Molecular clocks based upon amino acid sequences in proteins have played a major role in the clarification of evolutionary phylogenies. Creationist criticisms of these methods sometimes rely upon data that might initially seem to be paradoxical. For example, human cytochrome c differs from that of an alligator by 13 amino acids but differs by 14 amino acids from a much more closely related primate, Otolemur garnettii. The apparent anomaly is resolved by taking into consideration the variable substitution rate (...) of cytochrome c, particularly among primates. This paper traces some of the history of extensive research into the topic of rate heterogeneity in cytochrome c including data from cytochrome c pseudogenes. (shrink)

In this paper, I discuss several temporal aspects of paleontology from a philosophical perspective. I begin by presenting the general problem of “taming” deep time to make it comprehensible at a human scale, starting with the traditional geologic time scale: an event-based, relative time scale consisting of a hierarchy of chronological units. Not only does the relative timescale provide a basis for reconstructing many of the general features of the history of life, but it is also consonant with the cognitive (...) processes humans use to think about time. Absolute dating of rocks, fossils, and evolutionary events (such as branching events on the tree of life) can be accomplished through the use of radiometric dating, chronological signals extractable from fossil growth patterns, and the “molecular clock.” Sometimes these different methods of absolute dating, which start from largely independent assumptions and evidentiary bases, converge in their temporal estimates, resulting in a consilience of inductions. At other times they fail to agree, either because fossils and molecules are giving temporal information about different aspects of nature and should not be expected to agree, or because of flawed assumptions that give rise to an inaccurate estimate. I argue that in general, despite the fact that it can be difficult to integrate disparate kinds of evidence, the principle of total evidence should be applied to the dating of evolutionary events. As a historical science, paleontology studies past events we cannot observe directly. This raises questions of epistemic access, meaning that due to the fragmentary nature of the fossil record we may find ourselves without access to the relevant traces to adjudicate between rival hypotheses about the past. The problems and prospects of epistemic access are explored through a case study of the reconstruction of the colors of dinosaurs. The paper closes with a reflection on the Darwin- Lyell metaphor of the fossil record as a highly fragmentary history book, and a call for a reconsideration of the book metaphor in favor of a systems view of the geologic and fossil records. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence (...) of molecular structure cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

Across a wide range of cultural forms, including philosophy, cultural theory, literature and art, the figure of the clock has drawn suspicion, censure and outright hostility. In contrast, even while maps have been shown to be complicit with forms of domination, they are also widely recognised as tools that can be critically reworked in the service of more liberatory ends. This paper seeks to counteract the tendency to see clocks in this way, arguing that they have many more interesting (...) possibilities than they are usually given credit for. An analysis of approaches to clocks in continental philosophy critiques the way they have too often been dismissed as unworthy of further analysis, and argues that this dismissal is based upon an inadequate understanding of how clocks operate. Seeking to move towards more critical and curious approaches, the paper draws inspiration from critical cartography in order to call for the development of a ‘critical horology’ which would emphasise both the fundamentally political nature of clocks, and the potential for designing them otherwise. A discussion of temporal design provides a range of examples of how clocks might open up new horizons within the politics of time. (shrink)

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the (...) usual (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3- dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance. (shrink)

There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated based on (...) their explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

In her articles on the clock paradox and the relativity of time Luise Lange (1891–1978) defends the theory of relativity against philosophical refutations, by showing that the apparent clock paradox is not a paradox, but merely conflicts with common sense and is based on a misunderstanding of the theory. The following study explores, contextualizes and analyzes Lange’s clear and sophisticated contribution to the debate on the clock paradox for the first time.

This paper (i) gives necessary and sufficient conditions that clocks in an inertial lattice can be synchronized, (ii) shows that these conditions do not imply a universal light speed, and (iii) shows that the terrestrial redshift experiment provides evidence that clocks in a small inertial lattice in a gravitational field can be synchronized.

In a recent very interesting and important challenge to tracking theories of knowledge, Williams & Sinhababu claim to have devised a counter-example to tracking theories of knowledge of a sort that escapes the defense of those theories by Adams & Clarke. In this paper we will explain why this is not true. Tracking theories are not undermined by the example of the backward clock, as interesting as the case is.

Molecular biology is a relatively new and very successful branch of science but currently it faces challenges posed by very complex issues that cannot be addressed by a traditional reductionist approach. However, despite its origins in the providential shift of some theoretical physicists to biology, currently molecular biology is immersed in a blind trend in which high-throughput technology, able to generate trillions of data, is becoming the leading edge of a discipline that has traded rational and critical thinking (...) for computer power, data crunching and statistics in hope of finding, once more, its way. However, the complex questions facing MB may only be solved by a paradigm shift in the causal way of thinking, so that complex, emergent, non-linear phenomena may be effectively understood in top-down and not in bottom-up terms. (shrink)

This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries (...) to biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science. (shrink)

General Relativity’s Schwarzschild solution describes a spherically symmetric gravitational field as an utterly static thing. The Space Generation Model describes it as an absolutely moving thing. The light propagation time-delay experiment of Shapiro-Reasenberg [1] and the falling atomic clock experiment of Vessot-Levine [2] provide the ideal context for illustrating how, though the respective world views implied by these models are radically di fferent, they make nearly the same prediction for the results of these experiments.

We present Backward Clock, an original counterexample to Robert Nozick’s truth-tracking analysis of propositional knowledge, which works differently from other putative counterexamples and avoids objections to which they are vulnerable. We then argue that four ways of analysing knowledge in terms of safety, including Duncan Pritchard’s, cannot withstand Backward Clock either.

In this paper I propose to describe, in brief, a semiotic paradigm which results from the redefinition of the linguistic sign as a molecular sememe. Borrowing a tactic from Wittgenstein, I wish to use the game of chess as an analogy for the sake of describing what a molecular sememe is. Then I hope to use it further to sketch several implications of this semiotic paradigm for literary criticism and critical theory.

Without directly addressing the Demarcation Problem for logic—the problem of distinguishing logical vocabulary from others—we focus on distinctive aspects of logical vocabulary in pursuit of a second goal in the philosophy of logic, namely, proposing criteria for the justification of logical rules. Our preferred approach has three components. Two of these are effectively Belnap’s, but with a twist. We agree with Belnap’s response to Prior’s challenge to inferentialist characterisations of the meanings of logical constants. Belnap argued that for a logical (...) constant to exist, its rules must be conservative over a previously given consequence relation and guarantee the uniqueness of the constant. The twist is that we require logical vocabulary to be provably conservative, not over a previously given formal consequence relation, but over a previously given meaningful vocabulary of a language. Uniqueness is also a feature defined in terms of provability: if two syntactically distinguished expressions are governed by the same rules, then formulas with them as main operators are interderivable. Belnap’s criteria are not only those for the existence of a logical constant, but more: they are what distinguishes logical vocabulary from all other expressions. It is the defining mark of a logical constant that it is provably conservative over the fragment of the language which excludes it and that its rules guarantee its uniqueness. The third component is the topic neutrality of logic. The provable conservativeness of logic over a previously given vocabulary of a language is motivated, in part, by appeal to molecularism in the theory of meaning. Molecularity is a feature endorsed by the theory of meaning as a whole, so it does not distinguish logical constants from other expressions. The same is true for conservativeness. We argue that molecularity, and hence conservativeness, are implicit presuppositions of speakers’ use of language: the addition of new vocabulary to a language is presupposed to be conservative. But this presupposition is one that we should be able reflectively to endorse (such as when attempting a rational reconstruction of the use of the vocabulary). Thus, where conservativeness is found to fail, this defect should be remedied and the use of the vocabulary corrected (as in classical negation) or excised altogether (as in pejoratives). We go on to characterise a notion of topic neutrality, which we argue applies to logical vocabulary. We then note that reflective endorsement of the conservativeness of a topic neutral vocabulary requires a proof that the vocabulary is conservative relative to any base vocabulary. Thus we require that logical vocabulary be demonstrably conservative. Allying this requirement, distinctive of logic, to a general consideration about the commitments of assertion yields a mode of justification for logical constants akin to some conceptions of Harmony, i.e., to the idea that the consequences of assertion of a logical complex need to be warranted by the grounds and ought to be the strongest consequences warranted by the grounds. Intuitionistic logic acquires a somewhat familiar justification but emanating from a new motivation. (shrink)

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions (...) of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events. (shrink)

The question of what human consciousness “is,” how it “works,” and what it “does” is currently being approached by myriad fields of study, each with their own particular goals and research techniques. But despite the undeniably complex nature of this enigmatic phenomenon, the prevailing scientific and institutional paradigm seems to imply that only quantitative, experimentally focused approaches are a worthy means of illuminating “truth” about human consciousness. -/- In this paper, I begin by borrowing Popper’s metaphor of “clock systems” versus (...) “cloud systems,” applying each to quantitative and qualitative inquiry respectively. I make the case that, as Popper urged when articulating his ideas about physical determinism, the field of consciousness research must re-consider the possibility that rejecting the “cloud” or qualitative aspects of consciousness will lead to a stunted, incomplete picture of the phenomenon. Taking examples from my own work as an anthropologist and from the work of my colleagues within the field, I offer examples of and reflections on what qualitative research has to offer all of us who wish to gain insight into human consciousness; in particular, its nature, function, and potential. In response to the one-sidedness within the field, I urge researchers of all types to consider its “double nature” as a positive quality, and offer the reminder that no matter what differences in our particular goals and research styles, our meta-mission remains the same: to illuminate the great mystery that lies in the center of our personhood. (shrink)

One of the most plausible and widely discussed examples of strong emergence is molecular structure. The only detailed account of it, which has been very influential, is due to Robin Hendry and is formulated in terms of downward causation. This paper explains Hendry’s account of the strong emergence of molecular structure and argues that it is coherent only if one assumes a diachronic reflexive notion of downward causation. However, in the context of this notion of downward causation, the (...) strong emergence of molecular structure faces three challenges that have not been met and which have so far remained unnoticed. First, the putative empirical evidence presented for the strong emergence of molecular structure equally undermines supervenience, which is one of the main tenets of strong emergence. Secondly, it is ambiguous how the assumption of determinate nuclear positions is invoked for the support of strong emergence, as the role of this assumption in Hendry’s argument can be interpreted in more than one way. Lastly, there are understandings of causation which render the postulation of a downward causal relation between a molecule’s structure and its quantum mechanical entities, untenable. (shrink)

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers (...) yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

Unless one embraces activities as foundational, understanding activities in mechanisms requires an account of the means by which entities in biological mechanisms engage in their activities—an account that does not merely explain activities in terms of more basic entities and activities. Recent biological research on molecular motors exemplifies such an account, one that explains activities in terms of free energy and constraints. After describing the characteristic “stepping” activities of these molecules and mapping the stages of those steps onto the (...) stages of the motors’ hydrolytic cycles, researchers pieced together from images of the molecules in different hydrolyzation states accounts of how the chemical energy in ATP is transformed in the constrained environments of the motors into the characteristic activities of the motors. We argue that New Mechanism’s standard set of analytic categories—entities, activities, and organization—should be expanded to include constraints and energetics. Not only is such an expansion required descriptively to capture research on molecular motors but, more importantly from a philosophical point of view, it enables a non-regressive account of activities in mechanisms. In other words, this expansion enables a philosophical account of mechanistic explanation that avoids a regress of entities and activities “all the way down.” Rather, mechanistic explanation bottoms out in constraints and energetics. (shrink)

In “Beat the (Backward) Clock,” we argued that John Williams and Neil Sinhababu’s Backward Clock Case fails to be a counterexample to Robert Nozick’s or Fred Dretske’s Theories of Knowledge. Williams’ reply to our paper, “There’s Nothing to Beat a Backward Clock: A Rejoinder to Adams, Barker and Clarke,” is a further attempt to defend their counterexample against a range of objections. In this paper, we argue that, despite the number and length of footnotes, Williams is still wrong.

In this work, polystyrene/waste tires composites were prepared using the melt-mixing method.. The effect of the preparation conditions of the PS/waste tires composite is investigated in this work by using Gel permeation chromatography (GPC) technique. Stability at elevated temperatures were found to increase with the addition of waste tires to PS as confirmed by the results. GPC results indicate that the preparation conditions of the PS/waste tires composite has no effect on the Ps chains as indicated by GPC technique. The (...) signals of the GPC for unfilled and filled PS are similar. That evidences no thermo-mechanical chain degradation is taken place during the addition of the waste tires under the conditions of the melt-mixing process . (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how (...) the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

Existen inconsistencias fundamentales entre el paradigma de la biología molecular y el paradigma de la física contemporánea y, por lo tanto, el marco conceptual vigente en la biología molecular resulta insuficiente para abordar las cuestiones del origen y desarrollo de la forma y organización biológicas.

Manfred Eigen employs the terms language and communication to explain key recombination processes of DNA as well as to explain the self-organization of human language and communication: Life processes as well as language and communication processes are governed by the logic of a molecular syntax, which is the exact depiction of a principally formalizable reality. The author of the present contribution demonstrates that this view of Manfred Eigen’s cannot be sufficiently substantiated and that it must be supplemented by an (...) approach based on linguistic pragmatics. (shrink)

Contrary to John Bramhall and critics like him, Thomas Hobbes takes the view that no account of liberty or freedom can serve as the relevant basis on which to distinguish moral from nonmoral agents or explains the basis on which an agent becomes subject to law and liable to punishment. The correct compatibilist strategy rests, on Hobbes’s account, with a proper appreciation and description of the contractualist features that shape and structure the moral community. From this perspective human agents may (...) indeed use their liberty to make themselves moral agents. In doing this, however, they are not employing a distinct kind of liberty but rather using a liberty that they share with animals and other nonmoral agents to perform a distinct kind of act (i.e., consent) whereby they become moral agents subject to law and any punishments that are required to enforce it. ____ -/- Originally published in the Oxford Handbook of Philosophy in Early Modern Europe - eds. D. Clarke & C. Wilson, OUP 2011 -/- Republished in Recasting Hume and Early Modern Philosophy: Selected Essays - OUP 2021: Paul Russell]. (shrink)

Advanced medical imaging, such as CT, fMRI and PET, has undergone enormous progress in recent years, both in accuracy and utilization. Such techniques often bring with them an illusion of immediacy, the idea that the body and its diseases can be directly inspected. In this paper we target this illusion and address the issue of the reliability of advanced imaging tests as knowledge procedures, taking positron emission tomography in oncology as paradigmatic case study. After individuating a suitable notion of reliability, (...) we argue that PET is a highly theory-laden and non-immediate knowledge procedure, in spite of the photographic-like quality of the images it delivers; the diagnostic conclusions based on the interpretation of PET images are population-dependent; PET images require interpretation, which is inherently observer-dependent and therefore variable. We conclude with a three-step methodological proposal for enhancing the reliability of advanced medical imaging. (shrink)

Surface water sources in the oil producing Niger Delta region of Nigeria are highly susceptible to pollution by petroleum hydrocarbons and so it is important to understand the microbial diversity of such ecosystems. Water and sediment samples were collected between April-August, 2013 from Bodo creeks and taken to Environmental Microbiology laboratory of University of Portharcourt for analysis. A total of thirty aerobic heterotrophic bacterial strains isolated ranged from 3.0 - 7.0 × 104 cfu for surface water and 1.6 - 5.6 (...) × 104 cfu for sediment samples of Bodo creek using serial dilution and spread plate technique. Pure cultures of bacteria were obtained on the basis of their morphological characteristics and subjected to biochemical tests and further classified on the basis of 16S rRNA gene sequence analysis. The DNA was isolated from size fractionated samples and the diversity of bacteria in each fraction was studied using PCR amplification of partial 16S rRNA. The sequences were submitted to NCBIGen bank for identification and assigning of accession numbers. The isolated aerobic heterotrophic bacteria belong to the families of Enterobacteriaceae, Bacilliceae, Alcaligenaceae, Pseudomonadaceae, Flavobactericeae and Planococcaceae. (shrink)

Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to “transcend the laws of chemistry”. It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical “law”, for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its (...) biological role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters, which causally couple two properties or processes which would otherwise be uncorrelated. Additionally, adapters work by acting as intermediate rather than cooperating causes. (shrink)

The type-level abstraction is a formal way to represent molecular structures in biological practice. Graphical representations of molecular structures of biological objects are also used to identify functional processes of things. This paper will reveal that category theory is a formal mathematical language not only to visualize molecular structures of biological objects as type-level abstraction formally but also to understand how to infer biological functions from the molecular structures of biological objects. Category theory is a toolkit (...) to understand biological knowledge at the type-level formally, not individual token-level, as well as typical heuristic strategies in molecular biology. (shrink)

I will relate some social and epistemic aspects involved in the conceptual development of the genetic model in the early Molecular Biology. I will use the link between Biology and Physics as a framework, which supports such assumptions, providing new methodologies, but mainly as a framework that provides a model of objectivity developed within Modern Tradition. Finally, I will interpret this relationship from the pragmatist perspective to embrace Rorty’s thesis on «the ontological priority of the social» which implies understanding (...) biology as a part of a general cultural politics. (shrink)

Adrian Heathcote has proposed a truth-making account of knowledge that combines traditional conditions of justified true belief with the truth-making condition, which would jointly provide us with the sufficient condition of knowledge, and this truth-maker account of knowledge in turn explains why a gettiered justified true belief fails to be regarded as a genuine instance of knowledge. In this paper, by the comparison of two different casual models that are illustrated by the thermometer and the clock respectively, however, it will (...) be argued that Heathcote’s truth-making account of knowledge fails to cope with the Gettier case of the stopped clock and therefore is called for some further remedy. (shrink)

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows a new avenue for intertheoretic reduction to be seen. Reductions in biology are possible, when one fully recognises that a sufficient condition for a reduction in biology is a molecular model of 1) only the demonstrated causal parameters of a biological model and 2) only within a replicable experimental background. These intertheoretic identifications –which are ubiquitous in biology and (...) form the basis of ruthless reductions (Bickle 2003)- are criticised as merely “local” (Sullivan 2009) or “fragmentary” (Schaffner 2006). However, in an instructive case, a biological model is preserved in molecular terms, and a complex biological phenomenon has been successfully reduced. In doing this the molecular model remains valid in a broader range of background conditions and meaningfully unites disparate biological phenomena. (shrink)

A puzzle of an unmarked clock, used by Timothy Williamson to question the KK principle, was separately adapted by David Christensen and Adam Elga to critique a principle of Rational Reflection. Both authors, we argue, flout the received relationship between ideal agency and the classical distinction between systematic and random error, namely that ideal agents are subject only to the latter. As a result, these criticisms miss their mark.

Neil Sinhababu and I presented Backward Clock, an original counterexample to Robert Nozick’s truth-tracking analysis of propositional knowledge. Fred Adams, John Barker and Murray Clarke argue that Backward Clock is no such counterexample. Their argument fails to nullify Backward Clock which also shows that other tracking analyses, such as Dretske’s and one that Adams et al. may well have in mind, are inadequate.

In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...) visualize the arborizations of single neurons that were “colored brownish black even to their finest branchlets, standing out with unsurpassable clarity upon a transparent yellow background. All was sharp as a sketch with Chinese ink”. The high quality of both the visualization of individual nerve cells and the work performed on studying the anatomy of the central nervous system lead Ramon y Cajal to the conclusion that axons output the nervous impulses to the dendrites or the soma of other target neurons. (shrink)

The Aristotelian axiom that function follows form was beautifully instantiated in molecular biology by the discovery of DNA’s structure that immediately suggested how DNA might work as depository and vehicle for genetic information. However, later on molecular biology became infatuated with the gene that became the center of the universe. This gene-centered viewpoint is an obstacle for the emerging field of evo-devo aiming at finding the causal connections between evolution and biological development. Here it is argued that (...) class='Hi'>molecular biology must reject the narrow-minded causality associated with the gene-centered view and so it must recover to the spirit of Aristotelian natural history and its four types of causation in order to foster the evo-devo field of research. (shrink)

The layers of a solvent liquid flowing around a moving molecule have a finite thickness corresponding to the finite dimensions of the solvent molecules. Taking this feature into account leads to a modification of Stokes’ laws of the relation between friction and viscosity in continuous media. We derive the observed order of magnitude of the microfriction, for rotation as well as translation, and its approximately correct dependence on the radii of moving and solvent molecules.

In this paper, I defend the agent/patient distinction against critics who argue that causal interactions are symmetrical. Specifically, I argue that there is a widespread type of causal interaction between distinct entities, resulting in a type of ontological asymmetry that provides principled grounds for distinguishing agents from patients. The type of interaction where the asymmetry is found is when one of the entities undergoes a change in kind, structure, powers, or intrinsic properties as a result of the interaction while the (...) other does not. Interactions of this type are widespread in molecular biology and chemistry. I focus specifically on (i) the actions of enzymes on substrates and (ii) water molecules breaking the bonds of polarized molecules. Finally, I respond to objections by laying out and to a limited extent defending three commitments of my account: emergent entities and powers, realism about chemical kinds or structures, and the assumption of the agent/patient distinction in functional attributions in biology. (shrink)

The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, (...) I argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

1900 was a remarkable year for science. Several ground-breaking events took place, in physics, biology and psychology. Planck introduced the quantum concept, the work of Mendel was rediscovered, and Sigmund Freud published The Interpretation of Dreams . These events heralded the emergence of completely new areas of inquiry, all of which greatly affected the intellectual landscape of the 20 th century, namely quantum physics, genetics and psychoanalysis. What do these developments have in common? Can we discern a family likeness, a (...) basic affinity between them, so that we can use the one to deepen our understanding of the other? One common denominator is that they open up realms of inquiry that are significantly different from the world of everyday experience, namely the realm of elementary particles, of genes and genomes, and of the unconscious. But to what extent can we meaningfully argue, for instance, that the genome is the biological unconscious, and the unconscious the psychic genome? To address these questions, I will build on the work of two key intellectual figures who have explored the affinities of these developments in depth, namely Erwin Schrödinger (a quantum physicist and avid reader of Schopenhauer who initiated molecular biology) and Jacques Lacan (who reframed the specificity of psychoanalysis with the help of 20 th century science: the era of structural linguistics, but also of quantum physics, molecular biology, bioinformatics and DNA). (shrink)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

In this paper, I will reread the history of molecular genetics from a psychoanalytical angle, analysing it as a case history. Building on the developmental theories of Freud and his followers, I will distinguish four stages, namely: (1) oedipal childhood, notably the epoch of model building (1943–1953); (2) the latency period, with a focus on the development of basic skills (1953–1989); (3) adolescence, exemplified by the Human Genome Project, with its fierce conflicts, great expectations and grandiose claims (1989–2003) and (...) (4) adulthood (2003–present) during which revolutionary research areas such as molecular biology and genomics have achieved a certain level of normalcy—have evolved into a normal science. I will indicate how a psychoanalytical assessment conducted in this manner may help us to interpret and address some of the key normative issues that have been raised with regard to molecular genetics over the years, such as ‘relevance’, ‘responsible innovation’ and ‘promise management’. (shrink)

In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, (...) macroscopic and microscopic entities inhabit different “worlds”: the former is ruled by gravity and inertia, whereas the latter is governed by Brownian motion. One implication is that we should be extremely skeptical of models and analogies that seek to explain properties of microscopic entities by appealing to properties of macroscopic ones. Unfortunately, this is precisely what the appeal to engineering metaphors in molecular biology attempts to do. Molecular biologists routinely resort to such metaphors because they are familiar and intuitively intelligible. But if our machines were the size of molecules it would be impossible for them to function the way they do. It follows that we should avoid distorting biological reality by construing it in engineering terms. In this chapter I examine four key metaphors in molecular biology – “genetic program,” “cellular circuitry,” “molecular machine,” and “molecular motor” – and I argue that their deficiencies derive from their neglect of scale. I also try to explain why many biologists today appear to have forgotten the importance of scale that Haldane drew attention to in his essay. I suggest that the reason has to do with the influence of Schrödinger’s argument in 'What is Life?' regarding the stability of the gene. (shrink)

Denis Nobel looks at four important misinterpretations of molecular biology concerning evolutionary processes and demonstrates that the new synthesis today looks rather outdated. The modern synthesis is nearly 80 years old. The proponents who worked out the modern synthesis had no access to the current knowledge on cell biology, genetics, epigenetics, RNA biology and virology. Therefore this contribution adds several aspects which Nobel’s article does not explicitly mention, providing some examples for a better understanding of evolutionary novelty.

I consider three explanatory strategies from recent systems biology that are driven by mathematics as much as mechanistic detail. Analysis of differential equations drives the first strategy; topological analysis of network motifs drives the second; mathematical theorems from control engineering drive the third. I also distinguish three abstraction types: aggregations, which simplify by condensing information; generalizations, which simplify by generalizing information; and structurations, which simplify by contextualizing information. Using a common explanandum as reference point—namely, the robust perfect adaptation of chemotaxis (...) in Escherichia coli—I argue that each strategy invokes a different combination of abstraction types and that each targets its abstractions to different mechanistic details. (shrink)

The guide explains the basic concepts of natural, social and evolutionary components and methods of risk management and control of modern biotechnologies stemming from the general theory of human evolution. A a transdisciplinary approach is a feature of the presentation of the material The risk is considered from the point of view of evolutionary anthropology, as a basic element of a stable evolutionary strategy of our biological species and the basis of a combination of natural-scientific and humanitarian forms of presentation (...) and interpretation of the material. CONTENT BIOSAFETY AND BIOETHICS IN BIOTECHNOLOGY (Introduction). Part 1. BIOTECHNOLOGY AS A FACTOR OF EVOLUTION AND A SOURCE OF TECHNOGENIC RISK. Chapter 1. GENERAL THEORY OF TECHNOLOGICAL RISK. Chapter 2. RISK AS AN ATTRIBUTE OF STABLE HUMAN EVOLUTIONARY STRATEGY. Chapter 3. BIOTECHNOLOGY AS A SOURCE OF BIORISKS Chapter 4. COMPONENTS OF THE "BIOLOGICAL FACTOR" OF RISK. Chapter 5. BIOLOGICAL WEAPONS and BIOTERRORISM. Part 2. BIOLOGICAL, SOCIAL AND EVOLUTIONARY COMPONENTS OF THE RISK OF MODERN BIOTECHNOLOGIES Chapter 6. RISK MANAGEMENT DURING BIOTECHNOLOGICAL RESEARCH.. Chapter 7. BIOTECHNOLOGY AS A SOURCE OF SOCIAL INSTABILITY. Chapter 8. BIOTECHNOLOGY AS A SOURCE OF CIVILIZATIONAL RISK. -/- . (shrink)