Emergence in Biology

Bedau's influential (1997) account analyzes weak emergence in terms of the non-derivability of a system’s macrostates from its microstates except by simulation. I offer an improved version of Bedau’s account of weak emergence in light of insights from information theory. Non-derivability alone does not guarantee that a system’s macrostates are weakly emergent. Rather, it is non-derivability plus the algorithmic compressibility of the system’s macrostates that makes them weakly emergent. I argue that the resulting information-theoretic picture provides a metaphysical account of (...) weak emergence rather than a merely epistemic one. (shrink)

Inhere we expand the concept of Holobiont to incorporate niche construction theory in order to increase our understanding of the current planetary crisis. By this, we propose a new ontology, the Ecobiont, as the basic evolutionary unit of analysis. We make the case of Homo Sapiens organized around modern cities (technobionts) as a different Ecobiont from classical Homo Sapiens (i.e. Hunter- gatherers Homo Sapiens). We consider that Ecobiont ontology helps to make visible the coupling of Homo Sapiens with other biological (...) entities under processes of natural and cultural evolution. Not to see this coupling hidden systemic risks and enhance the probability of catastrophic events. So Ecobiont ontology is necessary to understand and respond to the current planetary crisis. -/- . (shrink)

Sciences of complex systems thrive on compositional theories – toolkits that allow the construction of models of a wide range of systems, each consisting of various parts put together in different ways. To be tractable, a compositional theory must make shrewd choices about the parts and properties that constitute its basic ontology. One such choice is to decompose a system into spatiotemporally discrete parts. Compositional theories in the high-level sciences follow this rule of thumb to a certain extent, but they (...) also make essential use of what I call distributed ontologies: divisions of the system into entities or states of affairs each depending on sets of fundamental-level facts that to a large extent overlap. The point is developed using the example of statistical theories in which the probabilities are ontologically distributed. (shrink)

Species’ adaptation to their environments occurs via a range of mechanisms of adaptation. These include genetic adaptations as well as non-traditional inheritance mechanisms such as learned behaviors, niche construction, epigenetics, horizontal gene transfer, and alteration of the composition of a host’s associated microbiome. We propose to supplement these with another modality of eco-evolutionary dynamics: cases in which adaptation to the environment occurs via what may be called a “distributed adaptation,” in which the adaptation is not conferred via something carried by (...) an individual of the adapted species (as with genes, behavior, or associated microbes), but by some structural or compositional aspect of the population. Put differently, the adaptively relevant information cannot be reduced to information possessed by a single individual, whether genetic or otherwise. Rather, the adaptively relevant information is distributed, and is found strictly at the population level. While human culture is presumably such a case, as may be cases found in social insects, we want to suggest that there are other cases that belong to this category and to explore its evolutionary implications. In particular, we discuss the factors that affect whether adaptive information is stored in a distributed way, to what degree, and what kinds of adaptive information are most likely to be found in this modality of adaptation. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...) employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

Debates concerning the units and levels of selection have persisted for over fifty years. One major question in this literature is whether units and levels of selection are genuine, in the sense that they are objective features of the world, or merely reflect the interests and goals of an observer. Scientists and philosophers have proposed a range of answers to this question. This Element introduces this literature and proposes a novel contribution. It defends a realist stance and offers a way (...) of delineating genuine levels of selection by invoking the notion of a functional unit. (shrink)

In recent decades, several theories have claimed to explain the teleological causality of organisms as a function of self-organising and self-producing processes. The most widely cited theories of this sort are variations of autopoiesis, originally introduced by Maturana and Varela. More recent modifications of autopoietic theory have focused on system organisation, closure of constraints and autonomy to account for organism teleology. This article argues that the treatment of teleology in autopoiesis and other organisation theories is inconclusive for three reasons: First, (...) non-living self-organising processes like autocatalysis meet the defining features of autopoiesis without being teleological; second, organisational approaches, whether defined in terms of the closure of constraints, self-determination or autonomy, are unable to specify teleological normativity, that is, the individuation of an ultimate beneficiary; third, all self-organised systems produce local order by maximising the throughput of energy and/or material (obeying the maximum entropy production (MEP) principle) and thereby are specifically organised to undermine their own critical boundary conditions. Despite these inadequacies, an alternative approach called teleodynamics accounts for teleology. This theory shows how multiple self-organising processes can be collectively linked so that they counter each other’s MEP principle tendencies to become codependent. Teleodynamics embraces – not ignoring – the difficulties of self-organisation, but reinstates teleology as a radical phase transition distinguishing systems embodying an orientation towards their own beneficial ends from those that lack normative character. (shrink)

How we ought to diagnose, categorise and respond to spectrum disabilities such as autism and Attention Deficit/Hyperactivity Disorder (ADHD) is a topic of lively debate. The heterogeneity associated with ADHD and autism is described as falling on various continua of behavioural, neural, and genetic difference. These continua are varyingly described either as extending into the general population, or as being continua within a given disorder demarcation. Moreover, the interrelationships of these continua are likewise often vague and subject to diverse interpretations. (...) -/- In this paper, I explore geneticists' and self-advocates’ perspectives concerning autism and ADHD as continua. These diagnoses are overwhelmingly analysed as falling on a continuum or continua of underlying traits, which supports the notion of “the neurodiversity spectrum”, i.e., a broader swath of human neural and behavioural diversity on which some concentrations of different functioning are diagnosed. I offer a taxonomy of conceptions of the genetic, phenotypic, and endophenotypic dimensionality within and beyond these diagnostic categories, and suggest that the spectrum of neurodiversity is characteristically endophenotypic. (shrink)

Islam gives legal precedence to purity of lineage and known parenthood of all children. In Islam treatment to infertility using IVF is permitted within validity of marriage contract with no genes mixing. The paper shows that the Qur’ān, the word of Allah, and science, the deeds of Allah are not in major conflicts in defining the start of human life. The Holy Qur’ān provides an elegant description of origin, developmental stages of intra-uterine life. The Hadith explains two positions one that (...) believes human embryo get ensouled at conception and the other after 40 days of conception. The paper aims to find that Islam confers moral respect to human embryo, but it also clarifies the absence of full human rights to a developing foetus. In Islam, human embryonic use is probably permissible for therapeutic and reproductive purpose keeping intact the principles of Shari’ah. (shrink)

Negli ultimi anni, il richiamo al concetto di emergenza si è fatto sempre più diffuso in molte aree della filosofia e della scienza. Il termine viene usato per riferirsi alla circostanza in cui un sistema (fisico, chimico, biologico, ma anche sociale) manifesta delle proprietà e dei comportamenti che sembrano nuovi rispetto a quelli delle sue parti più semplici. Questo libro si propone di chiarire questo fenomeno, tenendo conto, da un lato, che le discipline coinvolte nel dibattito sono molte, quindi un (...) approccio univoco all'emergenza potrebbe non bastare e, dall'altro, che per comprendere cosa sia l'emergenza è necessario delinearne le relazioni con altre questioni filosofiche di primaria importanza come quelle che coinvolgono la fondamentalità, la complessità e la causalità. (shrink)

Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...) Darwinism, is logically inconsistent. This has been demonstrated in some of my latest academic publications. The entire conceptual framework of Darwinism is inadequate. Organisms do not compete with each other for the survival of the fittest. The fundamental relationship in Nature is not competition or confrontation, but interconnectivity, complementarity, and relational meaningfulness. A new theory of evolution is necessary to explain how it is possible that organisms as simple as bacteria, protozoa and diatoms could have generated organisms as complex as primates, and among them, the human being, a being capable of feeling and thinking, of suffering and enjoying, a being capable of having ideals and purposes. A theory that explains how it is possible that this being so complex, rich, and to some extent still unknown, has emerged from a single cell, an egg-cell, lacking all the capacities, riches and depths of human existence. Such a theory already exists. (shrink)

This paper proposes an integrated-structure notion of interlevel emergence, from a dynamic relational ontological perspective. First, I will argue that only the individualist essentialism of atomistic metaphysics can block the possibility of interlevel emergence. Then I will show that we can make sense of emergence by recognizing the formation of structures of transformative and interdependent causal relations in the generation and development of a particular class of mereological complexes called integrated systems. Finally, I shall argue that even though the emergent (...) structural attributes of such systems are not micro-determined nor micro-reducible, they can still be accounted for by an interlevel integrative neo-mechanistic form of explanation. (shrink)

The notion of a physiological individuals has been developed and applied in the philosophy of biology to understand symbiosis, an understanding of which is key to theorising about the major transition in evolution from multi-organismality to multi-cellularity. The paper begins by asking what such symbiotic individuals can help to reveal about a possible transition in the evolution of cognition. Such a transition marks the movement from cooperating individual biological cognizers to a functionally integrated cognizing unit. Somewhere along the way, did (...) such cognizing units simultaneously have cognizers as parts? Expanding upon the multiscale integration view of the Free Energy Principle, this paper develops an account of reciprocal integration, demonstrating how some coupled biological cognizing systems, when certain constraints are met, can result in a cognizing unit that is in ways greater than the sum of its cognizing parts. Symbiosis between V. Fischeri bacteria and the bobtail squid is used to provide an illustration this account. A novel manner of conceptualizing biological cognizers as gradient is then suggested. Lastly it is argued that the reason why the notion of ontologically nested cognizers may be unintuitive stems from the fact that our folk-psychology notion of what a cognizer is has been deeply influenced by our folk-biological manner of understanding biological individuals as units of reproduction. (shrink)

The central question in the biological sciences for the past 100 years has concerned an understanding of how living systems differ from other general physical phenomena and what makes these systems unique. With new developments in the fields of nonequilibrium thermodynamics, systems theory, chaos, and information theory over the past few decades, there has been growing interest in finally answering the question first posed by Erwin Schrödinger in the 1940s concerning the true scientific nature of living systems. Similarly, there is (...) also increasing interest within the biologic community for a more holistic and non-reductionist methodology. The approach followed in this book builds on a foundation of information theory and semiotics while integrating basic thermodynamic considerations and systems theory to form a singular unifying concept that is proposed to be the essential process of living systems. However, the premise presented is much more than simply the exposition of a new hypothesis. This book describes the logical progression of thought incorporating a diverse array of established scientific ideas that were used in the conceptualization of a dynamic mathematical framework that can be employed as a novel analytic means for the study of living systems and their fundamental processes. (shrink)

Contemporary philosophy of science has seen a growing trend towards a focus on scientific practice over the epistemic outputs that such practices produce. This practice-oriented approach has yielded a clearer understanding of how reductive research strategies play a central role in contemporary scientific inquiry. In parallel, a growing body of work has sought to explore the role of non-reductive, or systems-level, research strategies. As a result, the relationship between reductive and non-reductive scientific practices is becoming of increased importance. In this (...) paper, I provide a framework within which research strategies can be compared. I argue that no strategy is reductive or non-reductive simpliciter, rather strategies are more, or are less, reductive than one another according to a frame of reference. That frame of reference is provided by a continuum of possible ways in which the target system might be conceptualised. I illustrate the utility of the framework by deploying it to analyse a recent debate in cancer research. When set within the framework, a prominent reductive strategy—the somatic mutation theory—and a prominent non-reductive strategy—the tissue organisational field theory—do not stand opposed to one another. Rather, they serve as boundary markers to chart the territory of approaches to carcinogenesis within which most strategies in the field fall. (shrink)

In this work the doctrine of organicism will be addressed, as explained and seen mainly by Bertalanffy. We will study how this doctrine represents and embodies the ambiguity of Kantian teleology as a regulative principle, and how this same problem leads to consider a real problem as a knowledge problem. It will be concluded that organicism, conceived in this way, does not represent a true holism, but what we will call a syn-holism, a synthesis or assembly, and that to obtain (...) a true holism we must resort to the concept of true form. Finally, it will be established that since the fundamental characteristic of an organism is its development, a historical theory of the organism is required for which the concept of field can be useful and necessary. (shrink)

Does the Big History of life on Earth disclose a trajectory that has been driven by selection? If so, will the trajectory continue to apply into the future? This paper argues that such a trajectory exists, and examines some of its key implications. The most important consequence is that humanity can use the trajectory to guide how it evolves and adapts into the future. This is because the trajectory identifies a sequence of adaptations that will be favoured by selection. If (...) humanity intentionally evolves its social systems and psychological capacities so that they follow the trajectory, humanity can avoid negative selection and instead survive and thrive indefinitely into the future. This would enable humanity to make a positive contribution to the future evolution of life in the universe. But it turns out that immediate selection will not drive the evolution of life on Earth further along this trajectory. Instead, intentional action by humanity is necessary. It is as if the evolution of life on any planet is a developmental process that has a very unusual characteristic: evolution will continue to develop successfully beyond a certain point only if it produces a sentient organism that: (i) awakens to the possibility it is embedded in a developing process; (ii) realizes that this developing process will continue successfully only if it chooses to intentionally drive the process forward; and (iii) commits to doing whatever is necessary to achieve this. On this planet, humanity is that sentient organism. The existence of such a key evolutionary role for humanity is capable of providing humanity with meaning and purpose in a larger scheme of things. For individuals who commit to driving the process forward, the nature of the trajectory has immediate consequences for what they should do with their lives, here and now. (shrink)

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms (...) of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...) been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what (...) the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems. (shrink)

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)

Description courte (Électre, 2019) : Une étude d'un des principaux axes de réflexion du philosophe des sciences et de la nature Raymond Ruyer (1902-1987). À la lumière des découvertes de l'embryogenèse et en s'appuyant par ailleurs sur la théorie de l'information, il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. -/- Short Descriptor (Electre 2019): A study of one of the main axes of reflection of the French philosopher of science and of nature Raymond Ruyer (1902-1987). Relying on (...) the discoveries about embryogenesis, and also with the use of information theory, Ruyer proposed an interpretation of the main unifying concepts of mechanistic cybernetics. -/- Cet ouvrage propose une étude fouillée d'un des principaux axes de réflexion du philosophe des sciences et de la nature français Raymond Ruyer (1902–1987) : la cybernétique. Après avoir proposé une philosophie structuraliste, Ruyer la modifia à la lumière des découvertes de l'embryogenèse, puis il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. Réfléchissant sur cette dernière et sur la théorie de l'information, en particulier sur l'origine de l'information, il défendit que cette cybernétique n'était qu'une lecture inversée de la vraie cybernétique, qui nous donnerait de lire dans l'expérience même les traces du pouvoir morphogénétique, appréhendé comme un champ axiologique. Dans un texte résumant son propre parcours, Ruyer affirma finalement que la critique de la théorie de l'information « peut donner […] l'espoir d'aboutir à quelque chose comme une nouvelle théologie. » Les idées directrices de Ruyer sont tout particulièrement contextualisées ici à partir de la question du développement des formes en biologie, et de celles de la génétique, de la genèse stochastique de l'ordre, et de l'identification mentale ou physique de l'information. Il se termine en départageant ce qui est théologique et axiologique dans ce projet de métaphysique qui, bien que resté inachevé, n'en représente pas moins le plus impressionnant conçu en France au siècle dernier. – This book offers an in-depth study of one of the main axes in the reflection of French philosopher of science and nature Raymond Ruyer. In a text summarising his own development, Ruyer stated about the philosophical critique of information theory that it "is what can give the most long-lasting hope of getting to something like a new theology." After propounding a structuralist philosophy, and distinguishing between form and structure, to then modify it in the light of discoveries in embryogenesis, Ruyer offered a re-evaluation of the unifying concepts of mechanistic cybernetics. Thinking about it and about information theory, he defended the idea that this cybernetics was in reality an inverted reading of the real one, which would allow us to read in experience itself traces of the morphogenetic power, apprehended as the axiological field. On some transversal points, the development of forms in biology and genetics, the stochastic genesis of order, the identification of information with either psychological and mental, or physical reality, behaviour, and the access to meaning, this work exposes the main ideas of Ruyer while situating them in the context of the breadth of others' contributions. It ends by determining what is theological and axiological in this project for a metaphysics which, although unfinished, is nevertheless the most impressive effort done in France in the last century. – Available on i6doc dot com (ISBN 978-2-930517-56-8 ; pdf 978-2-930517-57-5). (shrink)

Starting with the observation that there exist contradictory claims in the literature about the relationship between vitalism and emergentism—be it one of inclusion or, on the contrary, exclusion–, this paper aims at disentangling the vitalism–emergentism knot. To this purpose, after having described a particular form of emergentism, namely Lloyd Morgan’s emergent evolutionism, I develop a conceptual analysis on the basis of a distinction between varieties of monism and pluralism. This analysis allows me to identify and characterize several forms of vitalism (...) and emergentism, and a subsequent comparison between these forms constitutes the occasion for a clarification of the relationship between both doctrines. (shrink)

Brute facts are facts that don't have explanations. They are instrumental in our attempts to give accounts of other facts or phenomena, and so they play a key role in many philosophers' views about the structure of the world. This volume explores neglected questions about the nature of brute facts and their explanatory role.

Some claim that the notion of strong emergence as involving ontological or causal novelty makes no sense, on grounds that any purportedly strongly emergent features or associated powers 'collapse', one way or another, into the lower-level base features upon which they depend. Here we argue that there are several independently motivated and defensible means of preventing the collapse of strongly emergent features or powers into their lower-level bases, as directed against a conception of strongly emergent features as having fundamentally novel (...) powers. After introducing the project (Section 1), we motivate and present the powers-based account (Section 2); we then canvass the two main versions of the collapse objection, show how these apply to the powers-based account, and problematize certain strategies of response (Section 3); we then present and defend four better strategies of response (Section 4). (shrink)

Providing empirically supportable instances of ontological emergence is notoriously difficult. Typically, the literature has focused on two possible sources. The first is the mind and consciousness; the second is within physics, and more specifically certain quantum effects. In this paper, I wish to suggest that the literature has overlooked a further possible instance of emergence, taken from the special science of linguistics. In particular, I will focus on the property of truth-evaluability, taken to be a property of sentences as created (...) by the language faculty within human minds (or brains). The claim will not be as strong as to suggest that the linguistic data and theories prove emergence. Rather the dialectical aim here is to say that we have some good reasons (even if not conclusive reasons) to think that the property is emergent. (shrink)

The Einstein of the New Age holds forth in his unique and brilliant style on the history of world views and how to put spirit back in our life. If you have the patience to learn his jargon and read slowly there is alot of serious brainfood here. I read this and his Sex, Ecology and Spirituality(1995) with Hofstadter´s famous Godel, Escher, Bach(GEB) written in 1980(both of which I have reviewed here). Wilber´s work has many parallels with GEB, both of (...) them massive works attempting to tie together disparate fields and different views of life. Unlike Hofstadter, who was mainly interested in the nature of intelligence, Wilber does not treat math, music or DNA, and he concentrates on world views that have a spiritual relevance but like Hofstadter he lacks any grasp of the logical structure of rationality, the dual systems of thought or the works of Wittgenstein and Searle, which obviates much of his work. For an account of those see my articles. He spent a vast amount of time working out the relationships between ideas and how they relate to individual and society, spirit and science. If you don´t have the time or patience for the whole book, read Superconsciousness Parts 1 and 2 which are an excellent summary. His shortest book, `The Marriage of Self andSoul is a much easier read that gives you a good idea of his style and purpose. He details alot of intellectual history (philosophy, psychology, religion, ecology, feminism, sociology, etc) and shows where nearly everyone went too far in the direction of Ascent (to the spirit) or Descent (to science,materialism, reductionism or Flatland). He trys to show how to heal the rifts by combining sense and soul (spiritual and material life, science and religion, internal and external, individual and social). Everything is related to everything else (holons in holarchies). The Age of Enlightenment denied the the spirit, the individual and the interior life but developed art, morals and science and led to democracy, feminism, equality and ecology, but this reductionism compressed the intellect and the spirit into the Flatland of science, rationality and materialism. He sees the loss of the spiritual point of view with the Age of Enlightenment as the major factor responsible for the malaise of modern times, but real spirituality or ìntelligent religion (i.e., the quest for enlightenment) as opposed to primitive religion (everything else-see my review of Boyer´s 'Religion Explained') was always rare. It is intelligent religion he sees as the panacea, but it is primitive religion that the masses understand, and it too has only materialistic goals. In sum, in spite of its shortcomings it is still unique and well worth the effort. -/- Those wishing a comprehensive up to date framework for human behavior from the modern two systems view may consult my book ‘The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle’ 2nd ed (2019). Those interested in more of my writings may see ‘Talking Monkeys--Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet--Articles and Reviews 2006-2019 3rd ed (2019), The Logical Structure of Human Behavior (2019), and Suicidal Utopian Delusions in the 21st Century 4th ed (2019). (shrink)

You can get a quick summary of this book on p 135 or 326. If you are not up to speed on evolutionary psychology you should first read one of the numerous recent texts with this term in the title. One of the best is " The Handbook of Evolutionary Psychology " by Buss, but it is big and expensive. Until about 15 years ago, ´explanations´´of behavior have not really been explanations of mental processes at all, but rather vague and (...) largely useless descriptions of what people did and what they said, with no insight into why. We might say that people gather to commemorate an event, praise god, receive his (or her or their) blessings, etc, but none of this describes the relevant mental processes so we might say they are explanations in much the same way that it explains why an apple drops to the ground if we say its because we released it and it's heavy-there is no mechanism and no explanatory or predictive power. This book continues the elucidation of the genetic basis of human behavior which has been almost univerally ignored and denied by academia, religion, politics and the public(see Pinker´s excellent book``The BlankSlatè`). His statement (p3) that it is meaningless to ask if religion is genetic is mistaken as the percentage of variation due to genes and environment can be studied, just as they are for all other behaviors (see eg. Pinker). The title should be "Preliminary Attempts to Explain Some Aspects of Primitive Religion" since he does not treat higher consciousness at all (e.g., satori, enlightenment etc.) which are by far the most interesting phenomena and the only part of religion of personal interest to intelligent, educated people in the 21st century. Reading this entire book, you would never guess such things exist. Likewise for the immense field of drugs and religion. It lacks a framework for rationality and does not mention the dual systems of thought view which is now so productive. For these I suggest my own recent papers. Nevertheless, the book has much of interest and in spite of being dated is still worth reading. -/- Those wishing a comprehensive up to date account of Wittgenstein, Searle and their analysis of behavior from the modern two systems view may consult my article The Logical Structure of Philosophy, Psychology, Mind and Language as Revealed in Wittgenstein and Searle (2016). Those interested in all my writings in their most recent versions may download from this site my e-book ‘Philosophy, Human Nature and the Collapse of Civilization Michael Starks (2016)- Articles and Reviews 2006-2016’ by Michael Starks First Ed. 662p (2016). -/- All of my papers and books have now been published in revised versions both in ebooks and in printed books. -/- Talking Monkeys: Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet - Articles and Reviews 2006-2017 (2017) https://www.amazon.com/dp/B071HVC7YP. -/- The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle--Articles and Reviews 2006-2016 (2017) https://www.amazon.com/dp/B071P1RP1B. -/- Suicidal Utopian Delusions in the 21st century: Philosophy, Human Nature and the Collapse of Civilization - Articles and Reviews 2006-2017 (2017) https://www.amazon.com/dp/B0711R5LGX . (shrink)

This Letter to the Editor is a comment on a paper by Rodríguez Higuera (Biosemiotics 9, 155–167, 2016) that refers to a paper by van Hateren (Biosemiotics 8, 403–419, 2015). The comment argues that semiosis (i.e., the making of meaning) has biological roots in an internal process X occurring within all forms of life. This internal process produces, in effect, an approximation (i.e., an estimate) of the fitness of an organism. X subsequently drives a purely stochastic process of structural change (...) within the organism. This results in primordial forms of semiosos, agency, and aboutness. It is argued that the way this is produced should be regarded as a form of strong emergence, because it results in novel causal powers that are not equivalent to the combined causal powers of the composing parts of the system. -/- . (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

Life poses a threat to materialism. To understand the phenomena of animate nature, we make use of a teleological form of explanation that is peculiar to biology, of explanations in terms of what I call the ‘vital categories’ – and this holds even for accounts of underlying physico-chemical ‘mechanisms’. The materialist claims that this teleological form of explanation does not capture what is metaphysically fundamental, whereas her preferred physical form of explanation does. In this essay, I do three things. (1) (...) I argue that the ‘vital categories’, such as life form and life-process, do not reduce to the ‘physical categories’ and show that there are no grounds for the materialist's metaphysically limiting claim; (2) I sketch a positive view on how vital and physical explanations can both apply to a given phenomenon, and on how they interrelate; and (3) I show that this view meshes nicely with evolutionary theory, despite being committed to a form of ‘biological essentialism’. (shrink)

In this paper, I argue for the usefulness of pragmatism as a framework within which to develop the theological application of emergentist theory. I consider some philosophical issues relevant to the recent revival of interest, across various disciplines, in the concept of emergence and clarify some of the conceptual issues at stake in the attempts to formulate the philosophical position of emergentism and to apply it theologically. After highlighting some major problems arising from the main existing ways of formulating emergentism, (...) I build on the work of Sami Pihlström, outlining a less problematic, alternative proposal. I attempt to show that the philosophical problems can be circumvented by an appeal to the pragmatist tradition, which is a useful philosophical framework within which to develop an emergentist theory fit for theological application. (shrink)

Nicht Stabilität, sondern Instabilität sei der Grundcharakter der Natur, so hören wir von Jan Schmidt als Auftakt zu seinem Buch „Das Andere der Natur“ (Hirzel-Verlag, 2015). „Das Eine der Natur“, welches reduktionistisch zu erfassen ist, soll durch ein „Anderes“ ergänzt werden. Von dieser anderen Seite her zeigt sich „Natur ... auch (als) instabil, komplex, chaotisch, zufällig, emergent...“, und aus dieser Sicht des Naturgeschehens heraus will der Autor eine Philosophie der Instabilität entwerfen. Der gelernte Physiker und Philosoph lehrt an der Hochschule (...) Darmstadt (hda) Wissenschafts- und Technikphilosophie. Sein Buch beleuchtet das Thema „Instabilitäten“ aus vielen Blickwinkeln. Was sind Instabilitäten, was Selbstorganisation, was ist Zeit, was Zufall, was Kausalität? Diese Erkenntnisse bezieht der Autor dann auf den Kosmos, auf die Evolution bis hin zum menschlichen Gehirn und seinen Leistungen. Mit dieser Rezension gehe ich ausführlich auf dieses lesenswerte Buch ein. (shrink)

Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems (MACS). While taking the emergence of properties seriously, the notion of MACS enables at the same time the design (or “meta-design”) of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied (...) in the field of Artificial Life, the specificity of MACS essentially lies in the close relation between their emergent properties and functional properties. Second, we argue that to be a MACS a system does not need to display more than weak emergent properties. Third, since the notion of weak emergence is based on the possibility of simulation, whether computational or mechanistic via machines, we see MACS as good candidates to help design artificial self-architected systems (such as robotic swarms) but also harness and redesign living ones (such as synthetic bacterial films). (shrink)

Motivated by the seeming structure of the sciences, metaphysical emergence combines broadly synchronic dependence coupled with some degree of ontological and causal autonomy. Reflecting the diverse, frequently incompatible interpretations of the notions of dependence and autonomy, however, accounts of emergence diverge into a bewildering variety. Here I argue that much of this apparent diversity is superficial. I first argue, by attention to the problem of higher-level causation, that two and only two strategies for addressing this problem accommodate the genuine emergence (...) of special science entities. These strategies in turn suggest two distinct schema for metaphysical emergence---'Weak' and 'Strong' emergence, respectively. Each schema imposes a condition on the powers of entities taken to be emergent: Strong emergence requires that higher-level features have more token powers than their dependence base features, whereas Weak emergence requires that higher-level features have a proper subset of the token powers of their dependence base features. Importantly, the notion of “power” at issue here is metaphysically neutral, primarily reflecting commitment just to the plausible thesis that what causes an entity may bring about are associated with how the entity is---that is, with its features. (shrink)

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...) the cultures is necessary for understanding how they collaborate or compete, and how they are fragmented or integrated, in the rich interdisciplinary /trading zone/ (Galison 1997) of Evo-Devo. Evo-Devo is an important example of how science can progress through a radical plurality of perspectives and cultures. (shrink)

This thesis contributes to the growing literature surrounding the importance of weak emergence by showing it can account for more phenomena than originally conceived via the use of computational reduction. Weak emergence refers to unpredictable higher-level phenomena that are reducible to lower-level phenomena. The ability of weak emergence to reduce higher-level phenomena to their lower-level constituents is useful for establishing a mechanistic explanation of emergent features. The tension between holistic higher-level phenomena and lower-level parts is a classic argument in philosophy (...) and investigating emergent phenomena is one means of furthering the discussion. In particular I will look at theories of emergence and computational analysis related to systems biology. Systems biology uses modern computational analysis to model naturally occurring interactions of higher-level elements and, in combination with synthetic biology, can trace complex macro-level interactions back to micro-level occurrences without explanatory loss. What makes this interesting is that systems biology is able to explain and reduce phenomena that were once considered strongly emergent, therefore shrinking the number of phenomena we consider strongly emergent. Furthermore, systems biology offers a compelling milieu for philosophers to contribute to scientific discourse and vice versa. Hence, it is a worthwhile endeavor for philosophers to test their theories of emergence against actual practice as a way to inform their concepts. I will use examples traditionally considered strongly emergent to show that these cases can in fact be reduced and categorized as weakly emergent because they are unpredictable but not irreducible. The reclassification of these phenomena challenges strong emergence, and reveals it to be an ‘Emergence of the Gaps’ whereby the number of phenomena strong emergence can describe decreases in an inversely proportional relationship to increased computational capacity. (shrink)

Book Review of "Trinity in Relation: Creation, Incarnation, and Grace in an Evolving Cosmos" by Gloria L. Schaab.

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that (...) is incompressible and its behavior cannot be derived except by crawling through all of the gory details of the interactions in the web. The central thesis of this article is that synthetic biology centrally is the activity of engineering the desired weak emergent properties of synthetic cells. Synthetic biology has many different ways to engineer desired weak emergent properties of synthetic cells, including Edisonian trial and error, standardized parts, refactoring, and reprogramming synthetic genomes. The article ends by noting two philosophical consequences of engineering weak emergence. One is epistemological: synthesis is crucial for discovering weak emergent properties. The other is metaphysical: simple life forms are nothing but complex chemical mechanisms. (shrink)

In the framework of population dynamics, we start from the logistic equation describing the evolution of one species with limited food supply. A split device allows us to consider the population as two sub-populations x and y evolving analogously. The dynamical system has a one-parameter family of equilibria which is structurally unstable. Then small perturbations of the system lead in general to a new system involving a fast and a slow dynamics with a finite number of equilibria. In simple situations (...) where the differentiation is clearly either an advantage or an inconvenience for one of the subspecies, the stable equilibrium amounts to extinction of the disadvantaged subspecies. Oppositely more complex differentiations often lead to stable equilibria with well-defined non zero proportions of the sub-populations. Other examples are concerned with symbiosis-like differentiations, leading to preservation, whereas the opposite case has an unstable equilibrium and lead to extinction of one or the other subspecies according to the initial conditions. The case of a scission into three subspecies is more rich in consequences. In certain cases, predator-prey relations lead to auto-organization phenomena with stable diversity-preserving diversity. Cases of instability are also possible, leading to orbits tending towards a poly-cycle.This implies some kind of pseudo-extinction: this amounts to “pseudo-periodic-like” orbits with “pseudo-periods” larger and larger, tending to infinity; each pseudo-period contains parts where one of the sub-populations practically vanish. Other non-linear perturbations lead to stable orbits. (shrink)

The Emergic Cognitive Model (ECM) is a unified computational model of visual filling-in based on the Emergic Network architecture. The Emergic Network was designed to help realize systems undergoing continuous change. In this thesis, eight different filling-in phenomena are demonstrated under a regime of continuous eye movement (and under static eye conditions as well). -/- ECM indirectly demonstrates the power of unification inherent with Emergic Networks when cognition is decomposed according to finer-grained functions supporting change. These can interact to raise (...) additional emergent behaviours via cognitive re-use, hence the Emergic prefix throughout. Nevertheless, the model is robust and parameter free. Differential re-use occurs in the nature of model interaction with a particular testing paradigm. -/- ECM has a novel decomposition due to the requirements of handling motion and of supporting unified modelling via finer functional grains. The breadth of phenomenal behaviour covered is largely to lend credence to our novel decomposition. -/- The Emergic Network architecture is a hybrid between classical connectionism and classical computationalism that facilitates the construction of unified cognitive models. It helps cutting up of functionalism into finer-grains distributed over space (by harnessing massive recurrence) and over time (by harnessing continuous change), yet simplifies by using standard computer code to focus on the interaction of information flows. Thus while the structure of the network looks neurocentric, the dynamics are best understood in flowcentric terms. Surprisingly, dynamic system analysis (as usually understood) is not involved. An Emergic Network is engineered much like straightforward software or hardware systems that deal with continuously varying inputs. Ultimately, this thesis addresses the problem of reduction and induction over complex systems, and the Emergic Network architecture is merely a tool to assist in this epistemic endeavour. -/- ECM is strictly a sensory model and apart from perception, yet it is informed by phenomenology. It addresses the attribution problem of how much of a phenomenon is best explained at a sensory level of analysis, rather than at a perceptual one. As the causal information flows are stable under eye movement, we hypothesize that they are the locus of consciousness, howsoever it is ultimately realized. (shrink)

In this paper, we advocate the idea that an adequate explanation of biological systems requires appealing to organizational closure as an emergent causal regime. We first develop a theoretical justification of emergence in terms of relatedness, by arguing that configurations, because of the relatedness among their constituents, possess ontologically irreducible properties, providing them with distinctive causal powers. We then focus on those emergent causal powers exerted as constraints, and we claim that biological systems crucially differ from other natural systems in (...) that they realize a closure of constraints, i.e. a second-order emergent regime of causation such that the constituents, each of them acting as a constraint, realize a mutual dependence among them, and are collectively able to self-maintain. Lastly, we claim that closure can be justifiably taken as an emergent regime of causation, without admitting that it inherently involves whole-parts causation, which would require to commit to stronger ontological and epistemological assumptions. (shrink)

All the central assumptions of the Modern Synthesis (Neo-Darwinism) have been disproven. [1, 2] An article with the title, "Rocking the foundations of molecular genetics,” appearing in the prestigious Proceedings of the National Academy of Sciences at the end of 2012 [3] would have not been possible a decade ago. Groundbreaking experimental evidence of epigenetic maternal inheritance over several generations was published in the same journal, throwing the whole foundation of 21st century molecular genetics into question. Neo-Darwinism attributed genetic change (...) to random events, in which physiology was assumed to play little role. "The germ line was thought to be isolated from any influence by the rest of the organism and its response to the environment. [3] The fundamental concepts that constitute the foundations of contemporary systems biology include holism, emergentism, and robustness, compared to the concepts of reductionism, mechanism, and homeostasis, that form the foundations of molecular biology. [18] Holism is to be contrasted with reductionism which considers a system as merely composed of a sum of parts. Emergentism, the appearance of hierarchical levels of organization, is contrasted with mechanism of independent linear events. Robustness refers to the preservation of the functionality of a system to a certain degree despite external or internal changes, while homeostasis refers to maintaining the stability of the state of a system. The Vedantic view also proposes viewing life from the Organic Whole perspective, in which consciousness forms the supporting basis. The conscious agent is an important part of that view, but the absolute conception of a unifying center is not to be omitted if a proper conception is to be achieved. (shrink)