Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (...) (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist. (shrink)

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution (...) are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification. (shrink)

Organisms are organized both internally and externally. The centrality of the organism in examination of the hierarchy of biological organization and the kinds of “emergent properties” that develop from study of organization at one level relative to other levels are my themes. That centrality has not often been implicit in discussion of unifying concepts, even evolution. Few general or unifying principles integrate information derived from various levels of biological organization. However, as the genetic toolbox and other new techniques are now (...) facilitating broader views of organisms and their internal and external interactions, and their evolution, some fundamental perspectives are emerging for many kinds of studies of biology. In particular, more hierarchical approaches are gaining favor in several areas of biology. Such approaches virtually demand the integration of data and theory from different levels of study. They require explicit delineations of methodology and clear definition of terms so that communication per se among scientists can become more integrative. In so doing, a hierarchy of theory will develop that demands ever further integration, potentially leading to unifying concepts and a general theory for biology. (shrink)

In a macroevolutionary timescale, evolvability itself evolves. Lineages are sorted based on their ability to generate adaptive novelties, which leads to the optimization of their genotype-phenotype map. The system of translation of genetic or epigenetic changes to the phenotype may reach significant horizontal and vertical complexity, and may even exhibit certain aspects of learning behaviour. This continuously evolving semiotic system probably enables the origin of complex yet functional and internally compatible adaptations. However, it also has a second, “darker”, side. As (...) was pointed out by several authors, the same process gradually reduces the probability of the origination of significant evolutionary novelties. In a similar way to the evolution of societies, teachings, or languages, in which the growing number of internal linkages gradually solidifies their overall structure and the structure or interpretation of their constitutive elements, the evolutionary potential of lineages decreases during biological evolution. Possible adaptations become limited to small “peripheral” modifications. According to the Frozen Evolution theory, some of the proximate causes of this “macroevolutionary freezing” are more pronounced or present exclusively in sexual lineages. Sorting based on the highest evolvability probably leads to the establishment of certain structural features of complex organisms, e.g. the modular character of their development and morphology. However, modules also “macroevolutionary freeze” whereas the hypothetical “thawing” of modules or their novel adaptive combinations becomes rarer and rarer. Some possible ways out of this dead end include the rearrangement of individual development, e.g. neoteny, radical simplification, i.e. sacculinization, and transition to a higher level of organization, e.g. symbiosis or symbiogenesis. The evolution of evolvability is essentially a biosemiotic process situated at the intersection of the genocentric modern synthesis and the evo-devo-centric extended synthesis. Therefore, evolvability may eventually connect these three not necessarily contradictory approaches. (shrink)

In recent years, many philosophers of science have attempted to articulate a theory of non-epistemic emergence that is compatible with mechanistic explanation and incompatible with reductionism. The 2005 account of Fred C. Boogerd et al. has been particularly influential. They argued that a systemic property was emergent if it could not be predicted from the behaviour of less complex systems. Here, I argue that Boogerd et al.'s attempt to ground emergence in complexity guarantees that we will see emergence, but at (...) the cost of rendering it either trivial or epistemic. There are three basic problems. First, neither the measures of complexity explicitly mentioned by Boogerd et al. nor the most popular measures in the literature can do the practical and theoretical work that they assign to complexity. Second, I argue that while the success of their view depends on restricting the base of information available to the reductionist, this cannot be done in a way that is metaphysically neutral with respect to emer.. (shrink)

Cancer is typically spoken of as a “complex” disease. But, in what sense are cancers “complex”? Is there one sense, or several? What implications does this complexity have – both for how we study, and how we intervene upon cancers? The aim of this paper is first, to clarify the variety of senses in which cancer is spoken of as "complex" in the scientific literature, and second, to discover what explanatory and predictive roles such features play.

Richness theory offers an alternative to the paradigms that have dominated the short history of environmental ethics as a self-conscious field. This alternative theoretical paradigm defines intrinsic value as “richness”—a synonym for “organic unity” or “unity in diversity.” Richness theory can handily reconcile two kinds of ideas that seem to be in tension with each other:that (1) an individual human being has a greater worth than an individual organism of just about any other species; and (2) yet the world would (...) be a better place with substantially fewer humans and/or less consumption per capita, thus leaving more resources for other species.The mutual compatibility of such ideas within the framework of richness theory can be demonstrated both verbally and through a simplified mathematical model. (shrink)

The common opinion has been that evolution results in the continuing development of more complex forms of life, generally understood as more complex organisms. The arguments supporting that opinion have recently come under scrutiny and been found wanting. Nevertheless, the appearance of increasing complexity remains. So, is there some sense in which evolution does grow complexity? Artificial life simulations have consistently failed to reproduce even the appearance of increasing complexity, which poses a challenge. Simulations, as much as scientific theories, are (...) obligated at least to save the appearances! We suggest a relation between these two problems, understanding biological complexity growth and the failure to model even its appearances. We present a different understanding of that complexity which evolution grows, one that genuinely runs counter to entropy and has thus far eluded proper analysis in information-theoretic terms. This complexity is reflected best in the increase in niches within the biosystem as a whole. Past and current artificial life simulations lack the resources with which to grow niches and so to reproduce evolution’s complexity. We propose a more suitable simulation design integrating environments and organisms, allowing old niches to change and new ones to emerge. (shrink)

In this article, I will discuss possible differences between ecosystems and organisms on the basis of their intrinsic complexity. As the concept of complexity still remains highly debated, I propose here a practical and original way to measure the complexity of an ecosystem or an organism. For this purpose, I suggest using the concept of logical depth (LD) in a specific manner, in order to take into account the difficulty as well as the time needed to generate the studied object. (...) I illustrate this method with fully controlled Daisyworld simulations (i.e., simulations based on the Gaia hypothesis) that have often been proposed to mimic living systems. The method consists of the following sequential stages: (1) identification of the shortest program able to numerically model the studied system (also called the Kolmogorov–Solomonoff complexity); (2) running the program, once if there are no stochastic components in the system, several times if stochastic components are there; and (3) computing the time needed to generate the system with LD complexity. This measure is supposed to estimate the system complexity. It appears in this study that LD estimations fit well with the intuition we have of complex systems, with higher complexities being found for more realistic Daisyworlds. With such a method of capturing the time needed to build a system, we expect to detect in future studies any quantified differences between complex ecosystems and organisms. (shrink)

It is an ongoing controversy whether natural selection is a cause of population change, or a mere statistical description of how individual births and deaths accumulate. In this paper I restate the problem in terms of the reference class problem, and propose how the structure of stable equilibrium can provide a solution in continuity with biological practice. Insofar natural selection can be understood as a tendency towards equilibrium, key statisticalist criticisms are avoided. Further, in a modification of the Newtonian-force analogy, (...) it can be suggested that a better metaphor for natural selection is that of an emergent force, similar in nature to entropic forces: with magnitude and direction, but lacking a spatiotemporal origin or point of application. (shrink)

Philosophers and psychologists make many different, seemingly incompatible parsimony claims in support of competing models of cognition in nonhuman animals. This variety of parsimony claims is problematic. Firstly, it is difficult to justify each specific variety. This problem is especially salient for Morgan's Canon, perhaps the most important variety of parsimony claimed. Secondly, there is no systematic way of adjudicating between particular claims when they conflict. I argue for a view of parsimony in comparative psychology that solves these problems, based (...) on Sober's view that parsimony claims are claims that one model is more plausible given background theory. (shrink)

Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (shrink)

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken (...) in Clarke :413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided. (shrink)

Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the (...) context of such a “social protocell,” the outcome will be an evolutionary transition in individuality whereby traditions and hominins coalesce into a macroscopic bio-socio-technical system, with an organismal organization that is culturally inherited through irreversible fission events on the community level. We refer to the resulting hypothetical evolutionary individual as a “sociont.” The social protocell provides a preadapted source of alignment of fitness interests that addresses a number of open questions about the origins of shared adaptive cultural organization, and the derived genetic adaptations that support them. Also, social cooperation between hominins is no longer in exclusive focus since cooperation among traditions becomes salient in this model. This provides novel avenues for explanation. We go on to hypothesize that the fate of the hominin in such a setting would be mutualistic coadaptation into a part-whole relation with the sociont, and we propose that the unusual suite of derived features in Homo is consistent with this hypothesis. (shrink)

Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the (...) context of such a “social protocell,” the outcome will be an evolutionary transition in individuality whereby traditions and hominins coalesce into a macroscopic bio-socio-technical system, with an organismal organization that is culturally inherited through irreversible fission events on the community level. We refer to the resulting hypothetical evolutionary individual as a “sociont.” The social protocell provides a preadapted source of alignment of fitness interests that addresses a number of open questions about the origins of shared adaptive cultural organization, and the derived genetic adaptations that support them. Also, social cooperation between hominins is no longer in exclusive focus since cooperation among traditions becomes salient in this model. This provides novel avenues for explanation. We go on to hypothesize that the fate of the hominin in such a setting would be mutualistic coadaptation into a part-whole relation with the sociont, and we propose that the unusual suite of derived features in Homo is consistent with this hypothesis. (shrink)

Arguments for or against a trend in the evolution of complexity are weakened by the lack of an unambiguous definition of complexity. Such definitions abound for both dynamical systems and biological organisms, but have drawbacks of either a conceptual or a practical nature. Physical complexity, a measure based on automata theory and information theory, is a simple and intuitive measure of the amount of information that an organism stores, in its genome, about the environment in which it evolves. It is (...) argued that physical complexity must increase in molecular evolution of asexual organisms in a single niche if the environment does not change, due to natural selection. It is possible that complexity decreases in co‐evolving systems as well as at high mutation rates, in sexual populations, and in time‐dependent landscapes. However, it is reasoned that these factors usually help, rather than hinder, the evolution of complexity, and that a theory of physical complexity for co‐evolving species will reveal an overall trend towards higher complexity in biological evolution. BioEssays 24:1085–1094, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

This dissertation focuses on teleology and functions in biology. More precisely, it focuses on the scientific legitimacy of teleofunctional attributions and explanations in biology. It belongs to a multi-faceted debate that can be traced back to at least the 1970s. One aspect of the debate concerns the naturalization of functions. Most authors try to reduce, translate or explain functions and teleology in terms of efficient causes so that they find their place in the framework of the natural sciences. Our approach (...) here is radically different, as we question the premise that teleological explanations are disguised causal explanations. On the contrary, we defend that they are acceptable in natural sciences and in biology in particular. We challenge the idea that teleological explanations are immature causal explanations, as well as the idea that teleology and functions are some sort of intentional explanations. We therefore reject the accusations of anthropomorphism, vitalism and finalism. On the contrary, we defend that teleology, causality and intentionality correspond to different, autonomous and complementary modes of representation of the outside world. -/- ———[FRANÇAIS]——— -/- Ce travail de thèse porte sur la téléologie et les fonctions en biologie. Plus précisément, il porte sur la légitimité scientifique des attributions et des explications téléofonctionnelles en biologie. Il s’inscrit dans le cadre d’un débat à plusieurs facettes que l’on peut faire remonter au moins jusqu’aux années 1970 et qui est encore très actif aujourd’hui. L’un des aspects du débat porte sur la naturalisation des fonctions, c’est-à-dire sur la manière de les réduire, de les traduire ou de les expliciter en termes de causes efficientes de sorte qu’elles trouvent leur place dans le cadre des sciences de la nature. Notre approche ici est radicalement différente, car nous remettons en question la prémisse selon laquelle les explications téléologiques seraient des explications causales déguisées. Nous défendons au contraire qu’elles sont acceptables en tant que telles aussi bien de façon générale que dans le domaine scientifique et en particulier en biologie. De façon générale, nous remettons en question l’idée selon laquelle la pensée téléologique serait une pensée causale immature, ainsi que sa dépendance présumée vis-à-vis de la psychologie, c’est-à-dire de l’intentionnalité. Nous rejetons donc les accusations d’anthropomorphisme, de vitalisme et de finalisme formulées contre elle. Nous défendons au contraire que la téléologie, la causalité et l’intentionnalité correspondent à des modes différents, autonomes et complémentaires de représentation du monde extérieur. (shrink)

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the (...) origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology. (shrink)