Is the transition from chemistry to biology a mystery?

Abstract

Today most chemists think that the answer to how life on earth emerged is still unknown. They assume a gap between chemistry and biology that is still unbridged. For chemists, understanding the origin of life requires the experimental modeling of a process that bridges this gap. They will not consider the problem solved before they are able to perform such tasks. No gap appears when we are pursuing a less ambitious goal, namely, to present a sequence of hypothetical processes that lead to an apparatus with the basic structure and fundamental feature of the genetic apparatus of biosystems but strongly simplified. The modeled apparatus has the basic machinery of living entities. Its fundamental feature is Darwinian behavior. Living individuals have the power to evolve toward ever increasing complexity and intricacy if appropriate conditions are given. The task to understand life's origin as a rational process is closely related to the earlier attempts of the present author to design and construct supra-molecular machines. The skill of the experimentalist has to be replaced by the presence of very particular conditions given by chance in a very particular location. The resulting apparatus has a distinct basic structure and function.The essence of what happens is inevitable, not accidental. Thus the emergence of life is assumed to be described by a distinct theory. Today's great challenge is experimentally investigating chemical systems with the goal of creating artificial chemical life and the given theory provides a powerful stimulus. Life, from the perspective of physics, is the living state of matter and this view calls for a theory describing the fundamental requirements for the appearance of such a living state of matter (on the early earth and in the universe). The approach given here is an attempt in this direction. According to that approach the appearance of an entity with Darwinian behavior is instantaneous and linked with the creation of matter that carries information. Thus, Information (measured in bits according to Shannon) takes a meaning with that instant, the appearance of the first entity that evolves by multiplication, variation, selection and keeps that meaning during the entire evolution of the living (Information carrying) state of matter. Another consequence of this initial event is a spontaneous symmetry breaking due to the equal probabilities that the oligomer starting the process is right handed or left handed.

New concept for quantification of similarity relates entropy and energy of objects: First and Second Law entangled, group behavior of micro black holes expected

“…Theories from quite different domains such as, to name a few, probability theory [7][8][9][10], information theory and the emergence of complex systems [11][12][13][14][15][16][17][18], quantum relativity/cosmology [19][20][21][22][23][24][25][26][27][28][29] and string theory [30] operate with entropy and the Second Law of thermodynamics yet in conjunction with parameters different from the ones studied here. Urgent problems are being at least attacked, and possibly solved, through the insight into apparent and/or fundamental analogies between statistical thermodynamics and, for example (respectively), randomness of sequential irregularities ("algorithmic entropy", "approximate entropy"), computational compactness ("logical depth"), quality change of hereditary information (change in systemic "knowledge" through periodically discarded "Shannon entropy"), the dynamics of black holes ("Bekenstein-Hawking entropy"), and tracing back the microscopic origin of their area-entropy by counting the degeneracy of periodic and persistent topological defects (Bogomol'nyiPrasad-Sommerfield soliton bound states) in certain kinds of supersymmetric branes that mimic the thermodynamics of idealised extremal, highly charged black holes.…”

Interfacial Systems Chemistry: Out of the Vacuum—Through the Liquid—Into the Cell

“…In agreement with this conception, test experiments demonstrated that the conformation of the photosensitive molecule can be switched by irradiation with visible and ultraviolet light, as was expected. [1] With the help of scanning tunneling microscopy data of molecular resolution, the authors demonstrate that the TATA molecules form a well-defined network on the clean Au(111) gold substrate. Formation of such two-dimensional, supramolecular structures on solid surfaces by adsorption of suitable organic ligands is a highly interesting topic that met with considerable attention recently.…”

“…When considering implications for life science, it is worthwhile to mention the ongoing discussion about the origin of life (see for example, the recent paper by Kuhn [1] ). In some of the theoretical models put forward, chemical processes at surfaces have been proposed to play a crucial role.…”

Prebiotic Lipidic Amphiphiles and Condensing Agents on the Early Earth

“…Chang [ 17 ], Oró [ 18 ], Lazcano [ 19 ], Pace [ 20 ], Eschenmoser & Loewenthal [ 21 ], Orgel [ 22 ], Bada [ 23 ], Snooks [ 24 ], Root-Bernstein [ 25 ] and many others reviewed the chemical and biological constraints on life’s origin on Earth, including the inherent philosophical implications. Kuhn [ 26 ], Pross [ 27 , 28 ], Pascal & Pross [ 29 ], and Luisi [ 30 ] among others, highlighted the problems of understanding the transition from chemical to biological processes and the abiotic synthesis of biomolecules. The goal now is to understand, perhaps from experimental reproduction [ 31 ], the formation of a chemical system that is self-sustained, kinetically stable, dynamically evolvable, and far from thermodynamic equilibrium, which we then could call “alive” or “animate”.…”