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. (shrink)

Intersemiotic translation (IT) was defined by Roman Jakobson (The Translation Studies Reader, Routledge, London, p. 114, 2000) as “transmutation of signs”—“an interpretation of verbal signs by means of signs of nonverbal sign systems.” Despite its theoretical relevance, and in spite of the frequency in which it is practiced, the phenomenon remains virtually unexplored in terms of conceptual modeling, especially from a semiotic perspective. Our approach is based on two premises: (i) IT is fundamentally a semiotic operation process (semiosis) and (ii) (...) IT is a deeply iconic-dependent process. We exemplify our approach by means of literature to dance IT and we explore some implications for the development of a general model of IT. (shrink)

This paper is divided into two parts. Part I focuses on the manner in which the components of the face recognition system work together so that a perceiver, within several hundred milliseconds after seeing a familiar face, is able to both identify the face of the perceived and recall elements of the history of past encounters with the perceived. Face recognition plays a crucial role in enabling both human and nonhuman primates to interact in collaborative social groups. This critical function (...) is accomplished through the unidirectional coded transfer of informational elements from one component to another. Although these informational elements themselves are not meaningful to the perceiving agent, they do nevertheless contain essential bits of information that are necessary for the final formation of the meaningful message. The structural components of the system are identified and the manner in which informational elements are coded and transferred sequentially from component to component in the brain of the perceiver is described. The independent, physically separated components in the face recognition system are bridged by an additional component, an “adaptor”, that mediates the transfer of informational elements from one component to another. The nature of the independent systems, and the manner by which the bridging or adaptor apparatus enables coded information transfer from one system to another is discussed. Part II focuses on the analysis of recognition in human-designed sign systems such as Braille and Morse code. Recognition in human-designed sign systems is notable for the stability of the link between sign and meaning. Face recognition is characterized as being subjective, indicating that the meaning of a sign to a perceiver is variable and dependent on context, whereas human-devised sign recognition is characterized as being objective, indicating that the meaning of a sign is context independent and invariant. Human-designed sign systems require the presence in brain of a referent world. An example of a referent world is the set of letters of the alphabet. Representations of this set are installed in the brain through social mediated learning. Human-designed sets of signs are created to correspond, via a code enabling adaptor structure, to referent worlds in the brain. Human-designed sign systems are the foundations for literacy, a capability only found in humans. (shrink)

The sequence of nucleotide bases occurring in an organism’s DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of construction. In reality, any biochemical machine for which a DNA codescript is efficacious is itself produced through the mechanical interpretation of an identical or very similar codescript. In these (...) terms the origin of life can be described as a bootstrap process involving the simultaneous accumulation of genetic information and the generation of a machine that interprets it as instructions for its own construction. This problem is discussed within the theoretical frameworks of thermodynamics, informatics and self-reproducing automata, paying special attention to the physico-chemical origin of genetic coding and the conditions, both thermodynamic and informatic, that a system must fulfil in order for it to sustain semiosis. The origin of life is equated with biosemiosis. (shrink)

The concept of information has been extensively studied and written about, yet no consensus on a unified definition of information has to date been reached. This paper seeks to establish the basis for a unified definition of information. We claim a biosemiotics perspective, based on Gregory Bateson’s definition of information, provides a footing on which to build because the frame this provides has applicability to both the sciences and humanities. A key issue in reaching a unified definition of information is (...) the fundamental problem of identifying how a human organism, in a self-referential process, develops from a state in which its knowledge of the human-organism-in-its-environment is almost non-existent to a state in which the human organism not only recognizes the existence of the environment but also sees itself as part of the human-organism-in-its-environment system. This allows a human organism not only to self-referentially engage with the environment and navigate through it, but also to transform it in its own image and likeness. In other words, the Fundamental Problem of the Science of Information concerns the phylogenetic development process, as well as the ontogenetic development process of Homo sapiens sapiens from a single cell to our current multicellular selves, all in a changing long-term and short-term environment, respectively. (shrink)

All information results from a process, intrinsic to living beings, of info-autopoiesis or information self-production; a sensory commensurable, self-referential feedback process immanent to Bateson’s ‘difference which makes a difference’. To highlight and illustrate the fundamental nature of the info-autopoietic process, initially, two simulations based on one-parameter feedback are presented. The first, simulates a homeostatic control mechanism (thermostat) which is representative of a mechanistic, cybernetic system with very predictable dynamics, fully dependent on an external referent. The second, simulates a homeorhetic process, (...) inherent to biological systems, illustrating a self-referenced, autonomous system. Further, the active incorporation/interference of viral particles by prokaryotic cells and the activation of CRISPR-Cas can be understood as info-autopoiesis at the most fundamental cellular level, as well as constituting a planetary network of self-referenced information. Moreover, other examples of the info-autopoietic nature of information are presented to show the generality of its applicability. In short, info-autopoiesis is a recursive process that is sufficiently generic to be the only basis for information in nature: from the single cell, to multi-cellular organisms, to consideration of all types of natural and non-natural phenomena, including tools and artificial constructions. (shrink)

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. (shrink)

Molecular codes can be considered a special type of mapping among molecular species in biochemical systems. The formalization of molecular codes allows to identify these in network models of real world systems. Analyzing algorithmically identified codes leads to the observation that codes does not necessarily stand alone, but that we can identify certain relations among codes. In this paper I will define two types of relations that can occur among codes, code linkage and code nesting, and will discuss implications of (...) this finding. (shrink)

Acoustic codes assure the intra and interspecific communication of vocal animals. They are composed by a sequence of nominal entities and by magnitude modulation confirming in such a way contemporarily a behavioural and ecological nature. The acoustic codes find evidence in the acoustic niche hypothesis by which species in order to reduce interspecific competition occupy a restricted portion of the available frequencies modulating very precise acoustic cues . Their evolution, like other aspect of biology, is under control of the environmental (...) conditions assuming the more favourable configurations. These nominal entities respond also to the amount of energy by which are emitted allowing to the eavesdropping individuals to range the distance at which a potential competitor is broadcasting a signal. Environmental alterations, especially if of anthropogenic origin, can produce severe consequence of the acoustic codes that in turn may affect the prey–predator balance and the complexity of communities. In fact acoustic codes under an environmental constraint like human noise intrusion can be modified in order to reduce a masking effect, demonstrating their phenological plasticity. The new ecological discipline of soundscape ecology offers the possibility to investigate the nature and the evolution of the acoustic codes in different environmental conditions. (shrink)