In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such a (...) transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

Recalling the title of Yoxen’s classical paper on the influence of Schrödinger’s book, I analyze the role that the work of H. Pattee might have played, if any, in the development of Biosemiotics. I take his 1969 paper “How does a molecule become a message?” (Developmental Biology Supplement) as a first target due to several circumstances that make it especially salient. On the one hand, even if Pattee has obviously developed further his ideas on later papers, the significance of this (...) one springs out right from the title, the journal and date of publication and, of course, its content. On the other, this paper in particular has been somehow rediscovered recently and not only within the frame of biosemiotics (eg, in history and philosophy of biology by E.F. Keller). Following the parallelism with Yoxen’s perspective, I contend that Pattee’s work was relatively influential with respect to a good amount of attempts to rethink living systems within theoretical biology around the 70s. This influence diminished together with the decay or even collapse of those attempts under the impact of molecular biology as it was being developed those years. Eventually, Pattee’s work has been taken up again. Notwithstanding, it is quite clear that Pattee himself was not intending to contribute specifically to Biosemiotics and that he was probably unaware of any such discipline, at least until recently. Then, we should as well ask (as Yoxen wonders with respect to Schrödinger) to which extent Pattee’s influence has been a direct one or rather an indication of the relevance of his ideas and the resonance of his hypotheses with those of biosemiotics. For this task I will sketch a few points of convergence and divergence and examine the work of some authors who either address directly this issue or have contributed significantly to build up the history of Biosemiotics. (shrink)

Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically (...) inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to “boot,” i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell “body” into which genomes are placed. (shrink)

There are many ways that biological theory can inform ethical discussions of genetic engineering and biomedical enhancement. In this essay, we highlight some of these potential contributions, and along the way provide a synthetic overview of the papers that comprise this special issue. We begin by comparing and contrasting genetic engineering with programs of selective breeding that led to the domestication of plants and animals, and we consider how genetic engineering differs from other contemporary biotechnologies such as embryo selection. We (...) go on to consider the implications of genetic engineering for human nature, human evolution, and persistence of the human species. Finally, we question whether genetic interventions warrant the extraordinary ethical scrutiny they are often given, and we show how the misleading “genetic blueprint” metaphor has imposed a faulty structure on the enhancement debate. We conclude by considering the nature of biological development and the sobering limits it places on what genetic engineering can reasonably hope to achieve. (shrink)

The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” systems. Therefore, (...) what flows in the genetic system is not “information” but “value.” We define meaning, meaning-making, and value and then use these terms to explain the abstract dynamics of coding, which can illuminate many forms of sign-mediated activities in biosystems. (shrink)

A recent debate concerning the representational content of DNA in developmental processes has opposed “dynamicists” and “computationalists.” I review the arguments in favor of a representational interpretation of the role of genes, and show that they are inconclusive. There is a very restricted sense in which genes can be said to represent something, and stronger claims about DNA being a program for the construction of an organism are overstatements. I also show that arbitrariness, taken by representationalists to be a central (...) criterion for identifying representational vehicles, is neither a sufficient nor a necessary condition to qualify as a representation. Finally, I propose a relatively new way to define what programs are, which implies that genetic regulatory networks shouldn’t be thought of as being programs. As a consequence, insofar as cognition and development share similar mechanisms, any computational account of cognition should be significantly weakened. (shrink)

Durante las últimas décadas, la biología ha sido objeto de una considerable proliferación teórica y subdisciplinar, hecho que suscita la pregunta acerca de su unidad. Por ello, a partir del abandono del reduccionismo como estrategia unificadora, el interrogante filosófico es qué otras formas alternativas de relaciones subdisciplinares son posibles, y si dichas relaciones logran dar unidad a la biología. En el presente artículo, a partir de una breve consideración de algunos de los problemas que el programa reduccionista ha tenido en (...) biología, analizaremos diferentes tipos de relaciones que se encuentran entre las subdisciplinas de la biología contemporánea. En particular, indagaremos cuatro de las principales propuestas que pueden encontrarse en la literatura filosófica especializada; ofrecemos entonces dos nuevas propuestas de relación interdisciplinar: el isomorfismo de la biología evolutiva, e la importación/exportación de cuerpos teóricos, propia de la relación entre la ecología y la fisiología. Finalmente, presentaremos algunas consideraciones en torno al objetivo de la unidad de la ciencia en general, como también acerca de la clase de cohesión que creemos posible para la biología a partir de nuestros análisis, defendiendo la idea de un pluralismo de las relaciones interdisciplinares y de la unidad como un fenómeno local. Over the last decades, in biology there has been a proliferation of subdisciplines and theories, and this poses a question about its unity. Consequently, after reductionism was abandoned as a unifying strategy, philosophical questions have been raised about the possibility of alternative forms of relations among the subdisciplines, and whether they can effectively accomplish a unity of biology. This article starts with a brief consideration of some of the problems that the reductionist program confronts in biology, and then analyzes different kind of relations that are present among the subdisciplines of contemporary biology. In particular, we investigate four of the main proposals that can be found in the specialized philosophical literature; and then we propose two models of inter-disciplinary relations: isomorphism in evolutionary biology, and import/export of theoretical corpus, present in the relation between ecology and physiology. Finally, we offer a few ideas on unity as a goal for science in general, and also about the kind of cohesion that we think to be possible for biology based on our analysis. Thus, we defend the idea of pluralism of inter-disciplinary relations and of unity as a local phenomenon. (shrink)

Implicit God-like and ghost-in-the-machine metaphors underlie much current thinking about genomes. Although many criticisms of such views exist, none have succeeded in substituting a different, widely accepted view. Viewing the genome with its protein packaging as a brain gets rid of Gods and ghosts while plausibly integrating machine and information-based views. While the ‘wetware’ of brains and genomes are very different, many fundamental principles of how they function are similar. Eukaryotic cells are compound entities in which case the nuclear genome (...) might best be thought of more as a government than simply as a brain. (shrink)

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply (...) the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents. (shrink)