Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically 'the carriers of hereditary information.' Nevertheless, a number of researchers consider such talk as inadequate and 'just metaphorical,' thus expressing a skepticism about the use of the term 'information' and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis.

Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Abstract. Modern semiotics is a branch of logics that formally defines symbol-based communication. In recent years, the semiotic classification of signs has been invoked to support the notion that symbols are uniquely human. Here we show that alarm-calls such as those used by African vervet monkeys (Cercopithecus aethiops), logically satisfy the semiotic definition of symbol. We also show that the acquisition of vocal symbols in vervet monkeys can be successfully simulated by a computer program based on minimal semiotic and neurobiological constraints. The simulations indicate that learning depends on the tutor-predator ratio, and that apprenticegenerated auditory mistakes in vocal symbol interpretation have little effect on the learning rates of apprentices (up to 80% of mistakes are tolerated). In contrast, just 10% of apprentice-generated visual mistakes in predator identification will prevent any vocal symbol to be correctly associated with a predator call in a stable manner.Tutor unreliability was also deleterious to vocal symbol learning: a mere 5% of "lying" tutors were able to completely disrupt symbol learning, invariably leading to the acquisition of incorrect associations by apprentices.Our investigation corroborates the existence of vocal symbols in a non-human species, and indicates that symbolic competence emerges spontaneously from classical associative learning mechanisms when the conditioned stimuli are self-generated, arbitrary and socially efficacious. We propose that more exclusive properties of human language, such as syntax, may derive from the evolution of higher-order domains for neural association, more removed from both the sensory input and the motor output, able to support the gradual complexification of grammatical categories into syntax.

Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be applied to establish, in a general sense, a set of theoretical constraints for explaining the instantiation of different kinds of meaning processes (iconic, indexical, symbolic) in semiotic systems. We use it to model a semiotic process in the immune system, namely, B-cell activation, in order to offer insights into the heuristic role it can play in the development of explanations for specific semiotic processes.

Abstract. In this paper, we describe a digital scenario where we simulated the emergence of self-organized symbol-based communication among artificial creatures inhabiting a virtual world of unpredictable predatory events. In our experiment, creatures are autonomous agents that learn symbolic relations in an unsupervised manner, with no explicit feedback, and are able to engage in dynamical and autonomous communicative interactions with other creatures, even simultaneously. In order to synthesize a behavioral ecology and infer the minimum organizational constraints for the design of our creatures, we examined the well-studied case of communication in vervet monkeys. Our results show that the creatures, assuming the role of sign users and learners, behave collectively as a complex adaptive system, where self-organized communicative interactions play a major role in the emergence of symbol-based communication. We also strive in this paper for a careful use of the theoretical concepts involved, including the concepts of symbol and emergence, and we make use of a multi-level model for explaining the emergence of symbols in semiotic systems as a basis for the interpretation of inter-level relationships in the semiotic processes we are studying.

Meaning, Semiosis, Emergence, Simulation, C. S. Peirce,

Mimicry and deception are two important issues in studies about animal communication. The reliability of animal signs and the problem of the benefits of deceiving in sign exchanges are interesting topics in the evolution of communication. In this paper, we intend to contribute to an understanding of deception by studying the case of aggressive signal mimicry in fireflies, investigated by James Lloyd. Firefly femmes fatales are specialized in mimicking the mating signals of other species of fireflies with the purpose of attracting responding males to become their prey. These aggressive mimics are a major factor in the survival and reproduction of both prey and predator. It is a case of deception through active falsification of information that leads to efficient predation by femmes fatales fireflies and triggered evolutionary processes in their preys' communicative behaviors. There are even nested coevolutionary interactions between these fireflies, leading to a remarkable system of deceptive and counterdeceptive signaling behaviors. We develop here a semiotic model of firefly deception and also consider ideas advanced by Lloyd about the evolution of communication, acknowledging that deception can be part of the explanation of why communication evolves towards increasing complexity. Increasingly complex sign exchanges between fireflies evolve in an extremely slow pace. Even if deceptive maneuvers are played out time and time again between particular firefly individuals, the evolution of the next level of complexity-and thus the next utterance in the dialogue between species-is likely to take an immense amount of generations.

In his 1903 Syllabus, Charles S. Peirce makes a distinction between icons and iconic signs, or hypoicons, and briefly introduces a division of the latter into images, diagrams, and metaphors. Peirce scholars have tried to make better sense of those concepts by understanding iconic signs in the context of the ten classes of signs described in the same Syllabus. We will argue, however, that the three kinds of hypoicons can better be understood in the context of Peirce's sixty-six classes of signs. We analyze examples of hypoicons taken from the field of information design, describing them in the framework of the sixty-six classes, and discuss the consequences of those descriptions to the debate about the order of determination of the 10 trichotomies that form those classes.