The transmission sense of information

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.     

Response to commentaries on “The Transmission Sense of Information”

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.     

Theory of data transferal

A new approach to information is proposed with the intention of providing a conceptual tool adapted to biology, including a semantic value.Information involves a material support as well as a significance, adapted to the cognitive domain of the receiver and/or the transmitter. A message does not carry any information, only data. The receiver makes an identification by a procedure of recognition of the forms, which activate previously learned significance. This treatment leads to a new significance (or new knowledge).The notion of a probabilistic event is abandoned. The quantity of information is the product of the quantity of data (probability of recognition of the message) times the value of the significance, determined by its semantic level.     

Historic and functional biology: the inadequacy of a system theory of evolution

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.     

Explanations in evolutionary theory1

The theory of biological evolution is defined in many ways, leading to considerable confusion in its application and testing against objective empirical observations. Evolutionary change is usually defined as genetic which would exclude both cultural and template evolution; hence the qualifying adjective genetic should not be included in the definition of biological evolution. Darwin's theory, always described by him in the singular, is actually a bundle of five independent theories about evolution as advocated by Mayr. Furthermore only one of these theories, that of common descent, is historical, and the other four – evolution as such, gradualism, processes of phyletic evolution and of speciation, and causes of evolution – are nomological. Hence not all evolutionary theory is historical. Biological comparisons can be divided into horizontal and vertical ones and valid conclusions from one type of comparisons cannot be automatically extrapolated to the other. All phyletic evolutionary change, no matter how extensive it may be, never crosses species taxa boundaries; hence it is not possible to distinguish ‘trans‐specific evolution’ (= evolution beyond or above the level of the species) from evolution within the species level. Macroevolution does not differ from microevolution except in the scale of the overall change; no special causes or processes of macroevolution exist.     

A theory for the evolutionary game

We present an evolutionary game theory. This theory differs in several respects from current theories related to Maynard Smith's pioneering work on evolutionary stable strategies (ESS). Most current work deals with two person matrix games. For these games the strategy set is finite. We consider evolutionary games which are defined over a continuous strategy set and which permit any number of players. Matrix games are included as a bilinear continuous game. However, under our definition, such games will not posses an ESS on the interior of the strategy set. We extend previous work on continuous games by developing an ESS definition which permits the ESS to be composed of a coalition of several strategies. This definition requires that the coalition must not only be stable with respect to perturbations in strategy frequencies which comprise the coalition, but the coalition must also satisfy the requirement that no mutant strategies can invade. Ecological processes are included in the model by explicitly considering population size and density dependent selection.     

Evolution of structure,order and complexity in biological systems: Part III of a general theory

In this, Part III of a general theory, the large-scale features of evolution of structure, order, and complexity are considered as characteristic features of the biological state of matter. This starts with a rigorous formal definition of structure, classes of structural order, complexity, measures of complexity, and how these arise through evolution by a cumulative process of storing information in memory systems. Three such memory systems have evolved: the genetic memory, the immune memory, and the memories of the nervous system. The evolution, characteristic parameters and the limitations of these memory systems are explored. From these considerations emerge the large-scale features of the evolutionary pathways of biological structure, function, and complexity.     

生物进化的根本动因在于主体程序的内化

通过主体、主体程序、内化、外化(进化)等核心概念的揭示和接入,展开了生命演化的崭新画卷——导致生物外在进化的根本动因是基于宇宙演化而产生的主体程序。论述了基于主体程序内化的引领及其与外化(进化)的互动,才使生物不断由低级走向到高级,并最终导致人类及人类精神的产生。主体程序理论的提出主旨在于弥补进化论在内在动因方面的重大缺陷,并由此奠定根本性解释生命现象的理论基础。     

The evolution of theory of mind on welfare tradeoff ratios

People seem to attribute beliefs and desires to another person when interacting with them. Such a “theory of mind” capacity is essential for complex and uniquely human behavior such as language, but its evolutionary origin remains elusive. Using the formal tools of evolutionary game theory, we asked what environmental properties are necessary to select for a basic form of theory of mind—the ability to infer the prosociality, quantified by the welfare tradeoff ratio, of another person toward oneself. We found that none of the environments studied in classical or evolutionary game theory give an advantage to this form of theory of mind capacities; theory of mind is advantageous only in a new class of environments with stable opponents and variable payoff structures. In two behavioral experiments (n = 91) we verified that people can, and do use theory of mind in such an environment. These results suggest that some features of early humans’ social environment that were previously neglected in evolutionary game theory may be responsible for the evolution of people’s complex social capacities.     

The arbitrariness of the genetic code

The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently by previous, often rather implicit accounts of arbitrariness. They have drawn on the frozen accident theory, on evolutionary contingency, on alternative causal pathways, and on the absence of direct stereochemical interactions between codons and amino acids. It has also been suggested that the arbitrariness of the genetic code justifies attributing semantic information to macromolecules, notably to DNA. I argue that these accounts of arbitrariness are unsatisfactory. I propose that the code is arbitrary in the sense of Jacques Monod's concept of chemical arbitrariness: the genetic code is arbitrary in that any codon requires certain chemical and structural properties to specify a particular amino acid, but these properties are not required in virtue of a principle of chemistry. This notion of arbitrariness is compatible with several recent hypotheses about code evolution. I maintain that the code's chemical arbitrariness is neither sufficient nor necessary for attributing semantic information to nucleic acids.     

Parsimony in evolutionary theory: Law or methodological prescription?

Parsimony (Ockham's razor) is in widespread use in phylogenetic reconstruction (evolution takes the shortest route), however it is not quite obvious which is the rank that this principle should have in evolutionary theory. Parsimony is not of a single kind but, on the contrary, is at least of two kinds: ontological and methodological. Ontological parsimony involves an assumption about the “simplicity of nature”. Methodological parsimony is a purely logical precept, a case of the broad practical principle not to believe anything for which there is no evidence. The two kinds of parsimony are not compatible with one another. The ontological hypotheses that reality is simple has been refuted many times in the history of science, and evolution is not an exception to this. In spite of the fact, that direct evolutionary changes have higher probability than the ones that take “unnecessary” steps, evolutionary parsimony is merely a methodological precept, not a law of evolution. Probability is not enough to give evolutionary parsimony a rank of ontological axiom. Therefore, the reasons to use the principle of evolutionary parsimony are only methodological. A definition of evolutionary parsimony is: as long as no evidence is available to suggest an alternative pathway evolution may be considered to occur in the most parsimonious way.     

Modeling the evolution of interconnected processes: It is the song and the singers

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re‐produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re‐production but also the evolution and fitness of biological and ecosystemic interconnected processes.     

Evolution of altitudinal migration in passerines is linked to diet

Bird migration is typically associated with a latitudinal movement from north to south and vice versa. However, many bird species migrate seasonally with an upslope or downslope movement in a process termed altitudinal migration. Globally, 830 of the 6,579 Passeriformes species are considered altitudinal migrants and this pattern has emerged multiple times across 77 families of this order. Recent work has indicated an association between altitudinal migration and diet, but none have looked at diet as a potential evolutionary driver. Here, we investigated potential evolutionary drivers of altitudinal migration in passerines around the world by using phylogenetic comparative methods. We tested for evolutionary associations between altitudinal migration and foraging guild and primary habitat preference in passerines species worldwide. Our results indicate that foraging guild is evolutionarily associated with altitudinal migration, but this relationship varies across zoogeographical regions. In the Nearctic, herbivorous and omnivorous species are associated with altitudinal migration, while only omnivorous species are associated with altitudinal migration in the Palearctic. Habitat was not strongly linked to the evolution of altitudinal migration. While our results point to diet as a potentially important driver of altitudinal migration, the evolution of this behavior is complex and certainly driven by multiple factors. Altitudinal migration varies in its use (for breeding or molting), within a species, population, and even at the individual level. As such, the evolution of altitudinal migration is likely driven by an ensemble of factors, but this study provides a beginning framework for understanding the evolution of this complex behavior.