Origins of life: A comparison of theories and application to Mars

The field of study that deals with the origins of life does not have a consensus for a theory of life's origin. An analysis of the range of theories offered shows that they share some common features that may be reliable predictors when considering the possible origins of life on another planet. The fundamental datum dealing with the origins of life is that life appeared early in the history of the Earth, probably before 3.5 Ga and possibly before 3.8 Ga. What might be called the standard theory (the Oparin-Haldane theory) posits the production of organic molecules on the early Earth followed by chemical reactions that produced increased organic complexity leading eventually to organic life capable of reproduction, mutation, and selection using organic material as nutrients. A distinct class of other theories (panspermia theories) suggests that life was carried to Earth from elsewhere — these theories receive some support from recent work on planetary impact processes. Other alternatives to the standard model suggest that life arose as an inorganic (clay) form and/or that the initial energy source was not organic material but chemical energy or sunlight. We find that the entire range of current theories suggests that liquid water is the quintessential environmental criterion for both the origin and sustenance of life. It is therefore of interest that during the time that life appeared on Earth we have evidence for liquid water present on the surface of Mars.     

The stepwise evolution of early life driven by energy conservation

Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic metabolisms. With the exception of a role for CO, the theories have little common ground. Here we propose an alternative theory for the early evolution of the cell which combines principal features of the widely disparate theories. The theory is based on the extant pathway for conversion of CO to methane and acetate, largely deduced from the genomic analysis of the archaeon Methanosarcina acetivorans. In contrast to current paradigms, we propose that an energy-conservation pathway was the major force which powered and directed the early evolution of the cell. We envision the proposed primitive energy-conservation pathway to have developed sometime after a period of chemical evolution but prior to the establishment of diverse protein-based anaerobic metabolisms. We further propose that energy conservation played the predominant role in the later evolution of anaerobic metabolisms which explains the origin and evolution of extant methanogenic pathways.     

How the discovery of ribozymes cast RNA in the roles of both chicken and egg in origin-of-life theories

Scientific theories about the origin-of-life theories have historically been characterized by the chicken-and-egg problem of which essential aspect of life was the first to appear, replication or self-sustenance. By the 1950s the question was cast in molecular terms and DNA and proteins had come to represent the carriers of the two functions. Meanwhile, RNA, the other nucleic acid, had played a capricious role in origin theories. Because it contained building blocks very similar to DNA, biologists recognized early that RNA could store information in its linear sequences. With the discovery in the 1980s that RNA molecules were capable of biological catalysis, a function hitherto ascribed to proteins alone, RNA took on the role of the single entity that could act as both chicken and egg. Within a few years of the discovery of these catalytic RNAs (ribozymes) scientists had formulated an RNA World hypothesis that posited an early phase in the evolution of life where all key functions were performed by RNA molecules. This paper traces the history the role of RNA in origin-of-life theories with a focus on how the discovery of ribozymes influenced the discourse.     

J. B. S. Haldane and the origin of life

In 1929 the British biologist John Burdon Sanderson Haldane published a hypothesis on the origin of life on earth, which was one of the most emblematic of the interwar period. It was a scenario describing the progressive evolution of matter on the primitive earth and the emergence of life. Firstly, this paper presents the main ideas put forward by Haldane in this famous text. The second part makes comparisons between Haldane and Alexander Ivanovitch Oparin’s ideas regarding the origins of life (1924). These two theories, apparently very similar, presented distinct conclusions. The third part focusses on Haldane’s reflections on the emergence of life during the 1950s and 1960s, and shows how they were linked to the recent developments of prebiotic chemistry and molecular biology.     

分子人类学与现代人的起源*

1953年Watson & Crick 对于DNA双螺旋结构模型的提出及对其遗传机理的解释,标志着现代分子生物学的诞生。其后短短50年的时间里,分子生物学在各个学科之间广泛渗透,相互促进,不断深入和发展。在以研究人类的起源和进化为首要任务的人类学领域,由于现代分子生物学理论和方法的应用,诞生了分子人类学这一全新的结合型分支学科,为人类学的发展提供了科学可信的研究方法和具发展前景的研究方向。系统地介绍了分子人类学的发展历史、研究方法及原理;另外,结合分子人类学在古人类学研究中的应用,讨论了关于现代人起源的“非洲起源说”和“多地区连续演化说”。Abstract: Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include “out-of-African theory” and “theory of multiregional evolution” are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.     

Non-terrestrial origin of life: a transformative research paradigm shift

Theories and hypotheses in science are continually subject to verification, critical re-evaluation, revision and indeed evolution, in response to new observations and discoveries. Theories of the origin of life have been more constrained than other scientific theories and hypotheses in this regard, through the force of social and cultural pressures. There has been a tendency to adhere too rigidly to a class of theory that demands a purely terrestrial origin of life. For nearly five decades evidence in favour of a non-terrestrial origin of life and panspermia has accumulated which has not been properly assessed. A point has now been reached that demands the serious attention of biologists to a possibly transformative paradigm shift of the question of the origin of life, with profound implications across many disciplines.     

Biotin. Its place in evolution

Summary In the previous article we try to give an explanation for the success of models for enzymatic reactions in which coenzymes play a role. However, one vital cofactor that has thus far not yielded appreciably to this approach is biotin. We attempt to show that biotin presents a fundamentally new sort of problem to bioorganic chemistry; this problem requires consideration both of the origin of life and subsequent evolution in any attempt to understand the anomalies offered by this cofactor.     

Aging, evolvability, and the individual benefit requirement; medical implications of aging theory controversies

There is a class of theories of aging (variously termed adaptive aging, aging by design, aging selected for its own sake, or programmed death theories) that hold that an organism design that limits life span conveys benefits and was selected specifically because it limits life span. These theories have enjoyed a resurgence of popularity because of the discovery of genes that promote aging in various organisms.However, traditional evolution theory has a core tenet that excludes the possibility of evolving and retaining an individually adverse organism design, i.e. a design characteristic that reduces the ability of individual organisms to survive or reproduce without any compensating individual benefit. Various theories of aging dating from the 1950s and based on traditional evolution theory enjoy substantial popularity. Therefore, any theorist proposing an adaptive theory of aging must necessarily also propose some adjustment to traditional evolution theory that specifically addresses the individual benefit issue. This paper describes an adaptive theory of aging and describes how one of the proposed adjustments (evolvability theory) supports adaptive aging.This issue is important because adaptive theories are generally more optimistic regarding prospects for medical intervention in the aging process and also suggest different approaches in achieving such intervention.     

生命起源的历程始于何处?--从化学进化到生物进化的探索

生命起源开始于从化学进化进入生物进化．然而,在原始细胞出现之前,已存在一个有蛋白质、核酸等生命要素的过渡期．那么,生命起源的历程究竞从何处开始?对这个未解之迹,进行了讨论．首先,从化学进化到生物进化要实现3个相变,即：从随机的有机化学反应相变为定向代谢途径;从消旋体环境相变为生物手性环境：从化学混沌状态相变为生命耗散结构．通过比较分析发现,由于前生命化学时期出现了丙酮酸．它的独特性质导致了这3种相变同步发生,其中起驱动作用的是定向代谢途径．它起源于以丙酮酸为基质的逆向糖酵解(糖生成途径)．     

The young Ramón y Cajal as a cell-theory dissenter.

The intellectual development of scientists normally traverses several different phases as they mature in their professions. In many cases, strong support of certain ideas and theories gives way to more critical, productive views that set the stage for major theories and discoveries. This appears to have been the case of Santiago Ramón y Cajal (1852-1934). In his youth, he supported the protoplasmic theory of life, and as he matured he maintained a critical, yet open view of the cell theory, which postulated that life phenomena could not take place below the cellular level. In later years, however, an older and wiser Ramón y Cajal abandoned all traces of dissent and joined in fully supporting a refined version of cell theory, to which his own discoveries significantly contributed.     

Lethal mutants and truncated selection together solve a paradox of the origin of life

Background

Many attempts have been made to describe the origin of life, one of which is Eigen''s cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465–523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen''s theory, the maximum chain length that could be maintained is restricted to nucleotides, while for the most primitive genome the length is around . This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life.

Methodology/Principal Findings

We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life.

Conclusions/Significance

We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.     

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.     

On the Emergence of Living Systems

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts.     

The neutral theory of molecular evolution: a review of recent evidence

In sharp contrast to the Darwinian theory of evolution by natural selection, the neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are caused by random fixation (due to random sampling drift in finite populations) of selectively neutral (i.e., selectively equivalent) mutants under continued inputs of mutations. The theory also asserts that most of the genetic variability within species at the molecular level (such as protein and DNA polymorphism) are selectively neutral or very nearly neutral and that they are maintained in the species by the balance between mutational input and random extinction. The neutral theory is based on simple assumptions, enabling us to develop mathematical theories based on population genetics to treat molecular evolution and variation in quantitative terms. The theory can be tested against actual observations. Neo-Darwinians continue to criticize the neutral theory, but evidence for it has accumulated over the last two decades. The recent outpouring of DNA sequence data has greatly strengthened the theory. In this paper, I review some recent observations that strongly support the neutral theory. They include such topics as pseudoglobin genes of the mouse, alpha A-crystallin genes of the blind mole rat, genes of influenza A virus and nuclear vs. mitochondrial genes of fruit flies. I also discuss such topics as the evolution of deviant coding systems in Mycoplasma, the origin of life and the unified understanding of molecular and phenotypic evolution. I conclude that since the origin of life on Earth, neutral evolutionary changes have predominated over Darwinian evolutionary changes, at least in number.     

植物同源多倍体耐盐性研究进展

多倍化是高等植物进化最重要的动力之一,多倍体植物由于基因组组成以及基因表达方面的变化,通常会表现出不同的生理现象,多倍体的抗性优于其同源二倍体祖先。土壤盐碱化和次生盐渍化是影响农作物生产的重要因素,严重制约着我国农业的可持续发展。同源多倍体植物耐盐能力较强,是作物遗传改良的重要种质资源,了解其耐盐机理对培育耐盐品种具有重要意义。本文从与盐胁迫相关的耐盐性进化、生理生化水平、细胞结构和分子层面等多角度总结了植物同源多倍体盐胁迫研究进展,并以作者所在研究团队培育出的多倍体西瓜为例讨论了多倍体抗逆性研究存在的问题及未来的发展方向,以期为多倍体抗逆优势机理研究提供参考。     

Adaptation and habitat selection in the eco-evolutionary process

The struggle for existence occurs through the vital rates of population growth. This basic fact demonstrates the tight connection between ecology and evolution that defines the emerging field of eco-evolutionary dynamics. An effective synthesis of the interdependencies between ecology and evolution is grounded in six principles. The mechanics of evolution specifies the origin and rules governing traits and evolutionary strategies. Traits and evolutionary strategies achieve their selective value through their functional relationships with fitness. Function depends on the underlying structure of variation and the temporal, spatial and organizational scales of evolution. An understanding of how changes in traits and strategies occur requires conjoining ecological and evolutionary dynamics. Adaptation merges these five pillars to achieve a comprehensive understanding of ecological and evolutionary change. I demonstrate the value of this world-view with reference to the theory and practice of habitat selection. The theory allows us to assess evolutionarily stable strategies and states of habitat selection, and to draw the adaptive landscapes for habitat-selecting species. The landscapes can then be used to forecast future evolution under a variety of climate change and other scenarios.     

The ribotype theory on the origin of life

The ribotype is defined as the ribonucleoprotein system of any cell. The theory substitutes the genotype-phenotype duality with the trinity genotype-ribotype-phenotype, and proposes that life on earth originated with the ancestors of today's ribotypes.The first three chapters describe separate models on precellular evolution, the evolution of protocells and the nature of the cell respectively, and the unity of the theory comes from the fact that they form a consistent and interdependent whole.The core of the theory is the ribotype hypothesis, of which two formulations are given. The restricted version is based on a link between ribotypes and ribosome biogenesis, and provides an explanation for the difference between 70S and 80S ribosomes. The general version describes a link between ribotypes and cell-types and explains why prokaryotes have 70S ribosomes, eukaryotes 80S ribosomes and endosymbionts a type of ribosomes similar to the bacterial ones.If the creation hypothesis, panspermia and spontaneous generation are set aside, all alternative models of the origin of life belong to two schemes which are referred to as the genotype and the phenotype theories. It is shown that these theories rely on some discontinuity between past and present biological principles because of the need to break their inherent chicken-and-egg paradoxes, while the ribotype theory does not. Its hypotheses, free and arbitrary as they are or appear to be, have been built exclusively on properties and processes for which solid evidence exists, and the continuity between past and present biological laws is assumed as a corollary. Finally, it is shown that falsification tests are possible, and some of them are expected in the relatively near future.     

The Extended Synthesis: The Law of the Conditions of Existence

A unified theory of biology must incorporate a naturalistic explanation for the origin of life, namely that given certain conditions, it was highly probable that life would originate. That theory, however, cannot be solely a theory of the origin of life. The same general mechanisms that allowed life to originate must also explain its subsequent evolution as embodied in the Extended Synthesis, including the origin of the inherent constraints and regularities that allowed natural selection to emerge as a natural process. A naturalistic grounding for the origin of life and its subsequent evolution, what Darwin called the Law of the Conditions of Existence, can be found in the natural law of history, the Second Law of Thermodynamics.     

A fundamental plant evolutionary problem: the origin of land-plant sporophyte; is a new hypothesis possible?

The origin of the sporophyte in land plants represents a fundamental phase in the plant evolution. Today this subject is controversial and, in my opinion, scarcely considered in our textbooks and journals of botany, in spite of its importance. There are two conflicting theories concerning the origin of the alternating generations in land plants: the "antithetic" and the "homologous" theory. These have never been fully resolved. The antithetic theory maintains that the sporophyte and gametophyte generations are fundamentally dissimilar and that the sporophyte originated in an ancestor organism with haplontic cycle by the zygote dividing mitotically rather than meiotically, and with a developmental pattern not copying the developmental events of the gametophyte. The sporophyte generation was an innovation of critical significance for the land-plant evolution. By contrast, the homologous theory simply stated that a mass of cells forming mitotically from the zygote adopted the same developmental plan of the gametophyte, but giving origin to a diploid sporophyte. In this context, a very important question concerns the possible ancestor or ancestors of the land plants. Considerable evidences at morphological, cytological, ultrastructural, biochemical and, especially, molecular level, strongly suggest that the land plants or Embryophyta (both vascular and non-vascular) evolved from green algal ancestor(s), similar to those belonging to the genus Coleochaete, Chara and Nitella, living today. Their organism is haploid for most of their life cycle, and diploid only in the zygote phase (haplontic cycle). On the contrary, the land plants are characterized by a diplo-haplontic life cycle. Several questions are implied in these theories, and numerous problems remain to be solved, such as, for example, the morphological difference between gametophyte and sporophyte (heteromorphism, already present in the first land plants, the bryophytes), and the strong gap existing between these last with a sporophyte dependent on the gametophyte, and the pteridophytes having the gametophyte and sporophyte generations independent. On the ground of all of the evidences on the ancestors of the land plants, the antithetic theory is considered more plausible than the homologous theory. Unfortunately, no phylogenetic relationship exists between some green algae with diplontic life cycle and the land plants. Otherwise, perhaps, it should be possible to hypothesize another scenario in which to place the origin of the alternating generations of the land plants. In this case, could the gametophyte be formed by gametes produced from the sporophyte, through their mitoses or a delayed fertilization process?     

Concepts of nerve fiber development, 1839–1930

Conclusion It was thus the combination of observational and experimental approaches that ultimately led to confirmation of the outgrowth theory. The observational method was essential for defining various possible methods of nerve fiber development. The multicellular, protoplasmic bridge and outgrowth theories were each postulated to explain purely observational evidence. However, the lack of truly suitable equipment and techniques to study the developing nervous system made it impossible to agree on a single theory on this basis alone. The experimental method provided a means of choosing between these theories. Without the preceding observations that had led to the formulation of various hypotheses, however, the experimental approach might not have been so successful, for the power of this method is more of selection than of generation.Therefore it is impossible to weigh separately the contributions of the observational and experimental approaches to the question of nerve fiber development. Both were necessary for the ultimate acceptance of the outgrowth theory. *** DIRECT SUPPORT *** A8402051 00004