A thoughtful study which integrates Aristotle's philosophy of science in the Organon and in the Parts of Animals with his actual biological investigations.

Robert Brandon is one of the most important and influential of contemporary philosophers of biology. This collection of his recent essays covers all the traditional topics in the philosophy of evolutionary biology and as such could serve as an introduction to the field. There are essays on the nature of fitness, teleology, the structure of the theory of natural selection, and the levels of selection. The book also deals with newer topics that are less frequently discussed but are of growing (...) interest, for example the evolution of human language and the role of experimentation in evolutionary biology. A special feature of the collection is that it avoids jargon and is written in a style that will appeal to working evolutionary biologists as well as philosophers. (shrink)

Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of determining the parameter values from the output. In fact, structural identifiability becomes a particular case of observability if the parameters are considered as constant state variables. It is possible to simultaneously analyse the observability and structural identifiability of a model using the conceptual tools of differential geometry. Many (...) complex biological processes can be described by systems of nonlinear ordinary differential equations and can therefore be analysed with this approach. The purpose of this review article is threefold: to serve as a tutorial on observability and structural identifiability of nonlinear systems, using the differential geometry approach for their analysis; to review recent advances in the field; and to identify open problems and suggest new avenues for research in this area. (shrink)

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)

The “DNA is a program” metaphor is still widely used in Molecular Biology and its popularization. There are good historical reasons for the use of such a metaphor or theoretical model. Yet we argue that both the metaphor and the model are essentially inadequate also from the point of view of Physics and Computer Science. Relevant work has already been done, in Biology, criticizing the programming paradigm. We will refer to empirical evidence and theoretical writings in Biology, although our arguments (...) will be mostly based on a comparison with the use of differential methods (in Molecular Biology: a mutation or alike is observed or induced and its phenotypic consequences are observed) as applied in Computer Science and in Physics, where this fundamental tool for empirical investigation originated and acquired a well-justified status. In particular, as we will argue, the programming paradigm is not theoretically sound as a causal(as in Physics) or deductive(as in Programming) framework for relating the genome to the phenotype, in contrast to the physicalist and computational grounds that this paradigm claims to propose. (shrink)

In the last part of the Timaeus, where Plato presents his ideas about human physiology but also about biology in general, we find the combined activity of Intellect and Necessity. In this essay I investigate whether Plato, apart from his general statement about the combined activity of Reason and Necessity, proposes a more specific method of biological research. For this purpose I am going to examine some methodological passages as well as the way in which he exposes and develops (...) his views about the human body and its organs. (shrink)

This collection of essays by Robert Brandon spans two decades and most of the important problems in the philosophy of biology. Four of his five most important contributions to the philosophy of biology can be found here: the concept of relative adaptedness and its role in the propensity interpretation of fitness; the principle of natural selection; the use of the screening-off relation in defense of organismic selection; and the distinction between units of selection and levels of selection. The fifth major (...) contribution, an analysis of the concept of "environment," mentioned briefly in an essay on the co-evolution of organisms and environment, is given an extended treatment in his 1990 book, Adaptation and Environment. (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 biology major has developed rapidly in recent years. Biology is a science that penetrates every aspect of human life and is one of the core majors in most agricultural colleges and universities. However, many teachers lack practical experience in the subject. To overcome this problem, in recent years, we have been trying to introduce new reforms into our teaching. This article provides some insight into the way that biology majors have been reformed, which will help educators in agricultural colleges (...) and universities. At present, teachers implement the “Industrial Innovation and Entrepreneurship Talent Cultivation” model, but it is not clear whether this helps biology majors to master the course and improve their practical skills. In this study, the IIETC model is outlined, and the academic achievement and satisfaction of students taught under the IIETC model are assessed. A T-test is used to examine potential differences between IIETC and traditional teaching models. In-depth interviews and questionnaires were given to two groups of students who followed different teaching models as part of an exploratory study. The aim was to explore how effective IIETC is at helping biology majors master the course and improve students’ wellbeing. Our results show that compared with traditional teaching methods, the IIETC model has a significant positive impact on the academic performance and happiness of biology students. Students trained under the IIETC model were more active and scored more highly in their final exams. They were more likely to feel that they had achieved success and happiness through the course. The outcomes of this research reveal a novel teaching reform that improved students’ enthusiasm for innovation and entrepreneurship during the ongoing COVID-19 pandemic. The effects are very encouraging and deserve further exploration and expansion in future work. (shrink)

Aristotle's biological writings, largely ignored by generations of philosophically oriented scholars, have been receiving an increasing amount of attention of late. This is a good thing, because this recent work has confirmed what David Balme's publications have been suggesting since 1961: that there is much to be learned about central concepts and issues in Aristotle's metaphysics and theory of science from a careful, philosophically sensitive study of this 25% of the surviving corpus.

Biological taxonomists rely on the so-called ‘type method’ to regulate taxonomic nomenclature. For each newfound taxon, they lay down a ‘type specimen’ that carries with it the name of the taxon it belongs to. Even if a taxon’s circumscription is unknown and/or subject to change, it remains a necessary truth that the taxon’s type specimen falls within its boundaries. Philosophers have noted some time ago that this naming practice is in line with the causal theory of reference and its (...) central notion of rigid designation: a type specimen fixes the reference of a taxon name without defining it. Recently, however, this consensus has come under pressure in the pages of this journal. In a series of articles by Alex Levine, Joseph LaPorte, and Matthew Haber, it has been argued that type specimens belong only contingently to their species, and that this may bode problems for the relation between type method and causal theory. I will argue that this ‘contingency debate’ is a debate gone wrong, and that none of the arguments in defense of contingency withstand scrutiny. Taxonomic naming is not out of step with the causal theory, but conforms to it. However, I will also argue that this observation is itself in need of further explanation, since application of the type method in taxonomic practice is plagued by errors and ambiguities that threaten it with breaking down. Thus, the real question becomes why taxonomic naming conforms to the causal theory in the first place. I will show that the answer lies in the embedding of the type method into elaborate codes of nomenclature. (shrink)

This volume draws together Allan Gotthelf's pioneering work on Aristotle's biology. He examines Aristotle's natural teleology, the axiomatic structure of biological explanation, and the reliance on scientifically organized data in the three great works with which Aristotle laid the foundations of biological science.

Examining stem cell biology from a philosophy of science perspective, this book clarifies the field's central concept, the stem cell, as well as its aims, methods, models, explanations and evidential challenges. The first chapters discuss what stem cells are, how experiments identify them, and why these two issues cannot be completely separated. The basic concepts, methods and structure of the field are set out, as well as key limitations and challenges. The second part of the book shows how (...) rigorous explanations emerge from stem cell experiments, and compares these to other kinds of scientific explanation. Model organisms, the role of genes, and the significance of collaboration are also discussed. The last part of the book considers relations to systems biology and clinical medicine, arguing that both the mathematical models of the former, and ethical principles of the latter, are necessary for stem cell biology to deliver on its promises. (shrink)

The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in the (...) past few decades and it is likely that more will come to light in the future. The existence of many organic codes in Nature is therefore an experimental fact, but also more than that. It is one of those facts that have extraordinary implications. In this book it is shown that the genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the first cells into three primary kingdoms (Archaea, Bacteria and Eukarya), the splicing codes were instrumental to the origin of the eukaryotic nucleus, the histone code provided a new regulation system in eukaryotic genomes, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis. It is shown, furthermore, that organic codes had a key role in multicellular life, in particular in the origin of animals, the origin of mind and the origin of language. The great events of macroevolution, in other words, were associated with the appearance of new organic codes, and we can easily understand why. The reason is that a new code brings into existence something that has never existed before because it creates arbitrary associations, relationships that are not determined by physical necessity. Another outstanding implication is the fact that codes involve meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The research on biological codes, in conclusion, is bringing to light new mechanisms in evolution and new fundamental concepts in science. This research is the field of Code Biology, the study of all codes of life, from the genetic code to the codes of culture, from the origin of life to the origin of man. (shrink)

Synthetic biology is an emerging technology that asks for inclusive reflection on how people frame the field. To unravel how we can facilitate such reflection, this study evaluates the Frame Reflection Lab. Building upon playfulness design principles, the FRL comprises a workshop with video-narratives and co-creative group exercises. We studied how the FRL facilitated frame reflection by organizing workshops with various student groups. Analysis of 12 group conversations and 158 mini-exit surveys yielded patterns in first-order reflection as well as patterns (...) in second-order reflection. Also patterns in participants’ framing of synthetic biology could be induced; participants’ viewpoints converged to some extent, yet with openness to individual viewpoint differences. Although the FRL method fortified the reflection processes of participants, the narratives and the workshop’s flexible format could inhibit the reflection too. Therefore, we advise designers of future frame reflection methods to apply stronger conversational facilitation and narratives of slightly mysterious yet identifiable narrators, in case e.g. video-narratives are created and used to scaffold the reflection process. Nevertheless, we argue that the use of a playful frame reflection method like the FRL could function well as a step to precede more application-specific deliberation or decision-making on synthetic biology and as a method for the collection of contemporary citizen viewpoints plus rationales underlying these, for the further responsible development of the emerging field. (shrink)

The current study compared the effectiveness of two methods in biology teaching that are based on the science-as-inquiry approach: visits to authentic university laboratories and analyzing adapted primary literature. The methods’ effectiveness was measured in terms of high-school students’ increased understanding following a 6-week intervention that emphasized five major aspects of the nature of science : the tentativeness of scientific understanding, the cooperative nature of the scientific process, methodological diversity, the sociocultural embeddedness of scientific knowledge, and the aims (...) of scientific inquiry. A quasi-experimental, pre-post control design was applied, utilizing quantitative evaluation methods. Findings indicate that teaching NOS in biology high-school classes using science-as-inquiry methods is an effective approach for enhancing NOS understanding. Both of the proposed methods appear to be promising; however, the AUL method was found to be more effective for enabling advanced-level high-school biology students’ understanding of these NOS aspects. In conclusion, both AUL and APL are potentially effective methods that can be adapted for teaching various biology subjects in different cultural contexts. (shrink)

Synthetic biology is an emerging technology that asks for inclusive reflection on how people frame the field. To unravel how we can facilitate such reflection, this study evaluates the Frame Reflection Lab. Building upon playfulness design principles, the FRL comprises a workshop with video-narratives and co-creative group exercises. We studied how the FRL facilitated frame reflection by organizing workshops with various student groups. Analysis of 12 group conversations and 158 mini-exit surveys yielded patterns in first-order reflection as well as patterns (...) in second-order reflection. Also patterns in participants’ framing of synthetic biology could be induced; participants’ viewpoints converged to some extent, yet with openness to individual viewpoint differences. Although the FRL method fortified the reflection processes of participants, the narratives and the workshop’s flexible format could inhibit the reflection too. Therefore, we advise designers of future frame reflection methods to apply stronger conversational facilitation and narratives of slightly mysterious yet identifiable narrators, in case e.g. video-narratives are created and used to scaffold the reflection process. Nevertheless, we argue that the use of a playful frame reflection method like the FRL could function well as a step to precede more application-specific deliberation or decision-making on synthetic biology and as a method for the collection of contemporary citizen viewpoints plus rationales underlying these, for the further responsible development of the emerging field. (shrink)

RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence‐specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross‐linking immuno‐precipitation (CLIP) and other recently developed high‐throughput methods provide comprehensive, genome‐wide maps of protein‐RNA interactions in the cell. Structural biology gives detailed (...) insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high‐throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein‐RNA recognition in gene regulation, as we review in this article. (shrink)

This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...) themes discussed. (shrink)

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is (...) argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems. (shrink)