Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that (...) self-organization plays an important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

Attempts to ‘naturalize’ phenomenology challenge both traditional phenomenology and traditional approaches to cognitive science. They challenge Edmund Husserl’s rejection of naturalism and his attempt to establish phenomenology as a foundational transcendental discipline, and they challenge efforts to explain cognition through mainstream science. While appearing to be a retreat from the bold claims made for phenomenology, it is really its triumph. Naturalized phenomenology is spearheading a successful challenge to the heritage of Cartesian dualism. This converges with the reaction against Cartesian thought (...) within science itself. Descartes divided the universe between res cogitans, thinking substances, and res extensa, the mechanical world. The latter won with Newton and we have, in most of objective science since, literally lost our mind, hence our humanity. Despite Darwin, biologists remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow lawful entailment of the evolution of the biosphere. This dream is no longer tenable. We now have to recognize that science and scientists are within and part of the world we are striving to comprehend, as proponents of endophysics have argued, and that physics, biology and mathematics have to be reconceived accordingly. Interpreting quantum mechanics from this perspective is shown to both illuminate conscious experience and reveal new paths for its further development. In biology we must now justify the use of the word “function”. As we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails. In place of entailing laws, a post-entailing law explanatory framework is proposed in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world, becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. (shrink)

A fascinating exploration of the very essence of life itself sheds new light on the order and evolution in complex life systems and defines and explains autonomous agents and work within the contexts of thermodynamics and information theory, setting the stage for a dramatic technological revolution. 50,000 first printing.

Explores the possiblity and process of evolution beyond the standard and established scientific principles.

In this fascinating read, Kauffman concludes that the development of life on earth is not entirely predictable, because no theory could ever fully account for the limitless variations of evolution. Sure to cause a stir, this book will be discussed for years to come and may even set the tone for the next "great thinker.".

At Home in the Universe presents and extends the intellectual core ofKauffman's earlier book The Origins of Order (OUP 1993) for any intelligentgeneral reader can understand and appreciate. The reader is very effectivelyinvited into Kauffman's vision and thought processes, in one of the moreexhilarating and important books of popular science.

A new science, the science of complexity, is birthing. This science boldly promises to transform the biological and social sciences in the forthcoming century. My own book, Origins of Order: Self Organization and Selection in Evolution, (Kauffman, 1992), is at most one strand in this transformation. I feel deeply honored that Marjorie Grene undertook organizing a session at the Philosophy of Science meeting discussing Origins, and equally glad that Dick Burian, Bob Richardson and Rob Page have undertaken their reading (...) of the manuscript and careful thoughts. In this article I shall characterize the book, but more importantly, set it in the broader context of the emerging sciences of complexity. Although the book is not yet out of Oxford press’s quiet womb, my own thinking has moved beyond that which I had formulated even a half year ago. Meanwhile, in the broader scientific community, the interest in “complexity” is exploding. (shrink)

This article discusses my book, Origins of Order: Self Organization and Selection in Evolution, in the context of the emerging sciences of complexity. Origins, due out of Oxford University Press in early 1992, attempts to lay out a broadened theory of evolution based on the marriage of unexpected and powerful properties of self organization which arises in complex systems, properties which may underlie the origin of life itself and the emergence of order in ontogeny, and the continuing action of natural (...) selection. The three major themes are: 1) that such self organized properties lie to hand for selection's further molding; 2) hence that the order we see is not due to selection alone, but in part reflects the order selection has always acted upon; 3) and finally that the marriage of natural order and natural selection may inevitably lead living entitites to a novel organized state, lying on the edge between order and chaos, as the inevitable evolutionary attractor of selection for the capacity to adapt. (shrink)

Contemporary evolutionary theory, derived from the intellectual marriage of Darwin's and Mendel's discoveries, leads us to view organisms as successful, but essentially ad hoc, responses to chance and necessity. Biological universals, the code, the pentadactyl limb, are frozen accidents shared by descent. The source of biological order has come to be seen as selection itself. This paper argues that this view is fundamentally inadequate. It ignores those underlying sources of biological order which derive from the generic self-organizing properties of the (...) biological building blocks. Among these generic properties are almost universal aspects of phase resetting responses in biological rhythmic systems, fascinating properties of continuity, symmetry and handedness seen in pattern regeneration across distant phyla; and statistically robust properties expected of eukaryotic gene regulatory systems persistently subject to mutations which "scramble" regulatory interactions. These examples suggest that many properties in organisms reflect a balance between selection, and the rich generic properties which would occur in the absence of selection. Where the balance is "close" to generic, a new pattern of evolutionary inference, and an ahistorical source of biological universals may be found: Those properties reflect, not selection, but the self-organizing features of the building blocks. (shrink)

Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic reproduction; (...) work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications. (shrink)

Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, (...) freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection—and perhaps self-organization—could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere. Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe. (shrink)

For the ancient Greeks, the world was both Eros, the god of chaos and creativity, and Logos, the regularity of the heavens as law. From chaos the world came forth. The world was home to ultimate creativity. Two thousand years later Kepler, Galileo, and then mighty Newton created deterministic classical physics in which all that happens in the universe is determined by the laws of motion, initial and boundary conditions. The Theistic God who worked miracles became the Deistic God who (...) set up the universe and let Newton’s laws take over. Eros, raw creativity, is dead, all is Logos.Quantum mechanics replaced the determinism of classical physics with fundamental indeterminism. This was a major crisis in physics, but remained entirely within the Newtonian paradigm of laws, here the Schrödinger equation, initial and boundary conditions. The Schrödinger equation entails the deterministic propagation of a probability distribution. The probabilities concern the indeterminate outcomes of quantum measurement events.The central issue of this article is to show that no laws at all determine or entail the becoming of our biosphere or any other among the 1022 solar systems in the universe. This claim is radical. If no laws determine or entail the becoming of biospheres, and biospheres are part of the universe, the Pythagorean dream that All is Number, All is Logos, is dead. There is no Final Theory that entails all that become in the universe. Eros is again, and always was, rambunctiously alive in the raw creativity of the becoming of life anywhere in the universe. The becoming of life is based on physics, on Logos, but beyond it, emerging from Eros.The reasons Eros is at play in the evolution of biospheres are fourfold.First, the universe will not make all possible complex things. That is, the universe is vastly non-ergodic. Yet complex things such as the human heart exist.Second, the reason human hearts exist is that organisms are Kantian Wholes in which the parts exist for and by means of the whole. Hearts exist because they fulfill the function of pumping the blood that keeps the whole organism alive. Such organisms propagate progeny that carry with them the hearts that keep them alive.Third, adaptations like hearts, the flagellar motor, the loop of Henle in kidneys that concentrates urine, and flight feathers, are tinkered-together contraptions stumbled upon in evolution. Parts and processes that arise in evolution are jury-rigged for unprestatable new functions that help keep the entire Kantian Whole organism alive and propagating in the evolving biosphere. There is no deductive theory of jury rigging. We cannot deduce the emergence of such novel functions.Fourth, the functions of parts of organisms emerge in unprestatable ways and form the unprestatable and ever-changing phase space of evolution. Since we cannot prestate the ever-changing phase space of evolution, we can write no laws of motion in differential equation form, so cannot integrate the equations we do not have. Thus, no laws entail the becoming of any biosphere.Evolving biospheres are everywhere creative. This is Eros, the chaos from which the world emerges. This profound creative emergence is the stuff of story, of narrative. Evolving biospheres always were and always will be both Eros and Logos, the stuff of story and the stuff of law. We always live in a world of Art and Science. (shrink)

Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic reproduction; (...) work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications. (shrink)

We have lived under the hegemony of the reductionistic scientific worldview since Galileo, Newton, and Laplace. In this view, the universe is meaningless, as Stephen Weinberg famously said, and organisms and a court of law are "nothing but" particles in morion. This scientific view is inadequate. Physicists are beginning to abandon reductionism in favor of emergence. Emergence, both epistemological and ontological, embraces the emergence of life and of agency. With agency comes meaning, value, and doing, beyond mere happenings. More organisms (...) are conscious. None of this violates any laws of physics, but it cannot be reduced to physics. Emergence is real, and the tiger chasing the gazelle are real parts of the real universe. We live, therefore, in an emergent universe. This emergence often is entirely unpredictable beforehand, from the evolution of novel functionalities in organisms to the evolution of the economy and human history. We are surrounded on all sides by a creativity that cannot even be prestated. Thus we have the first glimmerings of a new scientific worldview, beyond reductionism. In our universe emergence is real, and there is ceaseless, stunning creativity that has given rise to our biosphere, our humanity, and our history. We are partial co-creators of this emergent creativity. It is our choice whether we use the God word. I believe it is wise to do so. God can be our shared name for the true creativity in the natural universe. Such a view invites a new sense of the sacred, as those aspects of the creativity in the universe that we deem worthy of holding sacred. We are not logically forced to this view. Yet a global civilization, hopefully persistently diverse and creative, is emerging. I believe we need a shared view of God, a fully natural God, to orient our lives. We need a shared view of the sacred that is open to slow evolution, because rigidity in our view of the sacred violates how our most precious values evolve and invites ethical hegemony. We need a shared global ethic beyond our materialism. I believe a sense of God as the natural, awesome creativity in the universe can help us construct the sacred and a global ethic to help shape the global civilization toward what we choose with the best of our limited wisdom. (shrink)

Deacon suggests the autogen as a minimal Kantian Whole where the parts exist for and by means of the whole. An Autogen is a “for whom” information is created. Semantics of information comes first, syntax later. There are no entailing laws for the emergence and evolution of new meanings, which likely happened long before template replication and the genetic code. The evolution of life and meaning are based on physics but rise creatively above physics.

This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all this might lead to a generalized theory of autocatalytic sets, which could possibly be applied to entire ecologies or even (...) economies. (shrink)

I wish to discuss a large, interwoven set of topics pointed at in the title above. Much of what I say is highly speculative, some is testable, some is, at present, surely not. It is, I hope, useful, to set these ideas forth for our consideration. What I shall say assumes quantum measurement is real, and that Bohm's interpretation of Quantum Mechanics is not true. The Stalemate: In our contemporary neurobiology and much of the philosophy of mind post Descartes we (...) are classical physics machines and either mindless, or mind is at best epiphenomenal and can have no consequences for the physical world. The first main point of this paper is that we are not forced to this conclusion, but must give up total reliance on classical physics. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}. (shrink)

It is argued that quantum theory is best understood as requiring an ontological duality of res extensa and res potentia, where the latter is understood per Heisenberg’s original proposal, and the former is roughly equivalent to Descartes’ ‘extended substance.’ However, this is not a dualism of mutually exclusive substances in the classical Cartesian sense, and therefore does not inherit the infamous ‘mind-body’ problem. Rather, res potentia and res extensa are proposed as mutually implicative ontological extants that serve to explain the (...) key conceptual challenges of quantum theory; in particular, nonlocality, entanglement, null measurements, and wave function collapse. It is shown that a natural account of these quantum perplexities emerges, along with a need to reassess our usual ontological commitments involving the nature of space and time. (shrink)

It is suggested that the apparently disparate cosmological phenomena attributed to so-called ‘dark matter’ and ‘dark energy’ arise from the same fundamental physical process: the emergence, from the quantum level, of spacetime itself. This creation of spacetime results in metric expansion around mass points in addition to the usual curvature due to stress-energy sources of the gravitational field. A recent modification of Einstein’s theory of general relativity by Chadwick, Hodgkinson, and McDonald incorporating spacetime expansion around mass points, which accounts well (...) for the observed galactic rotation curves, is adduced in support of the proposal. Recent observational evidence corroborates a prediction of the model that the apparent amount of ‘dark matter’ increases with the age of the universe. In addition, the proposal leads to the same result for the small but nonvanishing cosmological constant, related to ‘dark energy,’ as that of the causet model of Sorkin et al. (shrink)

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of these (...) variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles. (shrink)

We argue that the physics of complex materials and self-organizing processes should be made central to the biology of form. Rather than being encoded in genes, form emerges when cells and certain of their molecules mobilize physical forces, effects, and processes in a multicellular context. What is inherited from one generation to the next are not genetic programs for constructing organisms, but generative mechanisms of morphogenesis and pattern formation and the initial and boundary conditions for reproducing the specific traits of (...) a taxon. There is no inherent antagonism between this “physicalist” perspective and genetics, since physics acts on matter, and gene products are essential material components of living systems whose variability affects the systems’ parameters. We make this notion concrete by summarizing the concept of “dynamical patterning modules” (DPMs; Newman and Bhat, Phys Biol 5:1–14, 2008; Int J Dev Biol 53:693–705, 2009), an explicit physico-genetic framework for the origin and evolution of multicellular form in animals, as well as (when differences in interaction toolkit genes and applicable physical processes are taken into account) in multicellular plants (Hernández-Hernández et al., Int J Dev Biol 56:661–674, 2012). DPMs provide the missing link between development and evolution by revealing how genes acting in concert with physics can generate and transform morphology in a heritable fashion. (shrink)

During vertebrate limb development, various genes of the Hox family, the products of which influence skeletal element identity, are expressed in specific spatiotemporal patterns in the limb bud mesenchyme. At the same time, the cells also exhibit ‘self‐organizing’ behavior – interacting with each other via extracellular matrix and cell‐cell adhesive molecules to form the arrays of mesenchymal condensations that lead to the cartilaginous skeletal primordia. A recent study by Yokouchi et al.(1) establishes a connection between these phenomena. They misexpressed the (...) product of the Hoxa‐13 gene in chick limb buds and demonstrated both skeletal pattern perturbations and changes in cell‐cell adhesivity in mesenchyme aberrantly expressing this protein. (shrink)

Heyman's target article contributes to our understanding of addictions by offering solutions to several paradoxes and by recognizing the stable nature of addictive behavior. Previous classical and operant conditioning models have emphasized molecular processes, such as acquisition and extinction, and have failed to address the aggregate effects of long-term exposure to the contingencies of drug and alcohol use.

James E. Huchingson's Pandemonium Tremendum draws on a surprisingly fruitful analogy between metaphysics and thermodynamics, with the latter motivated through the more accessible language of communication theory. In Huchingson's model, God nurtures creation by the selective communication of bits of order that arise spontaneously in chaos.