We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical (...) and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)

Aristotle was the first thinker to articulate a taxonomy of scientific knowledge, which he set out in Posterior Analytics. Furthermore, the “special sciences”, i.e., biology, zoology and the natural sciences in general, originated with Aristotle. A classical question is whether the mathematical axiomatic method proposed by Aristotle in the Analytics is independent of the special sciences. If so, Aristotle would have been unable to match the natural sciences with the scientific patterns he established in the Analytics. In (...) this paper, I reject this pessimistic approach towards the scientific value of natural sciences. I believe that there are traces of biology in the Analytics as well as traces of the Analytics’ theory in zoological treatises. Moreover, for a lack of chronological clarity, I think it’s better to unify Aristotle’s model of scientific research, which includes Analytics and the natural sciences together. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to (...) develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Robert Henman’s article, Can brain scanning and imaging techniques contribute to a theory of thinking? came to my attention recently. My own work over the years has included applications of mathematics in the biological sciences, collaboration in experimental work in biochemistry, as well as work in the philosophy of the biological sciences. Henman suggests something that, at present, would be out of the ordinary.

In the paper we examine the method of axiomatic rejection used to describe the set of nonvalid formulae of Aristotle's syllogistic. First we show that the condition which the system of syllogistic has to fulfil to be ompletely axiomatised, is identical to the condition for any first order theory to be used as a logic program. Than we study the connection between models used or refutation in a first order theory and rejected axioms for that theory. We show (...) that any formula of syllogistic enriched with classical connectives is decidable using models in the domain with three members. (shrink)

The criticism of Hilbert's axiomatic system of geometry by Mate Meršić (Merchich, 1850-1928), presented in his work "Organistik der Geometrie" (1914, also in "Modernes und Modriges", 1914), is analyzed and discussed. According to Meršić, geometry cannot be based on its own axioms, as a logical analysis of spatial intuition, but must be derived as a "spatial concretion" using "higher" axioms of arithmetic, logic, and "rational algorithmics." Geometry can only be one, because space is also only one. It cannot be (...) reduced to manipulation with symbols but has to deal with concepts and provide real knowledge. According to Meršić, aiming at some particular proof of the consistency of the whole axiomatic system is meaningless because the consistency follows from the truth of individual axioms based on spatial intuition. It is impossible, according to Meršić, for the geometric axioms to be mutually independent because they must be interconnected as essential parts of a whole. Although Meršić did not recognize all the advantages of Hilbert's formalization of geometry, he clearly pointed out some crucial limitations of the axiomatic method. (shrink)

A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) scientists integrate the cognitive, social, material, and cultural dimensions of practice. Her findings and conclusions have broad implications for researchers in philosophy, science studies, cognitive science, and interdisciplinary studies, as well as scientists, educators, policy makers, and funding agencies. In studying the epistemic practices of scientists, Nersessian pushes the boundaries of the philosophy of science and cognitive science into areas not ventured before. She recounts a decades-long, wide-ranging, and richly detailed investigation of the innovative interdisciplinary modeling practices of bioengineering researchers in four university laboratories. She argues and demonstrates that the methods of cognitive ethnography and qualitative data analysis, placed in the framework of distributed cognition, provide the tools for a philosophical analysis of how scientific discoveries arise from complex systems in which the cognitive, social, material, and cultural dimensions of problem-solving are integrated into the epistemic practices of scientists. Specifically, she looks at how interdisciplinary environments shape problem-solving. Although Nersessian’s case material is drawn from the bioengineering sciences, her analytic framework and methodological approach are directly applicable to scientific research in a broader, more general sense, as well. (shrink)

I describe two traditions of philosophical accounts of evidence: one characterizes the notion in terms of signs of success, the other characterizes the notion in terms of conditions of success. The best examples of the former rely on the probability calculus, and have the virtues of generality and theoretical simplicity. The best examples of the latter describe the features of evidence which scientists appeal to in practice, which include general features of methods, such as quality and relevance, and general features (...) of evidence, such as patterns in data, concordance with other evidence, and believability of the evidence. Two infamous episodes from biomedical research help to illustrate these features. Philosophical characterization of these latter features—conditions of success—has the virtue of potential relevance to, and descriptive accuracy of, practices of experimental scientists. (shrink)

Ernst Mayr argued that the emergence of biology as a special science in the early nineteenth century was possible due to the demise of the mathematical model of science and its insistence on demonstrative knowledge. More recently, John Zammito has claimed that the rise of biology as a special science was due to a distinctive experimental, anti-metaphysical, anti-mathematical, and anti-rationalist strand of thought coming from outside of Germany. In this paper we argue that this narrative neglects the important (...) role played by the mathematical and axiomatic model of science in the emergence of biology as a special science. We show that several major actors involved in the emergence of biology as a science in Germany were working with an axiomatic conception of science that goes back at least to Aristotle and was popular in mid-eighteenth-century German academic circles due to its endorsement by Christian Wolff. More specifically, we show that at least two major contributors to the emergence of biology in Germany—Caspar Friedrich Wolff and Gottfried Reinhold Treviranus—sought to provide a conception of the new science of life that satisfies the criteria of a traditional axiomatic ideal of science. Both C.F. Wolff and Treviranus took over strong commitments to the axiomatic model of science from major philosophers of their time, Christian Wolff and Friedrich Wilhelm Joseph Schelling, respectively. The ideal of biology as an axiomatic science with specific biological fundamental concepts and principles thus played a role in the emergence of biology as a special science. (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)

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)

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)

While seeking novel food sources to feed the increasing population of the globe, several alternatives have been discussed, including algae, fungi or in vitro meat. The increasingly propagated usage of farmed insects for human nutrition raises issues regarding food safety, consumer information and animal protection. In line with law, insects like any other animals must not be reared or manipulated in a way that inflicts unnecessary pain, distress or harm on them. Currently, there is a great need for research in (...) the area of insect welfare, especially regarding species-specific needs, health, farming systems and humane methods of killing. Recent results from neurophysiological, neuroanatomical and behavioral sciences prompt caution when denying consciousness and therefore the likelihood of presence of pain and suffering or something closely related to it to insects. From an animal protection point of view, these issues should be satisfyingly solved before propagating and establishing intensive husbandry systems for insects as a new type of mini-livestock factory farming. (shrink)

[penultimate draft; prepared for publication in Aristotle’s Parts of Animals: A Critical Guide, ed. Sophia Connell – please cite final version] -/- Parts of Animals II.10 makes a new beginning in Aristotle’s study of animals. In it, Aristotle proposes to “now speak as if we are once more at an origin, beginning first with those things that are primary” (655b28-9). This is the start of his account of the non-uniform parts of blooded animals: parts such as eyes, noses, mouths, etc., (...) as opposed to uniform parts like blood and flesh. PA II.10 proposes a new strategy for studying these parts: “one ought to speak about the human kind first” (656a10). Beginning “first” with the “primary” things thus amounts to beginning with humans (655b28-9). -/- Why does Aristotle think this strategy is appropriate for his project? One answer is that it reflects a fundamental anthropocentrism. Lloyd, for instance, has raised the possibility that the basic assumptions that guide Aristotle’s biology may to some extent reflect the anthropocentrism of his culture, where the relation of humans to animals was “a preoccupation of popular beliefs”. In this paper, I develop an interpretation that both builds on and challenges this suggestion. I do so by investigating how Aristotle thinks this strategy works in theory and in practice: his justifications for adopting it and its interaction with his scientific commitments. I argue that Aristotle adopts it in part because he thinks that humans are such that his scientific concepts apply to them in a particularly clear way. (This too is a form of anthropocentrism: one that might be resisted by arguing that humans are not the best illustrations of these concepts—that Aristotle ought to look elsewhere for models with the features he desires.) -/- More specifically, Aristotle holds that starting with humans helps establish the causal explanations of the parts of other animals, particularly when they are recalcitrant. What makes humans suitable for this role is a special teleological relation between their parts and the ends they serve: in humans, he supposes, this connection is particularly tight (in a way I explain below). Consequently, Aristotle thinks he can use humans to illuminate which sorts of features tend to be for the sake of which ends, and then extend the results of this inquiry to the parts of the other animals. (shrink)

In his famous article “The Unreasonable Effectiveness of Mathematics in the Natural Sciences” Eugen Wigner argues for a unique tie between mathematics and physics, invoking even religious language: “The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve”. The possible existence of such a unique match between mathematics and physics has been extensively discussed by philosophers and historians of mathematics. Whatever the merits (...) of this claim are, a further question can be posed with regard to mathematization in science more generally: What happens when we leave the area of theories and laws of physics and move over to the realm of mathematical modeling in interdisciplinary contexts? Namely, in modeling the phenomena specific to biology or economics, for instance, scientists often use methods that have their origin in physics. How is this kind of mathematical modeling justified? (shrink)

Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory (...) could translate empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his (...) work was disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

In the light of the results obtained during the last two decades in analysis of signals by time series, it has become evident that the tools of non linear dynamics have their elective role of application in biological, and, in particular, in neuro-physiological and psycho-physiological studies. The basic concept in non linear analysis of experimental time series is that one of recurrence whose conceptual counterpart is represented from variedness and variability that are the foundations of complexity in dynamic processes. Thus, (...) the recurrence plots and the Recurrence Quantification Analysis (RQA) are discussed. It is shown that RQA represents the most general and correct methodology in investigation of experimental time series. By it we arrive to inspect the inner structure of the time series connected to the signals under investigation. Linked to RQA we prospect also the method CZF, recently introduced by us. It is able to account for a true estimation of variability of signals in time as well as in frequency domain. And, consequently, it may be used in conjunction with classical Fourier analysis, accounting however that it is inappropriate in analysis of non linear and non stationary experimental time series. The use of CZF method in fractal analysis is also considered in addition to standard index as Hurst exponent. A large field of possible applications in neurological as well as in psycho-physiological studies is given. Also, there are given examples of other and (possibly linked) applications as example the analysis of beat-to-beat fluctuations of human heartbeat intervals that is sovereign in psycho-physiological studies. We give applications on some different planes to evidence the particular sensitivity of such methods. We reach the objective to show that the previously exposed methods are also able to predict in advance the advent of ventricular tachycardia and/or of ventricular fibrillation. The RQA analysis gives good results. The CZF method gives the most excellent results showing that it is able to give very significant indexes of prediction. We also apply such methods in investigation of state anxiety, and proposing in detail a quantum like model of such phenomenological status of the mind. (shrink)

The philosophy of science of Patrick Suppes is centered on two important notions that are part of the title of his recent book (Suppes 2002): Representation and Invariance. Representation is important because when we embrace a theory we implicitly choose a way to represent the phenomenon we are studying. Invariance is important because, since invariants are the only things that are constant in a theory, in a way they give the “objective” meaning of that theory. Every scientific theory gives a (...) representation of a class of structures and studies the invariant properties holding in that class of structures. In Suppes’ view, the best way to define this class of structures is via axiomatization. This is because a class of structures is given by a definition, and this same definition establishes which are the properties that a single structure must possess in order to belong to the class. These properties correspond to the axioms of a logical theory. In Suppes’ view, the best way to characterize a scientific structure is by giving a representation theorem for its models and singling out the invariants in the structure. Thus, we can say that the philosophy of science of Patrick Suppes consists in the application of the axiomatic method to scientific disciplines. What I want to argue in this paper is that this application of the axiomatic method is also at the basis of a new approach that is being increasingly applied to the study of computer science and information systems, namely the approach of formal ontologies. The main task of an ontology is that of making explicit the conceptual structure underlying a certain domain. By “making explicit the conceptual structure” we mean singling out the most basic entities populating the domain and writing axioms expressing the main properties of these primitives and the relations holding among them. So, in both cases, the axiomatization is the main tool used to characterize the object of inquiry, being this object scientific theories (in Suppes’ approach), or information systems (for formal ontologies). In the following section I will present the view of Patrick Suppes on the philosophy of science and the axiomatic method, in section 3 I will survey the theoretical issues underlying the work that is being done in formal ontologies and in section 4 I will draw a comparison of these two approaches and explore similarities and differences between them. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical (...) taxonomists sought to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

Prompted by the thesis that an organism’s umwelt possesses not just a descriptive dimension, but a normative one as well, some have sought to annex semiotics with ethics. Yet the pronouncements made in this vein have consisted mainly in rehearsing accepted moral intuitions, and have failed to concretely further our knowledge of why or how a creature comes to order objects in its environment in accordance with axiological charges of value or disvalue. For want of a more explicit account, theorists (...) writing on the topic have relied almost exclusively on semiotic insights about perception originally designed as part of a sophisticated refutation of idealism. The end result, which has been a form of direct givenness, has thus been far from convincing. In an effort to bring substance to the right-headed suggestion that values are rooted in the biological and conform to species-specific requirements, we present a novel conception that strives to make explicit the elemental structure underlying umwelt normativity. Building and expanding on the seminal work of Ayn Rand in metaethics, we describe values as an intertwined lattice which takes a creature’s own embodied life as its ultimate standard; and endeavour to show how, from this, all subsequent valuations can in principle be determined. (shrink)

Distributive justice deals with allocations of goods and bads within a group. Different principles and results of distributions are seen as possible ideals. Often those normative approaches are solely framed verbally, which complicates the application to different concrete distribution situations that are supposed to be evaluated in regard to justice. One possibility in order to frame this precisely and to allow for a fine-grained evaluation of justice lies in formal modelling of these ideals by metrics. Choosing a metric that is (...) supposed to map a certain ideal has to be justified. Such justification might be given by demanding specific substantiated axioms, which have to be met by a metric. This paper introduces such axioms for metrics of distributive justice shown by the example of needs-based justice. Furthermore, some exemplary metrics of needs-based justice and a three dimensional method for visualisation of non-comparative justice axioms or evaluations are presented. Therewith, a base worth discussing for the evaluation and modelling of metrics of distributive justice is given. (shrink)

This chapter tries to answer the following question: How should we conceive of the method of mathematics, if we take a naturalist stance? The problem arises since mathematical knowledge is regarded as the paradigm of certain knowledge, because mathematics is based on the axiomatic method. Moreover, natural science is deeply mathematized, and science is crucial for any naturalist perspective. But mathematics seems to provide a counterexample both to methodological and ontological naturalism. To face this problem, some authors (...) tried to naturalize mathematics by relying on evolutionism. But several difficulties arise when we try to do this. This chapter suggests that, in order to naturalize mathematics, it is better to take the method of mathematics to be the analytic method, rather than the axiomatic method, and thus conceive of mathematical knowledge as plausible knowledge. (shrink)

The debate about the foundations of mathematical sciences traces back to Greek antiquity, with Euclid and the foundations of geometry. Through the flux of history, the debate has appeared in several shapes, places, and cultural contexts. Remarkably, it is a locus where logic, philosophy, and mathematics meet. In mathematical astronomy, Nicolaus Copernicus’s axiomatic approach toward a heliocentric theory of the universe has prompted questions about foundations among historians who have studied Copernican axioms in their terminological and logical aspects but (...) never examined them as a question of mathematical practice. Copernicus provides seven unproved assumptions in the introduction of the brief treatise entitled Nicolaus Copernicus’s draft on the models of celestial motions established by himself, better known as Commentariolus (ca. 1515), published circa 30 years before the final composition of his heliocentric theory (On the revolutions of the heavenly spheres, 1543). The assumptions deal with the renowned Copernican hypothesis of considering the Earth in motion and the Sun, not affected by motion, near the center of the universe. Although Copernicus decides to omit the proofs for the sake of brevity, the deductions in the Commentariolus are supposed to be drawn from the initial seven assumptions. Questions on the nature (are they postulates or axioms?) and the logic (is there an internal rigor?) of those assumptions have yet to be fully explored. By examining Copernicus’s seven assumptions as a question of mathematical practice, it is possible to hold historical, philosophical, and logical aspects of Copernican axiomatics together and understand them as part of Copernicus’s intuition and creativity. (shrink)

The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of (...) a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology. (shrink)

Cattle farming is a traditional agricultural system that contributes to the rural economic, social, and cultural values of the communities. Cattle as common with other livestock, are affected by many diseases that cause mortality and economic losses. In many rural households, the use of plants and associated knowledge are popular for managing cattle diseases, especially in areas experiencing challenges with conventional veterinary medicine. Evidence on the documentation of indigenous knowledge and biological evaluation of plants used against cattle diseases remain understudied (...) and fragmented. The aim of the review is to collate and analyze the ethnoveterinary knowledge and biological evaluation of plants used against cattle diseases in South Africa. Different scientific databases were systematically explored to extract data from 37 eligible studies. A total of 310 medicinal plants from 81 families were used to treat 10 categories of cattle diseases across seven (7) provinces in South Africa. Leguminosae (Fabaceae), Compositae (Asteraceae), Asparagaceae, and Xanthorrhoeaceae were the most frequently used plant families. Common plant parts used were leaves and roots. Twenty-seven (27) combination remedies involving 2–6 plants were identified as treatment regimes against cattle diseases. Common preparation methods were infusion and decoction while the administration mode was predominantly unspecified (52%) while oral and topical contributed 26 and 22%, respectively. In terms of diseases, the most treated ones were general systems infection, reproduction disorders, and gastrointestinal problems. Currently, an estimated 21% of the 310 plants have been evaluated for diverse biological activities using relevant bioassays related to cattle diseases. Antibacterial activity remained the most studied biological activity. Evidence from the review revealed the significance of ethnoveterinary medicine against cattle diseases especially in rural areas of South Africa. Nevertheless, the use of plants for cattle diseases among other ethnic groups, particularly in the Northern Cape and Western Cape, remains understudied. (shrink)

The idea of rejection originated by Aristotle. The notion of rejection was introduced into formal logic by Łukasiewicz [20]. He applied it to complete syntactic characterization of deductive systems using an axiomatic method of rejection of propositions [22, 23]. The paper gives not only genesis, but also development and generalization of the notion of rejection. It also emphasizes the methodological approach to biaspectual axiomatic method of characterization of deductive systems as acceptance (asserted) systems and rejection (refutation) (...) systems, introduced by Łukasiewicz and developed by his student Słupecki, the pioneers of the method, which becomes relevant in modern approaches to logic. (shrink)

In this paper I take evolutionary biology as an example to reflect on the role of philosophy and on the transformations that philosophy is constantly stimulated to do in its own approach when dealing with science. I consider that some intellectual movements within evolutionary biology (more specifically, the various calls for 'synthesis') express metascientific views, i.e., claims about 'what it is to do research' in evolutionary biology at different times. In the construction of metascientific views I see (...) a fundamental role to be played by philosophy, and, at the same time, a need to complement the philosophical methods with many more methods coming from other sciences. What leads philosophy out of itself is its own attention to scientific practice. My humble methodological suggestions are, at this stage, only meant to help us imagine metascientific views that are built with a more scientific, interdisciplinary approach, in order to attenuate partiality, subjectivity and impressionism in describing the scientific community. And yet, we should not be naïve and imbued with the myth of 'datadriven' research, especially in this field: other complex issues about metascientific views call for a serious, constant philosophical reflection on scientific practice. (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)

This chapter explores some of the major developments in the philosophical understanding of suicide in 19th Century Western thought. Two developments in particular are considered. The first is a widespread shift towards thinking about suicide in medical terms rather than moral terms. Deploying methods initiated by a number of French and German thinkers in the preceding century who worked at the then emerging interface between the social and biological sciences, a number of 19th century thinkers ejected what they took to (...) be old metaphysical superstitions about ‘good’ and ‘evil’, and replaced them with (allegedly) hard-nosed scientific diagnoses of ‘health’ and ‘sickness’. Dismissing traditional moral arguments against the permissibility of suicide, the phenomenon came to be viewed as a symptom of decline or degeneration. How variations of this view, in biological and social contexts, reorientated practical responses to suicide in terms of treatment rather than moral condemnation is explored. The second 19th century development in philosophical thought with respect to suicide the chapter considers concerns its place in one of the most significant controversies in Germany from 1860 to the turn of the century: the Pessimismusstreit or ‘pessimism dispute’. While philosophical pessimism might be thought to vindicate or even entail suicide, many of the most prominent pessimists—including Arthur Schopenhauer and Eduard von Hartmann—denied that this was the case, and perhaps surprisingly took suicide to involve a special kind of moral and/or epistemic failing. The chapter aims to elucidate the different arguments which pessimists appealed to in order to ground this position. (shrink)

This paper presents a formalization of the classical proof of completeness in Henkin-style developed by Troelstra and van Dalen for intuitionistic logic with respect to Kripke models. The completeness proof incorporates their insights in a fresh and elegant manner that is better suited for mechanization. We discuss details of our implementation in the Lean theorem prover with emphasis on the prime extension lemma and construction of the canonical model. Our implementation is restricted to a system of intuitionistic propositional logic with (...) implication, conjunction, disjunction, and falsity given in terms of a Hilbert-style axiomatization. As far as we know, our implementation is the first verified Henkin-style proof of completeness for intuitionistic logic following Troelstra and van Dalen's method in the literature. (shrink)

Study represents an application of the neutrosophic method, for solving the contradiction between communication and information. In addition, it recourse to an appropriate method of approaching the contradictions: Extensics, as the method and the science of solving the contradictions. The research core is the reality that the scientific research of communication-information relationship has reached a dead end. The bivalent relationship communicationinformation, information-communication has come to be contradictory, and the two concepts to block each other. After the critical (...) examination of conflicting positions expressed by many experts in the field, the extensic and inclusive hypothesis is issued that information is a form of communication. The object of communication is the sending of a message. The message may consist of thoughts, ideas, opinions, feelings, beliefs, facts, information, intelligence or other significational elements. When the message content is primarily informational, communication will become information or intelligence. The arguments of supporting the hypothesis are: a) linguistic (the most important being that there is "communication of information" but not "information of communication"; also, it is clarified and reinforced the over situated referent, that of the communication as a process), b) systemic-procedural (in the communication system is developing an information system; the informing actant is a type of communicator, the information process is a communication process), c) practical (the delimitation eliminates the efforts of disparate and inconsistent understanding of the two concepts), d) epistemological arguments (the possibility of intersubjective thinking of reality is created), linguistic arguments, e) logical and realistic arguments (it is noted the situation that allows to think coherently in a system of concepts - derivative series or integrative groups) f) and arguments from historical experience (the concept of communication has temporal priority, it appears 13 times in Julius Caesar’s writings ). In an axiomatic conclusion, the main arguments are summarized in four axioms: three are based on the pertinent observations of specialists, and the fourth is a relevant application of Florentin Smarandache’s neutrosophic theory. (shrink)

Biological conservation practices and approaches take many forms. Conservation projects do not only differ in their aims and methods, but also concerning their conceptual and normative background assumptions and their underlying motivations and objectives. We draw on philosophical distinctions from the ethics of conservation to explain variances of different positions on conservation projects along six dimensions: (1) conservation ideals, (2) intervention intuitions, (3) the moral considerability of nonhuman beings, (4) environmental values, (5) views on nature and (6) human roles in (...) nature. The result is a map of the moral landscape of biological conservation, on which these six dimensions are layered. This map functions as a heuristic tool to understand conceptual and normative foundations of specific conservation projects, which we will illustrate with four paradigmatic examples: the Pisavaara Strict Nature Reserve, Predator Free New Zealand, the Oostvaardersplassen Nature Reserve and the Great Green Wall Project. With this map as a heuristic tool, we aim to conceptually illuminate disagreement and clarify misunderstandings between representatives of different environmental protection strategies and to show that the same project can be supported (or criticised) on different grounds. (shrink)

We study the general problem of axiomatizing structures in the framework of modal logic and present a uniform method for complete axiomatization of the modal logics determined by a large family of classes of structures of any signature.

We study the general problem of axiomatizing structures in the framework of modal logic and present a uniform method for complete axiomatization of the modal logics determined by a large family of classes of structures of any signature.

The idea of rejection originated by Aristotle. The notion of rejection was introduced into formal logic by Łukasiewicz [20]. He applied it to complete syntactic characterization of deductive systems using an axiomatic method of rejection of propositions [22, 23]. The paper gives not only genesis, but also development and generalization of the notion of rejection. It also emphasizes the methodological approach to biaspectual axiomatic method of characterization of deductive systems as acceptance (asserted) systems and rejection (refutation) (...) systems, introduced by Łukasiewicz and developed by his student Słupecki, the pioneers of the method, which becomes relevant in modern approaches to logic. (shrink)

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten (...) stuck on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, (...) and physiology, which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

Corcoran’s 27 entries in the 1999 second edition of Robert Audi’s Cambridge Dictionary of Philosophy [Cambridge: Cambridge UP]. -/- ancestral, axiomatic method, borderline case, categoricity, Church (Alonzo), conditional, convention T, converse (outer and inner), corresponding conditional, degenerate case, domain, De Morgan, ellipsis, laws of thought, limiting case, logical form, logical subject, material adequacy, mathematical analysis, omega, proof by recursion, recursive function theory, scheme, scope, Tarski (Alfred), tautology, universe of discourse. -/- The entire work is available online free at (...) more than one website. Paste the whole URL. http://archive.org/stream/RobertiAudi_The.Cambridge.Dictionary.of.Philosophy/Robert.Audi_The.Cambrid ge.Dictionary.of.Philosophy -/- The 2015 third edition will be available soon. Before you think of buying it read some reviews on Amazon and read reviews of its competition: For example, my review of the 2008 Oxford Companion to Philosophy, History and Philosophy of Logic,29:3,291-292. URL: http://dx.doi.org/10.1080/01445340701300429 -/- Some of the entries have already been found to be flawed. For example, Tarski’s expression ‘materially adequate’ was misinterpreted in at least one article and it was misused in another where ‘materially correct’ should have been used. The discussion provides an opportunity to bring more flaws to light. -/- Acknowledgements: Each of these entries was presented at meetings of The Buffalo Logic Dictionary Project sponsored by The Buffalo Logic Colloquium. The members of the colloquium read drafts before the meetings and were generous with corrections, objections, and suggestions. Usually one 90-minute meeting was devoted to one entry although in some cases, for example, “axiomatic method”, took more than one meeting. Moreover, about half of the entries are rewrites of similarly named entries in the 1995 first edition. Besides the help received from people in Buffalo, help from elsewhere was received by email. We gratefully acknowledge the following: José Miguel Sagüillo, John Zeis, Stewart Shapiro, Davis Plache, Joseph Ernst, Richard Hull, Concha Martinez, Laura Arcila, James Gasser, Barry Smith, Randall Dipert, Stanley Ziewacz, Gerald Rising, Leonard Jacuzzo, George Boger, William Demopolous, David Hitchcock, John Dawson, Daniel Halpern, William Lawvere, John Kearns, Ky Herreid, Nicolas Goodman, William Parry, Charles Lambros, Harvey Friedman, George Weaver, Hughes Leblanc, James Munz, Herbert Bohnert, Robert Tragesser, David Levin, Sriram Nambiar, and others. -/- . (shrink)

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

Darwin’s treatment of morality in The Descent of Man has generated a wide variety of responses among moral philosophers. Among these is the dismissal of evolution as irrelevant to ethics by Darwin’s contemporary Henry Sidgwick; the last, and arguably the greatest, of the Nineteenth Century British Utilitarians. This paper offers a re-examination of Sidgwick’s response to evolutionary considerations as irrelevant to ethics and the absence of any engagement with Darwin’s work in Sidgwick’s main ethical treatise, The Methods of Ethics . (...) This assessment of Sidgwick’s response to Darwin’s work is shown to have significance for a number of ongoing controversies in contemporary metaethics. (shrink)

Social norms – rules governing which behaviours are deemed appropriate or inappropriate within a given community – are typically taken to be uniquely human. Recently, this position has been challenged by a number of philosophers, cognitive scientists, and ethologists, who have suggested that social norms may also be found in certain non-human animal communities. Such claims have elicited considerable scepticism from norm cognition researchers, who doubt that any non-human animals possess the psychological capacities necessary for normative cognition. However, there is (...) little agreement among these researchers about what these psychological prerequisites are. This makes empirical study of animal social norms difficult, since it is not clear what we are looking for and thus what should count as behavioural evidence for the presence (or absence) of social norms in animals. To break this impasse, we offer an approach that moves beyond contested psychological criteria for social norms. This approach is inspired by the animal culture research program, which has made a similar shift away from heavily psychological definitions of ‘culture’ and to become organized around a cluster of more empirically tractable concepts of culture. Here, we propose an analogous set of constructs built around the core notion of a normative regularity, which we define as a socially maintained pattern of behavioural conformity within a community. We suggest methods for studying potential normative regularities in wild and captive primates. We also discuss the broader scientific and philosophical implications of this research program with respect to questions of human uniqueness, animal welfare and conservation. (shrink)

Melinda Fagan’s book on the philosophy of stem cell biology is a superb discussion of this exciting field of contemporary science, and the first book-length philosophical treatment of the subject. It contains a detailed and insightful examination of stem cell science, its structure, methods, and challenges.The book does not require any previous knowledge of stem cell biology—all the relevant scientific details and concepts, the central experimental procedures and results, as well as the historical development of the field, are (...) presented in as clear and accessible a way as possible. The presentation of the science starts in Chapter 1, with a general characterisation of stem cell biology, and continues throughout the book, with every chapter deepening and complicating the initial picture. Fagan’s lucid style makes even the more technical and detailed discussions of the research on human embryonic stem cells and on blood stem cells easy to follow.After the first in .. (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)

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)

One potentially extremely fruitful use of the tools of corpus analysis in the philosophy of science is to help us understand disputed terrains within the sciences that we study. For philosophers of biology, for instance, few controversies are as heated as those over the concepts we use in taxonomy to classify the living world, with the definition of ‘species’ perhaps most fundamental among them. As many understandings of biodiversity, in turn, involve counting the number of species present in a (...) given area, these taxonomic concepts thus become crucially implicated in our efforts in conservation biology and our response to climate change. In this chapter, we present a corpus of taxonomic journal papers, and illustrate how it might be used to make progress in the history and philosophy of taxonomy. What parts of the biological world do taxonomists most often study? Are these areas of focus related to other methodological commitments, or perhaps to their underlying conceptual disagreement? Are species that are more important to conservation, or economic concerns, or more important to local cultures, more or less likely to be the target of biological study? Corpus-based methods, we argue, are uniquely powerful for approaching questions such as these, and we hope that the case we present can serve as a fruitful example for others considering their implementation. (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 (...) 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)

Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes (...) from the primary biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out—as a preliminary step in preparation for upcoming, more detailed treatments—the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute. (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)