Synthetic biology, as a research field, brings together molecular life scientists, computational biologists, and social scientists to engineer biological systems toward societally desired goals. Given the field’s broad multidisciplinarity and relatively young age, innovative educational methods are required to provide students with the needed background knowledge to push the field forward in the future. The international Genetically Engineered Machine competition is such an example where education and high-level research merge, providing the synthetic biology field with trained students, new ideas, and (...) novel results. In the 2021 edition alone, 343 teams from across the world completed the competition to tackle societal problems with synthetic biology. As Wageningen University & Research celebrates 10 years of participation in iGEM, we share our thoughts and experiences on supervising iGEM teams, which is especially relevant to organizers of current and new teams, and also others interested in the iGEM competition. (shrink)

Robert Batterman examines a form of scientific reasoning called asymptotic reasoning, arguing that it has important consequences for our understanding of the scientific process as a whole. He maintains that asymptotic reasoning is essential for explaining what physicists call universal behavior. With clarity and rigor, he simplifies complex questions about universal behavior, demonstrating a profound understanding of the underlying structures that ground them. This book introduces a valuable new method that is certain to fill explanatory gaps across disciplines.

But do animals know that other creatures have minds? And how would we know if they do? In "Mindreading Animals," Robert Lurz offers a fresh approach to the hotly debated question of mental-state attribution in nonhuman animals.

This article discusses minimal model explanations, which we argue are distinct from various causal, mechanical, difference-making, and so on, strategies prominent in the philosophical literature. We contend that what accounts for the explanatory power of these models is not that they have certain features in common with real systems. Rather, the models are explanatory because of a story about why a class of systems will all display the same large-scale behavior because the details that distinguish them are irrelevant. This story (...) explains patterns across extremely diverse systems and shows how minimal models can be used to understand real systems. (shrink)

It is relatively easy to state that information retrieval is a scientific discipline but it is rather difficult to understand why it is science because what is science is still under debate in the philosophy of science. To be able to convince others that IR is science, our ability to explain why is crucial. To explain why IR is a scientific discipline, we use a theory and a model of scientific study, which were proposed recently. The explanation involves mapping the (...) knowledge structure of IR to that of well-known scientific disciplines like physics. In addition, the explanation involves identifying the common aim, principles and assumptions in IR and in well-known scientific disciplines like physics, so that they constrain the scientific investigation in IR in a similar way as in physics. Therefore, there are strong similarities in terms of the knowledge structure and the constraints of the scientific investigations between IR and scientific disciplines like physics. Based on such similarities, IR is considered a scientific discipline. (shrink)

This paper examines contemporary attempts to explicate the explanatory role of mathematics in the physical sciences. Most such approaches involve developing so-called mapping accounts of the relationships between the physical world and mathematical structures. The paper argues that the use of idealizations in physical theorizing poses serious difficulties for such mapping accounts. A new approach to the applicability of mathematics is proposed.

Big Data’s calculative ontology relies on and reproduces a form of hyperindividualism in which the ontological unit of analysis is the discrete data point, the meaning and identity of which inheres in itself, preceding, separate, and independent from its context or relation to any other data point. The practice of Big Data governed by an ontology of hyperindividualism is also constitutive of that ontology, naturalizing and diffusing it through practices of governance and, from there, throughout myriad dimensions of everyday life. (...) In this paper, I explicate Big Data’s ontology of hyperindividualism by contrasting it to a coconstitutive ontology that prioritizes relationality, context, and interdependence. I then situate the ontology of hyperindividualism in its genealogical context, drawing from Patrick Joyce’s history of liberalism and John Dewey’s pragmatist account of individualism, liberalism, and social action. True to its genealogical provenance, Big Data’s ontological politics of hyperindividualism reduces governance to the management of atomistic behavior, undermines the contribution of urban complexity as a resource for governance, erodes the potential for urban democracy, and eviscerates the possibility of collective resistance. (shrink)

This paper concerns what Jerry Fodor calls a 'metaphysical mystery': How can there by macroregularities that are realized by wildly heterogeneous lower level mechanisms? But the answer to this question is not as mysterious as many, including Jaegwon Kim, Ned Block, and Jerry Fodor might think. The multiple realizability of the properties of the special sciences such as psychology is best understood as a kind of universality, where 'universality' is used in the technical sense one finds in the physics literature. (...) It is argued that the same explanatory strategy used by physicists to provide understanding of universal behavior in physics can be used to explain how special science properties can be heterogeneously multiply realized. (shrink)

This paper examines the role of mathematical idealization in describing and explaining various features of the world. It examines two cases: first, briefly, the modeling of shock formation using the idealization of the continuum. Second, and in more detail, the breaking of droplets from the points of view of both analytic fluid mechanics and molecular dynamical simulations at the nano-level. It argues that the continuum idealizations are explanatorily ineliminable and that a full understanding of certain physical phenomena cannot be obtained (...) through completely detailed, non-idealized representations. (shrink)

This paper aims to draw attention to an explanatory problem posed by the existence of multiply realized or universal behavior exhibited by certain physical systems. The problem is to explain how it is possible that systems radically distinct at lower-scales can nevertheless exhibit identical or nearly identical behavior at upper-scales. Theoretically this is reflected by the fact that continuum theories such as fluid mechanics are spectacularly successful at predicting, describing, and explaining fluid behaviors despite the fact that they do not (...) recognize the discrete nature of fluids. A standard attempt to reduce one theory to another, is shown to fail to answer the appropriate question about autonomy. (shrink)

A traditional view of mathematical modeling holds, roughly, that the more details of the phenomenon being modeled that are represented in the model, the better the model is. This paper argues that often times this ‘details is better’ approach is misguided. One ought, in certain circumstances, to search for an exactly solvable minimal model—one which is, essentially, a caricature of the physics of the phenomenon in question.

The 3Rs, or the replacement, reduction, and refinement of animal research, are widely accepted as the best approach to maximizing high-quality science while ensuring the highest standard of ethical consideration is applied in regulating the use of animals in scientific procedures. This contrasts with the muted scientific interest in the 3Rs when they were first proposed in The Principles of Humane Experimental Technique. Indeed, the relative success of the 3Rs has done little to encourage engagement with their original text, which (...) remains little read and out of print. By adopting a historical perspective, this article argues that one explanation for this disjunction may be found in another, more celebrated, event of 1959: C. P. Snow’s Rede lecture on The Two Cultures. The moral outlook of The Principles of Humane Experimental Technique derived from an earlier ethos wherein humanistic and scientific values occupied a shared culture. While the synthetic style of The Principles has hindered its readership, this article concludes that there is value to recovering the notion that the humanities and social sciences can contribute to the improvement of animal research. (shrink)

This volume is a collection of fourteen essays by leading philosophers on issues concerning the nature, existence, and our knowledge of animal minds. The nature of animal minds has been a topic of interest to philosophers since the origins of philosophy, and recent years have seen significant philosophical engagement with the subject. However, there is no volume that represents the current state of play in this important and growing field. The purpose of this volume is to highlight the state of (...) the debate. The issues which are covered include whether and to what degree animals think in a language or in iconic structures, possess concepts, are conscious, self-aware, metacognize, attribute states of mind to others, and have emotions, as well as issues pertaining to our knowledge of and the scientific standards for attributing mental states to animals. (shrink)

Autonomy -- Hydrodynamics -- Brownian motion -- From Brownian motion to bending beams -- An engineering approach -- The right variables and natural kinds.

We present a toy theory that is based on a simple principle: the number of questions about the physical state of a system that are answered must always be equal to the number that are unanswered in a state of maximal knowledge. Many quantum phenomena are found to have analogues within this toy theory. These include the noncommutativity of measurements, interference, the multiplicity of convex decompositions of a mixed state, the impossibility of discriminating nonorthogonal states, the impossibility of a universal (...) state inverter, the distinction between bipartite and tripartite entanglement, the monogamy of pure entanglement, no cloning, no broadcasting, remote steering, teleportation, entanglement swapping, dense coding, mutually unbiased bases, and many others. The diversity and quality of these analogies is taken as evidence for the view that quantum states are states of incomplete knowledge rather than states of reality. A consideration of the phenomena that the toy theory fails to reproduce, notably, violations of Bell inequalities and the existence of a Kochen-Specker theorem, provides clues for how to proceed with this research program. (shrink)

From the ferment of recent debates about the intellectual virtues, Roberts and Wood develop an approach they call 'regulative epistemology', exploring the connection between knowledge and intellectual virtue. In the course of their argument they analyse particular virtues of intellectual life - such as courage, generosity, and humility - in detail.

The principles of the 3Rs—replacement, refinement, and reduction—strongly shape discussion of methods for performing more humane animal research and the regulation of this contested area of technoscience. This special issue looks back to the origins of the 3Rs principles through five papers that explore how it is enacted and challenged in practice and that develop critical considerations about its future. Three themes connect the papers in this special issue. These are the multiplicity of roles enacted by those who use and (...) care for animals in research, the distribution of “feelings that matter” across species and spaces of laboratory animal practice, and the growing importance of “cultures of care” in animal research. (shrink)

If we are flexible, hybrid and unfinished creatures that tend to incorporate or at least employ technological artefacts in our cognitive lives, then the sort of technological regime we live under should shape the kinds of minds we possess and the sorts of beings we are. E-Memory consists in digital systems and services we use to record, store and access digital memory traces to augment, re-use or replace organismic systems of memory. I consider the various advantages of extended and embedded (...) approaches to cognition in making sense of E-Memory and some of the problems that debate can engender. I also explore how the different approaches imply different answers to questions such as: does our use of internet technology imply the diminishment of ourselves and our cognitive abilities? Whether or not our technologies can become actual parts of our minds, they may still influence our cognitive profile. I suggest E-Memory systems have four factors: totality, practical cognitive incorporability, autonomy and entanglement which conjointly have a novel incorporation profile and hence afford some novel cognitive possibilities. I find that thanks to the properties of totality and incorporability we can expect an increasing reliance on E-Memory. Yet the potentially highly entangled and autonomous nature of these technologie pose questions about whether they should really be counted as proper parts of our minds. (shrink)

In its broadest sense, "universality" is a technical term for something quite ordinary. It refers to the existence of patterns of behavior by physical systems that recur and repeat despite the fact that in some sense the situations in which these patterns recur and repeat are different. Rainbows, for example, always exhibit the same pattern of spacings and intensities of their bows despite the fact that the rain showers are different on each occasion. They are different because the shapes of (...) the drops, and their sizes can vary quite widely due to differences in temperature, wind direction, etc. There are different questions one might ask about such patterns. For instance, one might ask why the particular rainbow... (shrink)

Why does performing certain tasks cause the aversive experience of mental effort and concomitant deterioration in task performance? One explanation posits a physical resource that is depleted over time. We propose an alternative explanation that centers on mental representations of the costs and benefits associated with task performance. Specifically, certain computational mechanisms, especially those associated with executive function, can be deployed for only a limited number of simultaneous tasks at any given moment. Consequently, the deployment of these computational mechanisms carries (...) an opportunity cost – that is, the next-best use to which these systems might be put. We argue that the phenomenology of effort can be understood as the felt output of these cost/benefit computations. In turn, the subjective experience of effort motivates reduced deployment of these computational mechanisms in the service of the present task. These opportunity cost representations, then, together with other cost/benefit calculations, determine effort expended and, everything else equal, result in performance reductions. In making our case for this position, we review alternative explanations for both the phenomenology of effort associated with these tasks and for performance reductions over time. Likewise, we review the broad range of relevant empirical results from across sub-disciplines, especially psychology and neuroscience. We hope that our proposal will help to build links among the diverse fields that have been addressing similar questions from different perspectives, and we emphasize ways in which alternative models might be empirically distinguished. (shrink)

Canid and human barks and growls were examined in videotapes of 24 humans (Homo sapiens) and 24 dogs (Canis familiaris) playing with familiar and unfamiliar cross-species play partners. Barks and growls were exhibited by 9 humans and 9 dogs. Dogs barked and (less often) growled most frequently when being frustrated by humans and/or engaged in competitive games, and less often when being chased or inviting chase, and being instigated or captured. Dogs never growled when playing with an unfamiliar human, and (...) humans did so rarely when playing with an unfamiliar dog. Humans growled and (less often) barked most frequently when chasing and capturing the dog, less often when engaging in competitive games, being frustrated by the dog, and/or instigating the dog, and rarely when showing or throwing an object. Dog barks were most often requests for the human to make an object available to the dog. Dog growls were often pretend threats when competing for an object or being frustrated by the human’s actions. Human barks and growls were typically pretend threats, and were sometimes used to emphasize simultaneous behaviors. Human barks and growls allow humans to connect with their canid partner. (shrink)

While 4E cognitive science is fundamentally committed to recognising the importance of the environment in making sense of cognition, its interest in the role of artefacts seems to be one of its least developed dimensions. Yet the role of artefacts in human cognition and agency is central to the sorts of beings we are. Internet technology is influencing and being incorporated into a wide variety of our cognitive processes. Yet the dominant way of viewing these changes sees technology as an (...) outside force “impacting” on our minds. Within this context, Material Engagement Theory seems well poised to help make sense of our cognitive involvement with the Internet as MET is precisely concerned with grasping the role of material culture in human cognition. This paper explores some of the resources MET provides to think through the effects the internet is having on human agency. This paper uses MET as a starting point for examining the way Internet technology can be involved with human agency, both to the provide a much needed and more adequate theorization of these phenomena, but also to illustrate ways in which the consideration of artefacts can be given a more central and adequate place within the 4E cognitive sciences. (shrink)

This paper looks at emergence in physical theories and argues that an appropriate way to understand socalled “emergent protectorates” is via the explanatory apparatus of the renormalization group. It is argued that mathematical singularities play a crucial role in our understanding of at least some well-defined emergent features of the world.

Among discrete emotions, basic emotions are the most elemental; most distinct; most continuous across species, time, and place; and most intimately related to survival-critical functions. For an emotion to be afforded basic emotion status it must meet criteria of: (a) distinctness (primarily in behavioral and physiological characteristics), (b) hard-wiredness (circuitry built into the nervous system), and (c) functionality (provides a generalized solution to a particular survival-relevant challenge or opportunity). A set of six emotions that most clearly meet these criteria (enjoyment, (...) anger, disgust, fear, surprise, sadness) and three additional emotions (relief/contentment, interest, love) for which the evidence is not yet quite as strong is described. Empirical approaches that are most and least useful for establishing basic-emotion status are discussed. Basic emotions are thought to have a central organizing mechanism and to have the capacity to influence behavior, thoughts, and other fundamental processes. (shrink)

The study of insight in problem solving and creative thinking has seen an upsurge of interest in the last 30 years. Current theorising concerning insight has taken one of two tacks. The special-process view, which grew out of the Gestalt psychologists’ theorising about insight, proposes that insight is the result of a dedicated set of processes that is activated by the individual's reaching impasse while trying to deal with a problematic situation. In contrast, the business-as-usual view argues that insight is (...) brought about by the same processes that underlie ordinary thinking . Although those two views are typically treated as being in opposition, it has recently been proposed that a complete understanding of insight will require bringing together aspects of both views. The present paper carries that proposal further. Critical analysis of those two viewpoints demonstrates that each has a positive contribution to make to our understanding of insight, but also is.. (shrink)

We discuss the astronomical underpinning of the improved calendar of 1700. Starting from the astronomical motivation of the Gregorian calendar of 1582 and the rejection of this reform in Protestant states in Europe, we describe how the astronomical Easter reckoning based on Kepler’s Rudolphine tables led to the foundation of Berlin Observatory and enabled the founding of the Electoral Brandenburg Society of Sciences, which had to finance itself through a calendar monopoly.

This is the first book to evaluate the significance and usefulness of the practices of anthropomorphism and anecdotalism for understanding animals.

This paper addresses issues surrounding the concept of geometric phase or "anholonomy". Certain physical phenomena apparently require for their explanation and understanding, reference to toplogocial/geometric features of some abstract space of parameters. These issues are related to the question of how gauge structures are to be interpreted and whether or not the debate over their "reality" is really going to be fruitful.

Mesoscale modeling is often considered merely as a practical strategy used when information on lower-scale details is lacking, or when there is a need to make models cognitively or computationally tractable. Without dismissing the importance of practical constraints for modeling choices, we argue that mesoscale models should not just be considered as abbreviations or placeholders for more “complete” models. Because many systems exhibit different behaviors at various spatial and temporal scales, bottom-up approaches are almost always doomed to fail. Mesoscale models (...) capture aspects of multi-scale systems that cannot be parameterized by simple averaging of lower-scale details. To understand the behavior of multi-scale systems, it is essential to identify mesoscale parameters that “code for” lower-scale details in a way that relate phenomena intermediate between microscopic and macroscopic features. We illustrate this point using examples of modeling of multi-scale systems in materials science and biology, where identification of material parameters such as stiffness or strain is a central step. The examples illustrate important aspects of a so-called “middle-out” modeling strategy. Rather than attempting to model the system bottom-up, one starts at intermediate scales where systems exhibit behaviors distinct from those at the atomic and continuum scales. One then seeks to upscale and downscale to gain a more complete understanding of the multi-scale system. The cases highlight how parameterization of lower-scale details not only enables tractable modeling but is also central to understanding functional and organizational features of multi-scale systems. (shrink)

This paper presents a theory of scientific study which is regarded as a social learning process of scientific knowledge creation, revision, application, monitoring and dissemination with the aim of securing good quality, general, objective, testable and complete scientific knowledge of the domain. The theory stipulates the aim of scientific study that forms the basis of its principles. It also makes seven assumptions about scientific study and defines the major participating entities. It extends a recent process model of scientific study into (...) a detailed interaction model as this process model already addresses many issues of philosophy of science. The detailed interaction model of scientific study provides a common template of scientific activities for developing logical models in different scientific disciplines, or alternatively for developing ontologies of different scientific disciplines. Differences between research and scientific studies are discussed, and a possible way to develop a scientific theory of scientific study is described. (shrink)

In many evolutionary/functionalist theories, emotions organize the activity of the autonomic nervous system and other physiological systems. Two kinds of patterned activity are discussed: coherence, and specificity. For each kind of patterning, significant methodological obstacles are considered that need to be overcome before empirical studies can adequately test theories and resolve controversies. Finally, links that coherence and specificity have with health and well-being are considered.