Mechanisms of Evolution

Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont – that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome – be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part‐dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of the part (...) of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host‐relative or microbe‐relative. We support the claim that biological individuality is part‐dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the ‘demibiont’. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates. (shrink)

Generalized Darwinism models cultural development as an evolutionary process, where traits evolve through variation, selection, and inheritance. Inheritance describes either a discrete unit’s transmission or a mixing of traits. In this article, we compare classical models of cultural evolution and generalized population dynamics with respect to blending inheritance. We identify problems of these models and introduce our model, which combines relevant features of both. Blending is implemented as success-based social learning, which can be shown to be an optimal strategy.

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

This book offers a novel defence of a highly contested philosophical position: biological natural kind essentialism. This theory is routinely and explicitly rejected for its purported inability to be explicated in the context of contemporary biological science, and its supposed incompatibility with the process and progress of evolution by natural selection. Christopher J. Austin challenges these objections, and in conjunction with contemporary scientific advancements within the field of evolutionary-developmental biology, the book utilises a contemporary neo-Aristotelian metaphysics of "dispositional properties", or (...) causal powers, to provide a theory of essentialism centred on the developmental architecture of organisms and its role in the evolutionary process. By defending a novel theory of Aristotelian biological natural kind essentialism, Essence in the Age of Evolution represents the fresh and exciting union of cutting-edge philosophical insight and scientific knowledge. (shrink)

In Wilson (2019), I articulated and defended a version of the Westermarck Effect by developing a phylogenetic argument that has purchase within primatology but that has had more limited appeal for cultural anthropologists due to their commitment to conventionalist or culture-first accounts of incest avoidance. Here I look to advance the discussion of incest and incest avoidance beyond culture-first accounts in two ways. First, I shall dig deeper into the disciplinary grooves within cultural anthropology that make attractive the view that (...) incest has a naturalness to it that is countered only or primarily by explicit social rules, such as taboos. Second I further explore the emerging, post-conventionalist view of incest avoidance in a more positive vein by elaborating on the nature of the Westermarckian mechanism and how it relates to such explicit social rules and our innate biological endowments. One general aim here is to overcome the bifurcation between perspectives that are seen as biological and those seen as cultural, pre-empting or countering the claim that rejecting culture-first accounts entails a form of biological reductionism, a general aim I have pursued in related publications on bioessentialism about kinship (Wilson 2016a, 2016b). (shrink)

The Social Evolution of Human Nature: From Biology to Language. By Smit Harry.

James developed an evolutionary objection to epiphenomenalism that is still discussed today. Epiphenomenalists have offered responses that do not grasp its full depth. I thus offer a new reading and assessment of James’s objection. Our life-essential, phenomenal pleasures and pains have three features that suggest that they were shaped by selection, according to James: they are natively patterned, those patterns are systematically linked with antecedent brain states, and the patterns are “universal” among humans. If epiphenomenalism were true, phenomenal patterns could (...) not have been selected (because epiphenomenalism precludes phenomenal consciousness affecting reproductive success). So epiphenomenalism is likely false. (shrink)

The probability that the fitter of two alleles will increase in frequency in a population goes up as the product of N (the effective population size) and s (the selection coefficient) increases. Discovering the distribution of values for this product across different alleles in different populations is a very important biological task. However, biologists often use the product Ns to define a different concept; they say that drift “dominates” selection or that drift is “stronger than” selection when Ns is much (...) smaller than some threshold quantity (e.g., ½) and that the reverse is true when Ns is much larger than that threshold. We argue that the question of whether drift dominates selection for a single allele in a single population makes no sense. Selection and drift are causes of evolution, but there is no fact of the matter as to which cause is stronger in the evolution of any given allele. (shrink)

The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the main explanatory role. We defend the notion that symbiogenesis (...) is non-mechanistic in nature and that any attempt to explain some of the contemporary features of the eukaryotic cell mechanistically turns out to be at least insufficient and sometimes fails to address the question that is asked. Finally, we suggest that symbiogenesis is better understood as a pragmatic scientific law and present an alternative non-mechanistic model of scientific explanation. In the model we present, the use of scientific laws is supposed to be a minimal requirement of all scientific explanations, since the purpose of a scientific explanation is to make phenomena expectable. Therefore, this model would help to understand biologists’ appeal to the notion of symbiosis and thus is shown to be better, for the case under examination, than the mechanistic alternative. (shrink)

Although the concept of modularity is pervasive across fields and disciplines, philosophers and scientists use the term in a variety of different ways. This paper identifies two distinct ways of thinking about modularity, and considers what makes them similar and different. For philosophers of mind and cognitive science, cognitive modularity helps explain the capacities of brains to process sundry and distinct kinds of informational input. For philosophy of biology and evolutionary science, biological modularity helps explain the capacity of random evolutionary (...) processes to give rise to highly complex and sophisticated biological systems. Although these different ways of thinking about modularity are largely distinct, this paper proposes a unifying feature common to both: isolability, or the capacity of subsystems to undergo changes without resulting in substantial changes to neighboring or interconnected subsystems. (shrink)

Mechanisms are organized collections of objects and activities that underlie certain phenomena/behaviours. In this article, I shall argue that the organizations of mechanisms should be thought of as external relations, namely, as relations that do not entirely depend on their relata's existence, nor on their natures, nor on their intrinsic properties. After having introduced in the first two sections mechanisms and the ontology of relations, I shall analyse the organizations of mechanisms along four different dimensions: spatial, temporal, causal and hierarchical. (...) I shall demonstrate that each dimension requires that organizations be taken as external relations. Finally, in the last section, I shall anticipate and reply to two objections. (shrink)

The clonal evolution model and the cancer stem cell model are two independent models of cancers, yet recent data shows intersections between the two models. This article explores the impacts of the CSC model on the CE model. I show that CSC restriction, which depends on CSC frequency in cancer cell populations and on the probability of dedifferentiation of cancer non-stem cells into CSCs, can favor or impede some patterns of evolution and some processes of evolution. Taking CSC restriction into (...) account for the CE model thus has implications for the way in which we understand the patterns and processes of evolution, and can also provide new leads for therapeutic interventions. (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)

Gene drives are selfish genetic elements that use a variety of mechanisms to ensure they are transmitted to subsequent generations at greater than expected frequencies. Synthetic gene drives based on the clustered regularly interspersed palindromic repeats genome editing system have been proposed as a way to alter the genetic characteristics of natural populations of organisms relevant to the goals of public health, conservation, and agriculture. Here, we review the principles and potential applications of CRISPR drives, as well as means proposed (...) to prevent their uncontrolled spread. We also focus on recent work suggesting that factors such as natural genetic variation and inbreeding may represent substantial impediments to the propagation of CRISPR drives. CRISPR-based synthetic selfish genetic elements, or gene drives, have been proposed as a means by which to genetically alter natural populations to address issues in agriculture, conservation, and public health. We describe key concepts of CRISPR gene drives and limitations that must be addressed before their use in the wild. (shrink)

Evolution in its contemporary meaning in biology typically refers to the changes in the proportions of biological types in a population over time (see the entry on the concept of evolution to 1872 for earlier meanings). As evolution is too large of a topic to address thoroughly in one entry, the primary goal of this entry is to serve as a broad overview of contemporary issues in evolution with links to other entries where more in-depth discussion can be found. The (...) entry begins with a brief survey of definitions of evolution, followed by a discussion of the different modes of evolution and related philosophical issues, and ends with a summary of other topics in the philosophy of evolution focusing particularly on topics covered in this encyclopedia. (shrink)

The book discusses some of the stages in the development of genetics, biotechnology in terms of basic strategy of humanity towards the formation of a modern agrarian civilization. Agricultural civilization is seen as part of the biosphere and primary user of its energy flows. Consistently a steps of creation of management tools for live objects to increasing the number of food security of mankind are outlines. The elements of the biosphere degradation started in the results of human activities, and the (...) ways of their compensation. are discussed.The importance of the cooperation of experts in different areas of knowledge in the development of new approaches to the management of genetic resources of the planet is discussed too. (shrink)

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. (shrink)

In recent years, some have claimed that a Darwinian perspective will revolutionize the study of human society and culture. This project is viewed with disdain and suspicion, on the other hand, by many practicing social scientists. This article seeks to clear the air in this heated debate by dissociating two claims that are too often assumed to be inseparable. The first is the ‘ontological’ claim that Darwinian principles apply, at some level of abstraction, to human society and culture. The second (...) is the more ‘pragmatic’ claim that this observation necessitates substantial changes in the practices of social scientists. Even if some version of the first claim is true, I argue – which I believe is quite likely – the second does not follow. This observation ought to chasten the most overzealous advocates of Darwinian social science, as well as softening the instinctive resistance of many social scientists and historians to the genuine insights enabled by a Darwinian approach. The conclusion discusses these insights, the most important of which is a methodological prescription for normative theory. (shrink)

Doolittle :351–378, 2013) and Ereshefsky and Pedroso argue that selection can act at the level of biofilms and other microbial communities. Clarke is skeptical and argues that selection acts on microbial cells rather than microbial communities. Her main criticism is that biofilms lack one of the ingredients required for selection to operate: heritability. This paper replies to her concern by elaborating how biofilm-level traits can be inheritable.

Darwin's understanding of evolution as involving his original concept of natural selection involves discussions of development, progress, human pride, the construct o `primitivism,' and slavery. These discussions have to a remarkable extent been ignored by political theorists. This omission is all the more surprising in that these same discussions also call to mind Rousseau's often misunderstood concept of perfectibility.

It is desirable that the antecedents of existing, highly specialised, evolutionary mechanisms in animals be sought. The study of the lower Metazoa and especially of their simpler reproductive processes suggests that asexual reproduction is the primitive evolutionary mechanism from which the more advanced sexual mechanisms have evolved. A study of the metagenetic cycles of Coelenterata and Platyhelminthes seems to throw much light upon their prophylogeny and indicates that: Such cycles seem to provide the closest possible recapitulatory parallelism between phylogeny and (...) ontogeny. The Hydrozoa are ancestral to the other classes of Coelenterata. The polypoid adult is more primitive than the medusoid adult. The sporocysts, rediae and scolices represent the more primitive types of adults in their respective ontogenies and phylogenies.On avance la théorie qu'il y a eu une évolution des mécanismes évolutionnaires depuis les stades primitifs jusqu'aux stades avancés. D'après cette théorie les premières étapes dans l'évolution des Métazoaires inférieurs se sont effectuées par la reproduction asexuelle avant que les mecanismes sexuels très spécialisés se soient manifestés.Des preuves à l'appui de cette théorie découlent: de la rencontre actuelle d'une reproduction asexuelle chez des animaux, avec l'indication que sa simplicité est, dans la plupart des cas, originelle, et des cycles d'évolution des Coelentérés et Platyhelminthes qui sont métagénésiques. Leurs cycles peuvent s'interpréter comme partant de stades reproductifs asexuels pour évoluer vers des formes se reproduisant sexuellement.On croit que les organismes ne pouvant se reproduire que sexuellement sont plus avancés que ceux qui peuvent se reproduire asexuellement, ou à la fois sexuellement et asexuellement.Cette théorie a d'importantes implications pour l'étude de la métagenèse, de la récapitulation et de la phylogénie chez les Métazoaires inférieurs; elle exemplifie, dans l'étude de ces phénomènes, la nouvelle orientation qu'on a appelée Prophylogénie.In dieser Arbeit wird eine Theorie entwickelt, die besagt, dass eine Fortentwicklung der Evolutionsmechanismen von primitiven zu fortgeschrittenen Stufen besteht. Dieser Theorie nach haben sich die niedrigeren Metazoen ursprünglich nur ungeschlechtlich entwickelt und fortgepflanzt. Erst später haben sich die höchst spezialisierten geschlechtlichen Mechanismen entwickelt.Belege für diese Theorie sind: Noch heute kommt die geschlechtslose Fortpflanzung in Tieren vor, was dafür spricht, dass ihre Einfachheit in den meisten Fällen ursprünglich ist. Die Lebenskreisläufe der Metagenetischen Coelenteraten und Platyhelminthen lassen sich interpretieren als bestehend aus ursprünglich ungeschlechtlichen Fortpflanzungsstufen, die jedoch später in Formen mit geschlechtlicher Fortpflanzung übergehen.Es wird behauptet, dass Organismen mit nur geschlechtlicher Fortpflanzung weiter fortgeschritten sind als solche mit nur ungeschlechtlicher oder mit sowohl ungeschlechtlicher als auch geschlechtlicher Fortpflanzung.Diese Theorie ist wichtig für das Studium der Metagenese, Rekapitulation und Phylogenie in den niedrigen Metazoen und veranschaulicht die Prophylogenie, d.h. die neue Methode im Studium dieser Erscheinungen. (shrink)

From Arabidopsis and Antirrhinum to Arabia and Antioch: a review of cells to civilizations: the principles of change that shape life -/- Cells to Civilizations: The Principles of Change That Shape Life, Coen, E. 2012. Princeton University Press, Princeton, NJ. 312 pp. ISBN 978-0-691-14967-7.

Over the past decade philosophers of biology have discussed whether evolutionary theory is a causal theory or a phenomenological study of evolution based solely on the statistical features of a population. This article reviews this controversy from three aspects, respectively concerning the assumptions, applications, and explanations of evolutionary theory, with a view to arriving at a definite conclusion in each contention. In so doing I also argue that an implicit methodological assumption shared by both sides of the debate, namely the (...) overconfidence in conceptual analysis as a tool to understand the scientific theory, is the real culprit that has both generated the problem and precluded its solution for such a long time. (shrink)

Review of John Tyler Bonner: Randomness in Evolution. Princeton University Press, Princeton, 2013, 152 pp, £19.95 hbk, ISBN 978-0-691-15701-6.

For a population to undergo evolution by natural selection, it is assumed that the constituents of the population form parent-offspring lineages, that is, that they must reproduce. I challenge this assumption by dividing the notion of reproduction into two subprocesses, that is, multiplication and inheritance, that produce parent-offspring lineages between the parts of a population, and I show that their population-level roles, generation and memory, respectively, can be effected by processes that do not rely on such local-level lineages. I further (...) argue that these two population-level processes, not local parent-offspring lineages, are necessary conditions for a population to undergo Darwinian evolution. (shrink)

Analogies between Newtonian mechanics and evolutionary processes are powerful but not infinitely versatile tools for generating explanations of particular biological phenomena. Their explanatory range is sensitive to a preliminary decision about which processes count as background conditions and which as special forces. Here I argue that the defenders of the zero-force evolutionary law are mistaken in defending their decision as the only appropriate one. The Hardy–Weinberg principle remains a viable option that is consistent with the epistemic role of Newton’s own (...) first law, and the strengths and weaknesses of each analogy are sufficiently distinct to justify their continued coexistence. (shrink)

In this paper, I discuss the concept of complexity. I show that the principle of natural selection as acting on complexity gives a solution to the problem of reconciling the seemingly contradictory notion of generally increasing complexity and the observation that most species don’t follow such a trend. I suggest the process of evolution to be illustrated by means of a schematic diagram of complexity versus time, interpreted as a form of the Tree of Life. The suggested model implies that (...) complexity is cumulatively increasing, giving evolution a direction, an arrow of time, thus also implying that the latest emerging species will be the one with the highest level of complexity. Since the human species is the last species evolved in the evolutionary process seen at large, this means that we are the species with the highest complexity. The model implies that the human species constitutes an integral part of organic evolution, yet rendering us the exclusive status as the species of the highest complexity. (shrink)

The Hardy–Weinberg equilibrium has been argued by Sober, Stephens and others to represent the zero-force state for evolutionary biology understood as a theory of forces. I investigate what it means for a model to involve forces, developing an explicit account by defining what the zero-force state is in a general theoretical context. I use this account to show that Hardy–Weinberg equilibrium is not the zero-force state in biology even in the contexts in which it applies, and argue based on this (...) that drift should not be understood as an evolutionary force. (shrink)

What is the boundary between the animate and inanimate world? It is obvious that the animate world is under rules of inanimate world. Is the converse true? This paper is aimed at imposing the well-known Darwin's theory of evolution to inanimate world of atomic realm where bizarre behavior of electron challenges our everyday perception of inanimate world. This paper, suggests a weird, peculiar and highly elegant speculation of existing, leads suspicious about validity of the law of conservation of mass, provides (...) conceptual foundation for many odd explanations of quantum mechanics such wave-particle duality of elementary particles, the inherent randomness and probabilistic nature of world as quantum mechanics states, the Louis de Broglie proposition of wave-like behavior of moving particles, Schrödinger's wave function description of probability of finding electron at any location around the nucleus and even the roots of causality. It defines existence as follows: "All the elementary particles emerge spontaneously and randomly in space where the possibility of conforming the physical laws is higher and after appearing if they not conform the laws of physics, they vanish." It proposes, the emerging from nothing, as a natural process and in other word there is an inherent urge to existence not only for animate world but also for inanimate world. Assuming the correctness of the proposed speculation, leads to dramatic development of human perception of existing, reality and interaction with world. (shrink)

Here I advance two related evolutionary propositions. (1) Natural selection is most often considered to require competition between reproducing “individuals”, sometimes quite broadly conceived, as in cases of clonal, species or multispecies-community selection. But differential survival of non-competing and non-reproducing individuals will also result in increasing frequencies of survival-promoting “adaptations” among survivors, and thus is also a kind of natural selection. (2) Darwinists have challenged the view that the Earth’s biosphere is an evolved global homeostatic system. Since there is only (...) one biosphere, reproductive competition cannot have been involved in selection for such survival-promoting adaptations, they claim. But natural selection through survival could reconcile Gaia with evolutionary theory. (shrink)

A number of recent discussions have argued that George Price's equationfor representing evolutionary change is a powerful and illuminatingtool, especially in the context of debates about multiple levels ofselection. Our paper dissects Price's equation in detail, and comparesit to another statistical tool: the calculation and comparison ofaverage fitnesses. The relations between Price's equation and equationsfor evolutionary change using average fitness are closer than issometimes supposed. The two approaches achieve a similar kind ofstatistical summary of one generation of change, and they (...) achieve thisvia a similar loss of information about the underlying fitnessstructure. (shrink)