It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...) of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. (shrink)

Genes are often described by biologists using metaphors derived from computa- tional science: they are thought of as carriers of information, as being the equivalent of ‘‘blueprints’’ for the construction of organisms. Likewise, cells are often characterized as ‘‘factories’’ and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Impor- tantly, (...) modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists’ use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as ‘‘irreducible complexity’’ and on flawed analogies between living cells and mechanical factories. However, the living organ- ism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume’s criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume’s original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public. (shrink)

Abstract‘Serendipity’ is a category used to describe discoveries in science that occur at the intersection of chance and wisdom. In this paper, I argue for understanding serendipity in science as an emergent property of scientific discovery, describing an oblique relationship between the outcome of a discovery process and the intentions that drove it forward. The recognition of serendipity is correlated with an acknowledgment of the limits of expectations about potential sources of knowledge. I provide an analysis of serendipity in science (...) as a defense of this definition and its implications, drawing from theoretical and empirical research on experiences of serendipity as they occur in science and elsewhere. I focus on three interrelated features of serendipity in science. First, there are variations of serendipity. The process of serendipitous discovery can be complex. Second, a valuable outcome must be obtained before reflection upon the significance of the unexpected observation or event in respect to that outcome can take place. Therefore, serendipity is retrospectively categorized. Third, the primacy of epistemic expectations is elucidated. Finally, I place this analysis within discussions in philosophy of science regarding the impact of interpersonal competition upon the number and significance of scientific discoveries. Thus, the analysis of serendipity offered in this paper contributes to discussions about the social-epistemological aspects of scientific discovery and has normative implications for the structure of epistemically effective scientific communities. (shrink)

The need for European citizens to be more involved in scientific research has emerged from the conclusions of the studies commissioned by the EC and by independent bodies. In the first part of this contribution, I will discuss the question of whether a dialogue between society and science is desirable. I will attempt to claim that at least one of the reasons why the dialogue between science and society should be defended has been underestimated in the course of most of (...) the studies carried out: the fact the scientific knowledge helps to a create a better, more rounded, more aware human being which can only benefit society. Subsequently, I will deal with the various genres of scientific literature. While in modern times, communication of scientific discoveries has been reduced to the article, in the nineteenth century scientists made use of more varied literary forms such as journals, letters and narrative essays which were more accessible to those who were not specialists but nevertheless curious about scientific matters. I believe that these more popular forms of writing helped to close the gap between the public and science. (shrink)

This thematic issue addresses questions of constraints on the evolution of form—physical, biological, and technical. Here, form is defined as an embodiment of a specific structure, which can be hierarchically different yet emerge from the same processes. The focus of this contribution is about how developmental biology and paleontology can be better integrated and compared in order to produce hypotheses about the evolution of form. The constraints on current EvoDevo research stem from the disconnect in the focus of study for (...) developmental geneticists and evolutionary morphologists; the former being interested in early developmental events at a molecular level in a model animal, the latter in late developmental events or comparison between adult forms, at a structural level in non-model animals. In order to truly integrate information from both fields in our understanding of evolutionary processes, morphology needs to be reintegrated in the study of gene expression, and its time frame needs to be extended beyond early developmental stages. Gene expression in non-model organisms also needs to be studied in order to gain perspective into primitive patterning at evolutionary nodes. Hypotheses formed by the comparison of expression patterns and morphologies seen in extant species can then be tested against forms found in the fossil record, coming closer to understanding the mechanisms underlying evolution. (shrink)

A science is an intellectual activity defined by its mechanisms that prevent its scientists from always reaching the conclusions that they set out to reach. Such mechanisms are needed because, if scientists are given full control over what hypotheses they select, what data they discard, and what results they publish, they can communicate any conclusion that they desire. Synthesis, by setting a grand challenge, forces scientists across uncharted territory where they encounter and solve unscripted problems. When theory is inadequate, the (...) synthesis fails, and fails in a way that cannot be ignored. Therefore, synthesis drives discovery and paradigm change in ways that simple hypothesis testing cannot. Here, we describe the discoveries that emerged when synthetic biologists were challenged to create an alternative genetic system that has different molecular structures than DNA and RNA. In pursuit of this particular “grand challenge,” synthesis forced the recognition that the community did not know as much about the double helix as it had constructively assumed. In general, a field of science having access to synthesis as a research strategy can create knowledge even if its practitioners do not fit the ideal of a dispassionate, advocacy-free scientist. (shrink)

Both Aristotle and Ernst Mayr present theories of dual explanation in biology, with proximal, clearly physical explanations and more distal, biology-specific explanations. Aristotle’s presentation of final cause explanations in Posterior Analytics relates final causes to the necessary material, formal, and efficient causes that mediate them. Johnson and Leunissen demonstrate the problematic nature of historical and recent interpretations and open the door for a new interpretation consistent with modern evolutionary theory. Mayr’s differentiation of proximate and ultimate/evolutionary causes provides a key to (...) appropriating Aristotle for modern use, if care is taken to differentiate Mayr’s proximate/distal and mechanical/evolutionary distinctions from his intentional/non-intentional distinction. Building on Mayr, and noting his appropriation of ancient and recent commentary, a strong case can be made for nested explanation, wherein evolutionary explanations are instantiated in systems of mechanical explanations. Biological concepts of organism, gene, function, etc., are etiologically prior to mechanical explanations of function, but temporally posterior to mechanical explanations of historical adaptation. Such an analysis sheds light on recent arguments within evolutionary biology while highlighting the importance of epistemology in contemporary science. (shrink)

Since the discovery of the double helical structure of DNA, the standard account of the inheritance of features has been in terms of DNA-copying and DNA-transmission. This theory is just a version of the old theory according to which the inheritance of features is explained by the transfer at conception of some developmentally privileged material from parents to offspring. This paper does the following things: (1) it explains what the inheritance of features is; (2) it explains how the DNA-centric theory (...) emerged; (3) it clarifies the relation between the DNA-centric theory and the ‘unfolding’ theory of development; (4) it argues that (given what we now know about developmental processes and genetic activity) the DNA-centric theory should be abandoned in favour of a pluralistic (but not holistic) theory of the inheritance of features. According to this pluralistic theory, the reliable reoccurrence of phenotypes must be explained by appealing not only to processes responsible for the reliable reoccurrence of genetic developmental factors but also to processes responsible for the reliable reoccurrence (or persistence) of nongenetic developmental factors. (shrink)

Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning (...) from 1940 to 1983. This paper will complement such literature by focusing, for the first time, on the transition of Sanger’s sequencing strategies from degrading to copying the target molecule, which occurred in the late 1960s as he was shifting from protein and RNA to DNA sequencing, shortly after his move from the Department of Biochemistry to the Laboratory of Molecular Biology, both based in Cambridge (UK). Through a reinterpretation of Sanger’s papers and retrospective accounts and a pioneering investigation of his laboratory notebooks, I will claim that sequencing shifted from the working procedures of organic chemistry to those of the emergent molecular biology. I will also argue that sequencing deserves a history in its own right as a practice and not as a technique subordinated to the development of molecular biology or genomics. My proposed history of sequencing leads to a reappraisal of current STS debates on bioinformatics, biotechnology and biomedicine. (shrink)

Scientific hypotheses may either predict particular unknown facts or accommodate previously-known data. Although affirmed predictions are intuitively more rewarding than accommodations of established facts, opinions divide whether predictive hypotheses are also epistemically superior to accommodation hypotheses. This paper examines the contribution of predictive hypotheses to discoveries of several bio-molecular systems. Having all the necessary elements of the system known beforehand, an abstract predictive hypothesis of semiconservative mode of DNA replication was successfully affirmed. However, in defining the genetic code whose biochemical (...) basis was unclear, hypotheses were only partially effective and supplementary experimentation was required for its conclusive definition. Markedly, hypotheses were entirely inept in predicting workings of complex systems that included unknown elements. Thus, hypotheses did not predict the existence and function of mRNA, the multiple unidentified components of the protein biosynthesis machinery, or the manifold unknown constituents of the ubiquitin–proteasome system of protein breakdown. Consequently, because of their inability to envision unknown entities, predictive hypotheses did not contribute to the elucidation of cation theories remained the sole instrument to explain complex bio-molecular systems, the philosophical question of alleged advantage of predictive over accommodative hypotheses became inconsequential. (shrink)

A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively (...) parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems. (shrink)