Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal (...) processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

According to David Chalmers, the hard problem of consciousness consists of explaining how and why qualitative experience arises from physical states. Moreover, Chalmers argues that materialist and reductive explanations of mentality are incapable of addressing the hard problem. In this chapter, I suggest that Chalmers’ hard problem can be usefully distinguished into a ‘how question’ and ‘why question,’ and I argue that evolutionary biology has the resources to address the question of why qualitative experience arises from brain states. From this (...) perspective, I discuss the different kinds of evolutionary explanations (e.g., adaptationist, exaptationist, spandrel) that can explain the origins of the qualitative aspects of various conscious states. This argument is intended to clarify which parts of Chalmers’ hard problem are amenable to scientific analysis. (shrink)

The New World of the Organic CodesThe genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost 4 billion years later, at the end of life’s history. Today it is widely assumed that these are the only codes that exist in Nature, and if this were true we would have to conclude that codes are extraordinary exceptions because they appeared only at the beginning and at the end of evolution. In reality, various other (...) organic codes have been discovered in the past few decades.In 1975, the American biochemist Gordon Tomkins published a paper entitled The Metabolic Code. Biological symbolism and the origin of intercellular communication . That was the very first announcement of a new organic code after the discovery of the genetic code, but tragically Tomkins died that very year and his new world of organic symbolism remained unexplored. Some 10 years later, Edward Trifonov started a life-long campaign in favour .. (shrink)

This paper presents evidence for a psychological coding process that meets the criteria that define such processes in organic nature and culture. The recognition of these previously unknown encoding sequences is derived from the recent formulation of an adaptive mental module of the mind—the emotion processing mind—that has evolved to cope with traumatic events and the unique, language derived, explicit human awareness of personal mortality. The emergent awareness of death has served as a selection factor for the evolution of a (...) two-system, emotion-processing mind, with conscious and unconscious components, an arrangement that allows for the invocation of conscious denial, which in turn has fostered the use of encoding when faced with death-related traumas. The paper offers several ways in which evolved mental adaptations have features that are shared with those that are biological. Many aspects of these mental adaptive efforts are comparable to attempts at defense that are carried out by the immune system. In addition, the adaptive approach has been the foundation for the discovery of laws of communication, and thus of the mind, that are on a parallel with those found through mathematical models drawn from Newtonian physics. (shrink)

The evolutionary origin of consciousness has been a growing area of study in recent years. Nevertheless, there is intense debate on whether the existence of phenomenal consciousness without the cerebral cortex is possible. The corticocentrists have an empirical advantage because we are quasi-confident that we humans are conscious and have the well-developed cortex as the site of our consciousness. However, their prejudice can be an anthropic bias similar to the anthropocentric prejudice in pre-Darwinian natural history. In this paper, I propose (...) three basic principles to provide a conceptual basis for evolutionary studies of consciousness: the non-solipsistic principle, the evolution principle, and the anthropic principle. These principles collectively help us to avoid solipsism, anthropocentrism, and anthropomorphism to some degree, although we cannot be completely free from them. Also, the landscape metaphor associated with the anthropic principle provides an image of how different forms of consciousness can be acquired. (shrink)

The discovery of the genetic code has shown that the origin of life has also been the origin of semiosis, and the discovery of many other organic codes has indicated that organic semiosis has been the sole form of semiosis present on Earth in the first three thousand million years of evolution. With the origin of animals and the evolution of the brain, however, a new type of semiosis came into existence, a semiosis that is based on interpretation and is (...) commonly referred to as interpretive, or Peircean semiosis. This suggests that there are two distinct types of semiosis in Nature, one based on coding and one based on interpretation, and all the experimental evidence that we have does support this conclusion. Both in principle and in practice, therefore, there is no conflict between organic semiosis and Peircean semiosis, and yet they have been the object of a fierce controversy because it has been claimed that semiosis is always based on interpretation, even at the cellular level. Such a claim has recently been reproposed in a number of papers and it has become necessary therefore to reexamine it in the light of the proposed arguments. (shrink)

At the heart of evolutionary theory lays the notion of replication. Unfortunately, this notion is far less exact than the weight of its importance. In this paper, it is argued that replication always involves coding. Furthermore, when a theory of evolution is built on replication based on coding, a unifying and coherent picture arises that sheds new light on some of the controversies and open questions in contemporary biology, such as what are the roles of phylogeny and ontogeny in evolution, (...) and how to characterize and explain the increase of biological complexity. (shrink)

This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it (...) is a new and bold attempt to use semiotics to solve the problems created by the evolutionary paradigm’s commitment to produce a theory of how to connect the two sides of the Cartesian dualistic view of physical reality and consciousness in a consistent way. (shrink)

Four sequential, sub-processes are identified as the fundamental steps in the processing of signals by big-brained animals. These are, Detection of the signal, its Representation in correlated sensory brain structure, the Interpretation of the signal in another part of the brain and the Expression of the receiver’s response. We label this four-step spatiotemporal process DRIE. We support the view that when the context within which such signals are produced and received is relatively constant, the DRIE process can be ultimately assimilated (...) into the genome, with the Interpretation sub-phase is markedly decreased in duration as speed and efficiency are maximized. With frequent repetition and learning, an analogous result can be attained epigenetically as exemplified in human word and text recognition, allowing tasks critical to primate social function to be accomplished with rapidity and accuracy. (shrink)

Meaning is a central concept of (bio)semiotics. At the same time, it is also a word of everyday language. Here, on the example of the world information, we discuss the “reduction-inflation model” of evolution of a common word into a scientific concept, to return subsequently into everyday circulation with new connotations. Such may be, in the near future, also the fate of the word meaning if, flexed through objectified semantics, will become considered an objective concept usable in semiotics. We argue (...) that reducing meaning to a technical term essentially synonymous to code and stripped of most of the original semantic field is not a necessary prerequisite for a meaningful application of the concept in semiotics and in biology. (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)