The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by (...) drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice. (shrink)

Work on analogy has been done from a number of disciplinary perspectives throughout the history of Western thought. This work is a multidisciplinary guide to theorizing about analogy. It contains 1,406 references, primarily to journal articles and monographs, and primarily to English language material. classical through to contemporary sources are included. The work is classified into eight different sections (with a number of subsections). A brief introduction to each section is provided. Keywords and key expressions of importance to research on (...) analogy are discussed in the introductory material. Electronic resources for conducting research on analogy are listed as well. (shrink)

The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a (...) closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene. (shrink)

The purpose of this article is to invigorate debate concerning the nature of analogy, and to broaden the scope of current conceptions of analogy. We argue that analogizing is not a single or even a fundamental cognitive process. The argument relies on an analysis of the history of the concept of analogy, case studies on the use of analogy in scientific problem solving, cognitive research on analogy comprehension and problem solving, and a survey of computational mechanisms of analogy comprehension. Analogizing (...) is regarded as a macrocognitive phenomenon having a number of supporting processes. These include the apperception of resemblances and distinctions, metaphor, and the balancing of semantic flexibility and inference constraint. Psychological theories and computational models have generally relied on (a) a sparse set of ontological concepts (a property called “similarity” and a structuralist categorization of types of semantic relations), (b) a single form category (i.e., the classic four-term analogy), and (c) a single set of morphological distinctions (e.g., verbal vs. pictorial analogies). This article presents a classification based on a “naturalistic” exploration of the variety of uses of analogical reasoning in pragmatically distinct contexts. The resultant taxonomy distinguishes pre-hoc, ad-hoc, post-hoc, pro-hoc, contra-hoc, and trans-hoc analogy. Each will require its own macrocognitive modeling, and each presents an opportunity for research on phenomena of reasoning that have been neglected. (shrink)

This paper proposes a framework for representing in Bayesian terms the idea that analogical arguments of various degrees of strength may provide inductive support to yet untested scientific hypotheses. On this account, contextual information plays a crucial role in determining whether, and to what extent, a given similarity or dissimilarity between source and target may confirm an empirical hypothesis over a rival one. In addition to showing confirmation by analogy compatible with the adoption of a Bayesian standpoint, the proposal outlined (...) in this paper reveals a close agreement between the fulfillment of Hesse’s (Models and analogies in science, University of Notre Dame Press, 1963) criteria for analogical arguments capable of inductive support and the attribution of confirmatory power by the lights of Bayesian confirmation theory. In this sense, the Bayesian representation not only enriches a framework, Hesse’s, of enduring relevance for understanding scientific activity, but may offer something akin to a proof of concept of it. (shrink)

A prominent way through which wave-particle duality has been ascribed to photons is by illustrating their “wave-like” behaviour in the Mach-Zehnder interferometer and “particle-like” behaviour in the anti-correlation experiment. This duality has been formulated in two ways. Some have based the claim on the complementarity principle. This formulation, however, has already been shown to be problematic. Others have made a much simpler duality claim by considering that single-photons are analogous to waves and particles in the above experiments. I criticise this (...) formulation by arguing that the analogies cannot be distinctly established. Thus, this duality claim is found to be unsubstantiated. (shrink)

Critics of animal modeling have advanced a variety of arguments against the validity of the practice. The point of one such form of argument is to establish that animal modeling is pointless and therefore immoral. In this article, critical arguments of this form are divided into three types, the pseudoscience argument, the disanalogy argument, and the predictive validity argument. I contend that none of these criticisms currently succeed, nor are they likely to. However, the connection between validity and morality is (...) important, suggesting that critical efforts would be instructive if they addressed it in a more nuanced way. (shrink)

The image of a ball rolling along a series of hills and valleys is an effective heuristic by which to communicate stability concepts in ecology. However, the dynamics of this landscape model have little to do with ecological systems. Other landscape representations, however, are possible. These include the particle on an energy landscape, the potential landscape, and the Lyapunov function landscape. I discuss the dynamics that these representations admit, and the application of each to ecological modeling and the analysis and (...) representation of stability. (shrink)