What is Life? This is the question asked by Denis Noble in this very personal and at times deeply lyrical book. Noble is a renowned physiologist and systems biologist, and he argues that the genome is not life itself: to understand what life is, we must view it at a variety of different levels, all interacting with each other in a complex web. It is that emergent web, full of feedback between levels, from the gene to the wider environment, that (...) is life. (shrink)

The Modern Synthesis has dominated biology for 80 years. It was formulated in 1942, a decade before the major achievements of molecular biology, including the Double Helix and the Central Dogma. When first formulated in the 1950s these discoveries and concepts seemed initially to completely justify the central genetic assumptions of the Modern Synthesis. The Double Helix provided the basis for highly accurate DNA replication, while the Central Dogma was viewed as supporting the Weismann Barrier, so excluding the inheritance of (...) acquired characteristics. This article examines the language of the Modern Synthesis and reveals that it is based on four important misinterpretations of what molecular biology had shown, so forming the basis of the four Illusions: 1. Natural Selection; 2. The Weismann Barrier; 3. The Rejection of Darwin’s Gemmules; 4. The Central Dogma. A multi-level organisation view of biology avoids these illusions through the principle of biological relativity. Molecular biology does not therefore confirm the assumptions of the Modern Synthesis. (shrink)

What is Life? To answer this question, Denis Noble argues that we must look beyond the gene's eye view. For modern 'systems biology' considers life on a variety of levels, as an intricate web of feedback between gene, cell, organ, body, and environment. He shows how it is both a biologically rigorous and richly rewarding way of understanding life.

Conscious Agency is a major driver of evolution. Artificial Selection (i.e. Conscious Selection by human breeders) was the foil against which Charles Darwin defined Natural Selection. In later work, he extended Artificial Selection to other species. That ability for social (e.g. sexual) selection must have evolved. Jablonka and Ginsburg identify markers of conscious agency, such as Unlimited Associative Learning (UAL), and show that it must have existed at the time of the Cambrian Explosion. To their insights, my commentary argues that (...) the harnessing of stochasticity was also involved in the evolution of the faculty of choice in organisms. (shrink)

The extensive range and depth of the twenty commentaries on my target article confirms that something has gone deeply wrong in biology. A wide range of biologists has more than met my invitation for “others to pitch in and develop or counter my arguments.” The commentaries greatly develop those arguments. Also remarkably, none raise issues I would seriously disagree with. I will focus first on the more critical comments, summarise the other comments, and then point the way forward on what (...) I view as a necessary and long-overdue transition in the foundations of biology. (shrink)

In this paper, we demonstrate (1) how harnessing stochasticity can be the basis of creative agency; (2) that such harnessing can resolve the apparent conflict between reductionist (micro-level) accounts of behaviour and behaviour as the outcome of rational and value-driven (macro-level) decisions; (3) how neurophysiological processes can instantiate such behaviour; (4) The processes involved depend on three features of living organisms: (a) they are necessarily open systems; (b) micro-level systems therefore nest within higher-level systems; (c) causal interactions must occur across (...) all the boundaries between the levels of organization. The higher levels constrain the dynamics of lower levels. The experimental evidence and theoretical arguments are shown to be consistent with previous research on the neuronal mechanisms of conscious choice, and with the interconnected multi-level processes by which organisms harness stochasticity, whether conscious or unconscious. (shrink)

The is the Editorial of the 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics and Phenomenological Philosophy.

Mathematical models of the heart have developed over a period of about 40 years. Cell types in all regions of the heart have been modelled and they are now being incorporated into anatomically detailed models of the whole organ. This combination is leading to the creation of the first ‘virtual organ,’ which is being used in drug discovery and testing, and in simulating the action of devices, such as cardiac defibrillators. Simulation is a necessary tool of analysis in attempting to (...) understand biological complexity. We often learn as much from the failures as from the successes of mathematical models. It is the iterative interaction between experiment and simulation that is important. Examples are given where this process has been instrumental in some of the major advances in the field. BioEssays 24:1155–1163, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

Kathy Wilkes contributed to two books on Goal-directed Behaviour and Modelling the Mind based on interdisciplinary graduate classes at Oxford during the 1980s. In this article, I assess her contributions to those discussions. She championed the school of philosophers who prefer problem dissolution to problem-solution. She also addressed the problem of realism in psychology. But the contribution that has turned out to be most relevant to subsequent work was her idea that in modelling the mind, we might need to “use (...) as structural elements synthetic cells, or things that behaved very like neurones.” I show how this idea has been developed in my own recent work with zoologist and neuroscientist, Raymond Noble, to become a possible physiological basis for the ability of organisms to choose between alternative actions, and so become active agents. I consider that this insight became her seminal contribution in this field. (shrink)

This chapter describes the origin of the principle of biological relativity and its development since 2012. It was first formulated by distinguishing between the causal properties of initial and boundary conditions, regarded as a formal cause, compared to the dynamics of the differential functions themselves, regarded as an efficient cause. The concept of organisational level, and of boundaries between levels and environmental factors are also central to the principle. Work on the properties of boundaries reveals two important features: the nature (...) of causation differs significantly between different levels of organisation, and the top-down and bottom-up forms must act simultaneously. These developments of the principle are used to clarify the reasons why bottom-up causation alone is inadequate in multi-level biology. (shrink)

Athlete after athlete in this book found discipline, hope, and inspiration on the playing field, rising above their circumstances. Filled with first-hand accounts from stars who exemplify the idea of enduring at all costs, Rising Above will serve as a must-read source of inspiration for kids and sports fans of all ages.

The Weismann Barrier and the Central Dogma do not protect the assumptions of The Modern Synthesis.

Despite the unprecedented freedoms that decolonization has brought for many Black1 people – especially in specific regions of the African Diaspora – freedom and its fulfilment, adequate signs and contested meanings remain a preoccupation within Black cultural discourses and practices. At the same time, while political and cultural nationalisms have led to greater political and civil rights, racism has not been eradicated. Furthermore, the new postcolonial globalizations of capital, people and cultures have destabilized the collective identities that framed twentieth-century struggles (...) for national sovereignty and equal citizenship, without necessarily erasing them. Instead, they remain, no longer securely anchored in their old homogenous appearances, but re-configured through the inner differences and contradictions of gender, sexuality, ethnicity and religion. This article addresses these internal differences and the ways in which they produce new contestations over race, the meaning of Black representation and postcolonial freedom, negotiations that are increasingly traced on the intimate contours of the body and the self, through practices of personal consumption, erotic hedonism and style as key performances of freedom. It achieves this through examining two localized moments in the transnational and diasporic circulation of Jamaican dancehall culture, understood as a privileged public space for the performance of Black identifications and personal freedom. It argues that the eroticized discourses of ethnicity, race and gender found in dancehall culture articulate the dominance of neo-liberal conceptions of freedom at the same time as they express, resist and comment on new cultural hegemonies not reducible to racism or the power of the West; that is how dancehall expresses the new problematizations of postcoloniality. 1Except when quoting other writers, I will capitalise the word Black, in order to recognise Black identity as a historically and politically constituted experience and representational category, and not solely denoting skin colour. (shrink)

Papers from a seminar held in Paris, Sept. 1995, organized by the International Union of Physiological Sciences and UNESCO.

The Language of Symmetry is a re-assessment of the structure and reach of symmetry, by an interdisciplinary group of specialists from the arts, humanities, and sciences at Oxford University. It explores, amongst other topics order and chaos in the formation of planetary systems entropy and symmetry in particle physics group theory, fractals and self-similarity symmetrical structures in western classical music, and how biological systems harness disorder to create order. This book aims to open up the scope of interdisciplinary work in (...) the study of symmetry and is intended for scholars of any background - whether it be science, arts or philosophy. (shrink)

Systems Biology is the study of the interactions between the elements (genes, proteins and other molecules) of living systems. Genes do not act in isolation either from each other or from the environment, and so I replace the metaphor of the selfish gene with metaphors that emphasise the processes involved rather than the molecular biological components. This may seem a simple shift of viewpoint. In fact it is revolutionary. Nothing remains the same. There is no 'book of life', nor are (...) there 'genetic programs'. The consequences for the study of the brain and the nature of the self are profound. They lead naturally to the concept of anātman, no-self, and to a better understanding of the relation between the microscopic and macroscopic views of the world. Organisms are viewed as variable open systems, rather than as determinate closed systems. (shrink)

Life is definitively purposive and creative. Organisms use genes in controlling their destiny. This book presents a paradigm shift in understanding living systems. The genome is not a code, blueprint or set of instructions. It is a tool orchestrated by the system. This book shows that gene-centrism misrepresents what genes are and how they are used by living systems. It demonstrates how organisms make choices, influencing their behaviour, their development and evolution, and act as agents of natural selection. It presents (...) a novel approach to fundamental philosophical and cultural issues, such as free-will. Reading this book will make you see life in a new light, as a marvellous phenomenon, and in some sense a triumph of evolution. We are not in our genes, our genes are in us. (shrink)

Stimulation of airway myocytes by contractile agents such as acetylcholine (ACh) activates a Ca2+-activated Cl– current (IClCa) which may play a key role in calcium homeostasis of airway myocytes and hence in airway reactivity. The aim of the present study was to model IClCa in airway smooth muscle cells using a computerised model previously designed for simulation of cardiac myocyte functioning. Modelling was based on a simple resistor-battery permeation model combined with multiple binding site activation by calcium. In order to (...) validate the model, a combination of equations, used to mimic [Ca2+]i response to ACh stimulation, were incorporated into the model. The results indicate that the model developed in this article accounts for experimental recordings and electrophysiological characteristics of this current in airway smooth muscle cells, with parameter values consistent with those calculated from experimental data. Such a model may thus be used to predict IClCa functioning, though additional experimental data from airway myocytes would be useful to more accurately determine some parameter values of the model. (shrink)

With scale relativity theory, Laurent Nottale has provided a powerful conceptual and mathematical framework with numerous validated predictions that has fundamental implications and applications for all sciences. We discuss how this extended framework reviewed in Nottale (Found Sci 152 (3):101–152, 2010a ) may help facilitating integration across multiple size and time frames in systems biology, and the development of a scale relative biology with increased explanatory power.