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)

When two populations of cells within a tissue mass differ from one another in magnitude or type of intercellular adhesions, a boundary can form within the tissue, across which cells will fail to mix. This phenomenon may occur regardless of the identity of the molecules that mediate cell adhesion. If, in addition, a choice between the two adhesive states is regulated by a molecule the concentration of which is periodic in space, or in time, then alternating bands of non‐mixing tissue, (...) or segments, can form. But temporal or spatial periodicities in concentration will tend to arise for any molecule that is positively autoregu‐latory. It is therefore proposed that segmentation is a ‘generic’ property of metazoan organisms, and that metamerism would be expected to have emerged numerous times during evolution. A simple model of segmentation, based solely on differential adhesion and periodic regulation of adhesion, can account for segment properties as disparate as those seen in long and short germ band insects, and for diverse experimental results on boundary regeneration in the chick hind brain and the insect cuticle. It is suggested that the complex, multicom‐ponent segment‐forming systems found in contemporary organisms (e.g., Drosophila) are the products of evolutionary recruitment of molecular cues such as homeobox gene products, that increase the reliability and stability of metameric patterns originally templated by generic self‐organizing properties of tissues. (shrink)

This book is concerned with, and makes an important contribution to, answering the central question of evolutionary theory: By what mechanisms and processes do organisms undergo transformative change? Animals or plants may undergo alterations in morphology or activity during their lifetimes, but only if such alterations are conveyed to the next generation can they contribute to the establishment of new forms. Heritability by itself is not decisive: offspring can differ from their parents at a variety of genetic loci without this (...) constituting evolutionary change, notwithstanding the fact that on theoretical grounds the standard model, stemming from the Modern Synthesis, asserts that any such variation represents incipient evolution (i.e., evolution is change in allele frequency). Clearly, some gene changes make more of an evolutionary difference than others. By placing phenotype at center stage and treating genotypes not in terms of their selective advantage, but rather with respect to the changes they exert on the phenotype, the author subtly but significantly reorients the explanatory terrain of evolutionary theory. (shrink)

Much of the philosophical attention directed to Kant’s intervention into biology has been directed toward Kant’s idea of a transcendental limit upon what can be understood constitutively. Kant’s own wider philosophical practice, however, was principally oriented toward solving problems and the scientific benefits of his methodology of teleology have been largely underappreciated, at least in the English language literature. This paper suggests that all basic biology has had, and continues to have, a need for some form of heuristic “bracketing” and (...) that a renewal of some form of, albeit flexible, teleological methodological bracketing can better complement the productive assimilation into developmental biology of continuing advances in our understanding of the mesoscale physics and chemistry of soft, excitable condensed matter, than what has been the prevailing and de facto use of a form of bracketing shaped by the neoDarwinian Modern Synthesis. Further we offer a concept of biogeneric processes and a framework of physico-genetic “dynamical patterning modules”, that can begin to account for the appearance of new Kantian “stocks of Keime und Anlagen”, capable of potentiating some range of possible organismal forms, and provide grounds for moving up the teleological “goalposts”, i.e., expanding the range of what can be accounted for on a constitutive basis. (shrink)

San John Henry Newman es ampliamente entendido como un hombre de conciencia, tanto en su vida como en sus escritos. El objetivo de este artículo es explorar más profundamente los escritos de Newman sobre la conciencia, en orden a mostrar tanto la importancia que la categoría de conciencia aporta nuestro sentido moral como la percepción religiosa y existencial de lo que estamos llamados a hacer, así como vínculo de todas las criaturas humanas a su Creador. Una lectura cuidadosa (...) de unos textos nos ayudará a evitar la mala interpretación común del brindis de Newman por la conciencia que distorsiona su punto de vista como si colocase la conciencia y el Magisterio en oposición, o que si concediese mucho más respeto a la conciencia que a la enseñanza con autoridad de la Iglesia. (shrink)

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)

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.".

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)

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.

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.

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.

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)

Rips, in The Psychology of Proof, argues that, through the processes of evolution, logic (e.g., modus ponens) has become established in the human mind as the basis for thinking, and that production systems rest on this foundation. In this paper we defend the converse argument that, through evolution, a production system architecture has become the basis for human thinking, and that formal logics rest on this production system and the accompanying mechanisms for recognition and search. It is through the “automaticity” (...) of the execution of productions that we experience the compellingness of deductive arguments. (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)