Biological regulation is what allows an organism to handle the effects of a perturbation, modulating its own constitutive dynamics in response to particular changes in internal and external conditions. With the central focus of analysis on the case of minimal living systems, we argue that regulation consists in a specific form of second-order control, exerted over the core regime of production and maintenance of the components that actually put together the organism. The main argument is that regulation requires a distinctive (...) architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. We distinguish between two major ways in which control mechanisms contribute to the maintenance of a biological organisation in response to internal and external perturbations: dynamic stability and regulation. Based on this distinction an explicit definition and a set of organisational requirements for regulation are provided, and thoroughly illustrated through the examples of bacterial chemotaxis and the lac-operon. The analysis enables us to mark out the differences between regulation and closely related concepts such as feedback, robustness and homeostasis. (shrink)

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)

In this paper we explore the organizational conditions underlying the emergence of organisms at the multicellular level. More specifically, we shall propose a general theoretical scheme according to which a multicellular organism is an ensemble of cells that effectively regulates its own development through collective mechanisms of control of cell differentiation and cell division processes. This theoretical result derives from the detailed study of the ontogenetic development of three multicellular systems and, in particular, of their corresponding cell-to-cell signaling networks. The (...) case study supports our claim that a specific type of functional integration among the cells of a multicellular ensemble , is required for it to qualify as a proper organism. Finally, we argue why a multicellular system exhibiting this type of functionally differentiated and integrated developmental organization becomes a self-determining collective entity and, therefore, should be considered as a second-order autonomous system. (shrink)

In this short contribution we explore the historical roots of recent synthetic approaches in biology and try to assess their real potential, as well as identify future hurdles or the reasons behind some of the main difficulties they currently face. We suggest that part of these difficulties might not be just the result of our present lack of adequate technical skills or understanding, but could spring directly from the nature of the biological phenomenon itself. In particular, if life is conceived (...) as autonomy in open-ended evolution, which would help to explain the highly complex and dynamic organization of the simplest known organisms (i.e., genetically-instructed cellular metabolisms), external synthetic implementations of such systems, or interventions on them, are bound to interfere with some of their characteristic transformation processes, both at the ontogenetic and phylogenetic scales. In any case, this will prove very revealing and productive, technologically and scientifically speaking, since the knowledge gathered from those implementations/interventions will be extremely valuable in establishing our capacities and limitations to fully comprehend, utilize, and expand the living domain as we know it today. (shrink)

Since Darwin it is widely accepted that natural selection (NS) is the most important mechanism to explain how biological organisms—in their amazing variety—evolve and, therefore, also how the complexity of certain natural systems can increase over time, creating ever new functions or functional structures/relationships. Nevertheless, the way in which NS is conceived within Darwinian Theory already requires an open, wide enough, functional domain where selective forces may act. And, as the present paper will try to show, this becomes even more (...) evident if one looks into the problem of origins. If there was a time when NS was not operating (as it is quite reasonable to assume), where did that initial functional diversity, necessary to trigger off the process, come from? Self-organization processes may be part of the answer, as many authors have claimed in recent years, but surely not the complete one. We will argue here that a special type of self-maintaining organization, arising from the interplay among a set of different endogenously produced constraints (pre-enzymatic catalysts and primitive compartments included), is required for the appearance of functional diversity in the first place. Starting from that point, NS can progressively lead to new (and, at times, also more complex) organizations that, in turn, provide wider functional variety to be selected for, enlarging in this way the range of action and consequences of the mechanism of NS, in a kind of mutually enhancing effect. (shrink)

During the last decades the question of defining life has gained increased interest but, at the same time, the difficulty in reaching consensus on a possible answer has led many to skeptical positions. This, in turn, has raised a wider debate about why defining life is so hard and controversial. Such a debate introduces additional aspects to be considered, like the role and nature of a definition of life itself. In this paper, we will focus on those aspects, arguing that (...) progress can be made if we conceive definitions of life as open heuristic tools that contribute to develop specific research strategies in the biological sciences and, more generally, to increase our understanding of life’s complexity. In contrast with pragmatic or operationalist approaches, we will defend that definitions of life comprise a set of ontological assumptions, together with an inherent unifying vocation, so they should be subject to comparison and critical assessment, closely related to the success or failure of the corresponding research programs, but also to the success or failure in establishing well-grounded interconnections among the latter. We consider that the search for a more coherent, integrated and generalized theory of biology cannot be pursued without keeping an empirical standpoint, and the exercise of defining life should not be taken as an obstacle but as a valuable instrument to achieve that goal. (shrink)

In this paper we review and argue for the relevance of the concept of open-ended evolution in biological theory. Defining it as a process in which a set of chemical systems bring about an unlimited variety of equivalent systems that are not subject to any pre-determined upper bound of organizational complexity, we explain why only a special type of self-constructing, autonomous systems can actually implement it. We further argue that this capacity derives from the ‘dynamic decoupling’ (in its minimal or (...) most basic sense: the phenotype–genotype decoupling) by means of which a radically new way of material organization (minimal living organization) is achieved, allowing for the long-term sustenance of systems whose individual-metabolic and collective-historical pathways become thereafter deeply intertwined. (shrink)

In this chapter we offer a critical analysis of organizational models about the process of origins of life and, thereby, a reflection about life itself (understood in a general, minimal sense). We begin by demarcating the idea of organization as an explanatory construct, linking it to the complex relationships and transformations that the material parts of (proto-)biological systems establish to maintain themselves under non-equilibrium dynamic conditions. The diverse ways in which this basic idea has been applied within the prebiotic field (...) are then reviewed in relative detail. We distinguish between “network” and “protocell” approaches, discussing their specific implications and explaining the greater relevance of the latter in the current state of affairs. Despite the key role that such organizational approaches play (and should keep playing) to advance on the problem of primordial biogenesis, the second half of our contribution is devoted to argue that they must be combined with other explanatory accounts, which go beyond the physiology of any single (proto-)organism. With that aim, we underline the fundamental differences between the autonomous, metabolic dynamics that individual (proto-)cells perform and the evolutionary and ecological dynamics that take place in a collective and trans-generational dimension. Apart from obvious gaps in the characteristic temporal and spatial scales involved, the corresponding causal and interactive regimes also reveal themselves as neatly distinct, what is reflected in the unpaired functional integration and the agent behavior displayed by biological individuals. Nevertheless, any living organism (and life in a wider, general sense) derives from the deep interweaving of those two phenomenological domains: namely, the “individual-metabolic” and the “collective-evolutionary” domains. At the end of the chapter, we propose the principle of dynamical decoupling as the core idea to develop a more comprehensive theoretical framework to understand how this intricate, causally asymmetric connection must be articulated during the actual process of biogenesis (as it happened here on Earth or anywhere else in the universe), so that life’s minimal complexity threshold is reached. (shrink)

The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically (...) related to the living but not necessarily equivalent to it. More precisely, the idea of “minimal metabolism”, in contrast to previous, top‐down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here:https://youtu.be/DP7VMKk2qpA. (shrink)

En este artículo se ofrece una visión de la biología sintética alternativa a los planteamientos ingenieriles que marcan gran parte de la agenda de investigación del campo. Nuestro análisis se centra en enfoques, teóricos y experimentales, cuyo objetivo fundamental es la comprensión del fenómeno de la vida per se. Una revisión detallada de varios casos de implementación artificial, in vitro, de sistemas químicos ‘auto-productivos’ nos ayudará a reflexionar sobre el enorme reto que supone transformar una disciplina científica eminentemente descriptiva, como (...) la biología, en un proyecto que incluya y potencie líneas de investigación basadas en la idea de síntesis o fabricación. El reto es mayúsculo debido al carácter intrínsecamente metabólico de los sistemas biológicos, lo cual hace que nuestro empeño en controlarlos o en construirlos de novo sea mucho más dificultoso, forzándonos a desarrollar plataformas de intervención/implementación a nivel molecular que no pongan en compromiso esa inherente dimensión autónoma de lo vivo. (shrink)