The Fundamental Limit and Origin of Complexity in Biological Systems: A New Model for the Origin of Life (original) (raw)

The Origin of Cellular Life and Biosemiotics

BIOSEMIOTICS, 2013

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.

Complexity, self-organization and the origin of life: The happy liaison?

Origins of Life: Self-Organization and/or Biological Evolution?, 2009

The spontaneous assembly of amphiphiles into micelles and bilayer membranes, as well as the dynamical self-assembly properties of nucleic acids, suggest that selforganization phenomena played a role in the origin of life. However, current biology indicates that life could have not evolved in the absence of a genetic replicating mechanism insuring the stability and diversification of its basic components. This does not imply that explanations on the appearance of life should reduce themselves to the issue of the emergence of RNA or its predecessors.

The Origin and Evolution of Viruses as Molecular Organisms

Nature Precedings, 2009

Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for their origin from parasitic cellular species that fused with their host cells. By losing their membrane and cellular structure within the host cell, these new types of parasitic species gained full access to precursors for the synthesis of their specific molecules and to the host's information processing machineries, such as translation, which created unique parasitic and evolutionary opportunities. To identify viruses during their intracellular stage of their life cycle, in which their specific molecules are free or dispersed within the host cell, this paper introduces the concept of "molecular structure" and labels viruses as "molecular organisms." Among the extant viruses, the life cycle of poxviruses and other complex viruses that fuse with their host cells provides compelling evidence for the fusion model. One of the most remarkable implications of fusion model is that new viral lineages originated from parasitic cellular species throughout the history of life, and that this process might still be active. Surprisingly, it appears that several parasitic cellular species are currently evolving into molecular organisms. More remarkably though, according to this model, several parasites that are currently classified as cellular organisms are in fact genuine molecular organisms. The current evidence for the fusion hypothesis is strong and it is fully testable using both experimental and phylogenetic approaches. The academic and research implications of this model, which supports the inclusion of viruses in the Tree of Life, are highly significant. Some of these implications are discussed in more detail in two other articles of this series, which presents a unifying model for the origin and evolution of cellular and viral domains, including the origin of life. _______ _______________________________________________________________________________

What roles for viruses in origin of life scenarios

Important roles in origin of life (OL) scenarios have been and still are attributed to viruses. Yet the strict dependence of viruses on cells for their multiplication has been widely acknowledged since the first decades of the 20th century. How could viruses play critical roles in the OL if life relies on cellular organization and if viruses are defined as parasites of cells? In other words, how could viruses play a role in the emergence of cellular life if the existence of cells is a prerequisite for the existence of viruses? This paper investigates this issue and describes past and current OL scenarios conferring viruses with important roles, thereby completing the work of historian of science and physician Scott Podolsky who identified three major roles of viruses in past OL scenarios. Some objections raised by present OL scenarios conferring viruses with an important role are discussed. I argue that disagreements concerning the roles of viruses in OL scenarios stem from the different concepts of life and of virus scientists defend. Investigating the roles of viruses in OL scenarios not only helps identifying different ways to define life in the context of OL theorizing. It also offers the opportunity to better understand how viruses could be conceptualized. The relevance of the replication-first versus metabolism-first dichotomy in OL theorizing is briefly discussed.

THE CONCEPT OF COMPLEXITY IN EVOLUTIVE BIOLOGY: A SYNTHETIC REVIEW.

The complexity of living organisms is still debated within the scientific community, especially to define it formally. There seems to be a world of difference between on the one hand defenders of a significant complexity in the Universe as a whole, more specifically biological complexity, and on the other hand advocates of the worthlessness of such topics. Moreover, in spite of remaining doubts, particularly about the little conclusive evidence available, a growing consensus suggests that biological complexity is increasing. A number of scientific authors having addressed the issue for may years, I propose in this article a review of their various ideas, including the origin and the consequences of biological complexity.

On the Emergence of Biological Complexity: Life as a Kinetic State of Matter

Origins of Life and Evolution of Biospheres, 2005

A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an ongoing process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry.

An organisational systems-biology view of viruses explains why they are not alive

Biosystems, 2021

Whether or not viruses are alive remains unsettled. Discoveries of giant viruses with translational genes and large genomes have kept the debate active. Here, a fresh approach is introduced, based on the organisational definition of life from within systems biology. It views living as a circular process of self-organisation and self-construction which is ‘closed to efficient causation’. How information combines with force to fabricate and organise environmentally obtained materials, given an energy source, is here explained as a physical embodiment of informational constraint. Comparing a general virus replication cycle with Rosen’s -system shows it to be linear, rather than closed. Some viruses contribute considerable organisational information, but so far none is known to supply all required, nor the material nor energy necessary to complete their replication cycle. As a result, no known virus replication cycle is closed to efficient causation: unlike cellular obligate parasites, viruses do not match the causal structure of an -system. Analysis based in identifying a Markov blanket in causal structure proved inconclusive, but using Integrated Information Theory on a Boolean representation, it was possible to show that the causal structure of a virocell is not different from that of the host cell.

Self-organization at the origin of life

Journal of Theoretical Biology, 2008

The concept of an ðM; RÞ system with organizational invariance allows one to understand how a system may be able to maintain itself indefinitely if it is coupled to an external source of energy and materials. However, although this constitutes an important step towards understanding the difference between a living and a non-living system, it is not clear that an ðM; RÞ system with organizational invariance is sufficient to define a living system. To take a further step towards defining what it means to be alive it is necessary to add to a simple ðM; RÞ system some property that represents its identity, and which can be maintained and modified in subsequent generations.

2018.03.20-ESSENCE AND EMERGENCE OF BIOLOGICAL LIFE (2002)

2018.03.20-ESSENCE AND EMERGENCE OF BIOLOGICAL LIFE (2002)

Added probably the last missing element in the foundation of the biological sciences. This element consists in describing the nucleation of living molecules from inanimate ones. The origin of life coincides with the appearance of vibrations of molecular flagella under the action of quanta of energy flowing from a molecule to water. The evolution of living molecules to cellular organisms has been speculatively traced. An attempt has been made, while not rigorous, to inscribe this element in the existing system of biological knowledge. The role of living molecules in modern organisms has been established. Several new hypotheses have been formulated with the participation of a new element: on aging, on diabetes; about the causes of cancer and some others. For further advancement, it is necessary to concentrate theoretical efforts in the detected directions.

Power, Information and Complexity In the Origin of Life

This essay explores power, information and complexity in relation to the origin of life on earth. The origin of life requires decomposition of energy into power and information because such decomposition is necessary for feedback. The articulation of the decomposition of energy into power and information permits a significant correction of Francis Bacon’s dictum, Knowledge is power, which is one of the conceptual foundations of modern linear, reductionist science. Knowledge is not power; rather, knowledge orients power. The difference that life makes is seen as a different way of using energy, such as solar radiation, that is available to everything on earth. The difference in use is a consequence of living matter forming within the constraints of earth’s surface, which is the envelope of life or the biosphere. Complexity theory is used to conceptualize life as a consequence of morphogenetic constraints. Specific conditions of the earth, such as distance from the sun, speed of rotation and revolution, speed and extent of axis inclination, solar radiation, terrestrial and lunar gravitation, presence of free oxygen and protective ozone, Coriolis force, and ubiquity of water and land, are constraints on the existence of anything on or near the earth’s surface. Taken together, these constraints situate life on earth as neither a miracle, a mystery nor an accident. Life is rather a consequence. When we consider life as a consequence of morphogenetic constraints in the biosphere, then selection appears as an emergent feedback property of life. Viewed in this way, there are no random beginnings in life (Holland (2) 147-8), there are never infinite degrees of freedom in morphogenesis, there are no tinkered together contraptions in life (Kauffman 637 (1993)), and there is no order for free (Waldrop 120-5). This view also allows for a significant correction of the hypothesis that life occurs at the edge of chaos (Kauffman 29-279 (1993); Lewin 44-62; Waldrop 198-240): life occurs not at the edge of chaos but at the edges of different orders, none of which is chaotic. The viewpoint of this paper may be briefly characterized as structuralism with theories of transformation and structure. (Crutchfield 527-9)