Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other (...) mechanisms is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained by (...) original sin (we were all there). As another example of a theological motivation, some take the organism as an obvious starting point for a teleological argument for God’s existence, and this staring point is sometimes developed into a full-blown theory of pre-existence. The second category could be thought of as non-theological metaphysical, and paramount here is the desire to deal with the metaphysical problem of individuation. So, for example, Leibniz embraces a version of hylomorphism in order to overcome difficulties with Descartes’ theory of material substance, including the difficulty of how to account for enduring material individuals, and Leibniz’s hylomorphism is closely linked with his embrace of pre-existence. The third category might be termed “biological”, and one example of such a concern is how to explain the organic unity of living beings where the whole seems to ontologically precede the parts. This is frequently translated into a temporal priority of whole to parts, and thus pre-existence is posited. Of course, many natural philosophers of the early modern period embrace pre-existence for more than one reason, but in general, these are the three classes of motivations one might have for embracing the theory. In the second part of the paper I examine in detail one argument that appears in the work of Malebranche. On the face of it, this argument seems to be a biological one, specifically the biological or organic holism argument mentioned above. But upon closer examination, I shall argue, Malebranche’s reasons for endorsing pre-existence bring together several of the arguments discussed in the first part of the paper. I conclude with some considerations about what we can learn about Malebranche as a natural philosopher from his motivations for holding the pre-existence doctrine of generation. (shrink)

Open peer commentary on the article “Circularity and the Micro-Macro-Difference” by Manfred Füllsack. Upshot: The target article defends the fundamental role of circularity for systems sciences and the necessity to develop a conceptual and methodological approach to it. The concept of circularity, however, is multifarious, and two of the main challenges in this respect are to provide distinctions between different forms of circularities and explore in detail the roles they play in organizations. This commentary provides some suggestions in this direction (...) with the aim to supplement the perspective presented in the target article with some insights from theoretical biology. (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)

I go deep into the biology of the human organism to argue that the psychological features and functions of persons are realized by cellular and molecular parallel distributed processing networks dispersed throughout the whole body. Persons supervene on the computational processes of nervous, endocrine, immune, and genetic networks. Persons do not go with brains.

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way (...) toward a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

Synthetic organisms are at the same time organisms and artifacts. In this paper we aim to determine whether such entities have a good of their own, and so are candidates for being directly morally considerable. We argue that the good of non-sentient organisms is grounded in an etiological account of teleology, on which non-sentient organisms can come to be teleologically organized on the basis of their natural selection etiology. After defending this account of teleology, we argue (...) that there are no grounds for excluding synthetic organisms from having a good also grounded in their teleological organization. However, this comes at a cost; traditional artifacts will also be seen as having a good of their own. We defend this as the best solution to the puzzle about what to say about the good of synthetic organisms. (shrink)

This paper presents and defends an account of the coincidence of biological organisms with mereological sums of their material components. That is, an organism and the sum of its material components are distinct material objects existing in the same place at the same time. Instead of relying on historical or modal differences to show how such coincident entities are distinct, this paper argues that there is a class of physiological properties of biological organisms that their coincident (...) mereological sums do not have. The account answers some of the most pressing objections to coincidence, for example the so-called grounding problem , that material coincidence seems to require that coinciding objects have modal differences that do not supervene on any other properties. (shrink)

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the organism. To (...) account for how they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution. (shrink)

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have (...) different epistemic characters. Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (shrink)

Due to intensive agriculture, rapid industrialization and anthropogenic activities have caused environmental pollution, land degradation and increased pressure on the natural resources and contributing to their adulteration. Bioremediation is the use of biological organisms to destroy, or reduce the hazardous wastes on a contaminated site. Bioremediation is the most potent management tool to control the environmental pollution and recover contaminated soil. Use of biological materials, coupled to other advanced processes is one of the most promising and inexpensive (...) approaches for removing environmental pollutants. Bioremediation technology is a beneficial alternative which leads to degrade of pollutants. This article presents the important biological organisms used in bioremediation technologies. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, (...) together with the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden (...) its scope, contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (shrink)

The category of ‘organism’ has an ambiguous status: is it scientific or is it philosophical? Or, if one looks at it from within the relatively recent field or sub-field of philosophy of biology, is it a central, or at least legitimate category therein, or should it be dispensed with? In any case, it has long served as a kind of scientific “bolstering” for a philosophical train of argument which seeks to refute the “mechanistic” or “reductionist” trend, which has been perceived (...) as dominant since the 17th century, whether in the case of Stahlian animism, Leibnizian monadology, the neo-vitalism of Hans Driesch, or, lastly, of the “phenomenology of organic life” in the 20th century, with authors such as Kurt Goldstein, Maurice Merleau-Ponty, and Georges Canguilhem. In this paper I try to reconstruct some of the main interpretive ‘stages’ or ‘layers’ of the concept of organism in order to critically evaluate it. How might ‘organism’ be a useful concept if one rules out the excesses of ‘organismic’ biology and metaphysics? Varieties of instrumentalism and what I call the ‘projective’ concept of organism are appealing, but perhaps ultimately unsatisfying. (shrink)

The mathematical universe hypothesis is a theory that the physical universe is not merely described by mathematics, but is mathematics, specifically a mathematical structure. Our research provides evidence that the mathematical structure of the universe is biological in nature and all systems, processes, and objects within the universe function in harmony with biological patterns. Living organisms are the result of the universe’s biological pattern and are embedded within their physiology the patterns of this biological universe. (...) Therefore physiological patterns in living organisms can be used as models to structurally map analogies from the biological domain to any target domain to reveal and understand the biological nature of the target domain. Our paper explores various analogies, structurally mapping a red blood cell to a cup; proteins produced from ribosomes to music produced from instruments; a beating heart to the melting and freezing of Antartica; cells, tissue, organs and blood, to people, organizations, industries, and money, and; bio-economic concepts in cellular society to socioeconomic concepts in human society. It also discusses how phenomena in cellular mitosis can help explain phenomena in the universe, such as black holes, dark matter, dark energy, and the structure of the universe. Building upon the concept of perennial wisdom, our research has provided evidence that the ideas of a biological universe were expressed across many past cultures and historical periods. The implications of this theory are vast, encompassing fields such as physics, science, philosophy, religion, law, economics, politics, and engineering, thus serving as a unifying theory for all knowledge. Our theory is supported by meta-analysis of scientific, historic, and religious literature, observations and first principles logic. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in (...) my view, are as Godfrey-Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ as one (...) entity over time. In this paper, I offer a novel defence of substance ontology by arguing that the coherency and plausibility of the radical reconceptualisation of organisms proffered by process ontology ultimately depends upon its making use of the ‘substantial’ principles it purports to replace. (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)

Organisms receded from view in much of twentieth-century biology, only to undergo a sort of renaissance at the start of the twenty-first. The story of why this should be so is complicated and fascinating, but belongs primarily to the history of biology. On the other hand, to the extent that it is so, a question naturally arises: what, after all, are organisms? This question has a long and complicated history of its own, both within and without of biology; (...) an investigation of this history yields some guidance as to how organisms might yet be conceived today. One suggestion borne of these investigations is this: organisms are, for better or worse, normatively delineated unities. (shrink)

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that (...) the most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of (...) biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then (...) defines individual organisms as essentially possessing some mechanisms that play this role. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

A widespread view about early social functionalism is that its account of functional explanation was underpinned by an analogy between biological organisms and societies that suggested pseudo-explanations about the latter. I will challenge this view through a case study of the use G.W.F. Hegel made of the organismic analogy for the purpose of concept development in his theory of the state. My claim will be that the dismissal of this analogy is premature for two reasons. First, to claim (...) that the organismic analogy figured among the premises of an analogical argument and, thus, as explanans in an explanation misses its point. For Hegel made use of the analogy to model the apparent close cooperation among the parts of the state and, thus conceptualize its characteristic structure in terms of organization: the mutual dependence among distinct structures generated by the state as a whole. Second, the organizational view of social functions thus suggested by the organismic analogy has not obviously been made obsolete by evolutionary theory. Instead, reconsidering the organismic analogy in light of contemporary philosophy of biology puts an account of social functions that has fallen from view (and from grace) in the contemporary discussion back in focus: the organizational account. -/- . (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue (...) that this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

This article explores the use of model organisms in studying the cognitive phenomenon of decision-making. Drawing on the framework of biological control to develop a skeletal conception of decision-making, we show that two core features of decision-making mechanisms can be identified by studying model organisms, such as E. coli, jellyfish, C. elegans, lamprey, and so on. First, decision mechanisms are distributed and heterarchically structured. Second, they depend heavily on chemical information processing, such as that involving neuromodulators. We (...) end by discussing the implications for studying distinctively human decision-making. (shrink)

Consumers are increasingly aware of the health- and safety-related implications of the food which they can buy in the market. At the same time, households have become more aware of their environmental responsibilities. Regarding the production of food, a crucial and multifunctional role is played by agriculture. The way vegetables, fruits, and other crops are grown and how livestock is raised has an impact on the environment and landscape. Operations performed by farmers, such as water management, can be dangerous for (...) the soil and the whole ecosystem. Consequently, there is a search for natural ways of sustaining the impact of agriculture on the environment. In this context, one of the most popular ideas is organic agriculture. In the literature on the subject, there are many concepts that some authors consider to be synonymous even as others argue that these terms are not interchangeable. There is, for example, "organic agriculture," "alternative agriculture," "sustainable agriculture," "ecological agriculture," "biological agriculture," "niche farming," "community-supported agriculture," and "integrated pest management." Very often, techniques and products related to organic agriculture are described by marketing experts with the use of abbreviations such as "bio" and "eco." Products with such markings and labels are increasingly popular in stores that often give them separate shelves for their sale. Despite the higher price compared to conventional products, they are increasingly sought by consumers. The entry examines the various impacts of organic agriculture with a view to these trends. (shrink)

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a (...) phylogenetic tree will split differently than if the identity of an organism does not survive the fission process. (shrink)

Niche construction is a concept that captures a wide array of biological phenomena, from the environmental effects of metabolism to the creation of complex structures such as termite mounds and beaver dams. A central point in niche construction theory is that organisms do not just passively undergo developmental, ecological, or evolutionary processes, but are also active participants in them Evolution: From molecules to men, Cambridge University Press, Cambridge, 1983; Laland KN, Odling-Smee J, Feldman MW, In: KN Laland and (...) T Uller Evolutionary causation: Biological and philosophical reflections, MIT Press, Cambridge, MA, 2019). In this paper, we distinguish between two fundamentally different ways in which organisms are active participants: as agents and as contributors. Roughly, organisms act as agents when niche constructing effects are a result of a goal-directed behavior over which the organisms have some degree of control. Organisms act as contributors when the niche constructing effects do not arise from a goal to perform the constructive activity. As illustrative examples we discuss plants altering leaf-morphology to optimize light exposure as reported by Sultan and bacteria creating novel niches through excreting energy-rich metabolites. The difference between agential and contributional niche construction is important for understanding the different ways organisms can actively participate in development, ecology, and evolution. Additionally, this distinction can increase our understanding of how the capacity of agency is distributed across the tree of life and how agency influences developmental and evolutionary processes. (shrink)

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the (...) solution of all these three problems is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the “collapse” of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview. (shrink)

The concept of reaction norms plays a crucial role in connecting molecular and evolutionary biology.

As the world’s population grows and urbanization continues, the global waste crisis is becoming more severe, especially in developing countries. Without proper waste management, they may encounter various environmental and health risks. Biological technologies are regarded as promising waste management and recycling approaches in developing countries due to their cost-effectiveness and capability to handle diverse waste categories. One prominent technology in this aspect is the vermicomposting of organic waste utilizing the black soldier fly larvae. Nevertheless, significant financial resources are (...) still necessary to advance and expand biological waste treatment, which requires the participation of businesses. By examining waste management companies listed on the Vietnamese stock market, we highlight two challenges that hinder the adoption and scaling of the waste treatment system using black soldier flies and potentially other biological technologies in Vietnam. Specifically, the business regards the environmental services they offer primarily as a means to generate profit rather than as a genuine commitment to environmental preservation, and the values of companies operating in the environmental sector, particularly in waste management, have been significantly undervalued by the Vietnamese investing public. Therefore, we advocate for societal shifts toward the eco-surplus culture and apply the semiconducting principle of monetary and environmental values exchange to address the problem. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational (...) overtones, in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (shrink)

Defenders of evolutionary medicine claim that medical professionals and public health officials would do well to consider the role of evolutionary biology with respect to the teaching, research, and judgments pertaining to medical theory and practice. An integral part of their argument is that the human body should be understood as a bundle of evolutionary compromises. Such an appreciation, which includes a proper understanding of biological function and physiological homeostasis, would provide a crucial perspective regarding the understanding and securing (...) of human health needs currently lacking in the medical arena. (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)

We received several critical comments regarding the "The Science of Spiritual Biology." We reply to those criticisms in order to further clarify some of the important points that were made. It is only to be expected that a strong emotional response may be evoked by the revolution in scientific thinking that the modern paradigm of cognitive biology presents. We have to be prepared to accept that, and maintain the integrity of the scientific approach.

The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can (...) be approached in two ways: from a theoretical standpoint, exploring the centrality of the cognitive sciences in current theoretical biology; and from a historical perspective, examining the resemblance between the current state of theoretical biology and the Cognitive Revolution of the mid-20th century. Both inquiries yield affirmative answers, though important nuances will be emphasized. The cognitive sciences' explanatory framework is employed to elucidate the agentic characteristics of organisms, establishing a clear parallelism between the Cognitive Revolution and the present state of theoretical biology. (shrink)

Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to combinations of individuals and their attributes in the actual world. While the last decades of synthetic biology explorations have shown (...) biology to be much more difficult to engineer than originally conceived, synthetic biology has not given up its combinatorial approach. (shrink)

Reasoning from a naturalistic perspective, viewing the mind as an evolved biological organ with a particular structure and function, a number of influential philosophers and cognitive scientists claim that science is constrained by human nature. How exactly our genetic constitution constrains scientific representations of the world remains unclear. This is problematic for two reasons. Firstly, it often leads to the unwarranted conclusion that we are cognitively closed to certain aspects or properties of the world. Secondly, it stands in the (...) way of a nuanced account of the relationship between our cognitive and perceptual wiring and scientific theory. In response, I propose a typology or classification of the different kinds of biological constraints and their sources on science. Using Boden’s notion of a conceptual space, I distinguish between constraints relating to the ease with which we can reach representations within our conceptual space and constraints causing possible representations to fall outside of our conceptual space. This last kind of constraints does not entail that some aspects or properties of the world cannot be represented by us – as argued by advocates of ‘cognitive closure’ – merely that some ways of representing the world are inaccessible to us. It relates to what Clark and Rescher have framed as ‘the alien scientist hypothesis’. The purpose of this typology is to provide some much needed clarity and structure to the debate about biological constraints on science. (shrink)

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and (...) compare these two accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms. (shrink)

Genes and the Agents of Life undertakes to rethink the place of the individual in the biological sciences, drawing parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The 2005 book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the biological (...) sciences. The book is a companion to the author's Boundaries of the Mind (2004), also available from Cambridge, where the focus is the cognitive sciences. The book will appeal to a broad range of professionals and students in philosophy, biology, and the history of science. You can download the table of contents and the first chapter here. (shrink)

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions are (...) rejected; rather it is main arguments for them that are the focus. (shrink)

The perception of reality by biosystems is based on different, and in certain respects more effective, principles than those utilized by the more formal procedures of science. As a result, what appears as random pattern to the scientific method can be meaningful pattern to a living organism. The existence of this complementary perception of reality makes possible in principle effective use by organisms of the direct interconnections between spatially separated objects shown to exist in the work of J. S. (...) Bell. (shrink)

Biological sexes (male, female, hermaphrodite) are defined by different gametic strategies for reproduction. Sexes are regions of phenotypic space which implement those gametic reproductive strategies. Individual organisms pass in and out of these regions – sexes - one or more times during their lives. Importantly, sexes are life-history stages rather than applying to organisms over their entire lifespan. This fact has been obscured by concentrating on humans, and ignoring species which regularly change sex, as well as those (...) with non-genetic or facultatively genetic sex determination systems. But the general point applies equally to humans. Assigning sexes to pre-reproductive life history stages involves ‘prospective narration’ – classifying the present in terms of its anticipated future. Assigning sexes to adult stages of non-reproductive castes or non-reproductive individuals is a complex matter whose biological meaning differs from case to case. The chromosomal and phenotypic ‘definitions’ of biological sex that are contested in philosophical discussions of sex are actually operational definitions which track gametic sex more or less effectively in some species or group of species. Neither ‘definition’ can be stated for species in general except by defining them in terms of gametic sex. The gametic definition of sex also features in widely accepted models which explain why two biological sexes – either in separate individuals or combined in hermaphroditic individuals - are almost universal in multicellular species. Finally, the fact that a species has only two biological sexes does not imply that every member of the species is either male, female or hermaphroditic, or that the sex of every individual organism is clear and determinate. The idea of biological sex is critical for understanding the diversity of life, but ill-suited to the job of determining the social or legal status of human beings as men or women. (shrink)

Biological individuality is a notoriously thorny topic for biologists and philosophers of biology. In this paper we argue that biological individuality presents multiple, interconnected questions for biologists and philosophers that together form a problem agenda. Using a case study of an interdisciplinary research group in ecology, behavioral and evolutionary biology, we claim that a debate on biological individuality that seeks to account for diverse practices in the biological sciences should be broadened to include and give prominence (...) to questions about uniqueness and temporality. We show that broadening the problem agenda of biological individuality draws attention to underrecognized philosophical issues and discussions and thereby organizes and enriches the existing debate. (shrink)

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in (...) experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples. (shrink)

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the species as a Gene-Flow Community differs from Mayr’s definition (...) of the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand (...) in for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)