Pierre-Henri Castel provides a short but richly argued precis of his recently published two-volume 1,000-page masterwork on the history of obsessive-compulsive disorder. Having not read the as-yet-untranslated books, I write this commentary from Plato’s cave, trying to infer the reality of Castel’s analysis from expository shadows. I am unlikely to be more successful than Plato’s poor troglodytes, so I apologize ahead of time for any misunderstandings. Moreover, I cannot assess Castel’s detailed evidential case for his substantive theses.1 I thus focus (...) on some key philosophical issues that impinge on an area of my concern, the concept of mental disorder. Castel is a rare breed of French.. (shrink)

There are at least two kinds of design arguments for theism: fine-tuning arguments and biological design arguments. Dougherty and Poston (2008) have argued that the success of one requires the failure of the other, and vice versa. The reason is that the success of these arguments hinges on the following crucial probability: the probability that biological life exists somewhere in the universe given that (a) our universe is finely tuned and that (b) biological development is (...) unguided by intelligence. According to Dougherty and Poston, fine-tuning arguments require that the crucial probability is high while biological design arguments require that the crucial probability is low. As a result, at most one of these design arguments can factor into a cumulative case argument for theism. I argue that this is mistaken. Specifically, I show that fine-tuning arguments can succeed even if the crucial probability is low. (shrink)

There seems to be a widespread conviction — evidenced, for example, in the work of Mackie, Dawkins and Sober — that it is Darwinian rather than Humean considerations which deal the fatal logical blow to arguments for intelligent design. I argue that this conviction cannot be well-founded. If there are current logically decisive objections to design arguments, they must be Humean — for Darwinian considerations count not at all against design arguments based upon apparent cosmological fine-tuning. I (...) argue, further, that there are good Humean reasons for atheists and agnostics to resist the suggestion that apparent design — apparent biological design and/or apparent cosmological fine-tuning — establishes (or even strongly supports) the hypothesis of intelligent design. (shrink)

Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational (...) class='Hi'>design and directed evolution. Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its “methodological monism”, where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design. (shrink)

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these (...) two is the way they treat variation: rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they (...) exhibited a second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them. (shrink)

We consider first the most fundamental „design in Nature”, the explanatory structure of the Universe on the basis of the natural sciences, and the related problem of teleology in Nature. We point out that it is necessary to generalize the presently used explanatory scheme of physics. We derive here the first essentially complete scientific world picture, and obtain new insights answering to the problem of cosmic design. Considering some important objections against teleology, we present counter-arguments, give a new (...) classification of the main classes of teleology and their quantitative complexity measures. Comparing the new classification of teleology with that of Mayr, we give useful examples and indicate why teleology is useful for natural science. As a result, we outline a general picture of the basic types of design in Nature and provide their scientific explanation. (shrink)

Direct neurological and especially imaging-driven investigations into the structures essential to naturally occurring cognitive systems in their development and operation have motivated broadening interest in the potential for artificial consciousness modeled on these systems. This first paper in a series of three begins with a brief review of Boltuc’s (2009) “brain-based” thesis on the prospect of artificial consciousness, focusing on his formulation of h-consciousness. We then explore some of the implications of brain research on the structure of consciousness, finding limitations (...) in biological approaches to the study of consciousness. Looking past these limitations, we introduce research in artificial consciousness designed to test for the emergence of consciousness, a phenomenon beyond the purview of the study of existing biological systems. (shrink)

Abstract: Without directly taking sides in the design/anti-design debate, this paper defends the following position: the assertion that biological evolution “is” design-free presupposes the possibility to model biological evolution in a design-free way. Certainly, there are design-free models of evolution based on cumulative selection. But “to model” is a verb denoting “modeling” as the process leading to a model. So any modeling – trivially – needs “previous human design.” Nevertheless, contrary to other (...) scientific activities which legitimately consider models while ignoring the process leading to them, evolution theory must take into account the human activity of modeling required by its corresponding models. (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)

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)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, (...) yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

Much has been made of how Darwinian thinking destroyed proofs for the existence of God from ‘design’ in the universe. I challenge that prevailing view by looking closely at classical ‘teleological’ arguments for the existence of God. One version championed by Aristotle and Thomas Aquinas stems from how chance is not a sufficient kind of ultimate explanation of the universe. In the course of constructing this argument, I argue that the classical understanding of teleology is no less necessary in (...) modern Darwinian biology than it was in Aristotle's time. In fact, modern biology strengthens the claims that teleological arguments make by vindicating many of their key features. As a consequence, I show how Aristotle and Aquinas' teleological argument for an intelligent First Cause remains valid. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way of (...) articulating the questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)

In this essay I suggest that we view design principles in systems biology as minimal models, for a design principle usually exhibits universal behaviors that are common to a whole range of heterogeneous (living and nonliving) systems with different underlying mechanisms. A well-known design principle in systems biology, integral feedback control, is discussed, showing that it satisfies all the conditions for a model to be a minimal model. This approach has significant philosophical implications: it not only accounts (...) for how design principles explain, but also helps clarify one dispute over design principles, e.g., whether design principles provide mechanistic explanations or a distinct kind of explanations called design explanations. (shrink)

In this essay I propose that what design principles in systems biology and systems neuroscience do is to present abstract characterizations of mechanisms, and thereby facilitate mechanistic explanation. To show this, one design principle in systems neuroscience, i.e., the multilayer perceptron, is examined. However, Braillard (2010) contends that design principles provide a sort of non-mechanistic explanation due to two related reasons: they are very general and describe non-causal dependence relationships. In response to this, I argue that, on (...) the one hand, all mechanisms are more or less general (or abstract), and on the other, many (if not all) design principles are causal systems. (shrink)

Book Description (Blurb): Cognitive Design for Artificial Minds explains the crucial role that human cognition research plays in the design and realization of artificial intelligence systems, illustrating the steps necessary for the design of artificial models of cognition. It bridges the gap between the theoretical, experimental and technological issues addressed in the context of AI of cognitive inspiration and computational cognitive science. -/- Beginning with an overview of the historical, methodological and technical issues in the field of (...) Cognitively-Inspired Artificial Intelligence, Lieto illustrates how the cognitive design approach has an important role to play in the development of intelligent AI technologies and plausible computational models of cognition. Introducing a unique perspective that draws upon Cybernetics and early AI principles, Lieto emphasizes the need for an equivalence between cognitive processes and implemented AI procedures, in order to realise biologically and cognitively inspired artificial minds. He also introduces the Minimal Cognitive Grid, a pragmatic method to rank the different degrees of biologically and cognitive accuracy of artificial systems in order project and predict their explanatory power with respect to the natural systems taken as source of inspiration. -/- Providing a comprehensive overview of cognitive design principles in constructing artificial minds, this text will be essential reading for students and researchers of artificial intelligence and cognitive science. (shrink)

William Paley ( Natural Theology , 1802) developed the argument-from-design. The complex structure of the human eye evinces that it was designed by an intelligent Creator. The argument is based on the irreducible complexity ("relation") of multiple interacting parts, all necessary for function. Paley adduces a wealth of biological examples leading to the same conclusion; his knowledge of the biology of his time was profound and extensive. Charles Darwin’s Origin of Species is an extended argument demonstrating that the (...) "design" of organisms can be explained by natural selection. Moreover, the dysfunctions, defects, waste, and cruelty that prevail in the living world are incompatible with a benevolent and omnipotent Creator. They come about by a process that incorporates chance and necessity, mutation and natural selection. In addition to science, there are other ways of knowing, such as art, literature, philosophy, and religion. Matters of value, meaning, and purpose transcend science. (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)

What is it for an animal to be female, or male? An emerging consensus among philosophers of biology is that sex is grounded in some manner or another on anisogamy, that is, the ability to produce either large gametes (egg) or small gametes (sperm), though the exact nature of this grounding remains contentious. Here we argue for a new conception of this relation. In our view, one’s sex doesn’t depend on the kind of gamete one is capable of making, but (...) on the kind of gamete one is designed to make, where design is understood in terms of an evolutionary or ontogenetic selection process. Specifically, we argue that what it is to be, say, male, is to have a part or process that has the (proximal or distal) biological function of producing sperm. We outline and defend our view, and sketch some implications for scientific and social problems related to sex. (shrink)

Digital practices in design, together with computer-assisted manufacturing (CAM), have inspired the reflection of philosophers, theorists, and historians over the last decades. Gilles Deleuze’s The Fold: Leibniz and the Baroque (1988) presents one of the first and most successful concepts created to think about these new design and manufacturing practices.1 Deleuze proposed a new concept of the technological object, which was inspired by Bernard Cache’s digital design practices and computer-assisted manufacturing. Deleuze compared Cache’s practices to Leibniz’s differential (...) calculus-based notion of the parametric curve. From this perspective, the object is no longer an essential form: rather, it is functional, defined by a family of parametric curves. In Deleuze’s terms, it is an objectile. This definition grasps a particular aspect of modernity in the technological object, rendering possible the industrial production of “the unique object” (la pièce unique), while making obsolete the homogeneity that comes with industrial standardization. What follows introduces developmental biology into this design matrix, interrogating the relationship between parametric design and computer-assisted manufactory on the one hand and biological morphogenetic processes on the other. Is one necessary for the other? Does an architect need computation in order to render morphogenetic shapes? In answering these questions, this chapter displaces the centrality of digital technology in the design of shape-shifting forms within architecture and calls for a rethinking of design by way of analog prototypes. I argue that “thinking through analogs” offers another means of generating parametrically based morphogenetic forms. (shrink)

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted (...) by a sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (shrink)

I argue that Evolutionary Psychologists’ notion of adaptationism is closest to what Peter Godfrey-Smith (2001) calls explanatory adaptationism and as a result, is not a good organizing principle for research in the biology of human behavior. I also argue that adopting an alternate notion of adaptationism presents much more explanatory resources to the biology of human behavior. I proceed by introducing Evolutionary Psychology and giving some examples of alternative approaches to the biological explanation of human behavior. Next I characterize (...) adaptation and explain the range of biological phenomena that can count as adaptations. I go onto introduce the range of adaptationist views that have been distinguished by philosophers of biology and lay out explanatory adaptationism in detail. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to (...) describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...) ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes (...) from noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes. (shrink)

It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such, a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes or even whole organisms. In this paper, I argue that synthetic biology might also shed some novel and interesting (...) perspectives on the question of the origin of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origin. (shrink)

The function or intended use of a device such as a fire escape is escape from fire, whether or not it is ever actually used as such or it acquires other uses. Biological function, on the other hand, depends, in one way or another, on actual use. Philosophical attempts to explain artifact function by analogy with biological function or to build a unified theory of function are nonetheless common. What such attempts routinely overlook, however, is the role of (...) forethought in intentional function. I defend the traditional intended use view of function, emphasize the role of forethought and argue that design intentions are rationally grounded in a design brief, for which there is no obvious natural analogue. (shrink)

The scientific status of evolutionary theory seems to be more or less perennially under question. I am not referring here (just) to the silliness of young Earth creation- ism (Pigliucci 2002; Boudry and Braeckman 2010), or even of the barely more intel- lectually sophisticated so-called Intelligent Design theory (Recker 2010; Brigandt this volume), but rather to discussions among scientists and philosophers of science concerning the epistemic status of evolutionary theory (Sober 2010). As we shall see in what follows, this (...) debate has a long history, dating all the way back to Darwin, and it is in great part rooted in the fundamental dichotomy between what French biologist and Nobel laureate Jacques Monod (1971) called chance and necessity—i.e., the inevitable and inextricable interplay of deterministic and stochastic mechanisms operating during the course of evolution. (shrink)

Polger and Shapiro (2016) claim that unlike human-made artifacts cases of multiple realization in naturally occurring systems are uncommon. Drawing on cases from systems biology, I argue that multiple realization in naturally occurring systems is not as uncommon as Polger and Shapiro initially thought. The relevant cases, which I draw from systems biology, involve generalizable design principles called network motifs which recur in different organisms and species and perform specific functions. I show that network motifs with entirely different underlying (...) causal structures can perform the same function of interest. The article also considers the scope problem of multiple realization. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear reactions (...) are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

Intelligence in current AI research is measured according to designer-assigned tasks that lack any relevance for an agent itself. As such, tasks and their evaluation reveal a lot more about our intelligence than the possible intelligence of agents that we design and evaluate. As a possible first step in remedying this, this article introduces the notion of “self-concern,” a property of a complex system that describes its tendency to bring about states that are compatible with its continued self-maintenance. Self-concern, (...) as argued, is the foundation of the kind of basic intelligence found across all biological systems, because it reflects any such system's existential task of continued viability. This article aims to cautiously progress a few steps closer to a better understanding of some necessary organisational conditions that are central to self-concern in biological systems. By emulating these conditions in embodied AI, perhaps something like genuine self-concern can be implemented in machines, bringing AI one step closer to its original goal of emulating human-like intelligence. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important (...) respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

This article reviews two standard criticisms of creationism/intelligent design (ID): it is unfalsifiable, and it is refuted by the many imperfect adaptations found in nature. Problems with both criticisms are discussed. A conception of testability is described that avoids the defects in Karl Popper’s falsifiability criterion. Although ID comes in multiple forms, which call for different criticisms, it emerges that ID fails to constitute a serious alternative to evolutionary theory.

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...) particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

While a great deal of abuse has been directed at intelligent design theory (ID), its starting point is a fact about biological organisms that cries out for explanation, namely "specified complexity" (SC). Advocates of ID deploy three kind of argument from specified complexity to the existence of a designer: an eliminative argument, an inductive argument, and an inference to the best explanation. Only the first of these merits the abuse directed at it; the other two arguments are worthy (...) of respect. If they fail, it is only because we have a better explanation of SC, namely Darwin's theory of evolution by natural selection. (shrink)

Presenting an Open Peer Commentary on “In Maturana’s Wake: The Biology of Cognition’s Legacy and its Prospects” by Randall Whitaker, the article suggests that engaging with Maturana's biology of cognition in the context of design is a form of practice rather than application. Maturana's biology of cognition, the article argues, can be conceived of as initiating an educational process that supports agents to act “from within” rather than “from without.”.

In an effort to produce new and more sustainable technologies, designers have turned to nature in search of inspiration and innovation. Biomimetic design (from the Greek bios, life, mimesis, imitation) is the conscious imitation of biological models to solve today's technical and ecological challenges. Nowadays numerous different approaches exist that take inspiration from nature as a model for design, such as biomimicry, biomimetics, bionics, permaculture, ecological engineering, etc. This variety of practices comes in turn with a wide (...) range of different promises, including sustainability, increased resilience, multi-functionality, and a lower degree of risk. How are we to make sense of this heterogeneous amalgam of existing practices and technologies, and of the numerous promises attached to them? We suggest that a typology of biomimetic approaches would provide a useful hermeneutic framework to understand the different tensions that pull this variegated landscape in different directions. This is achieved through a critical analysis of the literature in different fields of biomimetic design and the philosophy of biomimicry, in order to derive conceptual and normative assumptions concerning the meaning and value of the imitation of nature. These two dimensions are then intersected to derive an analytical grid composed of six different biomimetic types, which enable the classification of existing and possible biomimetic approaches, practices, and technologies according to their specific conceptual assumptions and guiding norms. (shrink)

Modes of teaching and learning have had to rapidly shift amid the COVID-19 pandemic. As an emergency response, students from Philippine public schools were provided learning modules based on a minimized list of essential learning competencies in Biology. Using a cross-sectional survey method, we investigated students’ perceptions of the Biology self-learning modules (BSLM) that were designed in print and digitized formats according to a constructivist learning approach. Senior high school STEM students from grades 11 (n = 117) and 12 (n (...) = 104) participated in a survey using a 3-point Likert-scale questionnaire uploaded online through Google Forms. The survey results indicate that majority of the students perceived the modules positively, suggesting that aspects of the modules that were salient to students corresponded to essential elements of constructivist pedagogies. However, during interviews, students reported several difficulties in learning with BSLM as it was constrained by, to name a few, the use of unfamiliar words, lack of access to supporting resources, slow internet connection, and time constraints. To address these problems, teachers reported that they gave deadline extensions, complemented modules with other channels of support, and used online and offline platforms for reaching out to students to answer their queries and plan out their schedule for the week. The findings across the data sources point to the complex demands of emergency distance education that teachers, as curriculum designers and enactors, need to bear in mind in order to craft productive pedagogies, constructivist or otherwise, during this unprecedented time. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data (...) sets them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

Recently, the Intelligent Design (ID) movement has challenged the claim of many in the scientific establishment that nature gives no empirical signs of having been deliberately designed. In particular, ID arguments in biology dispute the notion that neo-Darwinian evolution is the only viable scientific explanation of the origin of biological novelty, arguing that there are telltale signs of the activity of intelligence which can be recognized and studied empirically. In recent years, a number of Catholic philosophers, theologians, and (...) scientists have expressed opposition to ID. Some of these critics claim that there is a conflict between the philosophy of St. Thomas Aquinas and that of the ID movement, and even an affinity between Aquinas’s ideas and theistic Darwinism. We consider six such criticisms and find each wanting. (shrink)

Denis Diderot’s natural philosophy is deeply and centrally ‘biologistic’: as it emerges between the 1740s and 1780s, thus right before the appearance of the term ‘biology’ as a way of designating a unified science of life (McLaughlin), his project is motivated by the desire both to understand the laws governing organic beings and to emphasize, more ‘philosophically’, the uniqueness of organic beings within the physical world as a whole. This is apparent both in the metaphysics of vital matter he puts (...) forth in works such as D’Alembert’s Dream (1769) and the more empirical concern with the mechanics of life in his manuscript Elements of Physiology, on which he worked during the last twenty years of his life. This ‘biologism’ obviously presents the interpreter of Diderot with some difficulties, notably as regards his materialism, given that contemporary forms of materialism have on the contrary strongly rejected notions of emergence, vitalism, teleology and any concepts appealing to unique, irreducible features of organisms. In response, some have described him as a ‘holist’ (Kaitaro) while others have emphasized his materialist, naturalist project (Bourdin, Wolfe). In what follows I examine a little-known aspect of Diderot’s articulation of his biological project: his statement in favour of epigenesis within the short but suggestive Encyclopédie article “Spinosiste.” Diderot was, of course, a partisan of epigenesis (the developmental-biological theory opposed to preformation, according to which beings develop by successive adjunction of layers of matter), but why include a statement in favour of a particular biological (or developmental) theory within an entry dealing with a philosopher, Spinoza, who does not seem to have been concerned at all with the specific properties of living beings, how they grow from embryonic to developed states, and so on? By trying to answer this question I also try and locate Diderot’s biological project in relation to what will become, in the years after his death, the project for a science called ‘biology’, with figures such as Treviranus and Lamarck. For it is not clear that the two can be easily correlated or causally linked: Diderot’s ‘epigenetic Spinozism’ is a different conceptual entity from what we find in histories of biology. (shrink)

Abstract: This study is designed to investigate the influence of menstruation on the academic achievement of senior secondary school Biology students in Irewole Local Government Area of Osun State, Nigeria. In the light of this, three specific objectives and research questions were highlighted not only to achieve but also to answer. The study employed quasi-experimental design. Besides, purposive sampling technique was used to take a sample of sixty-five (65) Grade 11 (Senior Secondary School II) students from three public high (...) school within the study area. The data generated from the instrument that is Biology Achievement Test (BAT) was analysed with the aid of a component of inferential statistics. The findings revealed a significant relationship between the academic achievement of students in Biology and menstruation. This is because, students before their menstrual period had mean score of 45 marks which was slightly higher than the one they had during (that is 42 marks) their menstrual period. A significant association between the academic achievement of students in Biology and menstrual pains was also observed. However, there was no significant relationship between the academic achievement in Biology among participants and duration of menstruation. This means that number of days used to complete menstruation period was insignificant to academic achievement of the participants in Biology. It is inferred from the study that there is relationship between menstruation and students’ academic performance in Biology among public secondary schools. Recommendations such as provision of conducive facilities in schools, constant awareness programme on the subject matter among others were made. (shrink)

The key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information guides biological systems, from bacteria (...) to ecosystems, in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

Water is the source of life for our planet, guided the ancient civilizations, and formed its current footprint on the earth. Water has always been a crucial element of our biological survival; consequently, humankind has permanently settled around it while carrying the responsibility of protecting it. To understand the water pattern in various cities throughout history and analyze how the emerging problems were overcome, Istanbul Technical University Landscape Architecture Department Graduate Level Design Studio was held under the theme (...) of "Around Water". Despite the adverse effects of the Covid-19 pandemic on education, international researchers contribute to the studio in a beneficial and diversified manner with the effective use of online tools. As a result of the literature review and the online, multidisciplinary education, and research-based design requirements, a new studio method was developed. Water-based case studies worldwide produced enriched outputs. While creating new discussion environments, the diversified outcomes of the studio "Around Water" contributed to the creation of cumulative studio knowledge. (shrink)

The so-called evolution wars (Futuyma 1995; Pigliucci 2002) between the scientific understanding of the history of life on earth and various religiously inspired forms of cre- ationism are more than ever at the forefront of the broader ‘‘science wars,’’ themselves a part of the even more encom- passing ‘‘cultural wars.’’ With all these conflicts going on, and at a time when a potentially historical case on the teach- ing of Intelligent Design (ID) in public schools is being de- bated (...) in Pennsylvania, it may be useful to consider a number of books that have come out recently to help scientists and the public at large to understand what all the fuss is about. (shrink)

Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the (...) contemporary philosophical debate on the scientific value of simulations, as we demonstrate its ability to form a scientific explanation of natural phenomena and to generate new emergent behaviors, making possible a prediction or hypothesis about the equivalent real-life phenomena. (shrink)

Racial constructionists, anti-naturalists, and anti-realists have challenged users of the biological race concept to provide and defend, from the perspective of biology, biological philosophy, and ethics, a biologically informed concept of race. In this paper, an ontoepistemology of biology is developed. What it is, by this, to be "biological real" and "biologically meaningful" and to represent a "biological natural division" is explained. Early 18th century race concepts are discussed in detail and are shown to be both (...) sensible and not greatly dissimilar to modern concepts. A general biological race concept (GBRC) is developed. It is explained what the GBRC does and does not entail and how this concept unifies the plethora of specific ones, past and present. Other race concepts as developed in the philosophical literature are discussed in relation to the GBRC. The sense in which races are both real and natural is explained. Racial essentialism of the relational sort is shown to be coherent. Next, the GBRC is discussed in relation to anthropological discourse. Traditional human racial classifications are defended from common criticisms: historical incoherence, arbitrariness, cluster discordance, etc. Whether or not these traditional human races could qualify as taxa subspecies – or even species – is considered. It is argued that they could qualify as taxa subspecies by liberal readings of conventional standards. Further, it is pointed out that some species concepts potentially allow certain human populations to be designated as species. It is explained why, by conventional population genetic and statistical standards, genetic differences between major human racial groups are at least moderate. Behavioral genetic differences associated with human races are discussed in general and in specific. The matter of race differences in cognitive ability is briefly considered. Finally, the race concept is defended from various criticisms. First, logical and empirical critiques are dissected. These include: biological scientific, sociological, ontological, onto-epistemological, semantic, and teleological arguments. None are found to have any merit. Second, moral-based arguments are investigated in context to a general ethical frame and are counter-critiqued. Racial inequality, racial nepotism, and the “Racial Worldview" are discussed. What is dubbed the Anti-Racial Worldview is rejected on both empirical and moral grounds. Finally, an area of future investigation – the politics of the destruction of the race concept – is pointed to. (shrink)