This article is arranged around two general claims and a thought experiment. I begin by suggesting that the genome should be studied as a developmental system, and that genes supervene on genomes (rather than the other way around). I move on to present a thought experiment that illustrates the implications a dynamic view of the genome has for central concepts in biology, in particular the information content of the genome, and the notion of responses to stress.

We propose that the sudden emergence of metazoans during the Cambrian was due to the appearance of a complex genome architecture that was capable of computing. In turn, this made defining recursive functions possible. The underlying molecular changes that occurred in tandem were driven by the increased probability of maintaining duplicated DNA fragments in the metazoan genome. In our model, an increase in telomeric units, in conjunction with a telomerase-negative state and consequent telomere shortening, generated a reference point equivalent to (...) a non-reversible counting mechanism. (shrink)

The ecological approach to perception-action is unlike the standard approach in several respects. It takes the animal-in-its-environment as the proper scale for the theory and analysis of perception-action, it eschews symbol based accounts of perception-action, it promotes self-organization as the theory-constitutive metaphor for perception-action, and it employs self-referring, non-predicative definitions in explaining perception-action. The present article details the complexity issues confronted by the ecological approach in terms suggested by Rosen and introduces non-well-founded set theory as a potentially useful tool for (...) expressing them. The issues and the tool are brought to focus in the concept of affordance that is the basis for explanation of prospective control of action in the ecological approach. (shrink)

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...) the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

In the past, philosophers, scientists, and even the general opinion, had no problem in accepting the existence of consciousness in the same way as the existence of the physical world. After the advent of Newtonian mechanics, science embraced a complete materialistic conception about reality. Scientists started proposing hypotheses like abiogenesis (origin of first life from accumulation of atoms and molecules) and the Big Bang theory (the explosion theory for explaining the origin of universe). How the universe came to be what (...) it is now is a key philosophical question. The hypothesis that it came from Nothing (as proposed by Stephen Hawking, among others), proves to be dissembling, since the quantum vacuum can hardly be considered a void. In modern science, it is generally assumed that matter existed before the universe came to be. Modern science hypothesizes that the manifestation of life on Earth is nothing but a mere increment in the complexity of matter — and hence is an outcome of evolution of matter (chemical evolution) following the Big Bang. After the manifestation of life, modern science believed that chemical evolution transformed itself into biological evolution, which then had caused the entire biodiversity on our planet. The ontological view of the organism as a complex machine presumes life as just a chance occurrence, without any inner purpose. This approach in science leaves no room for the subjective aspect of consciousness in its attempt to know the world as the relationships among forces, atoms, and molecules. On the other hand, the Vedāntic view states that the origin of everything material and nonmaterial is sentient and absolute (unconditioned). Thus, sentient life is primitive and reproductive of itself – omne vivum ex vivo – life comes from life. This is the scientifically verified law of experience. Life is essentially cognitive and conscious. And, consciousness, which is fundamental, manifests itself in the gradational forms of all sentient and insentient nature. In contrast to the idea of objective evolution of bodies, as envisioned by Darwin and followers, Vedānta advocates the idea of subjective evolution of consciousness as the developing principle of the world. In this paper, an attempt has been made to highlight a few relevant developments supporting a sentient view of life in scientific research, which has caused a paradigm shift in our understanding of life and its origin. (shrink)

In the framework of materialism, the major attention is to find general organizational laws stimulated by physical sciences, ignoring the uniqueness of Life. The main goal of materialism is to reduce consciousness to natural processes, which in turn can be translated into the language of math, physics and chemistry. Following this approach, scientists have made several attempts to deny the living organism of its veracity as an immortal soul, in favor of genes, molecules, atoms and so on. However, advancement in (...) various fields of biology has repeatedly given rise to questions against such a denial and has supplied more and more evidence against the completely misleading ideological imposition that living entities are particular states of matter. In the recent past, however, the realization has arisen that cognitive nature of life at all levels has begun presenting significant challenges to the views of materialism in biology and has created a more receptive environment for the soul hypothesis. Therefore, instead of adjudicating different aprioristic claims, the development of an authentic theory of biology needs both proper scientific knowledge and the appropriate tools of philosophical analysis of life. In a recently published paper the first author of present essay made an attempt to highlight a few relevant developments supporting a sentient view of life in scientific research, which has caused a paradigm shift in our understanding of life and its origin [1]. The present essay highlights the uniqueness of biological systems that offers a considerable challenge to the mainstream materialism in biology and proposes the Vedāntic philosophical view as a viable alternative for development of a biological theory worthy of life. (shrink)