith. Further on, I show how my interpretation relates to previous attempts to make sense of the notion of expected value in deterministic setups. The upshot of my analysis is a physical conception of drift that is compatible with both a deterministic and indeterministic world.

There are two ways evolution by natural selection (ENS) is conceptualized in the literature. One provides a 'recipe' for ENS incorporating three ingredients: variation, differences in fitness, and heritability. The other provides formal equations of evolutionary change and partitions out selection from other causes of evolutionary changes such as transmission biases or drift. When comparing the two approaches there seems to be a tension around the concept of heritability. A recent claim has been made that the recipe approach is flawed and should be abandoned. In this article, I show that the tension is only a superficial one. If one uses a concept of heritability strictly in line with the formal equations of evolutionary change, the recipe approach keeps its validity and generality. To demonstrate that the intuitive concept of heritability is not a general one, I use one formulation of the Price equation formulated by Okasha, show that the concept of heritability in his formulation incorporates both the intuitive notion of heritability as a measure of similarity between parent and offspring characters, and a measure of persistence. I advocate for persistence to be incorporated in the concept of heritability used in recipes for ENS in the same way heredity is, show that this is readily attainable and thereby dissolve any point of tension concerning heritability between the recipe and the analytical approach to ENS.

This thesis examines the theoretical and philosophical underpinnings of the concept of natural selection which is pervasively invoked in biology and other 'evolutionary' domains. Although what constitutes the process of natural selection appears to be very intuitive (natural selection results from entities exhibiting differences in fitness in a population), this conceals a number of theoretical ambiguities and difficulties. Some of these have been pointed out numerous times; others have hardly been noticed. One aim of this work is to unpack these difficulties and ambiguities; another is to provide new solutions and clarifications to them using a range of philosophical and conceptual tools. The result is a concept of natural selection stripped down from its biological specificities. I start by revisiting the entangled debates over whether natural selection is a cause of evolutionary change as opposed to a mere statistical effect of other causes, at what level this putative cause operates and whether it can be distinguished from drift. Borrowing tools from the causal modelling literature, I argue that natural selection is best conceived as a causal process resulting from individual level differences in a population. I then move to the question of whether the process of natural selection requires perfect transmission of types. I show that this question is ambiguous and can find different answers. From there, I distinguish the process of natural selection from some of its possible products, namely, evolution by natural selection and complex adaptation. I argue that reproduction and inheritance are conceptually distinct from natural selection, and using individual-based models, I demonstrate that they can be conceived as evolutionary products of it. This ultimately leads me to generalise the concepts of heritability and fitness used in the formal equations of evolutionary change. Finally, I argue that concepts of fitness and natural selection crucially depend on the grains of description at and temporal scales over which evolutionary explanations are given. These considerations reveal that the metaphysical status of the process of natural selection is problematic and why neglecting them can lead to flawed arguments in the levels of selection debate. Dedication À la mémoire de mon père, Michel, qui bien qu'il soit parti trop tôt m'a transmis sa curiosité Contents Abstract ....