Metaphors abound in both the arts and in science. Due to the traditional division between these enterprises as one concerned with aesthetic values and the other with epistemic values there has unfortunately been very little work on the relation between metaphors in the arts and sciences. In this paper, we aim to remedy this omission by defending a continuity thesis regarding the function of metaphor across both domains, that is, metaphors fulfill any of the same functions in science as they (...) do in the arts. Importantly, this involves the claim that metaphors in arts as well as science have both epistemic and aesthetic functions. (shrink)

Reductive representationalist theories of consciousness are yet to produce a satisfying account of pain’s affective component, the part that makes it painful. The paramount problem here is that that there seems to be no suitable candidate for what affective experience represents. This article suggests that affective experience represents the Darwinian fitness effects of events. I argue that, because of affective experience’s close association with motivation, natural selection will work to bring affect into covariance with the average fitness effects of types (...) of event, and that this covariance makes fitness effects a promising candidate for what affect represents. I also argue that this account is to be preferred to Cutter and Tye’s recent proposal that affect represents harmfulness, and answer an objection that Aydede and Fulkerson recently offered against representational accounts of affect. (shrink)

‘Gouldian arguments’ appeal to the contingency of a scientific domain to establish that domain’s autonomy from some body of theory. For instance, pointing to evolutionary contingency, Stephen Jay Gould suggested that natural selection alone is insufficient to explain life on the macroevolutionary scale. In analysing contingency, philosophers have provided source-independent accounts, understanding how events and processes structure history without attending to the nature of those events and processes. But Gouldian Arguments require source-dependent notions of contingency. An account of contingency is (...) source-dependent when it is indexed to some pattern and some process. Positions like Gould’s do not turn on the mere fact of life’s contingency—that life’s shape could have been different due to its sensitivity to initial conditions, path-dependence or stochasticity. Rather, Gouldian arguments require that the contingency is due to particular kinds of processes: in this case, those which microevolutionary theory cannot account for. This source-dependent perspective clarifies both debates about the nature and importance of contingency, and empirical routes for testing Gould’s thesis. (shrink)

Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so (...) by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. (shrink)

Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context (...) of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. (shrink)

Several tensions run through philosophical debates on the nature of pleasure: is it a feeling or an attitude? Is it excited engagement during activities, or satisfaction and contentment at their completion? Pleasure also plays fundamental explanatory roles in psychology, neuroscience, and animal behavior. I draw on this work to argue that pleasure picks out two distinct, but interacting neurobiological systems with long evolutionary histories. Understanding pleasure as having these two facets gives us a better account of pleasure and explains the (...) persistent tensions in the concept. This account of pleasure also sheds light on happiness and well-being. (shrink)

The concept of adaptation is employed in many fields such as biology, psychology, cognitive sciences, robotics, social sciences, even literacy and art,1 and its meaning varies quite evidently according to the particular research context in which it is applied. We expect to find a particularly rich catalogue of meanings within evolutionary biology, where adaptation has held a particularly central role since Darwin’s The Origin of Species (1859) throughout important epistemological shifts and scientific findings that enriched and diversified the concept. Accordingly, (...) a conceptual taxonomy of adaptation in evolutionary biology may help to disambiguate it. Interdisciplinary researches focused on adaptation would benefit from such a result. In the present work we recognize and define seven different meanings of adaptation: (1) individual fitness; (2) adaptation of a population; (3) adaptation as the process of natural selection; (4) adaptive traits; (5) molecular adaptation; (6) adaptation as structural tinkering; (7) plasticity. For convenience here, we refer to them as W-, P-, NS-, T-, M-, S- and PL-ADAPTATION. We present the seven meanings in some detail, hinting at their respective origins and conceptual developments in the history of evolutionary thought (references are offered for further deepening). However, it is important to point out that evolution researchers seldom if ever refer to a single meaning purified from the others. This applies also to the authors we cite as representatives of one of the seven meanings. In Discussion and Conclusion draw from our work some future perspectives for adaptation within evolutionary biology. (shrink)

Comparing engineering to evolution typically involves adaptationist thinking, where well-designed artifacts are likened to well-adapted organisms, and the process of evolution is likened to the process of design. A quite different comparison is made when biologists focus on evolvability instead of adaptationism. Here, the idea is that complex integrated systems, whether evolved or engineered, share universal principles that affect the way they change over time. This shift from adaptationism to evolvability is a significant move for, as I argue, we can (...) make sense of these universal principles without making any adaptationism claims. Furthermore, evolvability highlights important aspects of engineering that are ignored in the adaptationist debates. I introduce some novel engineering examples that incorporate these key neglected aspects, and use these examples to challenge some commonly cited contrasts between engineering and evolution, and to highlight some novel resemblances that have gone unnoticed. (shrink)

The smartphone can be considered a great example of how technology provides us with information at our fingertips anytime, anywhere. However, we have been operating mostly in the dark without a clear understanding of what our mobile devices have to offer and how people arrive at creative re-use as part of a problem-solving activity. This paper is an attempt to reach a better understanding of the conditions in which creative re-use of smartphones may take place. Our main goal is to (...) theoretically explore the role that the context of one’s activity may have in supporting creative re-use. We argue that the smartphone in itself cannot be separated from its cognitive ecology, but it is precisely the way in which it becomes permeable in the context that affords us to potentially come up with new uses and in doing so improve our ability to solve problems. (shrink)

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthe- sis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on (...) issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics. (shrink)

The idea of phenotypic novelty appears throughout the evolutionary literature. Novelties have been defined so broadly as to make the term meaningless and so narrowly as to apply only to a limited number of spectacular structures. Here I examine some of the available definitions of phenotypic novelty and argue that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that (...) these frameworks should be considered in addition to, and not as potential substitutes of, the modern synthesis. †To contact the author, please write to: Departments of Ecology and Evolution and Philosophy, Stony Brook University, Stony Brook, NY 11794; e‐mail: [email protected]. (shrink)

For many years the evolution of language has been seen as a disreputable topic, mired in fanciful “just so stories” about language origins. However, in the last decade a new synthesis of modern linguistics, cognitive neuroscience and neo-Darwinian evolutionary theory has begun to make important contributions to our understanding of the biology and evolution of language. I review some of this recent progress, focusing on the value of the comparative method, which uses data from animal species to draw inferences about (...) language evolution. Discussing speech first, I show how data concerning a wide variety of species, from monkeys to birds, can increase our understanding of the anatomical and neural mechanisms underlying human spoken language, and how bird and whale song provide insights into the ultimate evolutionary function of language. I discuss the “descended larynx” of humans, a peculiar adaptation for speech that has received much attention in the past, which despite earlier claims is not uniquely human. Then I will turn to the neural mechanisms underlying spoken language, pointing out the difficulties animals apparently experience in perceiving hierarchical structure in sounds, and stressing the importance of vocal imitation in the evolution of a spoken language. Turning to ultimate function, I suggest that communication among kin (especially between parents and offspring) played a crucial but neglected role in driving language evolution. Finally, I briefly discuss phylogeny, discussing hypotheses that offer plausible routes to human language from a non-linguistic chimp-like ancestor. I conclude that comparative data from living animals will be key to developing a richer, more interdisciplinary understanding of our most distinctively human trait: language. (shrink)

Some evolutionary psychologists contend that the best way to discover the functions of our present psychological systems is by appealing to the notion of functional mesh, that is, the assumed tight fit between a trait's design and the adaptive problem it is supposed to solve. In this paper, I argue that there exist theoretical considerations and empirical evidence that undermine this assumption of optimal design. Instead, I suggest that cognitive systems are constrained by what I call bounded functionality. This proposal (...) makes use of Jacob's (1977) notion of evolution as a bricoleur and Simon's (1981) idea that problems can have ``satisficing'' solutions. Functional mesh will thus be shown to neglect constraints that are necessary to explain the evolution of psychological mechanisms. (shrink)

This paper analyzes the notion of possibility in biology and demonstrates how synthetic biology can provide understanding on the modal dimension of biological systems. Among modal concepts, biological possibility has received surprisingly little explicit treatment in the philosophy of science. The aim of this paper is to argue for the importance of the notion of biological possibility by showing how it provides both a philosophically and biologically fruitful category as well as introducing a new practically grounded way for its assessment. (...) More precisely, we argue that synthetic biology can provide tools to scientifically anchor reasoning about biological possibilities. Two prominent strategies for this are identified and analyzed: the design of functionally new-to-nature systems and the redesign of naturally occurring systems and their parts. These approaches allow synthetic biologists to explore systems that are not normally evolutionarily accessible and draw modal inferences that extend in scope beyond their token realizations. Subsequently, these results in synthetic biology can also be relevant for discussions on evolutionary contingency, providing new methods and insight to the study of various sources of unactualized possibilities in biology. (shrink)

Evolutionary epistemology has experienced a continuous rise over the last decades. Important new theoretical considerations and novel empirical findings have been integrated into the existing framework. In this paper, I would like to suggest three lines of research that I believe will significantly contribute to further advance EE: ontogenetic considerations, key ideas from cognitive biology, and the framework of the Extended Evolutionary Synthesis. EE, in particular the program of the evolution of epistemological mechanisms, seeks to provide a phylogenetic account of (...) the generation of cognitive processes underlying knowledge creation. Traditionally, EE and EEM have been oriented towards an account of evolutionary theory that mainly drew from the tenets of the Modern Synthesis. The Modern Synthesis largely dismisses ontogenetic processes and considers them irrelevant for evolutionary explanations. If anything, the role of development in evolution is believed to be that of a constraint. There is, however, ample evidence for a tight intertwinement of developmental and evolutionary processes. Organisms employ their cognitive apparatus to interact with the environment in order to achieve a fully functioning perceptual and cognitive nervous system. Also, ontogeny provides generative potentials to enable variations that natural selection can act upon. EEM’s agenda may, therefore, strongly benefit from bringing together ontogenetic and phylogenetic approaches. To grapple with this challenge, an alternative vision of the evolutionary theory termed Extended Evolutionary Synthesis could be used. This extended evolutionary theory explores relationships between the processes of individual development and phenotypic change during evolution and can provide a more suitable framework for EEM to draw from. In recent years, cognitive biology has gained momentum as an independent research field. Cognitive biology builds on the concepts of EEM and understands knowledge as a biogenic phenomenon. Its main objective is also the formulation of substantiated interrelations between cognition and evolution but it focuses on cognitive functionality at all levels of biological organization. It thus employs a “vertical” approach that encompasses nested hierarchies which span from single molecules, cells, and tissues to the organismal level, communities, and societies. In contrast to cognitive biology, EEM is here understood to adopt a “horizontal” approach that focuses on phylogenetic explanations of cognition and knowledge acquisition. Linking EEM with the key ideas of cognitive biology could make EEM’s research program stronger as it can more easily accommodate phylogenetic and ontogenetic questions within a hierarchical, multilevel perspective. This is of particular importance for a more comprehensive account of cognition since living systems are subject to context-dependent causal influences from different organizational levels. In addition to EEM, there is a second program of EE. This program has been labeled evolutionary epistemology of theories and understands the increase in human knowledge, such as scientific theories, as naturalistic accounts of evolution. Both, EEM and EET initially drew from the core concepts of the Modern Synthesis. Several scholars have severely criticized the analogies made between EET and the Neo-Darwinian key processes of evolution. In particular processes of random mutation, the rate of variation, natural selection as the unique driving force, and the adaptationist agenda are believed to reveal disanalogies. In contrast to the Modern Synthesis, the Extended Evolutionary Synthesis not only recognizes developmental processes but also ecological interactions and systems dynamics as well as social and cultural evolutionary reciprocity as important evolutionary processes. Concepts of the Extended Evolutionary Synthesis are therefore expected to be more fruitful for re-conceptualizing parallels between scientific theorizing and biological evolution. (shrink)

Morphological EvoDevo is a field of biological inquiry in which explicit relations between evolutionary patterns and growth or morphogenetic processes are made. Historically, morphological EvoDevo results from the coming together of several traditions, notably Naturphilosophie, embryology, the study of heterochrony, and developmental constraints. A special feature binding different approaches to morphological EvoDevo is the use of formalisms and mathematical models. Here we will introduce anatomical network analysis, a new approach centered on connectivity patterns formed by anatomical parts, with its own (...) concepts and tools specifically designed for the study of morphological EvoDevo questions. Riedl’s concept of burden is tightly related to the use of anatomical networks, providing a nexus between the evolutionary patterns and the structural constraints that shape them. (shrink)

A participant–observer who is both informed and interested in ethical issues, and is embedded within a nanotechnology research and development facility may be able to influence the ethical awareness of researchers in nanotechnology, and tease out the societal implications of the work being conducted. Two inter-disciplinary methods were employed: (1) regular involvement in the technical and scientific research at the facility by the participant–observer, and (2) repeated interactions and discussions between the participant–observer and the scientists. As a result of this (...) qualitative approach, an ethics questionnaire was developed and tested. This questionnaire has been incorporated into the admissions procedures for researchers as they commence use of the nanotech facility. The questionnaire highlights the importance of ethical issues in nanotechnology research and draws researchers into an engagement with possible ethical consequences and with future societal implications of their work. (shrink)

Modularity has become a central and remarkably useful concept in evolutionary developmental biology, offering an explanation of how independent, interacting units make possible developmental events and evolutionary changes. These modules exist at several different levels of organization, from genes to signal transduction pathways to cell populations. Cell populations, which are multicellular modules, provide an opportunity both to clarify our notion of modularity and to reexamine such central concepts as cell-to-cell communication. Rosine Chandebois’s work on “cell sociology” is reframed in the (...) language of modularity in order to show how groups of cells maintain their collective identity during development and how signaling information from the group’s environment is received by the constituent cells. In a “test case” for our account of multicellular modules, we consider the vertebrate neural crest, a migratory cell population made up of several subpopulations. The neural crest proves yet again to be a complex case, showing the importance of taking into account both developmental and evolutionary transformations of multicellular modules. (shrink)

I characterize Wimsatt’s approach to philosophy of science as philosophy for science and then briefly consider a theme emerging from his work that informs just one of the many current developments in philosophy of biology that he inspired: scaffolding as a problem of mechanistic explanation for functionalists.

It is commonly argued that the rules of language, as distinct from its semantic features, are the characteristics which most clearly distinguish language from the communication systems of other species. A number of linguists (e.g., Chomsky 1972, 1980; Pinker 1994) have suggested that the universal features of grammar (UG) are unique human adaptations showing no evolutionary continuities with any other species. However, recent summaries of the substantive features of UG are quite remarkable in the very general nature of the features (...) proposed. While the syntax of any given language can be quite complex, the specific rules vary so much between languages that the truly universal (i.e. innate) aspects of grammar are not complex at all. In fact, these features most closely resemble a set of general descriptions of our richly complex semantic cognition, and not a list of specific rules. General principles of the evolutionary process suggest that syntax is more properly understood as an emergent characteristic of the explosion of semantic complexity that occurred during hominid evolution. It is argued that grammatical rules used in given languages are likely to be simply conventionalized, invented features of language, and not the result of an innate, grammar-specific module. The grammatical and syntactic regularities that are found across languages occur simply because all languages attempt to communicate the same sorts of semantic information. (shrink)

The interests of synthetic biologists may appear to differ greatly from those of evolutionary biologists. The engineering of organisms must be distinguished from the tinkering action of evolution; the ambition of synthetic biologists is to overcome the limits of natural evolution. But the relations between synthetic biology and evolutionary biology are more complex than this abrupt opposition: Synthetic biology may play an important role in the increasing interactions between functional and evolutionary biology. In practice, synthetic biologists have learnt to submit (...) the proteins and modules they construct to a Darwinian process of selection that optimizes their functioning. More importantly, synthetic biology can provide evolutionary biologists with decisive tools to test the scenarios they have elaborated by resurrecting some of the postulated intermediates in the evolutionary process, characterizing their properties, and experimentally testing the genetic changes supposed to be the source of new morphologies and functions. This synthetic, experimental evolution will renew and clarify many debates in evolutionary biology: It will lead to the explosion of some vague concepts as constraints, parallel evolution, and convergence, and replace them with precise mechanistic descriptions. In this way, synthetic biology resurrects the old philosophical debate about the relations between the real and the possible. (shrink)

Drawing on convergent work in a broad range of disciplines, this article uses the tipping point paradigm to frame a new account of how early human ancestors may have first broken free from, as Bickerton calls it, the “prison of animal communication.” Under building pressure for an enhanced signaling system capable of supporting joint attentional-intentional activities, a cultural tradition of disambiguated indexical pointing (a finger point disambiguated by a facial expression, vocalization, or other gesture), combined with increasingly sophisticated mindreading circuitry (...) and prosocial tendencies, may have sparked the first in the series of biocultural explosions that led from a simple protolanguage to fully modern human language. This account successfully integrates at least ten other competing hypotheses, and is shown to pass nine important tests that have been proposed for language origin scenarios of its type. (shrink)

C.H. Waddington is today remembered chiefly as a Drosophila developmental geneticist who developed the concepts of “canalization” and “the epigenetic landscape.” In his lifetime, however, he was widely perceived primarily as a critic of Neo-Darwinian evolutionary theory. His criticisms of Neo-Darwinian evolutionary theory were focused on what he saw as unrealistic, “atomistic” models of both gene selection and trait evolution. In particular, he felt that the Neo-Darwinians badly neglected the phenomenon of extensive gene interactions and that the “randomness” of mutational (...) effects, posited in the theory, was a false postulate. This last criticism dealt with the phenomenon known today as “developmental constraints.” Although population genetics itself has evolved considerably from its form at mid-20th century, much of Waddington’s critique, it is argued here, retains cogency. Yet, he did not attempt to develop a full-fledged alternative theory himself. Perhaps most surprisingly, in retrospect, is that he did not try to marry his work on gene interactions in development with his evolutionary interests, to create a theory of “genetic networks” and their evolution. Whether evolutionary genetics today will incorporate “network thinking” as a central element or whether there will be a general retreat to the more atomistic approach offered by genomics, remains an open question. (shrink)

Aspects of the history of behavioural science are reviewed, pointing to its fragmented and faction-ridden nature. The emergence of evolutionary psychology (EP) is viewed in this context. With the help of a dual-layered model of behavioural control, the case is made for a more integrative perspective towards EP. The model's application to both behaviour and complex human information processing is described. Similarities in their control are noted. It is suggested that one layer of control (‘on-line’) corresponds to the encapsulated modules (...) of EP whereas the off-line controls provide the plasticity and flexibility suggested by its critics. (shrink)

This paper analyzes three contrasting strategies for modeling intentional agency in contemporary analytic philosophy of mind and action, and draws parallels between them and similar strategies of scientific model-construction. Gricean modeling involves identifying primitive building blocks of intentional agency, and building up from such building blocks to prototypically agential behaviors. Analogical modeling is based on picking out an exemplary type of intentional agency, which is used as a model for other agential types. Theoretical modeling involves reasoning about intentional agency in (...) terms of some domain-general framework of lawlike regularities, which involves no detailed reference to particular building blocks or exemplars of intentional agency. Given the contrasting procedural approaches that they employ and the different types of knowledge that they embody, the three strategies are argued to provide mutually complementary perspectives on intentional agency. (shrink)

The figure of the chimera animates both mythology and the biotechnological imagination. The mythological construction of animals from the sections or attributes of different species parallels the surgical and genetic manipulations of animals in modern transformations. Chimerization also represents a hybridization that relationally links different species. Both the mythological imagination and biotechnical practice bear heavily on the definition and identity of the human animal. In mythology the chimera links the animal, the human, and the divine. In biotechnology like xenotransplantation and (...) genetic engineering, real patchwork combinations of humans and other animals are constructed. (shrink)

Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...) or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

A recurrent theme in the characterization of synthetic biology is the role of engineering. This theme is widespread in the accounts of scholars studying this field and the biologists working in it, in those of the biologists themselves, as well as in policy documents. The aim of this article is to open this black-box of engineering that is supposed to influence and change contemporary life sciences. Too often, both synthetic biologists and their critics assume a very narrow understanding of what (...) engineering is about, resulting in an unfruitful debate about whether synthetic biology possesses genuine engineering methodologies or not. By looking in more detail to the diversity of engineering conceptions in debates concerning synthetic biology, a richer perspective can be developed. In this article, I will examine five influential ways in which engineering is understood in these debates, namely engineering as applied science, as rational methodology, context-sensitive practice, cunning activity or design. The claim is first of all thus to argue that engineering must not be seen as something stable or characterized by a fixed essence. It rather has multiple meanings and interpretations. Secondly, the claim is that most of the debates on synthetic biology cannot be indifferent towards the question which conception of engineering is at play, since the specific questions and concerns that pop up depend to a great extent on the precise conception of engineering one has in account. Many of the existing debates around synthetic biology can thus be reinterpreted and readdressed once one is aware of which conception of engineering is at play. (shrink)

Since 2008, we witness the emergence of the Do-It-Yourself Biology movement, a global movement spreading the use of biotechnology beyond traditional academic and industrial institutions and into the lay public. Practitioners include a broad mix of amateurs, enthusiasts, students, and trained scientists. At this moment, the movement counts nearly 50 local groups, mostly in America and Europe, but also increasingly in Asia. Do-It-Yourself Bio represents a direct translation of hacking culture and practicesfrom the realm of computers and software into the (...) realm of genes and cells. Although the movement is still in its infancy, and it is even unclear whether it will ever reach maturity, the contours of a new paradigm of knowledge production are already becoming visible. We will subsequently sketch the economic, the epistemological and the ethical profile of Do-It-Yourself Bio, and discuss its implications and also its ambivalences. (shrink)

Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n ‘constitutive’ proteins at (...) concentrations exceeding individual threshold values (strong emergence). The latter algorithm is modified here to take account of protein redundancy with respect to a complex trait (‘full redundancy’). Irreducibility is considered a necessary and sufficient criterion for strong biological emergence; if one constitutive protein is missing, or its concentration drops below the threshold the trait is lost. A definition based on ‘unpredictability’ is dismissed, because this criterion is irrelevant for the evolution of a complex trait, and apparent unpredictability may rather reflect our basic deficits in understanding unless we can provide an unequivocal proof for it. The phenomenological approach advocated here allows to identify hidden rules according to which strongly emergent traits may be organized. This is of high value for understanding the evolution of complex traits which seems to require the saltational advent of all constitutive proteins ‘in one turn’ to arrive at a functional trait providing for an improved fitness of the organism. Rather than being a purely random process, it may be guided by fundamental structural principles. (shrink)

The comparison between natural evolution and the action of a tinkerer has become highly popular since its reintroduction by François Jacob at the end of the 1970s. It has been used as a weapon against the existence of an “intelligent design” as well as a way for synthetic biologists to promote their ambitious projects. I will describe the complex history of this metaphor, and examine its pertinence. Whereas Darwin considered it as a way to describe how evolution proceeded, Jacob linked (...) it with a description of the imperfections of organisms, while Stephen Jay Gould and Richard Lewontin criticized what they called the “Panglossian” vision of most evolutionary biologists. The distinction between the work of engineers and that of tinkerers is not obvious. There are limits to the process of evolution, but their alleged description so far reflects the limits of knowledge on the part of evolutionary biologists more than the existence of true barriers to the evolutionary process. And, in their work, synthetic biologists crucially need the optimizing action of natural selection. To give a definition of synthetic biology is no easy task; the false distinction drawn between the work of synthetic biologists and the action of evolution is of no help. (shrink)

Synthetic biology is not only a contemporary reformulation of the recombinant DNA technologies of the last 30 years, combined with descriptive language imported from electrical and industrial engineering. It is also a new way to interpret living systems and a statement of intent for the use and reprogramming of biological objects for human benefit. In this context, the notion of designer biology is often presented as opposed to natural selection following the powerful rationale formulated by François Jacob on evolution-as-tinkering. The (...) onset of synthetic biology opens a different perspective by leaving aside the question about the evolutionary origin of biological phenomena and focusing instead on the relational logic and the material properties of the corresponding components that make biological system work as they do. Once a functional challenge arises, the solution space for the problem is not homogeneous but it has attractors that can be accessed either through random exploration or rational design. Although these two paths are essentially different, they can lead to solutions to specific mechanistic bottlenecks that frequently coincide or converge—and one can easily help to understand and improve the other. Alas, productive discussions on these matters are often contaminated by ideological preconceptions that prevent adoption of the engineering metaphor to understand and ultimately reshape living systems—as ambitioned by synthetic biology. Yet, some possible ways to overcome the impasse are feasible. In parallel to Monod’s evolutionary paradox of teleo-logy vs. teleo-nomy, a mechanistic paradox could be entertained between techno-logy vs techno-nomy, all for the sake of understanding the relational logic that enables live systems to function as physico-chemical entities in time and space. This article thus proposes a radical vision of synthetic biology through the lens of the engineering metaphor. (shrink)