Graphical AbstractGene regulatory networks, which are crucial for the proper development of organisms, are extensively studied. From these investigations, coordinative mechanisms are shown to be instructive for further development. Competitive mechanisms as well as environmental and metabolic influences, however, are widely ignored so far but appear to be important for the emergence of shape.

Using the term world to mean a creative response to objective reality, this book considers the ways in which Eastern and Western peoples construct their natural, social, aesthetic, and religious worlds. It points the way to a view of Eastern and Western as complementary, rather than contradictory, descriptions.

Essays originally published ca. 1949-1989.

Invites the reader to examine the concept of the One in several complex cultural and philosophical mileux. The uniqueness of the study is its collation of Eastern and Western sources and systems.

This paper is concerned with the ambiguities and confusions that arise when studies of the ‘surveillance state’ are contrasted with studies of the ‘service state’. Surveillance studies take a largely negative view of the information capture and handling of personal data by Government agencies. Studies that examine Government service providing take a largely positive view of such data capture as Government is seen to be attempting to enhance service provision to individual citizens. This paper examines these opposing perspectives through a (...) series of case studies and concludes that a new understanding and methodology should be brought forward so as to create a reconciliation of these two points of departure for research. The call is for an holistic appreciation of data capture activities by Government so that researchers and public policy makers alike can appreciate and reconcile these competing perspectives. (shrink)

According to a once influential view of selection, it consists of repeated cycles of replication and interaction. It has been argued that this view is wrong: replication is not necessary for evolution by natural selection. I analyze the nine most influential arguments for this claim and defend the replication–interaction conception of selection against these objections. In order to do so, however, the replication–interaction conception of selection needs to be modified significantly. My proposal is that replication is not the copying of (...) an entity, the replicator, but the copying of a property. Thus, we can have a replication process without there being a replicator that is being copied. (shrink)

Graphical AbstractThe origins of asexuality in plants as well as animals have long puzzled researchers. In article 2000111, Diego Hojsgaard and Manfred Schartl integrate old ideas with recent molecular and genomic data and provide a single mechanistic model for this phenomenon. They highlight two usually overlooked conditions to understand the molecular nature of clonal organisms to explain asexuals' developmental diversity and biologically vague cases such as automixis and polyploidy.

The unusual occurrence and developmental diversity of asexual eukaryotes remain a puzzle. De novo formation of a functioning asexual genome requires a unique assembly of sets of genes or gene states to disrupt cellular mechanisms of meiosis and gametogenesis, and to affect discrete components of sexuality and produce clonal or hemiclonal offspring. We highlight two usually overlooked but essential conditions to understand the molecular nature of clonal organisms, that is, a nonrecombinant genomic assemblage retaining modifiers of the (...) sexual program, and a complementation between altered reproductive components. These subtle conditions are the basis for physiologically viable and genetically balanced transitions between generations. Genomic and developmental evidence from asexual animals and plants indicates the lack of complementation of molecular changes in the sexual reproductive program is likely the main cause of asexuals' rarity, and can provide an explanatory frame for the developmental diversity and lability of developmental patterns in some asexuals as well as for the discordant time to extinction estimations. (shrink)

In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicellular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means (...) in the case of unicellular organisms. In this article, we survey the concepts of PCD in the literature and the selective pressures associated with its evolution. We show that definitions of PCD have been almost entirely mechanistic and fail to separate questions concerning what PCD fundamentally is from questions about the kinds of mechanisms that realize PCD. We conclude that an evolutionary definition is best able to distinguish PCD from closely related phenomena. Specifically, we define “true” PCD as an adaptation for death triggered by abiotic or biotic environmental stresses. True PCD is thus not only an evolutionary product but must also have been a target of selection. Apparent PCD resulting from pleiotropy, genetic drift, or trade-offs is not true PCD. We call this “ersatz PCD.”. (shrink)

Ecological fitness has been suggested to provide a unifying definition of fitness. However, a metric for this notion of fitness was in most cases unavailable except by proxy with differential reproductive success. In this article, I show how differential persistence of lineages can be used as a way to assess ecological fitness. This view is inspired by a better understanding of the evolution of some clonal plants, colonial organisms, and ecosystems. Differential persistence shows the limitation of an ensemblist (...) noncausal understanding of evolution. Causal explanations are necessary to understand the evolution by natural selection of these biological systems. †To contact the author write to: Department of Philosophy, University of Montreal, P.O. Box 6128, Station Centre‐Ville, Montreal, Quebec, H3C 3J7 Canada; e‐mail: [email protected]. (shrink)

The somatic mutation theory (SMT) of cancer has been and remains the prevalent theory attempting to explain how neoplasms arise and progress. This theory proposes that cancer is a clonal, cell‐based disease, and implicitly assumes that quiescence is the default state of cells in multicellular organisms. The SMT has not been rigorously tested, and several lines of evidence raise questions that are not addressed by this theory. Herein, we propose experimental strategies that may validate the SMT. We also (...) call attention to an alternative theory of carcinogenesis, the tissue organization field theory (TOFT), which posits that cancer is a tissue‐based disease and that proliferation is the default state of all cells. Based on epistemological and experimental evidence, we argue that the TOFT compellingly explains carcinogenesis, while placing it within an evolutionarily relevant context.magnified imagemagnified imageAna Soto and Carlos Sonnenschein are at Tufts University School of Medicine, Boston, MA, USA. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Rhetoric 35.2 (2002) 153-174 [Access article in PDF] LSDNA: Rhetoric, Consciousness Expansion, and the Emergence of Biotechnology Richard Doyle I had to struggle to speak intelligibly. —Albert Hofmann on his self-experiment with LSD-25 Finding a place to start is of utmost importance. Natural DNA is a tractless coil, like an unwound and tangled audio tape on the floor of the car in the dark. —Kary Mullis on (...) the invention of Polymerase Chain Reaction 1. Undoing life What happened is this: Once upon a time there was a narrative of vitality. Ok, not a narrative, but an apprehension, a fear, a vision. It didn't have a beginning, middle, or end. It was. Its contours were no more determinable than those of consciousness. Indeed, our consciousness, as humans, was our sole alleged difference from it. From something called "life." We were more than life, but were also, tragically, confined to it. You know the story all too well. Some of its major authors were Cuvier, Lamarck, Darwin, Bichat. Even Shelley.Just because this sudden transformation happened on paper doesn't mean it was easy to endure. Enormous numbers of humans went on tranquilizers just to deal with the effects. Others, elsewhere, knew nothing but rumors. Nonetheless, they became increasingly implicated in its effects, the effects of understanding and experiencing both "life" and "consciousness" as informatic events. Suddenly—and it is sudden, a real surprise—both our vitality and our thought were distributed, scattered across a network and nowhere in particular. Timothy Leary and Francis Crick were speaking the same language, the language of information where the organic and the machinic enfold each other helically and, sometimes, the capacity for replication goes through the ceiling. This new language of information would [End Page 153] introduce a novel response and abyss: the pleasures and hells of eternal replication. The distribution of both life and consciousness enabled a dream of immortality from which we have not yet awakened, as the mere specter of infinite clonal replicants provokes entropies of identity even as it preserves the self from onslaughts of decay. 1In at least one of its characteristics this shift toward an informatic understanding of life is perhaps not really so novel. The seductions of control are hardly, historians of science tell us, foreign to the practices and effects of technoscience. Evelyn Fox Keller makes this point concisely and precisely in her not-quite eponymous essay, "From Secrets of Life to Secrets of Death," itself a self-professed sequel to her 1986 "Making Gender Visible." Here the scientific "impulse" is underwritten by a perennial motif that underlies much of scientific creativity, namely, the urge to fathom the secrets of nature and the collateral hope that, in fathoming the secrets of nature, we will fathom (and hence gain control of) our own mortality (Secrets, 29).Surely Keller is correct that the nascent practices of molecular biology were cryptographic in character, an espionage project unknowingly launched by Erwin Schrodinger during the Second World War. Surely it is crucial to this moment that while Schrodinger's 1943 Dublin lectures were introducing audiences to the concept of the code-script, Alan Turing again brilliantly decrypted a modified U-boat code, giving the Allies code superiority for the remainder of the war. 2 But in this segment on that strange growth called "biotechnology," I want to focus on what Keller has called the "collateral" of hope in this cryptographic impulse, namely the collateral equation between inquiry and control, specifically the control of mortality.For is "fathoming" a secret identical to the exercise of control? The very cadence and rhetorical encryption of Keller's formulation here, a general parenthetical syllogistic conclusion within and alongside a hyphenated invocation of particularity, suggest that concepts and practices of secrecy are more unstable than Keller implies with her invocation of Feynman's "disease" of lock picking: "One of my diseases, one of my things in life, is that anything that is secret, I try to undo" (40).For Keller, Feynman's confession is emblematic of a desire to control life and death... (shrink)

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level (...) fitness. Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives. (shrink)

Variation or rearrangement of regulatory genes is responsible for cellular malignant change. These types of chromosomal variations also produce heterochrony or paedomorphic evolution at the organismal level. Analogously, neoplasia represents a cellular macroevolutionary event, and a tumour can be said to be an evolved population of cells. To understand this cellular evolution to malignancy, it may be necessary to go beyond a clonal selection (adaptationist) explanation of neoplastic alteration. In the pericellular environment natural selection consists of the organizational restraints (...) of surrounding cells as well as the host's immunological surveillance and non-specific monocyte-macrophage systems. Indirect evidence suggests that success for the neoplasm depends not upon clonal selection, but solely upon a genetic methodology—the function of which is to elude selection.The author has coined the term cellular heterochrony to illustrate analogic similarities in the molecular modes of speciation between anaplastic cancer cells and the heterochronic evolution of organisms. By reverting to a juvenile (embryonic) repertoire of cellular behaviour a tumour secures its own tenure or niche by usurping the host's armamentarium of selection forces, employing many of the same or similar methods by which implanting and invading tissues of the mammalian embryo forestall maternal detection and rejection. A number of ways by which the tumour blocks, subverts or evades selection are discussed. (shrink)

The male gametes of most organisms lack cytoplasm. Consequently, most cytoplasmic genetic elements are maternally inherited: they cannot be transmitted patrilinnearly. The evolutionary interests of cytoplasmic elements therefore lie in transmission through the female. These elements may thus be in evolutionary conflict with nuclear genes which are transmitted by both sexes. This conflict is manifested in observations of cytoplasmically induced biased sex‐ratios. Some cytoplasmic genes avoid this fate by biasing the primary sex ratio towards females, or by inducing parthenogenesis. (...) Others kill male hosts, and either achieve transmission via dispersal, or benefit their clonal relatives in the dead male's female siblings. Still others cause the failure of zygotes resulting from pairings between males carrying specific microbes and females lacking them, causing an increase in the microbes through the sterilisation of non‐bearing females. Many, but not all, of these ‘ultra‐selfish’ microbes are closely related. Investigations of the significance of their phylogenetic affinities, or lack of them, their adaptability in terms of the methods by which they avoid, or ameliorate, the adverse effects of being in male hosts, and their importance as selective agents in the evolution of invertebrate sex determination systems, provide fertile spheres for future research. (shrink)

Human neoplasms develop following the progressive accumulation of genetic and epigenetic alterations to oncogenes and tumor suppressor genes. These alterations confer a growth advantage to the cancer cell, leading to its clonal proliferation, invasion into surrounding tissues, and spread to distant organs. Genes that are altered in neoplasia affect three major biologic pathways that normally regulate cell growth and tissue homeostasis: the cell cycle, apoptosis, and differentiation. While each of these pathways can be defined by a unique set of (...) molecular events, they are not biologically separate. Rather, they function more as an integrated molecular network, and perturbations in one pathway can have profound consequences on another. Insights into what distinguishes the regulation of growth and differentiation in a normal cell versus a cancer cell have led to the development of novel anticancer therapies. BioEssays 24:83–90, 2002. © 2002 John Wiley & Sons, Inc. (shrink)

Adult stem cell populations must coordinate their own maintenance with the generation of differentiated cell types to sustain organ physiology, in a spatially controlled manner and over long periods. Quantitative analyses of clonal dynamics have revealed that, in epithelia, homeostasis is achieved at the population rather than at the single stem cell level, suggesting that feedback mechanisms coordinate stem cell maintenance and progeny generation. In the central nervous system, however, little is known of the possible community processes underlying neural (...) stem cell maintenance. Recent work, in part based on intravital imaging made possible in the adult zebrafish, conclusively highlights that homeostasis in neural stem cell pools may rely on population asymmetry and long‐term spatiotemporal coordination of neural stem cell states and fates. These results suggest that neural stem cell assemblies in the vertebrate brain behave as self‐organized systems, such that the stem cells themselves generate their own intrinsic niche. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.