The Nature, Origin and Evolution of Life: Part II The Origin of Life

“the origin of life problem must be related to the quantum mechanical description of the mechanism of hereditary evolution itself which has generated all living cells”

-H.H Pattee

Introduction

Even before a more detailed understanding of molecular biology and the molecular basis of heredity was clarified, many of the most fundamental logical and physical requirements for the appearance of living matter had been elucidated (1). Most central to the requirements of life are the limitations imposed on atomic interactions by anatomic frameworks, akin to the perceptual and conceptual operations associated with an observer. Equally crucial is the requirement for a memory or storage system housing the information necessary for the construction of the living organism, as well as its hereditary processes which entail the stable and accurate replication of this information to be passed to succeeding generations. At the same time, there exists the possibility for mutations to occur, resulting in phenotypic alterations in the organism’s structure or function, rendering it susceptible to natural selection and evolution. Finally, it has become increasingly evident that both the structure and function of the emerging living substance, as well as its stored coded information, must be somehow protected from but not entirely excluded from the surrounding environment by some type of barrier. As highlighted by Pattee, the process of natural selection acts on the external traits or phenotype and not the description of the phenotype stored in the genetic code. The latter remains in a sort of quasi-virtual state with information stored and remembered from the past but mostly protected from direct interaction with the surrounding environment (2,3).

Despite our understanding of the fundamental logic required of living matter, there remains no consistent and universally accepted definition of life. In fact, dozens of authorities over the years have offered a wide range of varied and sometimes inconsistent definitions of life often focused primarily on the areas of their research interest or expertise. Most definitions are primarily focused on our current understanding of living matter based on DNA, proteins, and cellular structure derived from our vast understanding of complex cellular and multicellular organisms. On the other hand, efforts to create life even in its simplest form from nonliving matter likely available in the primitive earth environment have been unsuccessful in producing an entity with processes that most would accept as ‘living’. Thus, at the start, we have the fundamental challenge of agreeing upon the most basic definition and criteria for defining living matter or life.

Clearly, enormous advances have occurred in our understanding of the structure and function of living organisms including the basic elements of the structure and function of life, i.e., the cell, and the fundamental structure and function of the hereditary material of life, i.e., the gene. Our understanding of the complexity of modern life, while far from complete, is enormous and increasing daily. At the same time, we have proposed that a complete comprehension of life in all its complexity will require a detailed and more complete understanding of the origin of life. Our current knowledge of the likely steps involved in the development of life is far from complete. The gap between the proposed simple elements and processes of early life arising on the primordial earth and the nearly unlimited complexity of living organisms today leaves an enormous hole challenging the very credulity of the transition from one to the other. At the same time, this virtually unfathomable gap should also serve as an inspiration to current and future generations of researchers to achieve a greater understanding of life in all of its glory. Obviously, many factual and conceptual challenges exist that will be highlighted here and in subsequent commentaries. Perhaps, no area of knowledge is more lacking than an understanding of how the most basic and rudimentary forms of life evolved into the current forms of life of enormous complexity and how, at each point in time during this evolution, there remained a continuity of life. The evolution of life has required that there be no break at any step in the ability to sustain life among the final lineage that led to modern forms of life including ourselves.

As we will see, we now have compelling evidence that the early universe, including the sun and the Earth, already contained many of the fundamental atomic and simple molecular elements that are central to life. We also have increasing experimental evidence that from both these elements and available sources of energy (thermal, solar, electrical, chemical, nuclear) in the primitive earth that additional elements including simple biomolecules were created naturally. In addition, studies of asteroids, meteorites, and comets impacting the earth have contained traces of organic substances suggesting that these processes and substances were present in the interstellar dust clouds resulting from exploding early stars and are likely widespread and part of the evolution of our solar system, galaxy, and universe.

The complexity of even the most rudimentary and 'simple’ processes necessary to meet anyone’s definition of life creates incredible challenges as to how living matter could have arisen spontaneously or naturally on the early earth. Nevertheless, it did, and our challenge is to try to understand, even in its most incomplete form, how this might have occurred and subsequently led to progressive organizational complexity ultimately resulting in life today.

The conditions on the early earth

The atoms present in the modern world and constituting all life are actually billions of years old. Current evidence suggests that the universe is approximately 13.7 billion years old and has been expanding at an accelerating pace since the start. The observable universe, which is estimated to be less than one-quarter of the total size of the universe, consists of around 2 trillion galaxies, each of which is composed of 100s of billions of stars resulting from the gravitational effects on the initial protons of early hydrogen in the primordial clouds of gas. Many of these stars, in turn, have surrounding planetary systems like our solar system formed approximately 4.57 billion years ago.

Within the emerging stars, nuclear fusion reactions gave rise to the nucleosynthesis of additional elements including carbon, oxygen, nitrogen, phosphorus, and sulfur, among others, which are critical components of living matter (4). Within the core of each of these stars, the force of gravity competes with the outflow of energy resulting from nuclear fusion. Once a star’s core has depleted its hydrogen, increasingly heavier elements like carbon and oxygen form eventually leading to iron and nickel. At this point, the star either erupts into a supernova, seeding these elements throughout the cosmos or it undergoes a forceful collapse, giving rise to neutron stars and black holes. The freshly seeded elements from recent supernovae form the interstellar dust from which new stars, solar systems, and planets are formed.

As life emerged, it was composed of these atomic elements, much of which is in the form of water (H₂O) and carbon-based molecules making up proteins and nucleic acids. It is now believed that ultraviolet light and perhaps other sources of energy impacting interstellar dust may have resulted in these basic elements forming more complicated molecules such as carbon dioxide, hydrogen cyanide, and ammonia, and even the simplest amino acid, glycine, among others present in the early solar system and planets such as the earth where additional synthetic reactions occurred (4).

The molten planet, with a dense core of iron and nickel, accounted not only for the earth’s magnetic field but, importantly, the presence of active volcanos near which early life may have emerged from precipitating water although the early atmosphere was almost entirely nitrogen and carbon dioxide. Life on earth then emerged sometime before the first fossil evidence of life around 3.7 billion years ago but likely sometime after surface oceans appeared around 4.3 billion years ago as the surface temperature cooled (4).

Emergence of the first forms of life on earth

We know or can infer a great deal about the conditions on the early earth when life first emerged. We also know an incredible amount about the complexity of life today following billions of years of evolution. However, solid information on exactly how life first emerged, persisted, and evolved over this vast period of time is limited resulting in a great deal of speculation but little experimental or observational evidence. We do have considerable information about more advanced early life based on fossil records but must acknowledge that those forms of life were already quite advanced and lived long after the initial origins of life. Out of the virtually limitless arrangements of carbon-based organic molecules, evidence has emerged around geologic evidence of molecular biosignatures of life based on the very selective types of complex organic molecules. Among others, these biosignatures include the presence of sterols and features such as handedness associated with living matter identified in ancient rock formations utilizing mass spectrometry and other techniques. Nevertheless, large gaps remain specifically about the very earliest events in the origin of life.

Multiple theories on the essential processes of early life formation have been put forward with varying enthusiasm and support. However, most of these theories can be grouped into three broad general categories. All life requires a metabolic apparatus capable of capturing and utilizing energy from the environment. However, our understanding of metabolism in modern life requires already complex proteins including enzymes to control and accelerate such biochemical reactions. The complex tertiary structure of such molecules is directly determined by the primary structure (linear array of amino acids) along with secondary linkages associated with bonds between specific individual units. At the same time, this complex tertiary structure imposes selective functional constraints on the underlying detailed chemical elements and metabolic processes. At the same time, geothermal sources of chemical energy have been proposed for fueling primitive metabolism in early life.

In addition, all life requires stored information controlling the production and organization of living matter which is capable of replication. In modern cells, this is accomplished through DNA utilizing RNA for translation into structural and enzymatic proteins (DNA World). However, it is unlikely that DNA could have spontaneously emerged in the primordial environment of the earth. While others have argued that this role may have initially been played by RNA (RNA World), even this as a source of heredity and organizational control seems a stretch. Others have argued for even simpler and more plausible organizational molecular entities for this role in a ‘Pre-RNA World’ and several candidates have been proposed but none are completely convincing. Finally, life requires both structure and a barrier enabling concentration of metabolic and hereditary processes and protection from the external environment while selectively facilitating the incorporation of energy and nutrients along with the discarding of waste products. It is believed that, early in the origin of life, phospholipid membranes played an important role (Lipid World). While capable of self-assembly into spherical phospholipid bilayers or vesicles, their integration into the genetic and metabolic machinery of early life was also essential. Important to the membrane’s critical role in living cells is the ability of proteins and other molecules to become embedded with some representing channels in and out of the cell and others transmitting signals from the extracellular milieu or interacting with other cells.

The critical role of cell membranes

Cell membranes consist of aligned glycophospholipid molecules that concentrate, protect, and organize the contents of the cell and facilitate the production of energy needed for cellular metabolism and enables intercellular communication. Modern cell membranes are composed of a three-carbon backbone (glycerol), a phosphate group, and two fatty acid chains. In nature, as in the laboratory, phospholipids aggregate into bilayers with the fatty acid chains facing each other making up the hydrophobic internal portion of the bilayer and the hydrophilic phosphate groups facing outward facing either the water-based interior or the exterior. Approximately half of the mass of natural membranes consists of proteins, many of which are amphiphilic transmembrane molecules. At the temperatures likely in most living cells, membranes are semipermeable and behave as a liquid permitting lateral fluid mobility of many of the embedded molecules within the fluid mosaic structure. The mobility of many proteins is constrained from the outside or by internal cytoskeletal elements. Interestingly, the fluidity of phospholipid membranes may be altered either by other molecules within the membrane or by external influences that may relate to cellular differentiation as well as carcinogenesis (5, 6). While small hydrophobic molecules pass through cell membranes readily, polar elements such as protons and larger molecules require selective transport proteins to move against concentration gradients. Signal transduction proteins bind selectively to external signals resulting in conformational changes impacting on internal messenger molecules. Finally, some embedded membrane proteins function as enzymes facilitating internal metabolic processes as well as electron movement and proton transport. In addition to the external cell membrane, modern cells have an extensive internal membrane network constituting the endoplasmic reticulum, the nuclear membrane, mitochondria, and other intracellular organelles. How much of this complicated machinery was necessary at the emergence of life is unclear and the topic of extensive research (7,8).

The impact of salts on the ability of membranes to form and function favorably for life makes it far more likely that early life formed in diluted seawater or freshwater formed by precipitation. At the same time, alternating cycles of hydration and dehydration may be optimal for molecular polymerization essential for early life. Clearly, the ability of phospholipids to self-organize makes it a likely important step in the origin of early life enabling the separation of concentrated metabolic and hereditary elements from a more hostile environment while facilitating the metabolic processes and energy needed for life. Nevertheless, the transition from pre-cellular metabolic systems with some of the features of life to actual cellular-based life was likely a gradual one and shrouded in a cloak of mystery with many questions to be further explored.

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