Handbook of Astrobiology

Vera M. Kolb, Vera M. Kolb

• Publisher: CRC Press
• Year: 2018
• ISBN:
  9781351661102
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Astronomy & Astrophysics

Choice Recommended Title, August 2019

Read an exclusive interview with Professor Vera Kolb here.

Astrobiology is the study of the origin, evolution, distribution, and future of life on Earth. This exciting and significant field of research also investigates the potential existence and search for extra-terrestrial life in the Solar System and beyond.

This is the first handbook in this burgeoning and interdisciplinary field. Edited by Vera Kolb, a highly respected astrobiologist, this comprehensive resource captures the history and current state of the field. Rich in information and easy to use, it assumes basic knowledge and provides answers to questions from practitioners and specialists in the field, as well as providing key references for further study.

Features:

• Fills an important gap in the market, providing a comprehensive overview of the field
• Edited by an authority in the subject, with chapters written by experts in the many diverse areas that comprise astrobiology
• Contains in-depth and broad coverage of an exciting field that will only grow in importance in the decades ahead

Section V

Chemical Origin of Life

Prebiotic Chemistry

5.1	Prebiotic Chemistry That Led to Life Juli Peretó

CONTENTS

5.1.1 Introduction

5.1.2 Is Terrestrial Biochemistry One Among Many?

5.1.3 The Three Pillars of Classic Prebiotic Chemistry

5.1.4 A Preferred Route to Biomonomers?

5.1.4.1 The Cyanosulfidic Protometabolism

5.1.4.2 Prebiotic Prefiguration of Metabolism

5.1.4.3 Focusing the Metabolic Image

5.1.5 The Total Synthesis of Protocells

5.1.5.1 A Note of Caution: Origins of Life ≠ Last Universal Common Ancestor

5.1.6 Summary and Prospects

Acknowledgments

References

5.1.1 INTRODUCTION

Life belongs to the very fabric of the universe.

Christian de Duve (de Duve 1991)

Without doubt, explaining how life appeared on our planet is highly problematic, so daunting that some think it impossible. This fundamental question would fall outside the domain of science if the origin of life were the result of a highly improbable, almost unrepeatable phenomenon. In this case, we would lose all hope of finding an answer. However, the materialistic and evolutionary view adopted by contemporary scientists suggests that the origin of life is a chemical enigma of a historical nature, which, despite its intrinsic contingencies, we can understand and even test experimentally. It is a chemical enigma because the origin of life sprang from the transition from inert chemical matter (i.e., cosmo- and geochemistry) to the most primitive biochemical systems. It is historical since this is an evolutionary transition, that is, a long series of successive, contingent stages of increasing complexity, each one genealogically depending on the previous one (Lazcano 2010b), and since this took place on our planet in the past, more than 3,500 million years ago (see this Handbook, Section 8).

These chemical and historical facets of the riddle of life’s beginnings were obvious to Charles Darwin (Peretó et al. 2009). He was always reluctant to publicly express his ideas on the origin of life, but in a letter dated 1871 to his friend and colleague, the botanist Joseph Hooker, Darwin described a set of conditions and ingredients necessary to spark evolution: “It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, –light, heat, electricity, etc. present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.” (Letter reproduced in full in Peretó et al. 2009.)

Like Darwin, we accept that the primitive Earth was governed by the same laws of physics and chemistry as they are today. Those chemical events of the past are, thus, amenable to scientific examination and understanding, and therefore, any narration of the transition from inert to living matter must be compatible with all our scientific knowledge of the material world. Eventually, any model we propose must not only be plausible but also empirically verifiable. This does not mean that the answer to the origin-of-life enigma will be a detailed account of what exactly happened somewhere on the primitive Earth. This is something we will never know for certain in full detail, not only because of the complete absence of a chemical record of the first steps of life and the many unknowns about Archaean Earth’s physicochemical constraints but, essentially, also because of the historical nature of the problem, including emergent phenomena difficult to reduce to physics and chemistry and requiring other types of explanatory accounts. Rather, we seek a full explanation of how the origin of life might have happened on the primitive Earth or, in other words, an experimental demonstration of the outstanding potential of chemistry to generate life, a goal considered a Holy Grail in chemical science (Krishnamurthy 2017).

The prospect of reproducing the earliest steps of life in a laboratory is not new. Over a century ago, several pioneers of synthetic biology, such as Alfonso Herrera, John Burke, and Stéphane Leduc, tried to cross the boundaries dividing inert from living matter (Peretó and Català 2007; Peretó 2016). There is an epistemological continuity between these premature and naïve attempts to synthesize life and the ultimate objective of the scientific quest to reveal the origin of life, framed within an evolutionary and chemical context. This approach is represented by the original proposals of Aleksandr I. Oparin (1924) and John B. S. Haldane (1929), who independently argued that any proposal on the natural emergence of life would be mere speculation, unless we are able to offer empirical support for its plausibility on early Earth.

The classic research on prebiotic chemistry – the chemistry that led to life – initiated by Stanley L. Miller and Harold C. Urey in the United States in the 1950s and inspired by Oparin’s heterotrophic theory (Lazcano 2010a), promoted the notion of a primitive Earth rich in organic materials that could be a source of both raw materials and food for the earliest life forms. Thus, the chemical landscape on a young abiotic Earth (generated both from endogenous sources and from extraterrestrial delivery) offered a wide range of compounds, whose accumulation in the oceans shaped the primitive soup. Did life originate from an immense chemical diversity? Or rather, were there prebiotic processes providing a fairly reduced chemical repertoire that anticipated the subset of molecules operating in biochemistry? In this chapter, I will show that although these fundamental questions are not yet resolved, they are greatly clarified by current advances in prebiotic systems chemistry – an approach dealing with complex multicomponent, interacting reactions and processes (Powner and Sutherland 2011; Ruiz-Mirazo et al. 2014).

5.1.2 IS TERRESTRIAL BIOCHEMISTRY ONE AMONG MANY?

Life is the outcome of a complex network of chemical reactions and molecular interactions. Biological complexity is organized around a small set of organic molecules – amino acids, nucleotides, lipid molecules, and a suite of metabolic intermediates – used to build polymers and supramolecular architectures – proteins, nucleic acids, membranes, ribosomes, etc. The whole system is sustained by an almost universal metabolic network (Smith and Morowitz 2016), which, by gathering matter and energy from the environment, drives the idiosyncratic and paradoxical performance of life, namely, autonomous chemical systems able to make imperfect copies of themselves and, hence, evolve (Ruiz-Mirazo et al. 2004). But, how did this peculiar chemical phenomenon begin? We do not know for sure, but let’s start by quoting Richard Dawkins (Dawkins 2009, p. 419): it must have been whatever it took to get natural selection started. Once the extraordinary unfolding of natural selection has begun, the Darwinian evolutionary theory, conveniently updated and extended, explains much of what happened along the history of life. And for natural selection, a population of entities that replicated with imperfections was needed, resulting in a variety of survival and reproductive capacities. Although the specific characteristics of these “infra-biological” or “pre-biological” entities are not yet well determined, there is a broad consensus that natural selection was operative before cells were endowed with DNA as the genetic material, during the era of the so-called RNA world (de Duve 2005b). This situation can occur in primitive cells, in which catalytic RNAs (ribozymes) facilitate processes like the synthesis of monomers for their own replication (self-replicative ribozymes) and the synthesis of membrane components (Szostak et al. 2001). It is fascinating to see how – albeit in restricted circles – the development of molecular biology in the twentieth century ran parallel to the discussion on how evolution could have occurred using RNA before DNA (Lazcano 2010a, 2012).

But before the advent of RNA, was there some other kind of selection process taking place in this immense sea of chemical ​​possibilities, or was RNA the result of chemical determinism? Is terrestrial biochemistry just one among many? Was the use of RNA the result of a frozen accident, a matter of chance? It is reasonable to suppose that a variety of cosmic and geological processes took place on the primitive Earth, contributing to an extraordinarily diverse inventory of organic materials. When we scrutinize interstellar space, or analyze pieces of extraterrestrial matter such as meteorites or comets, we discover the astounding richness of organic cosmochemistry (see this handbook, Section 4). Likewise, when we simulate primitive atmospheric chemistry, as in the classic Miller experiments and its derivatives (see this handbook, Chapter 5.5), all the evidence points toward notable chemical wealth (Cleaves 2015). Processes of chemical selection would operate on this chemodiversity, aided by minerals and by the environmental conditions. We know very little about how the biological subset of amino acids, nitrogen bases, sugars, or lipids, all with a certain isomerism, could have been selected to ignite the earliest cellular systems.

However, the prevalent view of life emerging from a complex and diverse mixture of chemical building blocks was questioned by some evolutionary biochemists and, more recently, by Günther Wächtershäuser (Wächtershäuser 1988), Harold Morowitz (Morowitz 1992; Smith and Morowitz 2016), and Christian de Duve (de Duve 1993, 2011). With diverse emphasis and on different grounds, these scientists suggest that prebiotic chemistry was predisposed toward synthesizing a few components, which would be almost the same as those configuring the contemporary metabolic repertoire. In fact, chemical determinism in the origin of life is a central theme in de Duve’s thought and is one of the questions he posed in his posthumous book, which recounts the intellectual journey of this exceptional biologist (de Duve and Vandenhaute, Chapter 9, 2013). In short, de Duve argues that under certain environmental constraints, the outcome of chemical evolution would almost always be the same and that the specific polymers and systems that eventually turned into evolving cell populations would not have randomly emerged by chance from an immense ocean of molecular possibilities (Fry 2019a,b).

Thus, the “cosmic imperative” for life’s emergence proposed by de Duve is at the philosophical antipodes of the proposals considering the origin of life as an unlikely chance event (Fry 2000; Lazcano 2017). In his influential book Chance and Necessity, molecular biologist Jacques Monod accepted the almost-proven notion of an early Earth rich in organic compounds and the possible emergence of biopolymers, such as proteins and nucleic acids (Monod 1970). Yet, Monod attributed an exceedingly low chance to the emergence of the genetic code and the functional organization of a cell having the capacity to evolve by Darwinian mechanisms. He famously stated that the planet was not pregnant with life and that, as a consequence, ours was the only inhabited planet in the universe. Clearly, Monod was astounded by the advances in molecular biology in his time, showing that the intimacies of universal cell mechanisms were much more complex than expected, thus making the question of their natural emergence still more inextricable (Monod 1970). The historicity of the process of biogenesis would comprise not only contingencies of the type that Monod was conceiving (essentially, stochastic and irreversible events) but also the emergence of intermediate systems that allowed for further evolutionary transitions to take place. Nevertheless, as we will discuss in Section 5.1.4, recent discoveries in prebiotic systems chemistry indicate that the path leading from chemistry to the earliest evolving cells may be simpler than what Monod could ever have imagined (Islam and Powner 2017; Ruiz-Mirazo et al. 2017; Sutherland 2017).

5.1.3 THE THREE PILLARS OF CLASSIC PREBIOTIC CHEMISTRY

During the last six decades, many investigations in classic prebiotic chemistry have been conditioned by the search for reasonable mechanisms underlying the direct and robust synthesis of biomonomers. Miller’s spark discharge experiments elegantly showed the ease of amino acid synthesis from mixtures of simple molecules, such as H₂O, NH₃, CH₄, and H...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Table of Contents
• Preface
• Editor
• Contributors
• SECTION I Astrobiology: Definition, Scope, and Education
• SECTION II Definition and Nature of Life
• SECTION III Origin of Life: History, Philosophical Aspects, and Major Developments
• SECTION IV Chemical Origins of Life: Chemicals in the Universe and Their Delivery on the Early Earth; Geology and Atmosphere on the Early Earth
• SECTION V Chemical Origin of Life: Prebiotic Chemistry
• SECTION VI RNA and RNA World: Complexity of Life’s Origins
• SECTION VII Origin of Life: Early Compartmentalization—Coacervates and Protocells
• SECTION VIII Origin of Life and Its Diversification. Universal Tree of Life. Early Primitive Life on Earth. Fossils of Ancient Microorganisms. Biomarkers and Detection of Life
• SECTION IX Life under Extreme Conditions—Microbes in Space
• SECTION X Habitability: Characteristics of Habitable Planets
• SECTION XI Intelligent Life in Space: History, Philosophy, and SETI (Search for Extraterrestrial intelligence)
• SECTION XII Exoplanets, Exploration of Solar System, the Search for Extraterrestrial Life in Our Solar System, and Planetary Protection
• Index