Biosemiotics Within and Without Biological Holism: A Semio-historical Analysis

On the basis of a comparative analysis of the biosemiotic work of Jakob von Uexküll and of various theories on biological holism, this article takes a look at the question: what is the status of a semiotic approach in respect to a holistic one? The period from 1920 to 1940 was the peak-time of holistic theories, despite the fact that agreement on a unified and accepted set of holistic ideas was never reached. A variety of holisms, dependent on the cultural and disciplinary contexts, is sketched here from the works of Jan Smuts, Adolf Meyer-Abich, John Scott Haldane, Kurt Goldstein, Alfred North Whitehead and Wolfgang Köhler. In contrast with his contemporary holists, who used the model of an organism as a unifying explanatory tool for all levels of reality, Jakob von Uexküll confined himself to disciplinary organicism by extending the borders of the definition of “organism” without any intention to surpass the borders of biology itself. The comparison reveals also a significant difference in the perspectives of Uexküll and his contemporary holists, a difference between a view from a subjective centre in contrast with an all-encompassing structural view. Uexküll’s theories are fairly near to J. S. Haldane’s interpretation of an organism as a coordinative centre, but even here their models do not coincide. Although biosemiotics and holistic biology have different theoretical starting points and research-goals, it is possible nonetheless to place them under one and the same doctrinal roof.     

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.     

The Origin of Cellular Life and Biosemiotics

Recent successes of systems biology clarified that biological functionality is multilevel. We point out that this fact makes it necessary to revise popular views about macromolecular functions and distinguish between local, physico-chemical and global, biological functions. Our analysis shows that physico-chemical functions are merely tools of biological functionality. This result sheds new light on the origin of cellular life, indicating that in evolutionary history, assignment of biological functions to cellular ingredients plays a crucial role. In this wider picture, even if aggregation of chance mutations of replicator molecules and spontaneously self-assembled proteins led to the formation of a system identical with a living cell in all physical respects but devoid of biological functions, it would remain an inanimate physical system, a pseudo-cell or a zombie-cell but not a viable cell. In the origin of life scenarios, a fundamental circularity arises, since if cells are the minimal units of life, it is apparent that assignments of cellular functions require the presence of cells and vice versa. Resolution of this dilemma requires distinguishing between physico-chemical and biological symbols as well as between physico-chemical and biological information. Our analysis of the concepts of symbol, rule and code suggests that they all rely implicitly on biological laws or principles. We show that the problem is how to establish physico-chemically arbitrary rules assigning biological functions without the presence of living organisms. We propose a solution to that problem with the help of a generalized action principle and biological harnessing of quantum uncertainties. By our proposal, biology is an autonomous science having its own fundamental principle. The biological principle ought not to be regarded as an emergent phenomenon. It can guide chemical evolution towards the biological one, progressively assigning greater complexity and functionality to macromolecules and systems of macromolecules at all levels of organization. This solution explains some perplexing facts and posits a new context for thinking about the problems of the origin of life and mind.     

Evolutionary Biosemiotics and Multilevel Construction Networks

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents.     

Chemistry and biodiversity: Darwinism, evolution, and speciation. An opposing view

Complex structures produced by noncatalyzed multi‐step chemical processes must have highly probable origins and assembly routes. Within any frame of reference, life is easily the most‐complex self‐assembled structure known to man. It is not possible to calculate a finite time for biogenesis by statistical mechanics, but the abundance of life makes it reasonable to propose an accelerating principle of nature that naturally shortened the time for cell formation to a billion years or less. This hypothetical principle, which I have called valence‐orbital bias, is thought to be responsible for the discrepancy between statistics and observation, and carries with it, as a conditio sine qua non, multiple origins of life. The new concept resolves the differences between the predictions based on statistical mechanics and the relatively rapid appearance of life during the post‐accretion period. It suggests as well that species and variants, the units of propagation, may also have been the units of evolution. Produced in profusion by chemistry, the origins are culled by natural selection, whereby failure means extinction, not adaptation. Biodiversity, thus, becomes a direct consequence of chemistry without positive feedback from the environment and without a constructive role for mutation.     

Evolution by epigenesis: farewell to Darwinism, neo- and otherwise.

In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. The critics advanced other theories instead of 'natural selection' and the survival of the fittest'. 'Saltatory ontogeny' and 'epigenesis' are such new theories proposed to explain how variations in ontogeny and novelties in evolution are created. They are reviewed again in the present essay that also tries to explain how Darwinians, artificially kept dominant in academia and in granting agencies, are preventing their acceptance. Epigenesis, the mechanism of ontogenies, creates in every generation alternative variations in a saltatory way that enable the organisms to survive in the changing environments as either altricial or precocial forms. The constant production of two such forms and their survival in different environments makes it possible, over a sequence of generations, to introduce changes and establish novelties--the true phenomena of evolution. The saltatory units of evolution remain far-from-stable structures capable of self-organization and self-maintenance (autopoiesis).     

Formal Darwinism,the individual-as-maximizing-agent analogy and bet-hedging

The central argument of The origin of species was that mechanical processes (inheritance of features and the differential reproduction they cause) can give rise to the appearance of design. The ''mechanical processes'' are now mathematically represented by the dynamic systems of population genetics, and the appearance of design by optimization and game theory in which the individual plays the part of the maximizing agent. Establishing a precise individual-as-maximizing-agent (IMA) analogy for a population-genetics system justifies optimization approaches, and so provides a modern formal representation of the core of Darwinism. It is a hitherto unnoticed implication of recent population-genetics models that, contrary to a decades-long consensus, an IMA analogy can be found in models with stochastic environments (subject to a convexity assumption), in which individuals maximize expected reproductive value. The key is that the total reproductive value of a species must be considered as constant, so therefore reproductive value should always be calculated in relative terms. This result removes a major obstacle from the theoretical challenge to find a unifying framework which establishes the IMA analogy for all of Darwinian biology, including as special cases inclusive fitness, evolutionarily stable strategies, evolutionary life-history theory, age-structured models and sex ratio theory. This would provide a formal, mathematical justification of fruitful and widespread but ''intentional'' terms in evolutionary biology, such as ''selfish'', ''altruism'' and ''conflict''.     

Darwinism and cultural change

Evolutionary models of cultural change have acquired an important role in attempts to explain the course of human evolution, especially our specialization in knowledge-gathering and intelligent control of environments. In both biological and cultural change, different patterns of explanation become relevant at different 'grains' of analysis and in contexts associated with different explanatory targets. Existing treatments of the evolutionary approach to culture, both positive and negative, underestimate the importance of these distinctions. Close attention to grain of analysis motivates distinctions between three possible modes of cultural evolution, each associated with different empirical assumptions and explanatory roles.     

Cultural Darwinism and Language

This article examines the effect of cultural selection on the development of language in humans. First, it is claimed that directive and expressive types of speech acts are commonly found in many animal species. Representative speech acts, on the other hand, with the exception of animal "calls," are found primarily among humans. !t is argued that a cultural environment is a probable selective factor for the capacity to produce representative speech acts. Second, it is argued that representative speech acts, once they became part of language, acted as a selective factor for increased intelligence and associated greater brain size. And, finally, it is argued that the capacity to create representative speech acts selected for brains that could store great numbers of memory episodes and narratives, as well as plan for the future. [Key words: evolution, language, cultural selection, brain, intelligence, memory]     

Darwinism and cultural change

Evolutionary models of cultural change have acquired an important role in attempts to explain the course of human evolution, especially our specialization in knowledge-gathering and intelligent control of environments. In both biological and cultural change, different patterns of explanation become relevant at different ‘grains’ of analysis and in contexts associated with different explanatory targets. Existing treatments of the evolutionary approach to culture, both positive and negative, underestimate the importance of these distinctions. Close attention to grain of analysis motivates distinctions between three possible modes of cultural evolution, each associated with different empirical assumptions and explanatory roles.     

Biosemiotics and Hominidae history: technicity,animals, and the limitations of human exceptionalism

This article is focused on problematic distinctions of difference among animals in the lineage of great apes. It combines several theoretical perspectives on evolutionary relationships, technological innovation, the development of body parts as tools, and a semiotic interpretation of what André Leroi-Gourhan called technicity. Foundational questions in social theory are developed using biosemiotics, particularly as concerns a materialist understanding of religion and the magical aspects of cultural representation. This, it is argued, provides a framework for theorizing social history in terms of real ecological relations, embodied meaning, and the transference of meaning onto objects. Understood semiotically, the material history of Hominidae, encompassing animals with different kinds of motility, dexterity, and techno-semiotic orientations towards the world, is inclusive and relational rather than exclusively anthropocentric, as is the case for social theory based on the artifice of language and articulations of belief, creativity, and cultural distinction that are thought to be distinctive of the genus Homo.     

On the Concept of Code in Linguistics and Biosemiotics

Biosemioticians use language and linguistic concepts as a window onto phenomena and processes on all levels of life. Like most biologists, some biosemioticians use language and linguistic concepts as metaphors for phenomena and processes on the cellular level. Even mainstream biologists may be aware that with concepts like code, information or communication on the level of the cell, they are anthropomorphizing the living things they study. The paradox of linguistics is that the object of study is at the same time the cognitive tool for its analysis. Like everyone else, biologists depend on the species-specific cognitive tool of language to study the laws and phenomena of all kinds of living organisms. Biosemioticians face both paradoxes and the challenge of mediating between the terminologies of the disciplines they navigate. At the 11^th Gatherings in Biosemiotics in New York, several papers commented on inadequate concepts in the field of linguistics and the failure of the discipline of linguistics as a whole. In this paper, I comment on some of the claims that were made specifically about the distinctive feature and the notion of code in linguistics.     

Merging microsatellite data.

Genotype calling procedures vary from laboratory to laboratory for many microsatellite markers. Even within the same laboratory, application of different experimental protocols often leads to ambiguities. The impact of these ambiguities ranges from irksome to devastating. Resolving the ambiguities can increase effective sample size and preserve evidence in favor of disease-marker associations. Because different data sets may contain different numbers of alleles, merging is unfortunately not a simple process of matching alleles one to one. Merging data sets manually is difficult, time-consuming, and error-prone due to differences in genotyping hardware, binning methods, molecular weight standards, and curve fitting algorithms. Merging is particularly difficult if few or no samples occur in common, or if samples are drawn from ethnic groups with widely varying allele frequencies. It is dangerous to align alleles simply by adding a constant number of base pairs to the alleles of one of the data sets. To address these issues, we have developed a Bayesian model and a Markov chain Monte Carlo (MCMC) algorithm for sampling the posterior distribution under the model. Our computer program, MicroMerge, implements the algorithm and almost always accurately and efficiently finds the most likely correct alignment. Common allele frequencies across laboratories in the same ethnic group are the single most important cue in the model. MicroMerge computes the allelic alignments with the greatest posterior probabilities under several merging options. It also reports when data sets cannot be confidently merged. These features are emphasized in our analysis of simulated and real data.