On some theoretical grounds for an organism-centered biology: Property emergence, supervenience, and downward causation

In this paper, we investigate some theoretical grounds for bridging the gap between an organism-centered biology and the chemical basis of biological explanation, as expressed in the prevailing molecular perspective in biological research. First, we present a brief survey of the role of the organism concept in biological thought. We advance the claim that emergentism (with its fundamental tenets: ontological physicalism, qualitative novelty, property emergence, theory of levels, irreducibility of the emergents, and downward causation) can provide a metaphysical basis for a coherent sort of organicism. Downward causation (DC) is the key notion in emergentist philosophy, as shown by the tension between the aspects of dependence and nonreducibility in the concept of supervenience, preferred by many philosophers to emergence as a basis for nonreductive physicalism. As supervenience physicalism does not lead, arguably, to a stable nonreductive physicalist account, we maintain that a philosophical alternative worthy of investigation is that of a combination of supervenience and property emergence in the formulation of such a stance. Taking as a starting-point O’Connor’s definition of an emergent property, we discuss how a particular interpretation of downward causation (medium DC), inspired by Aristotelian causal modes, results in an explanation of property emergence compatible with both physicalism and non-reductionism. In this account of emergence, one may claim that biology, as a science of living organization, is and remains a science of the organism, even if completely explained by the laws of chemistry. We conclude the paper with a new definition of an emergent property.     

Systems biology,emergence and antireductionism

This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed.Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist–antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.     

Agential autonomy and biological individuality

What is a biological individual? How are biological individuals individuated? How can we tell how many individuals there are in a given assemblage of biological entities? The individuation and differentiation of biological individuals are central to the scientific understanding of living beings. I propose a novel criterion of biological individuality according to which biological individuals are autonomous agents. First, I articulate an ecological–dynamical account of natural agency according to which, agency is the gross dynamical capacity of a goal-directed system to bias its repertoire to respond to its conditions as affordances. Then, I argue that agents or agential dynamical systems can be agentially dependent on, or agentially autonomous from, other agents and that this agential dependence/autonomy can be symmetrical or asymmetrical, strong or weak. Biological individuals, I propose, are all and only those agential dynamical systems that are strongly agentially autonomous. So, to determine how many individuals there are in a given multiagent aggregate, such as multicellular organism, a colony, symbiosis, or a swarm, we first have to identify how many agential dynamical systems there are, and then what their relations of agential dependence/autonomy are. I argue that this criterion is adequate to the extent that it vindicates the paradigmatic cases, and explains why the paradigmatic cases are paradigmatic, and why the problematic cases are problematic. Finally, I argue for the importance of distinguishing between agential and causal dependence and show the relevance of agential autonomy for understanding the explanatory structure of evolutionary developmental biology.     

Organic Codes: A Unifying Concept for Life

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.

     

From autopoiesis to neurophenomenology: Francisco Varela's exploration of the biophysics of being

This paper reviews in detail Francisco Varela's work on subjectivity and consciousness in the biological sciences. His original approach to this "hard problem" presents a subjectivity that is radically intertwined with its biological and physical roots. It must be understood within the framework of his theory of a concrete, embodied dynamics, grounded in his general theory of autonomous systems. Through concepts and paradigms such as biological autonomy, embodiment and neurophenomenology, the article explores the multiple levels of circular causality assumed by Varela to play a fundamental role in the emergence of human experience. The concept of biological autonomy provides the necessary and sufficient conditions for characterizing biological life and identity as an emergent and circular self-producing process. Embodiment provides a systemic and dynamical framework for understanding how a cognitive self--a mind--can arise in an organism in the midst of its operational cycles of internal regulation and ongoing sensorimotor coupling. Global subjective properties can emerge at different levels from the interactions of components and can reciprocally constrain local processes through an ongoing, recursive morphodynamics. Neurophenomenology is a supplementary step in the study of consciousness. Through a rigorous method, it advocates the careful examination of experience with first-person methodologies. It attempts to create heuristic mutual constraints between biophysical data and data produced by accounts of subjective experience. The aim is to explicitly ground the active and disciplined insight the subject has about his/her experience in a biophysical emergent process. Finally, we discuss Varela's essential contribution to our understanding of the generation of consciousness in the framework of what we call his "biophysics of being."     

Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents

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.     

Principles of a new biological theory: A summary

This is a review of the present state of the author's efforts, extending over many years, to construct a formal biological theory that is entirely compatible with quantum mechanics. We point out that the correspondence between detailed realizations on the molecular level and the characteristics of a class or organisms is exceedingly multivalued with respect to the former. Biological theory deals with the process of selection of actual biological states among the very large manifold of possible ones. This may also be expressed by saying that biological theory deals with (biologically) necessary conditions but not with sufficient ones. Conditions that are both necessary and sufficient pertain to physical science (molecular biology). In conformity with a well-known theorem of von Neumann, the selective process (being partly non-mechanistic) is not assumed controlled by simple mathematical rules. The selection from a very large reservoir of possible states is here described as creativity of the organism. The ordinary process of hereditary reproduction may then be represented as creativity with constraints, where the constraints (partly non-mechanistic but compatible with quantum mechanics) are such that the progeny tends to resemble the progenitors. This scheme differs from the usual view of heredity as purely mechanistic molecular replication with possible small errors. In the new scheme a gene appears as an operative symbol which functions as the releaser of a creative process.     

Tma108, a putative M1 aminopeptidase,is a specific nascent chain-associated protein in Saccharomyces cerevisiae

The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, defines a subpopulation of cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Using ribonucleoparticle dissociation experiments we established that Tma108 directly interacts with the nascent protein chain. Additionally, we have shown that translation of the first 35 amino acids of Asn1, one of the Tma108 targets, is necessary and sufficient to recruit Tma108, suggesting that it is loaded early during translation. Comparative genomic analyses, molecular modeling and directed mutagenesis point to Tma108 as an original M1 metallopeptidase, which uses its putative catalytic peptide-binding pocket to bind the N-terminus of its targets. The involvement of Tma108 in co-translational regulation is attested by a drastic change in the subcellular localization of ATP2 mRNA upon Tma108 inactivation. Tma108 is a unique example of a nascent chain-associated factor with high selectivity and its study illustrates the existence of other specific translation-associated factors besides RNA binding proteins.     

Cycles and the Qualitative Evolution of Chemical Systems

Cycles are abundant in most kinds of networks, especially in biological ones. Here, we investigate their role in the evolution of a chemical reaction system from one self-sustaining composition of molecular species to another and their influence on the stability of these compositions. While it is accepted that, from a topological standpoint, they enhance network robustness, the consequence of cycles to the dynamics are not well understood. In a former study, we developed a necessary criterion for the existence of a fixed point, which is purely based on topological properties of the network. The structures of interest we identified were a generalization of closed autocatalytic sets, called chemical organizations. Here, we show that the existence of these chemical organizations and therefore steady states is linked to the existence of cycles. Importantly, we provide a criterion for a qualitative transition, namely a transition from one self-sustaining set of molecular species to another via the introduction of a cycle. Because results purely based on topology do not yield sufficient conditions for dynamic properties, e.g. stability, other tools must be employed, such as analysis via ordinary differential equations. Hence, we study a special case, namely a particular type of reflexive autocatalytic network. Applications for this can be found in nature, and we give a detailed account of the mitotic spindle assembly and spindle position checkpoints. From our analysis, we conclude that the positive feedback provided by these networks'' cycles ensures the existence of a stable positive fixed point. Additionally, we use a genome-scale network model of the Escherichia coli sugar metabolism to illustrate our findings. In summary, our results suggest that the qualitative evolution of chemical systems requires the addition and elimination of cycles.     

Trypanocidal agents with low cytotoxicity to mammalian cell line: a comparison of the theoretical and biological features of lapachone derivatives

Starting from alpha- and beta-lapachones, in this work we compared the biological and theoretical profile of several oxyran derivatives of lapachone as potential trypanocidal agents. Our biological results showed that the oxyrans tested act as trypanocidal agents against Trypanosoma cruzi with minimal cytotoxicity in the VERO cell line compared to naphthoquinones. The oxyran derivative of alpha-lapachone (7a) showed to be one of the most potent compounds. In our molecular modeling study, we analyzed the C-ring moiety and the redox center of beta-lapachone molecule as the moieties responsible for the trypanocidal and cytotoxic effects on mammalian cell line. The computational methods used to delineate the structural requirements for the trypanocidal profile pointed out that the transposition of the C-ring moiety of beta-lapachone, combined with its oxyran ring, introduced important molecular requirements for trypanocidal activity in the HOMO energy, HOMO orbital coefficient, LUMO density, electrostatic potential map, dipole moment vector, and calculated logP (clogP) parameter. This study could lead to the development of new antichagasic medicines based on alpha-lapachone analogs.     

Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.     

Cell theory, specificity, and reproduction, 1837-1870

The cell is not only the structural, physiological, and developmental unit of life, but also the reproductive one. So far, however, this aspect of the cell has received little attention from historians and philosophers of biology. I will argue that cell theory had far-reaching consequences for how biologists conceptualized the reproductive relationships between germs and adult organisms. Cell theory, as formulated by Theodor Schwann in 1839, implied that this relationship was a specific and lawful one, that is, that germs of a certain kind, all else being equal, would produce adult organisms of the same kind, and vice versa. Questions of preformation and epigenesis took on a new meaning under this presupposition. The question then became one of whether cells could be considered as autonomous agents producing adult organisms of a given species, or whether they were the product of external, organizing forces and thus only a stage in the development of the whole organism. This question became an important issue for nineteenth-century biology. As I will demonstrate, it was the view of cells as autonomous agents which helped both Charles Darwin and Gregor Mendel to think of inheritance as a lawful process.     

Cells as irreducible wholes: the failure of mechanism and the possibility of an organicist revival

According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy. While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. Organicists hold that organisms unlike machines are ‘more than the sum of their parts’ and predict that the vital properties of living things can never be explained in terms of mechanical analogies and that the reductionist agenda is doomed to failure. Here we review the current status of the mechanist and organicist conceptions of life particularly as they apply to the cell. We argue that despite the advances in biological knowledge over the past six decades since the molecular biological revolution, especially in the fields of genetics and cell biology the unique properties of living cells have still not been simulated in mechanical systems nor yielded to reductionist—analytical explanations. And we conclude that despite the dominance of the mechanistic–reductionist paradigm through most of the past century the possibility of a twentyfirst century organicist revival cannot be easily discounted.     

Evolution of a multi-agent system in a cyclical environment

The synchronisation phenomena in biological systems is a current and recurring subject of scientific study. This topic, namely that of circadian clocks, served as inspiration to develop an agent-based simulation that serves the main purpose of being a proof-of-concept of the model used in the BitBang framework, that implements a modern autonomous agent model. Despite having been extensively studied, circadian clocks still have much to be investigated. Rather than wanting to learn more about the internals of this biological process, we look to study the emergence of this kind of adaptation to a daily cycle. To that end we implemented a world with a day/night cycle, and analyse the ways the agents adapt to that cycle. The results show the evolution of the agents’ ability to gather food. If we look at the total number of agents over the course of an experiment, we can pinpoint the time when reproductive technology emerges. We also show that the agents adapt to the daily cycle. This circadian rhythm can be shown by analysing the variation on the agents metabolic rate, which is affected by the variation of their movement patterns. In the experiments conducted we can observe that the metabolic rate of the agents varies according to the daily cycle.     

The other side of molecular biology

The question is raised whether in addition to the well-known causal processes of molecular mechanics there are other effects of atomic physics which might appear significantly in biology. We find one, namely the process of molecular synthesis that involves ambiguities due to the competition of isomers. The ambiguities, mathematically called bifurcations, represent binary decisions buried in noise. The assumption is made that collectively there are enough causally undefined decisions to speak of the creativity of the organism as a basic phenomenon in its own right. Creativity, in the past a purely literary term, becomes then a scientific one for which exact definitions are required. We point out that in such a case theory can only specify necessary conditions of phenomena not sufficient ones, as distinct from physics. A very brief survey is made of the major features of a biological theory based on such assumptions.     

Rehabilitating Reductionism

SYNOPSIS: Reductionism has become the object of a great dealof criticism from a variety of quarters within evolutionarybiology in recent years. Many contemporary anti-reductionistsargue that reductionism is inappropriate in biological inquirygiven the prevalence of hierarchies, scales of complexity andlevels of organization in the organic world. They further contendthat a commitment to reductionism has led evolutionary theoriststo make a large number of methodological blunders and conceptualerrors in constructing explanations of biological evolution. The contemporary critics of reductionism have not made a persuasivecase for the ontological peculiarity of the organic world. Muchof their argument concerning hierarchy and levels appears torest on assertion rather than metaphysical necessity or ontologicalpeculiarity. Moreover, the interpretations of reductionism attackedby contemporary critics in biology are narrow and overly simplistic. The modern synthetic theory of evolution may well have explanatoryinadequacies that demand the attention of biologists workingin many fields. But attempts to motivate theoretical alternativesto this theory based solely on ontological grounds appear toplace the ontological cart before the theoretical horse. Theoriesdictate ontological commitments and, as a result, it is at thelevel of theoretical rather than ontological adequacy that theassessment of the modern synthetic theory ought to proceed.     

一类离散Leslic捕食-食饵系统的捕获策略

应用生物数学理论研究生态平衡与可持续发展是生态系统的一个热门课题.在海洋渔业的捕捞过程中,既要保证生态平衡,又要使捕捞收益最大更是海洋渔业关注的重要课题.目前对离散系统的捕捞研究较少.运用离散差分方程的稳定性理论,讨论一类具有捕获的离散Leslic捕食-食饵种群的系统,获取正平衡点的局部渐近稳定的充分条件.通过构造适当的Liapunov函数,利用二元函数的泰勒展开式讨论正平衡点存在必全局稳定性的结果.利用函数的极值判定法讨论在维持稳定捕获前提下的最优捕获策略,来获取最优经济效益.最后,通过一个适当的例子及数值模拟的说明主要结果是合理的.给实际生产提供了理论依据,具有一定的指导意义.     

Multiallelic selection polymorphism

The existence and stability of an internal (i.e., completely polymorphic) equilibrium for viability selection at a single multiallelic locus is investigated. Generations are discrete and nonoverlapping; the population is panmictic, monoecious, and diploid. Various necessary and sufficient conditions for the existence of an internal equilibrium are established and applied to the loss of alleles. Some necessary conditions for the existence of an asymptotically stable internal equilibrium are also established. All these conditions are simpler and yield general biological conclusions more easily than the classical necessary and sufficient conditions.