Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...) proposing autonomy as the main concept to grasp it. In the second part of the article we show how autonomy is also fundamental to explaining major evolutionary transitions, in an attempt to rethink evolution from the point of view of the organizational structure of the entities/organisms involved. This gives further support to the idea of autonomy not only as a key to understanding life in general but also the complex expressions of it that we observe on our planet. Finally, we suggest a possible general principle that underlies those evolutionary transitions, which allow for the open-ended redefinition of autonomous systems: namely, the relative dynamic decoupling that must be articulated among distinct parts, modules or modes of operation in these systems. (shrink)

The phrase “regenerative medicine” is used so often and for so many different things, with such enthusiasm or worry, and often with a sense that this is something radically new. This paper places studies of regeneration and applications in regenerative medicine into historical perspective. In fact, the first stem cell experiment was carried out in 1907, and many important lines of research have contributed since. This paper explores both what we can learn about the history and what we can learn (...) from the history of regenerative medicine research. (shrink)

In his 1987 book "Controlling Life: Jacques Loeb and the Engineering Ideal in Biology", Philip Pauly presented his readers with the biologist Jacques Loeb and his role in developing an emphasis on control of life processes. Loeb's work on artificial parthenogenesis, for example, provided an example of bioengineering at work. This paper revisits Pauly's study of Loeb and explores the way current research in regenerative medicine reflects the same tradition. A history of regeneration research reveals patterns of thinking and research (...) methods that both echo Loeb's ideology and point the way to modern studies. Pauly's work revealed far more than we readers realized at the time of its publication. (shrink)

This paper argues in defense of theanti-reductionist consensus in the philosophy ofbiology. More specifically, it takes issues with AlexRosenberg's recent challenge of this position. Weargue that the results of modern developmentalgenetics rather than eliminating the need forfunctional kinds in explanations of developmentactually reinforce their importance.

The relationship of man himself to his environment is an inseparable part of ecology; for he also is an organism and other organisms are a part of his environment. Ecology, therefore, broadly conceived and rightly understood, instead of being an academic science merely, out of touch with humanistic interests, is really that part of every other biological science which brings it into immediate relation to human kind. The proper place of humans in ecological study has been a recurring issue for (...) ecology. Of course humans are part of Nature writ large, but are they part of the ecologist's nature? The question bothered biologists even before the discipline of ecology was firmly institutionalized.... (shrink)

Canada is the world’s highest per capita municipal solid waste producer. By 2000, Canadians produced more annual waste per person than Americans; and by 2005, Canada produced nearly twice as much garbage as Japan (Conference Board of Canada 2008). By 2006, Canadians produced over 1000 kg of waste per person; 35 million tons of waste in a single calendar year (Statistics Canada 2008). The bulk of this waste ended up in landfills (ibid). In 2010, thirty percent of existing Canadian landfills (...) reached or surpassed capacity. Over one million tons of waste were exported out of Canada in 2002, much of it headed from southern Ontario to rural regions of Canada or to the United States (Statistics Canada 2005). Some cities .. (shrink)

Embryonic development and ontogeny occupy whatis often depicted as the black box betweengenes – the genotype – and the features(structures, functions, behaviors) of organisms– the phenotype; the phenotype is not merelya one-to-one readout of the genotype. Thegenes home, context, and locus of operation isthe cell. Initially, in ontogeny, that cell isthe single-celled zygote. As developmentensues, multicellular assemblages of like cells(modules) progressively organized as germlayers, embryonic fields, anlage,condensations, or blastemata, enable genes toplay their roles in development and evolution.As modules, condensations are (...) fundamentaldevelopmental and selectable units ofmorphology (morphogenetic units) that mediateinteractions between genotype and phenotype viaevolutionary developmental mechanisms. In ahierarchy of emergent processes, gene networksand gene cascades (genetic modules) link thegenotype with morphogenetic units such ascondensations, while epigenetic processes suchas embryonic inductions, tissue interactionsand functional integration, link morphogeneticunits to the phenotype. To support theseconclusions I distinguish units of heredityfrom units of transmission and discussepigenetic inheritance by tracing the historyof relationship between embryology andevolution, especially the role(s) assigned tocells or to cellular components in generatingtheories of morphological change in evolution.The concept of cells as modular morphogeneticunits is modeled and illustrated using themammalian dentary bone. (shrink)

From the 1930s through the 1970s, C. H. Waddington attempted to reunite genetics, embryology, and evolution. One of the means to effect this synthesis was his model of the epigenetic landscape. This image originally recast genetic data in terms of embryological diagrams and was used to show the identity of genes and inducers and to suggest the similarities between embryological and genetic approaches to development. Later, the image became more complex and integrated gene activity and mutations. These revised epigenetic landscapes (...) presented an image of how mutations could alter developmental pathways to yield larger phenotypic changes. These diagrams became less important as the operon became used to model differential gene regulation. (shrink)

Agnes Arber (1879-1960) was a British botanist who was a leading plant morphologist during the first half of the 20th century. She also wrote on the history and philosophy of botany. I argue in this article that her philosophical work on form and on how the work of the mind and the eye relate to each other in morphological research are relevant to the science of today. Arber's unusual blend of interests - in botany, history, philosophy, and art - put (...) her in a unique position to examine issues of form. Even her unorthodox ideas on evolution can now be seen as fitting in well with discussions of natural selection as the predominant engine of evolutionary change. Arber's views also throw light on present work dealing with developmental plant genetics and with the study of protein form. I will further argue that her marginal position relative to institutional science, while it may have left her vulnerable to criticism, also made possible her deep philosophical reflections on morphology. (shrink)

Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This simple abstract model represents (...) development as an undulating surface of hills and valleys. Originally constructed by C. H. Waddington to visually explicate an integrated theory of genetics, development and evolution, the landscape model can play an updated unificatory role. I examine this model’s structure, representational assumptions, and uses in all three contexts, and argue that explanations of cell development require both mathematical models and concrete experiments. On this view, the two approaches are interdependent, with mathematical models playing a crucial but circumscribed role in explanations of cell development. (shrink)

In this chapter I investigate the prospects of integrated history and philosophy of science, by examining how philosophical issues raised by “hidden entities”, entities that are not accessible to unmediated observation, can enrich the historical investigation of their careers. Conversely, I suggest that the history of those entities has important lessons to teach to the philosophy of science. Hidden entities have played a crucial role in the development of the natural sciences. Despite their centrality to past scientific practice, however, several (...) of them (e.g., phlogiston, caloric, and the ether) turned out to be fictitious. For this reason, they have figured prominently in recent debates on scientific realism. The issues I explore in this paper are entangled with those debates. I argue that our understanding of hidden entities and their role in experimental practice can be enhanced by adopting an integrated historical-cum-philosophical approach. On the one hand, philosophical reflection on the reality of those entities has a lot to gain by examining historically how they were ntroduced and investigated. On the other hand, the historical reconstruction of the careers of those entities may profit from philosophical reflection on their existence. (shrink)

C.H. Waddington’s concepts of ‘chreods’ (canalized paths of development) and ‘homeorhesis’ (the tendency to return to a path), each associated with ‘morphogenetic fields’, were conceived by him as a contribution to complexity theory. Subsequent developments in complexity theory have largely ignored Waddington’s work and efforts to advance it. Waddington explained the development of the concept of chreod as the influence on his work of Alfred North Whitehead’s process philosophy, notably, the concept of concrescence as a self-causing process. Processes were recognized (...) as having their own dynamics, rather than being explicable through their components or external agents. Whitehead recognized the tendency to think only in terms of such ‘substances’ as a bias of European thought, claiming in his own philosophy ‘to approximate more to some strains of Indian, or Chinese, thought, than to western Asiatic, or European, thought.’ Significantly, the theoretical biologist who comes closest to advancing Waddington’s research program, also marginalized, is Mae-Wan Ho. Noting this bias, and embracing Whitehead’s and Waddington’s efforts to free biology from assumptions dominating Western thought to advance an ontology of creative causal processes, I will show how later developments of complexity theory, most importantly, Goodwin’s work on oscillations, temporality and morphogenesis, Vitiello’s dissipative quantum brain dynamics, Salthe’s work on hierarchy theory, biosemiotics inspired by Peirce and von Uexküll, Robert Rosen’s work on anticipatory systems, together with category theory and biomathics, can augment while being augmented by Waddington’s work, while further advancing Mae-Wan Ho’s radical research program with its quest to understand the reality of consciousness. (shrink)

ABSTRACT. This paper contemplates Organicism and its relation with molecular and evolutionary biology. We explore whether twentieth-first century biology is returning to positions held at the beginning of the twentieth century and then abandoned. The guiding line is a history of theoretical biology in which we distinguish three periods: 1. The 20s-30s, and the Theoretical Biology Club (Needham, Woodger, and Waddington, among others); 2. An intermediate period in the 60s-70s, in which, in spite of the eclosion of the molecular and (...) evolutionary biologies, there is some recovery of organicist positions, and 3. The present post-genomic situation, which is demanding a systemic approach. (shrink)