From his earliest published writings to his last, Roman Ingarden displayed an interest in theoretical biology and its efforts to clarify what distinguishes living organisms from other types of entities. However, many of his explorations of such issues are easily overlooked, because they don’t appear in works that are primarily ontological, metaphysical, or anthropological in nature but are “hidden” within his works on literary aesthetics, where Ingarden sought to define the nature of living organisms in order to compare (...) literary works to such entities. This article undertakes a historical textual analysis that traces the evolution of Ingarden’s thought regarding the nature of the literary work of art as an organism-like entity and uncovers its links with the simultaneous development of his systems theory and its central concept of the “relatively isolated system”: for Ingarden, a literary work and an organism are each a systematically transforming, “living,” functional-structural whole that comprises a system of hierarchically arranged and partially isolated elements whose harmonious interaction allows the literary work or organism to fulfill its chief function. Having completed that historical analysis, we test Ingarden’s assessment of works of art as organism-like entities in a novel context by investigating the organism-like qualities of the contemporary computer game; insofar as their AI-driven behavior displays a form of agency, such games might appear to be even more “alive” than traditional works of art. We show that Ingarden’s conceptual framework provides a useful tool for understanding the “organicity” of such games as works of art, despite the fact that they differ qualitatively from those art forms with which Ingarden was directly familiar. (shrink)

In this paper we define two types of formal biological entities corresponding to biological levels of organization, thebiolons and theorgons, the properties of which are phenomenologically analyzed and discussed.We examine then, in a rather speculative manner, how some characteristics of these entities may suggest analogies between properties of biological systems and some special features of quantum systems.

The French school of theoretical biology has been mainly initiated in Poitiers during the sixties by scientists like J. Besson, G. Bouligand, P. Gavaudan, M. P. Schützenberger and R. Thom, launching many new research domains on the fractal dimension, the combinatorial properties of the genetic code and related amino-acids as well as on the genetic regulation of the biological processes. Presently, the biological science knows that RNA molecules are often involved in the regulation of complex genetic networks as (...) effectors, e.g., activators, inhibitors or hybrids. Examples of such networks will be given showing that there exist RNA “relics” that have played an important role during evolution and have survived in many genomes, whose probability distribution of their sub-sequences is quantified by the Shannon entropy, and the robustness of the dynamics of the networks they regulate can be characterized by the Kolmogorov–Sinaï dynamic entropy and attractor entropy. (shrink)

Structurally, microtubules (MTs) are composed of protofilaments of the subunit protein. They are prominent components of the cytoplasmic matrix and perform important functions as cytoskeletal elements for the determination of cell shape and as key elements in intracellular motility such as mitosis and the translocation of cell organelles. These functions are thought to depend on the controlled assembly and disassembly of MTs in the cytoplasm and on the interaction of MTs with each other and with other cytoplasmic components. I think (...) that apart from these cellular functions, MTs have the function of message transmission. Although no direct evidence is available to explain this point at present, a number of inddirect evidences have been obtained by many scientists e.g.: brain tissue has circumstantial the highest tubulin concentration, MTs have the property of self-assembly and disassembly, microtubule(MT) network is a key factor in differentiation of plant cells. (shrink)

The ArgumentBiology, understood in turn-of-the-century Germany to include psychology, held a central but enigmatic place in the philosopher Ernst Cassirer's work. From his earliest studies with Hermann Cohen through his long engagement with the theoretical biology of Jakob von Uexküll and Adolf Meyer-Abich, Cassirer consistently used the history and practice of biology to examine and delineate a set of characteristic tensions between the natural and cultural sciences. This paper examines Cassirer's treatment of this theme by addressing two (...) contrasting interpretations he gave — in hisPhilosophy of Symbolic Forms and in hisEssay on Man — to the benchmark case from empirical psychology of the “talking” horse “Clever Hans.” The original case involved the horse's ability to signal answers to remarkably complex questions by stamping its hooves, an ability that ultimately appeared to rest on a capacity to detect extremely minute unintentional movement cues in its auditors as it reached the appropriate answer. Due to both Cassirer's shifting description of the case within his philosophy and the case's inherent polyvalence, Cassirer's remarks provide a useful window onto the social, epistemological, and stylistic meaning of his “unified” philosophy of human culture and science. (shrink)

Proceeding of the Third International Conference of the French-Speaking Society for Theoretical Biology Content Type Journal Article Category Editorial Pages 1-2 DOI 10.1007/s10441-012-9156-2 Authors Slimane Ben Miled, ENIT-LAMSIN, Tunis el Manar University, 13, place Pasteur, Belvédère, B.P. 74, 1002 Tunis, Tunisia Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342.

Recent interest in the social and ethical aspects of biology raises the question of the disciplinary status of the study of these aspects of biology . In the traditional interpretations of theoretical biology the social and ethical aspects are usually not explicitly mentioned. In this article arguments are given for inclusion of the study of these aspects of biology within a broadened conception of theoretical biology.

Theses on the semiotic study of life as presented here provide a collectively formulated set of statements on what biology needs to be focused on in order to describe life as a process based on semiosis, or sign action. An aim of the biosemiotic approach is to explain how life evolves through all varieties of forms of communication and signification (including cellular adaptive behavior, animal communication, and human intellect) and to provide tools for grounding sign theories. We introduce the (...) concept of semiotic threshold zone and analyze the concepts of semiosis, function, umwelt, and the like as the basic concepts for theoretical biology. (shrink)

The theoretical biology movement originating in Britain in the early 1930’s and the biosemiotics movement which took off in Europe in the 1980’s have much in common. They are both committed to replacing the neo-Darwinian synthesis, and they have both invoked theories of signs to this end. Yet, while there has been some mutual appreciation and influence, particularly in the cases of Howard Pattee, René Thom, Kalevi Kull, Anton Markoš and Stuart Kauffman, for the most part, these movements (...) have developed independently of each other. Focussing on morphogenesis understood as vegetative semiosis, in this paper I will argue that the ideas of these movements are commensurate. Furthermore, synthesising them would enable us to see life processes as proto-narratives. Doing so will involve synthesising biohermeneutics, Peircian biosemiotics with Waddington’s theoretical biology and Piagetian genetic structuralism, and this, I claim, would strengthen the challenge of these traditions to mainstream biology. At the same time, this should contribute to overcoming the opposition between the sciences and the humanities, developing a broader tradition of Schellingian thought which involves developing the humanities and then demanding of the physical and biological sciences that they are consistent with and can make intelligible the emergence of humans as conceived by the humanities. (shrink)

The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can be approached (...) in two ways: from a theoretical standpoint, exploring the centrality of the cognitive sciences in current theoretical biology; and from a historical perspective, examining the resemblance between the current state of theoretical biology and the Cognitive Revolution of the mid-20th century. Both inquiries yield affirmative answers, though important nuances will be emphasized. The cognitive sciences' explanatory framework is employed to elucidate the agentic characteristics of organisms, establishing a clear parallelism between the Cognitive Revolution and the present state of theoretical biology. (shrink)

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as (...) well as with philosophers of biology. (shrink)

A theory in natural science is a comprehensive formula or doctrine which describes and correlates in a unified abstract form of statement the general determining factors of some special group of natural facts. It is at once inclusive, realistic and understandable. If a theoretical statement holds good, the existence and characteristics of many individual events can be inferred deductively from it. It thus gives a logical basis for empirical fact. But it is based on experience of nature, and must (...) conform to the facts of nature; these are primary, and a valid theory, no matter how broad it may be, is to be considered as itself a statement of fact, i.e., a true description of some condition which has a real and stable existence in the natural world. In its scientific usage, the term “fact” refers primarily to some datum of experience having the special character of permanence or regular recurrence; this is why scientific facts are verifiable; in this respect they differ from the passing individual events of history. Any scientific theory presupposes the stability and unequivocality of the natural facts. Hence if a theory is sound, it furnishes a reliable basis for prediction, discovery and invention. Scientific or technological creation then becomes possible; modern engineering and medicine could never have become what they are without a background of theoretical physics and biology. Obviously any natural science must always have at its disposal an ample body of observational and experimental data, but in most cases the work of collecting and verifying these is carried out under the guidance of theory. (shrink)

Adolf Meyer-Abich spent his career as one of the most vigorous and varied advocates in the biological sciences. Primarily a philosophical proponent of holistic thought in biology, he also sought through collaboration with empirically oriented colleagues in biology, medicine, and even physics to develop arguments against mechanistic and reductionistic positions in the life sciences, and to integrate them into a newly disciplinary theoretical biology. He participated in major publishing efforts including the founding of Acta Biotheoretica. He (...) also sought international contacts and worked for long stretches in Chile, the Dominican Republic, El Salvador, and the United States. His career straddled the Nazi period, which led him into a complex dance of support for and resistance to the regime. Despite the relative failure of his conceptual innovations to catch on, his ideas and writings sit squarely within the trajectory of thought and argument that has led to today’s reinvigoration of thought about conceptual integration in evolutionary developmental biology. (shrink)

This book originated as a Festschrift to mark the publication of Volume 50 of the journal `Acta Biotheoretica' in 2002 and the journal's 70th anniversary in ...

Philosophical biologists have attempted to define the distinction between life and non-life to more adequately define what it is to be human. They are reacting against idealism, but idealism is their point of departure, and they have embraced the reaction by idealists against the mechanistic notion of humans developed by the scientific materialists. Theoretical biologists also have attempted to develop a more adequate conception of life, but their point of departure has been within science itself. In their case, it (...) has involved efforts to overcome the reductionism of scientific materialism to develop a form of science able to identify and explain the distinctive characteristics of living beings. So, while both philosophical biologists and theoretical biologists are struggling to overcome scientific materialism, they are approaching the question: What is Life? from different directions. Focussing on the work of Robert Rosen, I will try to show what revisions in our understanding of science theoretical biologists need to accept in order to do justice to the insights of the philosophical biologists. I will suggest that not only will this involve major revisions in what we understand science to be, but that scientists must accept that science is indissociable from natural philosophy, and that to properly comprehend life mathematics must ultimately be subordinated to stories. (shrink)

The potential and realized impact of Bohm's views on biology are briefly discussed.

Peterson’s The Organic Life is a history of the development of the theoretical biology of organicism in the late nineteenth and early twentieth centuries. Its focus on a group of polymaths who defined the organic philosophy against the status quo is still very much alive today as theorists debate the extent to which the dominant biological paradigm of mechanism, as advanced in the Modern Synthesis, is sufficient to all biological explanation. If science is to be empirical it cannot (...) ignore the large body of evidence of what makes an organism an organism. (shrink)

The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what theory (...) is right, but what is real science. Peirce's work, as he acknowledged, is really a continuation of efforts of Schelling to challenge the heritage of Newtonian science for the very good reason that the deep assumptions of Newtonian science had made sentient life, human consciousness and free will unintelligible, the condition for there being science. Pointing out the need for such a revolution in science has not succeeded as a defence of Peircian biosemiotics, however. In this paper, I will defend the scientific credentials of Peircian biosemiotics by relating it to the theoretical biology of the bio-mathematician, Robert Rosen. Rosen's relational biology, focusing on anticipatory systems and giving a place to final causes, should also be seen as a rigorous development of the Schellingian project to conceive nature in such a way that the emergence of sentient life, mind and science are intelligible. Rosen has made a very strong case for the characterization of his ideas as a real advance not only in science, but in how science should be understood, and I will argue that it is possible to provide a strong defence of Peircian biosemiotics as science through Rosen's defence of relational biology. In the process, I will show how biosemiotics can and should become a crucial component of anticipatory systems theory. (shrink)

To study the interaction of forces that produce chest wall motion, we propose a model based on the lever system of Hillman and Finucane :951–961, 1987) and introduce some dynamic properties of the respiratory system. The passive elements are considered as elastic compartments linked to the open air via a resistive tube, an image of airways. The respiratory muscles force is applied to both compartments. Parameters of the model are identified in using experimental data of airflow signal measured by pneumotachography (...) and rib cage and abdomen signals measured by respiratory inductive plethysmography on eleven healthy volunteers in five conditions: at rest and with four level of added loads. A breath by breath analysis showed, whatever the individual and the condition are, that there are several breaths on which the airflow simulated by our model is well fitted to the airflow measured by pneumotachography as estimated by a determination coefficient R2 ≥ 0.70. This very simple model may well represent the behaviour of the chest wall and thus may be useful to interpret the relative motion of rib cage and abdomen during quiet breathing. (shrink)

At the beginning of this special issue of Acta Biotheoretica carrying the above title, we present a brief overview on currently important topics that have been brought up during the last “European Conference on Mathematical and Theoretical Biology” in Edinburgh. After emphasizing the need for a “synthetic biology” also from the side of theory, model building and analysis, we survey most plenary talks of this Conference and a selected series of eigth review articles, which are mainly related (...) to corresponding minisymposia, reflecting the current state of the art and the lively discussion within this interdisciplinary field. (shrink)

In this note some epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure and life.

The inanimate world, including Man's wheeled vehicles, follow the classical mechanical laws: trajectories of objects in phase-space are predictable on the basis of the vectors of forces acting on the objects. Animal locomotion does not involve wheels, but relies on antagonistic contractile fibre systems, and defies prediction of trajectories. These features are tied up with the faculty of immediate steering in response to momentaneous physiological and environmental stimuli. Thus, animal motor systems have two relatively independent inputs: the sensory/information system, which (...) is the cause for specific trajectories, and the erfolg system which permits for the execution of the thus instructed motion. The problem of relative energetic magnitudes between the two systems — in that the causative system involves small, yet the executive system large energies — is specially considered in relation to locomotion by antagonistically functioning mechanical elements. (shrink)

Observations on the morphological and functional similarity between embryonic or trophoblast tissues and tumors are very old. Over a period of time many investigators have created different hypotheses on the origin of cancerogenesis or tumor efficiency in relation to the host immune system. Some of these ideas have been rejected but many of them are still current. A presumption of the inefficiency of anti-tumor immunity in mammals due to the high similarity between trophoblast and embryonic cells to tumor cells is (...) very real. The mechanisms for the escape of tumors from the immune response are very similar to the mechanisms for the escape of a fetoplacental unit from the maternal immune response. The similarity between these two mechanisms is so great that any randomness must be banished. At the same time, an incidence of malignant tumors and the types of more frequent tumors in non-mammalian vertebrates is significantly different to that in mammals. Lastly, the mechanisms of anti-tumor immunity in mammals are substantially different from the mechanisms of anti-tumor immunity in other classes of vertebrates. These facts indicate that the immune system of mammals during anti-tumor immune response is tricked by the similarity between tumor cells and trophoblast or other placental cells. From this aspect, our conclusion is that anti-tumor immunity failure in mammals can be defined as an immunoreproductive phenomenon, which is developed under the evolutionary pressure of autoimmunity and reproductive effectiveness. (shrink)

It is generally believed, that when the surface/volume ratio is high, fractal structure is expected to exist. The branched fractal structure of the lung has been cited as a classical example of this statement. In this short paper I would like to demonstrate that an alternative lung structure (namely sponge-like fractal) is at least as good as, or even better than the branched one, concerning this ratio, therefore, the cause of the lung''s fractality lies elsewhere.

With a previous paper (Niu & Wang, 1995), a general, hypothetical outline of the mechanism of carcinogenesis was proposed. With reference to the fact of starvation-induced hypermutation in micro-organisms, we propose that the hypoxia commonly seen in the cells at the centre of solid tumours might also result in hypermutation, and then p53-dependent programmed cell death. Like the apparently adaptive mutations in micro-organisms, only those genes (e.g. p53) that enable the cells to escape from apoptosis may be selected.

In this paper I will reconstruct and analyze a famous argument by Stuart Kauffman about complex systems and evolution, in order to highlight the use in theoretical biology of a kind of non-mechanistic and non-causal explanation which I propose to call, following Kauffman, ensemble explanation. The aim is to contribute to the ongoing philosophical debate about non-causal explanations in the special sciences, kinds of explanation apparently extraneous to the received causal-mechanistic view. Ensemble explanations resemble quite closely the explanations (...) of the structural kind proposed by Philippe Huneman, which—unlike mechanistic explanations—do not explain by exposing the causal structure of a phenomenon, but... (shrink)

(1991). Life as emergence: The roots of a new paradigm in theoretical biology. World Futures: Vol. 32, Creative Evolution in Nature, Mind, and Society, pp. 133-149.

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented (...) but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. (shrink)