Nature of life

This is a review of current ideas on the nature of life from a molecular biology perspective. It summarizes contributions of well known scientists to the major current ideas on the nature of life based on experimental evidence and critical scientific thinking. For historical views on the nature of life, and perspectives other than those encompassed within the molecular biology perspective, see the article Life. For ideas on philosophical questions concerning the significance of life or existence in general, see the article Meaning of life.
Starting in the 1930s, as physics, chemistry and biology were maturing as sciences, a number of scientists proposed thoughtful perspectives on the nature of life. Initially specific chemical reactions were proposed that could have given rise to the molecular precursors of life on the primitive earth. Further ideas centered on how biological order could be created out of disordered material. These considerations gave rise to the idea that genetic information is stored in an “aperiodic crystal,” a conception whose predicted properties later proved to be fulfilled by RNA and DNA. Also, consideration was given to the question of whether forms of life could conceivably arise that were different from the carbon-centered life forms generated by conditions on earth. Further, it was shown that the emergence of life from non-life was clearly consistent with the second law of thermodynamics, a fundamental law of physics.
Starting in the 1950s, laboratory experiments were performed demonstrating the chemical synthetic reactions that likely occurred under the conditions thought to have been present on early earth, and that may have given rise to life. In the early 1960s, attention began to be focused on RNA as an early self-replicating molecule that would be subject to natural selection, and therefore to further evolution as the first step in the emergence of life. Explorations of the surface of Mars in the 1960s and 1970s stimulated further considerations on the nature of extraterrestrial life, and led the idea that the particular properties of the carbon atom are such that life --- even exotic life on other planets---would very likely be based on carbon chemistry. Later work in the 2000s described the major evolutionary transitions that occurred subsequent to the formation of the earliest pre-cellular RNA replicators. The common Darwinian principles that likely governed these transitions were clarified. These transitions took life from early RNA replicators, to cooperating RNAs, to membrane-enclosed proto-cells, to the emergence of sex, to eukaryotes, multicellular organisms and then to social groups.
The scientists primarily responsible for these ideas, and further details of their contributions, are described in this article.
Aleksandr I. Oparin
Aleksandr I Oparin (1894 - 1980) was Associate Director, Biochemical Institute, U.S.S.R. Academy of Science. His book “Origin of Life” was first published in English translation in 1938, and subsequently republished in 1953. The views presented by Oparin reflected the state of knowledge before the transformative influence of molecular biology and modern biochemistry on the study of life. Oparin’s views on the nature of life seem dated by current standards. However his was the first detailed attempt to show how organic molecules might have gradually evolved, step by step, to acquire newer properties leading to simple living organisms.
According to Oparin, organic compounds were initially formed on Earth by the reaction of superheated water vapor with carbides giving rise to hydrocarbons (the simplest organic matter). He thought it highly improbable that free oxygen was contained in the original Earth atmosphere. However he considered that hydrocarbons gave rise to a great variety of derivatives (alcohols, aldehydes, ketones, organic acids, etc.) through oxidation by the oxygen component of water. At the same time these hydrocarbons also reacted with ammonia. Consequently, amides, amines and other nitrogenous derivatives arose. These organic substances are endowed with great chemical potentialities, and thus entered into a variety of chemical reactions. Oparin proposed that by such processes, proteins first arose.
Initially proteins and other substances were present in the seas and oceans in the form of colloidal solutions (i.e. suspensions of particles resistant to sedimentation). As the colloidal solutions of various substances were mixed, new and special formations arose, the so-called coaservates. These are clusters of molecules that are aggregates of colloidal particles. By this process organic substances became concentrated in definite, spatial arrangements and separated from the solvent medium by a more or less distinct membrane. Inside these coaservates, the colloidal particles assumed a definite position towards each other; i.e. the beginnings of some elementary structure appeared within them. Each coaservate droplet acquired a certain degree of individuality so that its further fate was determined not only by the properties of the external medium but also by its own specific internal structure.
Oparin assumed that the internal structure of the droplets determined their ability to absorb and incorporate into itself organic substances dissolved in the surrounding water. The rate of growth depended upon the internal structure of individual droplets. Growth was greater the more the droplet was adapted for absorption and for chemical transformation of the absorbed materials. This characteristic led to a situation that Oparin described as the “growth competition of coacervate gels.” Due to the addition of new substances and chemical interactions the physico-chemical structure of coacervate droplets during growth tended to change. Such a change could either result in further perfection of organization or, on the contrary, induce the loss of structure and degradation of a droplet. Only those changes which enabled a coacervate to adsorb dissolved substances more rapidly and thus to grow faster acquired importance for continued existence and development. Oparin considered that by such a sequence of events “a peculiar selective process came into play which finally resulted in the origin of colloidal systems with a highly developed physico-chemical organization, namely, the simplest primary organisms.”
Oparin’s ideas were similar to ideas independently proposed by his contemporary J. B. S. Haldane (see J. B. S. Haldane), who suggested that before life emerged the accumulated organic compounds in the sea could have reached the consistency of hot dilute soup. And so the concoction from which life is presumed to have emerged became known as the “Oparin - Haldane primitive soup.”
Erwin Schrödinger
Erwin Schrödinger, a physicist most well known for his contributions to quantum theory published a book in 1944 entitled “What is Life?” This book was based on a course of public lectures delivered by Erwin Schrödinger in February 1943, under the auspices of the Dublin Institute for Advanced Studies at Trinity College, Dublin. Schrödinger's lecture focused on one important question: "how can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?"
In the book, Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. In the 1950s, this idea stimulated enthusiasm for discovering the genetic molecule. Although the existence of DNA had been known since 1869, its role in reproduction and its helical shape were still unknown at the time of Schrödinger's lecture. In retrospect, Schrödinger's aperiodic crystal can be viewed as a well-reasoned theoretical prediction of what biologists should have been looking for during their search for genetic material. Both James D. Watson, and independently, Francis Crick, co-discoverers of the structure of DNA, credited Schrödinger's book with presenting an early theoretical description of how the storage of genetic information would work, and each respectively acknowledged the book as a source of inspiration for their initial researches.
Fred Hoyle
Fred Hoyle (1915 - 2001) was a prominent English astronomer who worked mainly at the Institute of Astronomy at Cambridge, and served as its director for a number of years. He made important scientific contributions to the theory of stellar nucleosynthesis, the theory of how chemical elements heavier than helium in our Universe are manufactured within stars. He is also remembered for his coining of the term “Big Bang” theory, although this was done in the context of rejecting this theory; he favored an alternative steady state theory. In addition to his publications in scientific journals and his non-fiction books, he published 19 science fiction novels. The first of these, “The Black Cloud,” written in 1957, describes the interaction of Earth scientists with an intelligent life form, an immense black cloud of gas that moves towards the solar system and temporarily obscures the sun. On receiving radio signal from humans, the black cloud is surprised to learn that intelligent life can also exist on the surface of planets. Although Fred Hoyle described this novel as a “frolic,” he also noted that there is little here that could not conceivably happen. This novel was widely read and critically praised (see The Black Cloud). The novel is notable for raising and providing a scientific rationale for the idea that the existence of “life” may not be limited to the conditions that are conventionally considered to be necessary based on the singular occurrence of life on Earth.
Henry Quastler
The book “The Emergence of Biological Organization” is based on lectures given by Henry Quastler (1908 - 1963) during the spring term of 1963 while he was Visiting Professor of Theoetical Biology at Yale University. These lectures reflected the rapid development of molecular biology in the late 1950s and early 1960s that had generated new perspectives on the nature of life. In these lectures Quastler argued that the formation of single-stranded polynucleotides was well within the limits of probability of what could have occurred during the pre-biologic period of the Earth. However, he noted that polymerization of a single-stranded polymer from mononucleotides is slow, and its hydrolysis is fast; therefore in a closed system consisting only of mononucleotides and their single-stranded polymers, only a small fraction of the available molecules will be polymerized. However, a single-stranded polymer may form a double-stranded one by complementary polymerization, using a single-stranded polynucleotide as a template. Such a process is relatively fast and the resulting double-stranded polynucleotide is much more stable than the single single-stranded one since each monomer is bound not only along the sugar phosphate backbone, but also through inter-strand bonding between the bases.
The capability for self-replication, a fundamental feature of life, emerged when double-stranded polynucleotides disassociated into single-stranded ones and each of these served as a template for synthesis of a complementary strand, producing two double-stranded copies. Such a system is mutable since random changes of individual bases may occur and be propagated. Individual replicators with different nucleotide sequences may also compete with each other for nucleotide precursors. Mutations that influence the folding state of polynucleotides may affect the ratio of association of strands to dissociation and thus the ability to replicate. The folding state would also affect the stability of the molecule. Thus Quastler speculated that a nucleic acid system is even capable, in a primitive way, of Darwinian evolution. These ideas were then developed to speculate on the emergence of genetic information, protein synthesis and other general features of life.
Forty-five years after Quastler’s 1964 proposal, Lincoln and Joyce described a cross-catalytic system that involves two RNA enzymes (ribosymes) that catalyze each other’s synthesis from a total of four component substrates. This synthesis occurred in the absence of protein and could provide the basis for an artificial genetic system.
Stanley L.Miller and Leslie F. Orgel
Stanley L. Miller (1930 - 2007), at the University of California, San Diego and Leslie E. Orgel (1927 - 2007) at the Salk Institute published a book in 1974 entitled “The Origins of Life on the Earth.” In this book the authors presented detailed information concerning the synthesis of important biochemicals, both monomers and polymers, under the presumed primitive Earth conditions, and argued that this evidence throws light on pre-biotic biochemical evolution and the early emergence of life. In 1953, Miller had provided the first definitive experimental evidence for the “Oparin - Haldane primitive soup” theory. Working as a graduate student with his faculty advisor Harold Urey at the University of Chicago, Stanley Miller carried out an experiment to simulate the ocean - atmospheric conditions on the primitive Earth (see Miller-Urey experiment). Miller and Urey, like Oparin, considered that the atmosphere of the Earth soon after its formation must have been much more reducing than the current atmosphere, and that only a trace amount of molecular oxygen could have been present.) Despite their reservations at the time, Miller and Orgel thought that it would likely become possible to eventually demonstrate all of the required prebiotic reactions in a convincing way. They considered that natural selection acting on a system of polymers (some of which are able to replicate) was responsible for the emergence of organized biological structures. They argued that since complementary replication of nuclei acids makes use of certain structural characteristics inherent in the bases themselves, it is quite plausible that reasonably accurate replication is possible even in the absence of protein synthesis. Miller and Orgel considered that “the greatest contribution of molecular biology to the understanding of the origin of life is the realization that the emergence of biological order was neither more nor less than the production of imperfectly replicating polymers on which natural selection could operate.”
Harold Morowitz
Harold Morowitz, Professor of Molecular Biophysics and Biochemistry at Yale University was called in 1981, to testify in the Federal District Court in Little Rock Arkansas in the case McLean v. Arkansas dealing with “Balanced Treatment of Creation - Science and Evolution Science in the Public Schools,” a trial of considerable public interest at the time. He described this occasion in his somewhat whimsical set of essays “Mayonnaise and the Origin of Life.” Morowitz’s presence in the courtroom related to the aspect of the case dealing with “the emergence of life from nonlife.” It had been argued in support of creationism that the second law of thermodynamics precludes biogenesis by a natural process; therefore supernatural events were required. The second law states that isolated systems move towards the maximum degree of molecular disorder. Isolation, in this case, means the absence of flows of both matter and energy into and out of the system.
Morowitz had devoted the greater part of his career to the thermodynamic foundations of biological organization. In his expert testimony he pointed out that Ludwig Bolzmann, the noted Austrian physicist (see Ludwig Boltzmann), in 1886, had resolved the confusion concerning the applicability of the second law to living systems. Boltzmann had made clear that the Earth is an open system undergoing a flow of solar energy. Because of this, the surface of the Earth is not limited by a law that is restricted to isolated entities. Morowitz also noted that according to newer developments in the field of irreversible thermodynamics ushered in by Lars Onsager (see Irreversible Process and Lars Onsager), systems become ordered under a flow of energy. Thus Morowitz concluded that the existence of life involves no contradictions to the laws of physics.
In another area, Morowitz created a prebiotically plausible proto-cell in which RNA replication occurs within a fatty acid vesicle.)
In an article coauthored with Carl Sagan, of Harvard College Observatory, (also see also Morowitz) Harold Morowitz speculated on the possibility of an indigenous biology in the clouds of the planet Venus.
Norman H. Horowitz
In 1986, Norman H. Horowitz (1915 - 2005), a biology professor at the California Institute of Technology published “To Utopia and Back: The search for life in the solar system” Norman Horowitz (see ) entitled his first Chapter “What is Life?” Since Horowitz was the head of the Jet Propulsion Laboratory bioscience section for the Mariner and Viking missions to Mars (1965-1976), the question of what is life was of practical significance for his planning of experiments for these missions. Horowitz noted that our concept of “life” must be broad enough to let us recognize it in any guise and yet precise enough to prevent our finding it where it does not exist. He considered that the capacities for self-replication and mutation underlie the evolution of all structures and functions that distinguish living objects from inanimate ones. Any such system almost invariably evolves in directions that will ensure its preservation. Over time the system will acquire the complexity, variety and purposefulness that we recognize as “alive.” Horowitz noted that this particular view of life was first stated clearly by Herman J. Muller (1890-1967; see Hermann Joseph Muller), long before anything was known about the chemical nature of genes or their relation to proteins. Muller perceived that the characteristics of self-replication and mutability were at the center of the phenomenon called life.
Since the genes and proteins of all species on Earth are constructed out of the same nucleotides and amino acids, and since the genetic code is, with minor exceptions also universal, Horowitz considered that all terrestrial organisms are fundamentally alike. Hence he concluded that despite appearances, there is only one form of life on the Earth and this life need have originated only once. Life on Earth is based on the chemistry of carbon. Carbon compounds, with a few other elements, mainly the light elements hydrogen, nitrogen and oxygen, form the components of genetic systems. Horowitz considered that the unique characteristics of carbon made it unlikely that any other element could replace carbon, even on another planet, to generate the biochemistry necessary for life. First, the carbon atom has the unique ability to make four strong chemical bonds, termed covalent bonds, with other atoms, including other carbon atoms. These covalent bonds have direction in space, so that carbon atoms can form the skeletons of complex 3-dimensional structures with definite architectures, such as nucleic acids and proteins. Carbon compounds also tend to be relatively unreactive under the conditions that prevail on the Earth's surface, but can be activated by catalysts or heat. Horowitz noted that carbon forms more compounds than all other elements combined. He also pointed out that carbon is so superior for the building of complex molecules that the possibility of forming genetic systems with other elements has never been seriously considered, and he personally thought this possibility to be remote. This does not imply that the genetic systems of extraterrestrial species must be chemically identical with our own, but only that they must be built up of carbon molecules. This conclusion, he thought, has far reaching consequences for the possibility of life on other planets. The great versatility of the carbon atom makes it the element most likely to provide solutions—even exotic solutions—to the survival of life on other planets.
Horowitz’s views on the origin of life were similar to those of others, such as Quastler, Miller and Orgel (see above). He thought it highly likely that the first genetic system needed only short polymers to get started, not the large highly evolved molecules that are found in modern organisms. The first organism need not have been efficient, since it lived in an environment with no enemies and no problems of food supply. Thus it only had to reproduce itself fast enough to stay ahead of its own chemical decomposition. Horowitz also thought that a primitive genetic system might have been built up from RNA alone, without protein.
Richard E. Michod
Richard E. Michod, Professor and long-term Head of the Department of Ecology and Evolutionary Biology at the University of Arizona published a book in 2000 entitled “Darwinian Dynamics; evolutionary transitions in fitness and individuality.” In this book Michod analyzed the major transitions in evolution. Previous scientific investigators had proposed, as discussed above, that “life” was likely initiated when an informational molecule, usually assumed to be RNA, acquired the ability to replicate itself and undergo natural selection. Michod considered the major evolutionary transitions that occurred after this initial event. Michod viewed individual self-replicating RNA molecules as being analogous to autonomous individual genes, so that the first major evolutionary transition occurred when these genes formed pre-cellular interdependent networks. The second major transition was for gene networks to become encapsulated, forming bacteria-like proto-cells. The additional major transitions considered were: from bacteria-like cells to unicellular eukaryotic cells with organelles; from eukaryotic cells to multicellular organisms, and then from solitary organisms to societies. The first two of these transitions are the most relevant to the question of what is life and so these will be discussed further below.
As Michod points out, similar principles apply to all of these major transitions. New evolutionary units start out as groups of existing units. To create a new level of selection, adaptations must arise that promote cooperation among the lower level units in the functioning of the group, while at the same time mitigating the inherent tendency of the lower-level units to compete with one another. Cooperation is a critical factor in the emergence of new units of selection precisely because it trades fitness at the lower level (its costs) for increased fitness at the group level (its benefits).
Using a population genetics approach, Michod discusses how “fitness,” a key concept in Darwinian selection, arose when the earliest life forms first appeared in the pre-biotic world. Relative fitness, presumably in the form of different sequence-dependent configurations of the RNA replicators, predicts the outcome of natural selection among the different replicators. The continued evolution of these single-stranded RNA (ssRNA) replicators would lead to sequences that balanced the conflicting needs of replication and survival.
Michod suggested that there were limits to what any ssRNA sequence could attain by itself. Thus he thought that separate ssRNA molecules could possibly aid each other’s replication by providing catalytic surfaces for facilitating pairing with complementary mononucleotides and for linking the mononucleotides. (In 2007, a ssRNA polymerase ribozyme was reported to catalyze synthesis of at least a 20 nucleotide sequence with good fidelity.). Michod referred to the transition from independent molecular replicators to networks of cooperating genes as the first major transition in evolution. He also discussed the theory that Manfred Eigen and Ruthild Winkler-Oswatitsch had developed to explain how such cooperating groups of genes, referred to as “hypercycles” could emerge in communities of molecular replicators.
The evolution of networks of cooperating genes ultimately led to the enclosure of separate hypercycles within protective membranes to form proto-cells, the second major evolutionary transition. The proto-cells’ membrane would protect the enclosed genes from the damaging effects of the environment. It also would allow resources, and possibly early proteins specified by the genes, to be kept close at hand, instead of diffusing away to be used by others. If one of the genes in a proto-cellular hypercycle should turn selfish (for instance, by using its neighbors’ proteins to facilitate its own replication but not contributing to its neighbors replication), all the genes in the same proto-cell would be threatened, including the selfish gene. Michod proposed that by putting everybody in the same boat so to speak, everybody’s self-interest becomes more closely aligned with the interests of the group. Such a process leads to emergence of a higher level of selection than the individual gene, namely the individual proto-cell.
Michod also worked on the evolutionary emergence of sex, a fundamental aspect of life. This work involved a cost-benefit analysis that he carried out with several co-workers (see also RNA world hypothesis). In this analysis it was assumed that a basic problem facing early proto-cells was RNA damages arising from endogenous sources such as heat induced hydrolysis or from exogenous sources such as UV light and damaging chemicals. These damages can block replication and/or interfere with catalytic function.
Proto-cells having only one copy of each RNA gene (a haploid proto-cell) could be killed by even a single damage to an essential RNA gene. Thus a haploid proto-cell is vulnerable to genome damage. This vulnerability could be reduced by retaining more than one copy of each RNA gene in each proto-cell, i.e., by maintaining diploidy or polyploidy. This tactic would allow a damaged gene to be replaced by an additional replication of its homolog. However, the proto-cell’s rate of reproduction would likely be reduced by the costs of maintaining two sets of genes rather than one. Consequently, coping with genome damage while minimizing the costs of redundancy was likely a fundamental problem for early proto-cells. A cost-benefit analysis led to the conclusion that, under a wide range of circumstances, the selectively advantageous strategy would be for a haploid proto-cell to fuse with another haploid protocell to form a transient diploid.<ref name=Bernstein /> The retention of the haploid state maximizes the growth rate, while the periodic fusions allow mutual reactivation of otherwise lethally damaged proto-cells. If at least one damage-free copy of each RNA gene is present in the transient diploid, viable progeny can be produced. The cycle of haploid reproduction, with occasional fusion to a transient diploid state followed by splitting to the haploid state, can be considered to be the sexual cycle in its most primitive form. In the absence of this sexual cycle, haploid protocells with a damage in an essential RNA gene would simply die.

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