Table of Contents

Chapter 1. Introduction—What Is Astrobiology?

1.1. What is astrobiology?

Astrobiology is the science that seeks to understand the story of life in our universe. Astrobiology includes investigation of the conditions that are necessary for life to emerge and flourish, the origin of life, the ways that life has evolved and adapted to the wide range of environmental conditions here on Earth, the search for life beyond Earth, the habitability of extraterrestrial environments, and consideration of the future of life here on Earth and elsewhere. It therefore requires knowledge of physics, chemistry, biology, and many more specialized scientific areas including astronomy, geology, planetary science, microbiology, atmospheric science, and oceanography.

However, astrobiology is more than just a collection of different disciplines. In seeking to understand the full story of life in the Universe in a holistic way, astrobiology asks questions that transcend all these individual scientific subjects.

Astrobiological research potentially has much broader consequences than simply scientific discovery, as it includes questions that have been of great interest to human beings for millennia (e.g., are we alone?) and raises issues that could affect the way the human race views and conducts itself as a species (e.g., what are our ethical responsibilities to any life discovered beyond Earth?).

1.2. Have we already found life beyond Earth?

No. There have been many exciting discoveries that suggest life is possible on other planets and moons, but we have not yet detected any definite signs of life beyond Earth. That does not necessarily mean life exists only on Earth, but only that there is not yet compelling evidence for its existence elsewhere. Space missions have explored only a tiny portion of our solar system, and in the few years since we first discovered planets around other stars, the number of such exoplanets known has increased into the hundreds. The search for life beyond Earth has therefore only just begun.

Astrobiology is an exciting subject with new ideas that can easily capture the imaginations of both scientists and nonscientists. But like all areas of science, new ideas are subject to detailed scrutiny by the scientific community as part of the quality control process. Only ideas that are considered to be well-supported by evidence are accepted by the scientific community as a whole. This can lead to lively debate within the scientific community and sometimes within the public arena. Whether the new idea is ultimately accepted or not, the process of testing the evidence results in increased knowledge and understanding, not just about the possibility for life beyond Earth but about our own planet as well. Two high-profile announcements within the field of astrobiology illustrate this.

In 1996, scientists announced that they had found evidence of fossilized life contained within martian meteorite ALH84001 (McKay et al., 1996). In subsequent years, astrobiologists completed research on the meteorite itself and on the types of “biosignatures” contained within it. As a result, we now know that abiological processes could have created these signals, and the meteorite is not therefore widely considered proof of life beyond Earth (Bradley et al., 1996, 1997; Frankel and Buseck, 2000; Buseck et al., 2001; McKay et al., 2003; Treiman, 2003). For example, one of the “biosignatures” cited by McKay et al. were structures in the meteorite that appeared to resemble fossilized bacteria when viewed under an electron microscope, but later work showed that similar structures can be produced as an artifact of the techniques used to prepare mineral samples for electron microscopy (Bradley et al., 1997). Although the claims made by McKay et al. have not been generally accepted, in the process of testing them astrobiologists advanced research on a variety of topics, including the minimum size of an individual cell and production mechanisms for tiny grains of magnetite. Additionally, astrobiologists were forced to reexamine what constitutes conclusive evidence for past or present life.

More recently, a team announced the discovery of a bacterium they claimed could substitute arsenic for phosphorus in its DNA (Wolfe-Simon et al., 2011). These claims have been largely rejected by the scientific community, which has generally concluded that they are not proven by the evidence presented in the paper (Benner, 2011; Borhani, 2011; Cotner and Hall, 2011; Csabai and Szathmáry, 2011; Foster, 2011; Oehler, 2011; Redfield, 2011; Schoepp-Cothenet et al., 2011; Erb et al., 2012; Reaves et al., 2012). Nevertheless, this paper has stimulated a very active debate, and further research will undoubtedly lead to improved understanding of microbial arsenic metabolism. For example, investigations into the claims made by the paper have already led to the hypothesis that the bacteria isolated by Wolfe-Simon et al. may contain a high-affinity phosphorus transporter that is stimulated by arsenic (Foster, 2011).

1.3. What is the Astrobiology Primer?

The Astrobiology Primer is designed to provide a basic, but comprehensive, introduction to the field of astrobiology. It is longer than a typical review paper but much shorter in length than a textbook, with the goal of being detailed enough to provide a brief overview of the variety of questions investigated by astrobiologists.

The Astrobiology Primer is the product of a strong, vibrant, early-career astrobiology community. This is the second version of the Primer, and like the first (Mix et al., 2006), it is a grassroots effort, written by graduate students and postdoctoral researchers. In total, we are a group of 49 authors and editors from 14 different countries. This second edition has been rewritten from scratch. It updates content and is organized around the questions that currently drive research in the field.

Our target readers for this document are other early-career astrobiologists, in particular graduate students who are new to the field, but we hope that it will also be useful to a wide range of people for both personal study and teaching.

This primer begins with the question of the nature of life (Chapter 2), then goes on to discuss the origins of life and its planetary environment (Chapter 3), the interactions of life with our planet through time (Chapter 4), what we know of habitability from these interactions (Chapter 5), what we know about the habitability of environments outside Earth (Chapter 6), and how we might search for life in those environments (Chapter 7). We close with chapters on the implications of this research for society (Chapter 8) and resources for astrobiologists (Chapter 9).

Chapter 2. What Is Life?

This simple question is surprisingly difficult to answer yet is fundamental to the success of astrobiological research. Imagine the difficulty of identifying life on other worlds without a clear understanding of what similarities it may or may not share with life on Earth. Or consider the limitations of interpreting possible origin-of-life scenarios without distinguishing between primitive life-forms and the nonliving entities from which they must have emerged. So far, and not without significant effort, no single definition of life has achieved universal acceptance. But the very exercise of attempting to define life reveals and tests its most essential characteristics.

2.1. Can we define life?

The goal is not to define “life,” the word, as it is used and understood in language, but rather to understand “life” as an objective concept that can guide scientific research (Oliver and Perry, 2006). Successful scientific definitions of life attempt to include everything that we already intuitively consider alive and exclude everything that we would not consider alive. For our purposes, such definitions should also be sufficiently broad to include unknown forms of life that independently arose on Earth or elsewhere. If these criteria are satisfied, the definition will be a useful guide in the search for life on other worlds and the study of its origin here on Earth (Ruiz-Mirazo et al., 2004; Oliver and Perry, 2006).

This objective, however, is made more difficult to achieve by our lack of a second known instance of life. Because all known life evolved from a single ancestor or ancestral community, every life-form shares a common set of inherited properties (Woese, 1998; Becerra et al., 2007; Theobald, 2010). Consequently, it can be difficult to distinguish general features of life in the Universe from those specific to our own form of life (Gayon, 2010). Cleland and Chyba (2002) were the first to argue that, without additional examples of life and the greater understanding they may provide, it is even impossible to know whether the concept of life describes an objective natural phenomenon or a subjective category that cannot be perfectly defined (Cleland and Chyba, 2002; Robus et al., 2009).

Such objective phenomena, which philosophers call “natural kinds,” can be defined completely by principles of the natural world without depending on human-made conventions, for example water defined as the molecule H 2 O. Cleland and Chyba used the term “bachelor,” defined as “an unmarried adult human male,” to illustrate the sort of category that is not a natural kind. This definition “explain(s) the meaning of (the term) by relating (it) to expressions that we already understand,” but the term “bachelor” is not a natural kind in that the terms “adult” and “unmarried” are understood only as cultural concepts, not natural ones. Cleland and Chyba pointed out that “water” was a concept much like this before it became possible to describe water as its molecular formula. Life may be like water, a natural kind waiting for a scientific definition, or may be more like bachelor, a category that can be easily understood but that cannot be defined completely by natural principles.

A successful definition of life must not only delineate life and nonlife but also deal with the intermediate stages that may exist between life and nonlife. The origin of life presents just such a test. Our current understanding of life's origin suggests that there were intermediate states through which all forms of life must emerge (Fry, 1995; Luisi, 1998; Perry and Kolb, 2004). In addition, the biosphere today includes entities that may represent intermediate states between life and nonlife. For example, viruses, which some do not consider bona fide organisms, possess many features similar to organisms and may present further evidence that there is a continuum between life and nonlife. All the arguments listed above demonstrate that the goal of creating a clear and objective scientific definition of life is not at all straightforward.

2.2. What are the common characteristics of life on Earth?

While life on Earth represents only one example, it is the only known example and, therefore, a good place to begin. Any universal characteristic of life on Earth may be universal either because it was inherited from a common origin or because it is a necessary feature of all life in the Universe. The lack of a second example of life frustrates our ability to conclusively differentiate between these two possibilities.

The chemistry of life is predominated by only a handful of carbon-based macromolecules common to all organisms: cellular membranes and intracellular compartments are primarily composed of a type of molecule called a “phospholipid,” a lipid with a charged phosphate group on one end; genetic information is stored and processed by the nucleic acids DNA and RNA; the catalytic and infrastructural functions of the cell are performed mainly by proteins. Many of these so-called macromolecules are formed through the polymerization of subunits, for example, nucleotides (forming nucleic acids) and amino acids (forming proteins). The cellular pathway that creates proteins from genetic information is also common across life, and the genetic code that translates genetic information into protein molecules is also nearly universal (Knight et al., 2001).

In addition to a common biochemistry, all known life-forms exhibit many of the same general traits. Campbell and Reece (2002) listed the following traits that are common to life on Earth:

• Ordered structure refers to the high level of organization observed both within cells and within multicellular organisms as well as the bilateral or radial symmetry observed in many organisms.

• Reproduction can refer to either the nearly exact duplication of an organism or the production of a new organism through sex between two parent organisms.

• Growth and development refers to the processes by which organisms reach maturity, which can take drastically different forms depending on the type of organism.

• Energy utilization refers to the capture of energy from sources such as sunlight, inorganic chemical reactions, or organic material produced by other organisms, and subsequent use of that energy for cellular processes and the biosynthesis of cellular components.

• Response to the environment refers to the ability of organisms to sense external stimuli and alter their internal environments accordingly.

• Homeostasis refers to the maintenance of a steady internal environment regardless of the external environment.

• Evolutionary adaptation refers to the process by which populations of organisms adapt to external pressures such as environmental changes through evolution by natural selection.

Some phenomena that are clearly not alive demonstrate one or more, but not all, of these features. Crystals, fire, and hurricanes are all able to grow, reproduce, and utilize forms of potential energy. Crystals also demonstrate ordered structure, albeit composed of fewer distinct subunits. Elements of culture, or “memes” as originally coined by Dawkins (1976), reproduce and evolve by selection in ways that are similar to genes (Dawkins, 1976; Dennet, 1995). Many artificial intelligence algorithms are also based on learning by a process similar to evolution by selection (Dennet, 1995).

A much more ambiguous example is that of viruses, which are compartmentalized biological elements that contain genomes and reproduce by co-opting the metabolism of an infected cell. Viruses evolve, demonstrate ordered structure, and in some cases undergo a maturation process that could be construed as growth and development. But they cannot reproduce without co-opting the metabolism of their infected hosts. Viruses, themselves, also do not demonstrate homeostasis, energy utilization, or response to the environment. However, many pathogenic bacteria are also unable to reproduce outside a host cell. If complete metabolic autonomy were a requirement for life, animals, plants, and many other forms of life on Earth would not qualify.

Viruses are an especially important case for consideration because they are not only similar to cellular organisms in character, but they also use the same chemistry and genetic code that is discussed below. This similarity is necessary because, otherwise, viruses would not be able to take advantage of the host's biosynthetic machinery to reproduce. Several recently discovered viruses have genomes and physical dimensions comparable in size to some cellular organisms and can be infected, themselves, by other viruses (La Scola et al., 2003, 2008).

Biological entities smaller than viruses are also capable of evolution by natural selection. For example, transposons are stretches of DNA found in genomes that, at a minimum, encode genes responsible for extracting or copying themselves and inserting themselves or their copies elsewhere in the genome. About 40% of the human genome is composed of transposons (Lander et al., 2001). Such minimal biological agents appear to blur the line between life and nonlife. The line becomes a bit less blurry through the observation that the majority of natural selection in the biosphere acts on genes rather than organisms or populations (Williams, 1966).

2.3. So what is life?

At a workshop in 2003, every member of the International Society for the Study of the Origin of Life was asked to give his or her definition for life, resulting in 78 different answers (Palyi et al., 2002). Most often, definitions of life draw on one or more of the attributes of life on Earth that were listed above, usually involving some combination of metabolism, reproduction, and evolution. For the reasons described in Section 2.2, no single feature of life is sufficient to define it, as each of these features is shared by other entities that are not generally considered life.

In his 1943 lecture series “What is Life?,” published in 1944, Erwin Schrodinger introduced several important concepts that would shape future considerations of the question. The first of these is the concept of genetic information or what he called “code-script.” At the time of this insight, DNA had not yet been confirmed as the genetic molecule, and its mechanisms of heredity and genetic encoding would not be described until the following decade. A second insight is that life appears to disobey the second law of thermodynamics. That is, the ordered structures of life do not entropically decay toward chemical equilibrium. Life is able to achieve this far-from-equilibrium state by “feeding” on disequilibrium in the environment. We now understand that this maintenance of order is achieved through the coupling of energy metabolism to biosynthetic metabolism.

Currently, the most popular definition of life was conceived by a NASA effort to create a “working definition” for their Exobiology and Astrobiology research programs. The result, most often cited as Joyce (1994), defines life as “a self-sustaining chemical system capable of Darwinian evolution.” A major strength of this simple and concise definition is that it distinguishes life by the evolutionary process rather than its chemical composition. The definition alludes to biological chemistry through the general term of “self-sustainment.” By invoking evolution as a foundational feature of life, the definition also separates the property of life from the characteristics of individual organisms, which are not, themselves, capable of Darwinian evolution. This is because the evolutionary forces discovered by Darwin (e.g., natural selection) operate through the reproductive success of organisms rather than the alteration of individual organisms during their own lifetimes.

Critics of the definition find that the stipulation of Darwinian evolution is overly specific (Cleland and Chyba, 2002). They argue that an extraterrestrial life-form may have a genetic system that evolves through changes accumulated during an organism's lifetime (i.e., Lamarckian evolution) rather than Darwinian selection processes. Nevertheless, the NASA/Joyce definition is perhaps the most widely accepted definition of life within the astrobiological research community.

2.4. How should we use our concepts of life?

Even a less-than-perfect definition of life may be employed in the search for life on other worlds. For example, any “self-sustained chemical system” must differ in composition from its surroundings. Because life must also be “capable of undergoing Darwinian evolution,” this will result in successful species that amplify this chemical signature. McKay (2004) proposed that this chemical signature is a universal feature of all life and may be used for life detection. But while the Joyce (1994) definition gives us a useful way to identify candidate life-forms, it also requires that the life-form be verified by no less than clear evidence of evolution (Luisi, 1998; Cleland and Chyba, 2002).

A more pragmatic approach, and the only one used for life-detection experiments so far, is to look for signatures of life that are similar to those that would be produced by life on Earth (see Chapter 7). The first such attempts were made by experimental modules on NASA's Viking Mars landers in the mid-1970s (Klein et al., 1976). These attempts focused on the search for the organic molecules of which Earth-based organisms are composed, and experiments designed to detect the production and consumption of gases by any organisms using similar metabolisms to those used by Earth-based organisms. A more recent approach to develop a life-detection experiment is the Life Marker Chip, designed to detect a broad range of biomolecules in either their pristine or degraded states (Parnell et al., 2007). To do so, the Life Marker Chip would consist of an array of antibody proteins that are designed to bind biomolecules common to life on Earth.

Scientific research will continue to enhance our understanding of life on Earth and its effect on the planet. Considering which of the traits demonstrated by life on Earth may be universal to all life in the Universe will expand our understanding even further. With this broader concept of life, future astrobiological searches should be capable of detecting a greater variety of life-forms. If future astrobiological missions are successful in finding life beyond Earth, they may fundamentally change our concept of life. In this way, the effort to find life on other worlds and the effort to define life universally will always be interconnected.

Chapter 3. How Did Earth and Its Biosphere Originate?

The study of how life began on Earth offers information we can use to consider the possibilities for the existence of life elsewhere. This chapter starts with the availability of elements that could form the building blocks of life (Section 3.1). It continues with the origin of our planet and its volatile inventory (compounds with a low vaporization temperature/pressure) and considers what we know about the environment of early Earth (Section 3.2). The final section (Section 3.3) covers what we can determine about events that could have led to the origin and earliest evolution of life on Earth, given what we know about the environmental context.

3.1. How do elements, stars, and planets form?

3.1.1. How are the elements formed and distributed?

All chemical elements are formed in nucleosynthetic processes involving addition or removal of nucleons (protons and neutrons). The earliest synthesis of elements in the Universe took place during Big Bang nucleosynthesis, which produced the vast majority of the hydrogen and helium present in the Universe today. Since then, stellar nucleosynthesis in stars has produced the majority of other naturally occurring elements (Burbidge et al., 1957) (Fig. 1).

FIG. 1. A periodic table showing the major nucleosynthetic sources of naturally occurring elements. The three lightest elements formed mostly in the first three minutes after the Big Bang (Big Bang nucleosynthesis). Other lightweight elements formed in fusion reactions in stars, and these elements in turn served as fuel for the production of even heavier elements in larger stars. Slow neutron capture in massive stars synthesized elements beyond iron. Still heavier elements formed in explosive environments, such as in a supernova, through a rapid neutron-capture reaction. (Credit: Aditya Chopra)

Other known processes that have made minor contributions toward the production of elements in the Universe include photodisintegration of existing nuclei by gamma rays (cosmic ray spallation); radioactive decay of unstable elements; fission reactions in natural nuclear reactors; and recently, high-energy particle accelerators, nuclear bombs, and nuclear reactors. Together with Big Bang nucleosynthesis and stellar nucleosynthesis, these processes collectively yield all the isotopes of elements that exist in nature.

Big Bang nucleosynthesis began approximately 13.8 billion years ago, during the first 3 min after the Big Bang. The high temperature and density of the Universe during this time resulted in energies and collision frequencies that were high enough to overcome the electrostatic repulsion between nuclei and bring nucleons close enough for the attractive nuclear force to be sufficiently strong to achieve fusion. A series of fusion reactions of different isotopes could then produce the heavier elements helium and lithium. This period lasted for about 17 min and was responsible for the formation of the stable isotopes of hydrogen, helium, and lithium (the three lightest elements in the periodic table) from combinations of fundamental particles (Weinberg, 1993). Unstable (radioactive) isotopes of hydrogen and beryllium were also synthesized but decayed or fused with other nuclei to form stable isotopes.

Over time, this matter (also referred to as baryonic matter) fell into existing cold matter clumps to form clouds mostly composed of neutral molecular hydrogen. As densities increased in regions within the cloud, gravitational collapse triggered cloud fragmentation. Further collapse of the clouds led to increasing pressures and temperatures at their cores. Eventually, temperatures and densities in these cores reached levels required for nuclear fusion. This is how the first stars were born, beginning the era of stellar nucleosynthesis of heavier elements (Brom, 2013). This era of element formation began about 100 million years after the Big Bang and continues to this day (Fig. 2).

FIG. 2. Chronology of nucleosynthesis in the Universe. (Credit: Aditya Chopra)

The nucleosynthetic pathways that are possible in a star are closely coupled to stellar evolution; different types of stars synthesize a range of different elements during their lifetimes (Baross and Sullivan, 2007; Ryan and Norton, 2010). The successive nuclear fusion processes, commonly referred to as nuclear burning (not to be confused with “burning” meaning combustion in the presence of oxygen), are hydrogen burning, helium burning, carbon burning, neon burning, oxygen burning, and silicon burning. These nuclear burning (or fusion) reactions occur sequentially within a single star or series of different generations of stars. Collectively, they create isotopes as heavy and energetic as 56Ni through exothermic (energy-yielding) reactions that release the energy needed to sustain stars (see Section 3.1.2).

Isotopes with masses larger than 56Ni can only be generated with endothermic (energy-consuming) reactions. Therefore, elements heavier than Ni require energy to form and are not produced through the exothermic nuclear fusion reactions that take place at the centers of stars. (While 56Ni is the last fusion product produced in the cores of high-mass stars, this isotope undergoes radioactive decay into 56Fe, significantly increasing the abundance of iron relative to other first-row transition elements in the periodic table. This phenomenon is often referred to as the “iron peak.”)

Elements heavier than iron are assembled when there is a high abundance of highly energetic neutrons and protons in the star. Such scenarios often occur in the last few seconds to minutes before the end of the star's life, as in core-collapse supernovae (Arnett, 1996) (see Section 3.1.2). There are a number of “bottlenecks” in various nucleosynthetic pathways due to the dependence of reaction rates on each other, and these determine the relative abundances of the isotopes of the elements that are created (Lodders, 2010).

Generations of stars have gradually converted the products of Big Bang nucleosynthesis into heavier elements such as oxygen, iron, silicon, and magnesium. These elements are now available to form planets, moons, and life (Fig. 3). Most rocks on the surface of Earth are composed of minerals made of lithophilic (“rock-forming”) elements (Fig. 4). Input of material from comets and primitive meteorites such as chondrites in Earth's early history led to a biosphere (containing life and its environment) rich in the volatile elements hydrogen and oxygen (mostly as water) along with carbon, nitrogen, sulfur, and phosphorus (mostly as dissolved salts or gases) (Chyba et al., 1990).

FIG. 3. Elemental composition of the Sun (a typical star) by mass. The word “metal” here is used in the way commonly applied to stellar compositions and includes all elements heavier than H and He. (Credit: Martin Asplund)

FIG. 4. The abundance of elements (by number of atoms normalized to silicon) in Earth's crust. The crust is depleted in siderophilic (“iron-loving”) elements relative to the bulk Earth as siderophiles were partitioned into the Earth's core. Compared with the mantle, Earth's crust is enriched in lithophilic (rock-forming) elements. (Credit: Aditya Chopra)

3.1.2. How do stars form, evolve, and die?

A star forms when a cloud of predominantly hydrogen gas collapses under its own gravity. As it collapses, the temperature and pressure at the core become great enough to fuse hydrogen into helium. Further collapse of the star is halted when the pressure in the star's interior is high enough to counteract the force of gravity.

Nucleosynthesis is the process by which stars create progressively heavier elements (see Section 3.1.1). Starting at the core, the nucleosynthetic region within the star moves outward as its temperature within that region increases. As each region hosts nuclear fusion of progressively heavier elements at higher temperatures, different shells of nuclear burning define an onionlike structure within the star as illustrated in Fig. 5. The energy-releasing fusion process continues until iron is formed in the core of the star.

FIG. 5. Onionlike structure caused by progressive nucleosynthesis in stars. Nearest to the core are the sites of the hottest and heaviest nuclear fusion, while regions farther away near the surface host the coolest and lightest nuclear fusion reactions. (Credit: NASA)

Under the conditions found in stellar interiors, iron cannot be turned into a heavier element through the fusion process because, unlike fusion of lighter elements, iron fusion requires energy. Thus, once iron is formed at the core of a star, fusion ceases to operate in that region of the star. This places an upper limit on the amount of radiation pressure produced by fusion, and because radiation pressure is what prevents gravitational collapse, this leads to the death of stars. This same process also limits the heaviest element that can be formed in any given star. Iron is the heaviest element that can form in the most massive stars, but less massive stars may only be capable of forming lighter elements.

Lifetimes of stars are thought to be as long as trillions of years for the lightest stars and as short as a few millions of years for the most massive stars (Phillips, 1999). There are two pathways a dying star can take (Fig. 6). For low- to intermediate-mass stars, the core collapses to become a “white dwarf”—a hot, compact ball of helium, carbon, and oxygen—while the outer layers are ejected into space. In the most massive stars, the collapse initiates an explosion, known as a supernova, that triggers the formation of elements heavier than iron (see Section 3.1.1). Depending on the star's initial mass, the remaining core collapses to become either a neutron star (a dense city-sized ball of neutrons) or a black hole (an entity whose gravity is so strong that even the fastest particles in the Universe, photons, cannot escape its gravity well; as a result, black holes emit no light). In most cases, the newly formed elements that are not incorporated into the neutron star or black hole are dispersed back into the interstellar medium and become incorporated into the next generation of stars and planets (Whittet, 2003).

FIG. 6. Life cycle of stars, for both Sun-like stars and massive stars. (Credits: NASA and the Night Sky Network)

3.1.3. How do protoplanetary disks and planetary systems form?

Protoplanetary disks are diffuse regions of gas and dust and are the eventual birthplaces of stellar and planetary systems. During the gravitational collapse of a molecular hydrogen cloud, conservation of angular momentum causes the cloud's rotation to increase, and the rotation causes the cloud to flatten into a disk. The center of the disk contains the newly forming star, and the disk is the site of planet formation.

Planetary bodies are widely believed to have formed through the method of core accretion (Ida and Lin, 2004). Under this paradigm, dust accretes over time to produce rocky bodies known as planetesimals that range from kilometer size to approximately the size of Earth's Moon. These bodies interact gravitationally with each other, colliding and accreting to produce planetary embryos (Moon- to Mars-sized solid bodies) or being broken apart by violent collisions. An alternative planet formation model that has been hypothesized is that of gravitational instability (Zel'Dovich, 1970; Boss, 1997). In the instability model, protoplanetary disks fragment during the collapse of the disk, creating high-density regions that rapidly pull in surrounding material to form planetary bodies. This model, however, has not been widely adopted by the modeling community and encounters difficulties in producing the observed architecture of extrasolar planetary systems. As such, we will focus on the accretion model.

In the planetary accretion model, planets with relatively high metallic and rocky content, such as Mercury and Earth, are expected to form closer to their host star. Conversely, planets with greater volatile content (molecules that have low boiling points), such as the giant planets of the outer Solar System, are expected to form farther from their host star. The latter group of planets can become much more massive than their rocky counterparts due to addition of extra mass in the form of accreted volatiles. This explanation is consistent with—and historically driven by—the arrangement of planets in the Solar System: smaller, rocky planets exist closer to the star and larger, volatile-rich planets farther from the star.

However, Jupiter-mass and Neptune-mass exoplanets have been found closer to their host than Mercury is to the Sun (Butler et al., 2006; Borucki et al., 2010), so planetary migration through the disk has been suggested to explain how these hot giant planets moved from their birth locations to their current locations (see below). Combined, core accretion and orbital migration form the general framework for planet formation, both within our solar system and within extrasolar planetary systems (Kley and Nelson, 2012).

Two dominant models have emerged under the planetary accretion paradigm to explain the formation of planets and long-term evolution of the Solar System: the Grand Tack model, which focuses on planet formation (Walsh et al., 2011), and the Nice model, which focuses on long-term evolution (Gomes et al., 2005; Morbidelli et al., 2005; Tsiganis et al., 2005; Levison et al., 2011). Both models involve large-scale migration of the giant planets before settling in their current orbits and can explain a variety of features of the Solar System. However, they focus on very different time periods (Nice occurred approximately 500 million years after the Solar System formed, while the Grand Tack occurred within the first 5 million years). The two models also have somewhat different end results in that the Nice model reproduces the outer Solar System well, while the Grand Tack reproduces the inner Solar System.

The Grand Tack model addresses formation events that occurred in the earliest stages of the formation of the planets within the Solar System. Under this model, Jupiter and subsequently Saturn began their formation considerably closer to the Sun than they are now (approximately 3.5 AU; Walsh et al., 2011). Once large enough, both protoplanets began to experience type II migration wherein they were coupled to the gas disk and slowly migrated inward, along with the gas. This migration brought the bodies in to 1.5 astronomical units (AU), where Saturn effectively caught up with Jupiter (as Saturn-mass planets tend to migrate faster) and the cleared area around each of the bodies overlapped. This caused the planets’ migration to change direction (i.e., “tack,” hence the name of the model) and begin to migrate outward. As they migrated outward, they encountered Uranus and Neptune and caused the outward migration of these two planets to their current orbits.

The Grand Tack model has the benefit of explaining the structure and composition of the asteroid belt. There are two very different types of asteroids in the asteroid belt—ordinary chondrites and carbonaceous chondrites—which have very different compositions and therefore must have formed in different locations. According to the Grand Tack model, the giant planets scatter planetesimals throughout the disk as they migrate outward from 1.5 AU. Some of these are scattered inward, which results in the introduction of carbonaceous chondrites to the asteroid belt and explains the presence of two vastly different types of asteroids within the asteroid belt—ordinary chondrites in the inner asteroid belt and carbonaceous chondrites in the outer belt. The Grand Tack model allows for the combination of the two types in one location.

The Grand Tack model also has the added benefit of potentially resolving the longstanding issue of Mars’ low mass. The formation of Mars has been difficult to simulate correctly, as most models produce planets that are too massive (Wetherill, 1991; O'Brien et al., 2006; Raymond et al., 2009). One solution to this problem is to truncate the disk of planetesimals that accrete to produce the terrestrial planets at 1 AU (Hansen, 2009). The Grand Tack model provides a mechanism to achieve this, as the presence of (a still-forming) Jupiter at 1.5 AU results in a pileup of planetesimals at 1 AU and depletes the feeding zone for proto-Mars.

The Nice model, on the other hand, is focused on the evolution of the Solar System and results from the giant planets (Jupiter, Saturn, Neptune, and Uranus) initially being located farther from the Sun and closer to each other. Dynamical interactions with a large remnant planetesimal population result in orbital instabilities for Jupiter and Saturn. These orbital instabilities resulted in gravitational interactions with Uranus and Neptune, also affecting their orbits. Subsequent gravitational interactions between the giant planets and a planetesimal disk on the outer edges of the Solar System not only produce the influx of impactors observed in the inner Solar System during the Late Heavy Bombardment (LHB) period (see Section 3.2) (Gomes et al., 2005) but also serve to remove the majority of the planetesimal population from the outer Solar System, which explains the current dearth of trans-Neptunian bodies. The Nice model can also explain not only the structure of the asteroid belt but also some of the compositional variations observed therein (Levison et al., 2009), along with the structure of both Jupiter and Neptune's trojan population (Morbidelli et al., 2005; Tsiganis et al., 2005; Sheppard and Trujillo, 2010). This initial model has been modified, with the giant planets being suggested to have initially started in a quadruple resonance (Levison et al., 2011), migrating largely together due to gravitational interactions with the outer planetesimal disk.

Combined together, the Nice and Grand Tack models may represent the formation and evolution pathway of the planets within our solar system and potentially within other extrasolar systems. For further details regarding terrestrial planet formation models, see Morbidelli et al. (2012) for a Solar System–based discussion and Raymond et al. (2014) for discussion of planet formation within both the Solar System and extrasolar planetary systems. See also Chapter 6 for more information on our current knowledge of planets in other solar systems.

Once a planet forms (under any model) there can be further changes that result in the differentiation of elements between layers (Chambers, 2004). If enough heat is present in a planet's interior, the planet effectively melts into a liquid form, so different elements can rise or sink depending on their density, causing differentiation between metal-rich (siderophilic), silica-rich (lithophilic), and/or gas-rich (atmophilic) components. During this differentiation, relatively dense components such as iron, nickel, or metallic hydrogen tend to sink to the center to form the planet's core, whereas relatively less dense materials such as silica and gases become preferentially incorporated into the mantle and crustal layers above. Differentiation plays a major role in the distribution of elements in a planetary body.

3.2. How did Earth, including its oceans and atmosphere, form?

Earth formed via accretion (see Section 3.1.3) from the solar nebula 4.53–4.47 billion years ago (Ga). The age of Earth was established based on the combination of both Earth-based and meteoritic samples. Earth-based evidence includes the age of the oldest minerals currently persevered on Earth's surface (4.4 Ga; Wilde et al., 2001) and the oldest whole rock known to exist on Earth (4.208 Ga; O'Neil et al., 2008). Meteoritic evidence includes the age of the first solids to condense within the Solar System, known as calcium-aluminum inclusions (4.565 Ga; Connelly et al., 2008) and radiometric dating of various meteorite samples (ages clustering from 4.68 to 4.50 Ga).

Earth accreted and differentiated over a 10–150 million-year time period, based on the 182hafnium-182tungsten (182Hf-182W) isotope system. 182Hf decays into 182W with a half-life of 9 million years. Hafnium is a lithophile (i.e., an element that preferentially bonds with silicon) and as such portioned into proto-Earth's silicate-rich crust. Tungsten, on the other hand, is a siderophile and as such portioned into the core during Earth's formation. Thus, the observed 182W enrichment in Earth's crust (relative to other W and Hf isotopes) must be a result of 182Hf decay, meaning formation and differentiation must have occurred while 182Hf was still active and present within the system. Thus, the formation of Earth commenced no earlier than 10 million years after the formation of the Solar System (Kleine et al., 2004; Jacobsen, 2005; Touboul et al., 2007). There is some debate about whether a rapid accretion (10–30 million years) or slower accretion (50–150 million years) occurred, based on the timing of the Moon-forming impact (discussed below). This issue currently remains unresolved. The 182Hf-182W isotope system has also been applied to dating Mars (Dauphas and Pourmand, 2011).

The Hadean marks the first geological eon in Earth's history and spans the period from the end of the accretion to the beginning of the Archean eon at 3.8 Ga. During the Hadean, impactors pummeled proto-Earth. The most dramatic event during this period occurred within the first 100 million years of Earth's history. According to the most widely accepted hypothesis, this is when young Earth collided with a Mars-sized object, which led to the formation of the Moon (Canup and Asphaug, 2001). Heat from the impact left Earth's surface in a molten state, and due to the lack of an atmosphere immediately following impact, cooling occurred quickly. Within 150 million years a solid basaltic crust reformed. Steam escaping from the crust and gases released from volcanoes generated the prebiotic atmosphere and contributed to the formation of oceans (see Section 3.2.1). The bombardment of Earth by impactors continued after the Moon-forming impact, resulting in the delivery of the “late veneer.” This late veneer of material is evidenced by the presence of highly siderophilic elements within Earth's mantle and crust (as opposed to the core, where such elements would preferentially appear). Eventually, delivery of the late veneer material essentially ceased. According to the most well-known, though not universally accepted, hypothesis, this terminated with the LHB period (between 4.1 and 3.8 Ga), which marks the most intense period of bombardment after Earth's formation. Some geological models suggest that Earth could not have been continuously habitable during this period because the impacts would have sterilized the planet (Maher and Stevenson, 1988). However, there is some debate as to the global lethality of such impacts (Sleep et al., 1989), and more recent modeling suggests that, if life existed before the LHB, it could have survived (Abramov and Mojzsis, 2009), which leaves an absolute time frame for life's origin undetermined.

3.2.1. How were volatiles brought to Earth?

The emergence of life (as we know it) requires the presence of a variety of volatile elements and species. However, Earth's feeding zone is believed to have been dry and depleted in volatiles (species that readily enter into the gaseous phase due to a lower temperature of vaporization), especially water (based on the volatile-poor composition of the innermost asteroids). As such, delivery of these species (or their precursors) needed to occur during the formation and early evolution of Earth. Water delivery is understood to have occurred throughout the formation of Earth, primarily through the accretion of asteroidal material, with comets and other sources providing limited water. Organics were delivered via asteroids, with a very small amount being derived from cometary material.

Given their ice-rich composition, comets were originally suggested as the primary source of Earth's water (e.g., Owen and Bar-Nun, 1995; Delsemme, 2000). This idea has since been largely discredited due to the low probability of cometary collisions with Earth (Morbidelli et al., 2000) and the high D/H ratio of many, though not all, comets (e.g., Marty and Yokochi, 2006). Although water-poor in comparison with comets, asteroidal material has also been suggested as a water source, given its higher probability of colliding with Earth (Morbidelli et al., 2000; Raymond et al., 2004). This scenario has been altered somewhat by the Grand Tack model (discussed previously, see Section 3.1.3). Currently, our understanding is that the bulk of Earth's current water was derived from material analogous to asteroids and planetary embryos, delivered early in Earth's history, and later from larger planetary embryos that formed the outer, volatile-rich regions of the protoplanetary disk. This model has traditionally been difficult to simulate (Raymond et al., 2009), yet the Grand Tack model has proved to be promising, with the migration of material inward and then later outward within the Solar System providing the required mechanism to deliver volatile-rich material to a dry proto-Earth. Although it is unlikely that a significant fraction of the earliest water delivered would be retained, the later water delivery by embryos would supply sufficient water to account for Earth's water budget. No more than 10% of Earth's water was delivered by comets originating from the trans-uranian region, based on the differences in observed D/H ratio between comets and Earth's current water supply (Morbidelli et al., 2000).

Impacts from comets and asteroids delivered a variety of organics to early Earth, even though they provided only a very small fraction of Earth's water budget (Morbidelli et al., 2000). The interstellar medium, asteroids, and meteorites have been shown to host organics necessary for life (Sephton, 2005; Ehrenfreund and Cami, 2010; Pizzarello and Shock, 2010). The inventory of organics synthesized from the elements in interstellar space contains at least 120 identified species, including the simplest amino acid, glycine (C 2 H 5 NO 2 ). Additionally, formaldehyde, cyanide, acetaldehyde, water, and ammonia—all precursors in different synthesis pathways for amino acids—have been detected. (Amino acids are molecules that contain an amine group, a carboxylic acid group, and a side chain, which play a prominent role in modern biology as the primary building blocks of proteins.) During the formation of the Solar System, some of this interstellar organic material would have been integrated in the presolar nebula (the gas cloud from which the Solar System condensed—see Section 3.1) and incorporated into comets, asteroids, and other planetesimals.

Impacts of these objects (specifically asteroids) delivered volatile organics to ancient Earth (Chyba and Sagan, 1992). Sample return missions provide some of the best data about the composition of early impactors, as returned samples will have the most pristine records of the earliest Solar System (Matzel et al., 2010; Nittler, 2010). Additionally, comets likely contributed small amounts of carbonaceous material during the heavy bombardment (4.5–4 Ga). A surprise from the initial analysis of the Stardust samples retrieved from the comet Wild 2 was that the mineralogy was similar in composition to inner Solar System asteroids (Ishii et al., 2008). Other major extraterrestrial sources of carbon include interplanetary dust particles and carbonaceous meteorites (Chyba et al., 1990; Pizzarello and Shock, 2010). The Japan Aerospace Exploration Agency (JAXA) mission Hayabusa returned samples from the asteroid Itokawa, the study of which confirmed that asteroids are also similar in composition to ordinary meteoritic chondrites (Tomoki et al., 2011), and the OSIRIS-REx mission will return samples from a near-Earth asteroid. These extraterrestrial sources would have added to the endogenous inventory of carbon already existing on early Earth (Chyba and Sagan, 1992). Phosphorus is often the limiting resource for biological systems on Earth, as it is essential for all known life, but the geochemical cycling of phosphate is slow, and most phosphate minerals are insoluble (Pasek, 2008). A challenge for prebiotic chemistry is, therefore, to find sources for reactive and soluble phosphorus (Bryant and Kee, 2006; Pasek, 2008). In particular, meteorites may have been an important source of reactive phosphorus—such as the P-bearing ions pyrophosphate and triphosphate, key components for metabolism in modern life—a likely requirement for the emergence of life (Pasek and Lauretta, 2005).

Once delivered to proto-Earth and early Earth, geological activity provided many of the volatiles necessary for the emergence of life. In particular, Earth's early atmosphere formed via volcanic degassing (see Section 3.2.2), which would have provided N 2 , CO 2 , and water, with small quantities of H 2 , CO, and CH 4 , and negligible amounts of O 2 (Zahnle et al., 2010). This composition was at least mildly reducing, although how reducing it was is debated (Tian et al., 2005; Catling, 2006). Reactions of these volatiles in a weakly reducing early atmosphere could have produced molecular precursors to life (see Section 3.3). In addition, recycling of bioessential elements such C, N, O, and P on modern Earth is important to sustained habitability (see Chapter 5) and may have been crucial in the early development of life on Earth (Sleep, 2010).

3.2.2. What was the environment of prebiotic Earth like?

There is evidence that life on Earth was well established as early as 3.5 Ga (Schopf, 1993; Wacey et al., 2011) and possibly as early as 3.8 Ga (Mojzsis et al., 1996). However, the ages of the most ancient fossils are difficult to determine and typically subject to debate (e.g., Brasier et al., 2002; Bradley et al., 2009). If life was in fact thriving as early as 3.8 Ga or even 3.5 Ga, two possible scenarios emerge. The first is that life may have originated before or during the LHB and survived this tumultuous period in the early history of Earth. This viewpoint is strengthened by evidence that indicates Earth may never have been fully sterilized during the LHB (Abramov and Mojzsis, 2009). A second possibility is that, just after the LHB, the conditions on primitive Earth were conducive to the rapid emergence of life (Oberbeck and Fogleman, 1989; Sleep et al., 2001).

Over time, as the He/H content of the Sun's core increases, it burns increasing amounts of He relative to H in stellar fusion reactions (see Section 3.1.2 for a description of this process). Because He burning gives off more energy than H burning, the Sun has become brighter over the course of Earth's geological history. Going back in time, the Sun was about 30% less luminous 4.5 billion years ago than it is today (Sagan and Mullen, 1972) and 20% less luminous 2.5 billion years ago than it is today. This leads to the faint young Sun paradox: a planet with Earth's current atmospheric composition orbiting the faint early Sun would have had cold global temperatures that would have frozen all water at the surface of the planet, yet there is evidence for liquid water on early Earth. One resolution is that the early atmosphere was probably very different from the atmosphere of modern Earth and may have contained higher levels of greenhouse gases (Pavlov et al., 2000; Haqq-Misra et al., 2008). This is still an area of extensive research, and no definite theory has been widely accepted.

By the start of the Archean, global oceans covered most of the surface of Earth. Evidence of mineral interactions with water suggest that oceans may have started to form by 4.2 Ga (Cavosie et al., 2005) or possibly as early as 4.4 Ga (Wilde et al., 2001). Water would have degassed along with volatiles such as N 2 and CO 2 to form the primitive atmosphere. Condensation of the steam produced from volcanic degassing would have occurred as Earth cooled and led to the formation of global oceans. However, it is widely agreed that the primary source of water on Earth was delivery by material similar to C-type asteroids (Morbidelli et al., 2000) via the Grand Tack model, as discussed above.

3.3. How did life emerge?

Generally, five major stages of the origin of life can be distinguished, as follows:

• First, the simplest organic building blocks were synthesized, starting from the inorganic substrates.

• Second, small organic molecules started self-organizing, giving rise to the larger, more complex organic molecules.

• Third, complex molecules started interacting with each other, giving rise to the first reaction pathways, and the network of reactions among molecules in different reaction cycles began.

• Fourth, macrostructures arose from the spontaneous aggregation of the simpler molecules, which led to compartmentalization, and the chemical reaction cycles started to interact with the compartments.

• Fifth, the system was capable of being shifted from chemical equilibrium, maintaining homeostasis and undergoing evolution.

These stages are shown in Fig. 7. Events of the five described stages could have been overlapping in time and space, and it is often difficult, if not impossible, to uniquely assign particular processes to one stage.

FIG. 7. General schemes of possible stages of prebiotic evolution. (Credit: K. Adamala, adapted from scenario proposed by Eigen and Schuster, 1982)

To understand how life could have originated, we need to understand the types of environments that were present on Earth, the energy sources and raw materials that were available, the chemical reactions that might have been possible given the environmental conditions, and the processes that would have set a sequence of events in motion that resulted in the origin of life.

3.3.1. What do we know about the environment in which life originated?

Section 3.2.2 covers what we know about the overall environment of early Earth (in the Hadean age, 4.5–3.8 Ga), but it is important to consider the dynamics and composition of localized environments (microenvironments) that could have existed and that might have provided suitable settings for the origin of life. Each would have provided unique sources of energy, specific raw materials, and different mechanisms to facilitate chemical reactions. Apart from organic synthesis, three broad categories of reactions would have been required, including concentration of ingredients from a dilute medium, selection of biochemically useful compounds, and polymerization of monomers. Several possible microenvironments are listed in Table 1. The various sources of energy, the availability of raw materials, and the numerous types of chemical processes that could have taken place on early Earth are discussed in the sections below. Stüeken et al. (2013) provided a more detailed review of environmental linkages and their relevance to prebiotic chemistry.

Table 1. Potential Settings for the Origin of Life and a Description of How Each of These Settings Could Fulfill General Requirements for Life to Emerge Potential settings Energy sources Major sources of organic matter Concentration mechanisms Mechanisms enhancing organic reactions Surface ocean/lakes/ponds Lightning, UV radiation, redox gradient Meteorite deposition, Miller-Urey-type processes Mineral surfaces, evaporation/rehydration Clays at the bottom of lakes Sea ice Lightning, UV radiation, redox gradient Uptake from seawater, atmospheric deposition Brine pockets Dehydration Hydrothermal vents Redox gradients, e.g., between H 2 and CO 2 Serpentinization in peridotite-hosted vents Carbonate or sulfide mineral pores Metal sulfides, mineral surfaces, heat Beaches Lightning, redox gradient, radioactive radiation from accumulated uraninite grains, UV radiation Meteorite input, Urey-Miller-type processes, in situ production by nuclear fission Evaporation/rehydration of pore spaces Dehydration, nuclear fission by radioactive uraninite

3.3.2. Which energy sources were available?

Energy would have been required for a variety of necessities for the origin of life: the synthesis of important prebiotic precursors, concentration of potentially reactive solutes, energetically unfavorable polymerization reactions, global mixing of prebiotic reactants and products, and metabolisms (Deamer, 2007; Deamer and Weber, 2010). This energy could have been provided in various environments from ultraviolet (UV) and visible light (see Chapter 7 for an introduction to the electromagnetic spectrum), chemical reduction–oxidation (redox) processes, and geothermal heat. Visible and UV radiation could only have been available near the ocean's surface or on land, since UV radiation cannot penetrate far into water. Geothermal energy could have been available at hydrothermal sites such as vents on the seafloor and provided both heat to increase rates of reactions as well as redox gradients (Simoncini et al., 2011; Russell et al., 2013). Redox gradients are chemical gradients of oxidized molecules that can gain electrons (oxidized species are “reduced” in a redox reaction) and reduced molecules that can donate electrons (reduced species are “oxidized” in a redox reaction). (See Section 4.2.1 for more on redox as a source of energy for life.) These redox gradients provide both reduced and oxidized compounds in relatively close physical and temporal space. This redox disequilibrium creates the potential for energy-releasing redox reactions to occur. In fact, all modern organisms drive metabolic synthesis reactions by using electrochemical energy from redox reactions. Even photosynthetic organisms, which derive their energy from sunlight, use redox reactions as part of the mechanism by which this energy is harnessed (see Chapter 4). Some researchers have therefore suggested that early metabolisms developed in environmental settings where redox gradients occur naturally (Baross and Hoffman, 1985; Martin and Russell, 2007). Lateral transport and mixing could have brought together reaction products from various settings around the globe.

3.3.3. What raw materials were present on early Earth?

One of the most commonly used definitions of life is that it is a chemical reaction system capable of Darwinian evolution (see Chapter 2). The complex chemical reaction systems that exist today must have originated as a result of a long series of simpler, more primitive processes. The initial raw materials for these chemical reactions are the individual chemical elements, which react with each other and combine to form molecules. Section 3.1 (above) explains what is known about how the elements were formed and incorporated into planets, while Section 3.2.1 covers the way in which volatile compounds, which would have been lost during the accretion of Earth due to the intense heat, would have been replenished. While many molecules, including organic carbon molecules, can form abiotically (without the intervention of life), one of the characteristics of life is the presence of highly complex organic carbon compounds that are not known to form by any nonliving processes (see Chapter 7 for more detail). Theories about the origin of life must therefore explain how complex organic molecules could have formed (see Section 3.3.5 below).

3.3.4. What types of prebiotic chemical reactions could have occurred?

The characteristics of the microenvironments on early Earth would have directly influenced the type of chemical processes—prebiotic chemical reactions—that could have taken place and led to the origin of life.

3.3.4.1. Reaction medium

The environment of prebiotic reactions on Earth is considered to be predominately aqueous (Nisbet and Sleep, 2001). Some processes are postulated to take place in the gas phase in the atmosphere (Dobson et al., 2000), but the majority of prebiotic reactions need to be compatible with prebiotic Earth ocean conditions.

The prebiotic ocean was radically different from the modern ocean (Derry and Jacobsen, 1990). As the atmosphere on early Earth was non-oxidizing (Catling and Claire, 2005), the ocean would not have been oxidized, so it is believed to have contained high levels of the reduced form of iron (Fe2+), which may have played a significant role in prebiotic redox reactions. Some have suggested that, unlike the oceans of today, the early ocean was more alkaline, lower in Mg and Ca cations, and lower in NaCl (Kempe and Degens, 1985). Others have concluded that the early ocean was similar to those of the present, perhaps even mildly more acidic given the higher abundance of atmospheric CO 2 gas (Grotzinger and Kasting, 1993). Large gradients in pH and alkalinity probably occurred in the vicinity of hydrothermal vents (Holm, 1992). On modern Earth, vent fluids can range from pH 2 to pH 11, depending on whether they are driven by magmatic heating or serpentinization, and it is likely that both processes occurred under prebiotic conditions.

Many prebiotic chemistry processes may have occurred in lagoons or pools, where tides drove cyclic changes of concentrations that provided the increase of concentration necessary for increasing the yields and efficiency of the prebiotic reactions (Nelson et al., 2001). Arguments against this theory are that the initial concentration of substrates required for the “lagoon theory” was higher than the possible concentration of organic compounds in the primordial ocean and that side reactions and the presence of inhibitors would have decreased the overall yield when the solution was concentrated (Shapiro, 2002). Nevertheless, the so-called “lagoon theory” has strong proponents (Orgel, 2004) and may have been an important component of the global chemical reactor (Stüeken et al., 2013). Another setting that has been gaining support in recent years is the oceanic crust with its associated hydrothermal alteration zones. Multiple experimental and theoretical studies have demonstrated that organic synthesis, polymerization, and selection of compounds can occur under hydrothermal conditions (Baross and Hoffman, 1985; Martin et al., 2008; He et al., 2010; Amend et al., 2013; Barge et al., 2014; Kreysing et al., 2015). The advantages of subaerial lagoons and hydrothermal systems were perhaps combined in terrestrial hot springs (Mulkidjanian et al., 2012; Schrenk et al., 2013). Importantly, hydrothermal vents may exist on icy moons such as Enceladus (Glein et al., 2015), which lacks continental lagoons. If life exists on those bodies, then it would underscore the importance of hydrothermal processes in prebiotic chemistry.

3.3.4.2. Temperature

The range of temperatures available for prebiotic reactions vary greatly. The building blocks of life can be synthesized in interstellar clouds and on comets, in temperatures approaching absolute zero, and near hydrothermal vents where temperatures may be over 100°C. Also, the temperatures postulated for the actual origin of life vary, some hypotheses favoring a hot environment (Miller and Lazcano, 1995), others favoring a cold environment (Bada and Lazcano, 2002). The average temperature on prebiotic Earth may have been higher than it is today (Arrhenius, 1987), but this is a topic of current debate. Given the lower luminosity of the young Sun and uncertainties about the abundance of greenhouse gases and continental area at the time, it is also possible that Earth cooled down relatively quickly to lower temperatures after its formation (Sleep et al., 2001; Rosing et al., 2010; Pope et al., 2012). For prebiotic chemistry, the average surface temperature is less important than the occurrence of liquid water at the surface. Evidence for liquid water dates back to 4.3 Ga (Mojzsis et al., 2001). Favorable temperatures for specific reactions could have been encountered in environmental niches, such as in local ice caps or hydrothermal systems.

3.3.4.3. Sources of catalysis

In all modern life-forms, enzymes lower the activation energy of numerous biochemical reactions necessary to sustain the living cell. In a world of prebiotic chemistry, none of those enzymes would have been available; hence important steps in the origin of life would have had to take advantage of a nonbiological catalytic mechanism or arise with the slower kinetics of uncatalyzed reactions.

Nonbiological catalysts that would have been available on prebiotic Earth include naturally occurring minerals such as clays (Meng et al., 2004; Ferris, 2005), zeolite (Smith, 1998, 2005; Munsch et al., 2001), sulfides (Wächtershäuser, 1988, 1990; Cody, 2004; Roldan et al., 2015), and calcite (Hazen et al., 2001; Hazen and Sholl, 2003). Other mechanisms that facilitated reactions could have been the concentration of reactants in compartments or on surfaces, and evaporation. Examples of concentrating processes include progressive shrinkage of brine pockets in sea ice during freezing (Kanavarioti et al., 2001; Price, 2007, 2009; Pierre-Alain and Hans, 2008), dehydration of pore spaces in subaerial beach sand or vesicular volcanic rocks, enrichment of hydrophobic organics at the ocean-atmosphere interface (Sieburth, 1983), or encapsulation in porous carbonate or pyrite precipitates that form near alkaline and acidic hydrothermal systems, respectively (Russell and Hall, 1997; Baaske et al., 2007). All these mineralogical and hydrological subsettings would have exchanged reactants and products via various mixing processes, which would include ocean and atmospheric circulation; thermal convection in the subseafloor; tidal interaction; and catastrophic events such as impacts, seismic activity, or volcanic eruptions.

3.3.4.4. Causes of stereoselectivity

Stereoselectivity is a key feature of many modern biological reactions (see Chapter 4), but it is unknown at what stage in the origin of life stereoselectivity arose. There are numerous studies on obtaining stereoselective (enantiomerically enriched) products in putative prebiotic reactions between monomers (Popa, 1997). Even the smallest possible enantiomeric enrichment could be significant in prebiotic synthesis, as it could build up over time or in subsequent reactions (Mason, 1991). Some, however, consider that, on prebiotic Earth, obtaining any enantiomerically enriched products was impossible, and the abiogenic synthesis was either achiral or occurred elsewhere (Salam, 1991).

In mixtures of products from processes that researchers agree are abiotic (i.e., do not involve life), such as syntheses on comets and in interstellar clouds, some enantiomerically enriched compounds can be found (Pizzarello, 2006). Some inorganic processes, such as polarized light (Balavoine et al., 1974) or mineral catalysis (Kavasmaneck and Banner, 1977), are claimed to be responsible for enantiomeric enrichment of prebiotic syntheses products. When some chiral asymmetry is introduced to the pool of substrates or catalysts, it can be amplified in the subsequent reactions, resulting in almost enantiomerically pure mixtures (Soai et al., 1995; Blackmond et al., 2001).

3.3.4.5. Yields

Reactions between plausible prebiotic monomers in mixed media generate a huge variety of products; the yields for specific, biochemically “useful” compounds are therefore usually much lower than in controlled experiments with fewer reagents. However, given the fact that prebiotic processes likely had a huge reaction volume and many hundreds of years to accumulate products, single-digit percentage yields may have been sufficient. Also, in prebiotic processes, several analog compounds often have similar activity. Often prebiotic reactions result in a whole class of compounds, different species with a certain functional group, rather than a single well-defined product structure.

The low yields and lack of selectivity are among the major problems of prebiotic chemistry (Sutherland and Whitfield, 1997). Modern biochemical processes, and most probably those of the first cell metabolism, are very selective. This high selectivity is achieved by using advanced enzymatic machinery. One of the biggest challenges of prebiotic chemistry (synthesis of building blocks) and protobiology (assembling the simplest biochemical reaction cycles) is to control the selectivity of the syntheses. One possible solution may be cyclical exchange of reagents and products between environmental niches that each favored and enhanced the abundance of very specific compounds (Stüeken et al., 2013). A recently highlighted example of such a niche is the pore space of rocks that preferably adsorb long over short oligonucleotides (Kreysing et al., 2015).

3.3.5. What processes could have formed the first organic carbon molecules?

Prebiotic chemistry is the study of chemical reactions that result in the formation of organic carbon molecules, without the involvement of biological catalysts. This covers chemical reactions that take place under conditions such as those of the primordial Earth environment or the interstellar medium, where organic molecules can be synthesized from inorganic building blocks (Guillemin et al., 2004). Organic carbon molecules, such as precursors to lipids, nucleotides, amino acids, and carbohydrates, were necessary building blocks for the origin of life, but there is little agreement as to what the principal source would have been (McCollom, 2013; Trainer, 2013).

One of the first origin-of-life experiments, the Miller-Urey experiment (Miller, 1953), produced amino acids and other organic compounds by passing an electric charge through a mixture of gases that were considered to be components of Earth's early atmosphere at the time of the experiment (H 2 O, CH 4 , and H 2 , see Section 3.2). Impactors and interplanetary dust could also have delivered organic material (Chyba and Sagan, 1992; Pizzarello and Shock, 2010; Schmitt-Kopplin et al., 2010) and phosphorus (Pasek and Lauretta, 2005). The chemical processes that occur in hydrothermal vents, particularly those driven by serpentinization, are known to produce organic compounds through abiotic reactions. This could have resulted in the abiotic production of formate, acetate, methane, and larger hydrocarbons, including potentially amino acids, on early Earth (McCollom and Seewald, 2007; Proskurowski et al., 2008; Lang et al., 2010; Huber et al., 2012). Vents of this type may have been common on early Earth if oceanic crust was richer in olivine (e.g., Nna-Mvondo and Martinez-Frias, 2007) and if volcanic and tectonic activity was more widespread than today (e.g., Hargraves, 1986; Martin et al., 2007). Many simple organic compounds can be obtained with high yields in redox reactions catalyzed by iron, which was present in prebiotic, non-oxidizing oceans in much higher concentrations than in present-day oceans (Derry and Jacobsen, 1990) and might have served as a redox catalyst on prebiotic Earth (Cairns-Smith, 1978).

Ammonia, as a source of nitrogen for prebiotic synthesis of amino acids and amines, is readily synthesized by iron-catalyzed reduction of inorganic nitrites in simulated prebiotic ocean conditions (Summers and Chang, 1993). Amino acids and other simple carboxylic acids can also be synthesized in iron-catalyzed redox reactions (Schoonen et al., 2004). Various methods of prebiotic amino acid synthesis have been described (Pascal et al., 2005), and amino acids were products of the first successful prebiotic chemical synthesis experiment (Miller, 1953).

One of the oldest known methods of amino acid synthesis, the Strecker synthesis (Fig. 8), can yield enantiomerically enriched products when catalyzed by chiral catalysts (Li et al., 2003). Although currently known catalysts are not likely to have been available under prebiotic conditions, it is not impossible that some other types of chiral catalysts would have been used in the Strecker syntheses on primordial Earth.

FIG. 8. Amino acid synthesis in the Strecker reaction.

It has been proposed that racemic mixtures of amino acid alkyl and thio-alkyl esters that self-assemble on the water/air interface can undergo spontaneous condensation, forming randomly sequenced peptide chains (Zepik et al., 2002). However, recent studies show that, in the case of short side chain natural amino acids, the reaction does not proceed beyond the stage of di- and tripeptides (Eliash et al., 2004), so it cannot be regarded as a prebiotic way of obtaining enantiomerically pure peptides and selecting amino acid products of a specific chirality.

A readily available source of carbohydrate derivatives on prebiotic Earth was reactions in the atmosphere that resulted mainly in formaldehyde formation. This simplest aldehyde can be formed under a variety of conditions, including UV irradiation of the primordial atmosphere composed of H 2 O, CO 2 , and H 2 (Pinto et al., 1980) or even simply H 2 O and CO 2 (Bar-Nun and Hartman, 1978); electric discharge, possible in a wide range of atmospheric compositions based on CH 4 , H 2 , H 2 O, N 2 , and CO or CO 2 (Miller and Schlesinger, 1984); or photoreduction reactions (Chittenden and Schwartz, 1981). Various other aldehydes and sugars can be synthesized by condensation of formaldehyde (Weber, 1992) or by direct synthesis pathways similar to those of formaldehyde formation. Formaldehyde is also a substrate in the formose-type reactions—the sugar polymerization—which has been proposed as a historically first prebiotic route to obtain various mixtures of sugars (Breslow, 1959; Fig. 9).

FIG. 9. Example of a prebiotic sugar synthesis: elements of the formose reaction system.

It has been shown that amines (as amino acid derivatives or free primary amines) also can effectively catalyze sugar backbone formation (Weber, 2001). Long-chain carboxylic acids can be synthesized in Fisher-Tropsch-type syntheses, producing aliphatic chains and carbonyl groups in the inorganic gas condensations catalyzed on the mineral beds (McCollom et al., 1999). Several methods of prebiotic synthesis of heterocyclic nucleobases, pyrimidines, and purines are known (Pavey et al., 1995; Shapiro, 1999). All four nucleobases can be synthesized from formamide, in the reaction catalyzed by various inorganic mineral catalysts (Saladino et al., 2001). Cyanoacetaldehyde condensation, catalyzed by guanidine hydrochloride, is a possible pathway to pyrimidines, and starting from thiourea, a thiopyrimidine product can be obtained (Robertson et al., 1996). Hydrogen cyanide condensation in the presence of ammonia yields purines and purine derivatives (Lowe et al., 1963).

Phosphorus was probably introduced into prebiotic synthesis at an early stage of prebiotic evolution (Macia et al., 1997). Phosphorus can be obtained from various inorganic sources (Brown and Kornberg, 2004). For example, phosphonic acid, synthesized from sodium phosphite (Fig. 10), was found in the Murchison meteorite (De Graaf et al., 1997). In fact, extraterrestrial delivery of the phosphide mineral schreibersite may have introduced a highly reactive form of phosphorus into prebiotic chemistry (Pasek et al., 2013, 2007).

FIG. 10. Phosphonic acid synthesis based on inorganic sources of phosphorous; pathway proved by the existence of vinyl phosphonic acid in the Murchison meteorite (De Graaf et al., 1997).

A separate branch of prebiotic chemistry research is focused on the problem of polymerization of previously synthesized building blocks. Various studies have shown that amino acids can randomly polymerize to peptides (Plankensteiner et al., 2005), and nucleobases can form nucleic acid chains (Sutherland and Whitfield, 1997) under prebiotic, template-free conditions. The exact mechanism and conditions of such polymerizations are now the subject of extensive study.

All major organic functional groups can therefore be synthesized prebiotically; there are known reactions that can lead to the formation of amines, carboxylic acids, aldehydes and ketones, and heterocycles. All key components of the metabolic reactions can be synthesized, in various pathways leading to the amino acids, carbohydrates, lipids, and nucleobases. Also, inorganic sources of phosphorus and sulfur can be used to introduce these atoms to the organic compounds (Fig. 11).

FIG. 11. Examples of prebiotic syntheses of major organic molecules. 1: nucleobase synthesis, a: formamide condensation (Saladino et al., 2001), b: cyanoacetaldehyde condensation (Robertson et al., 1996); 2: amino acid synthesis, c: Strecker reaction (Li et al., 2003); 3: lipid synthesis, d: Fisher-Tropsch-type syntheses on mineral catalysts (McCollom et al., 1999); 4: phosphorylation of organic compounds, e: inorganic phosphates yield phosphonic acid derivatives (De Graaf et al., 1997); 5: carbohydrate synthesis, f: formose reaction (Breslow, 1959). Red: nucleic acid building blocks; blue: peptide building block; green: membrane building blocks.

3.3.6. What are the proposed sequences of events in the origin of life?

Prebiotic Earth provided many different sites for possible prebiotic chemical reactions, including the open water of the prebiotic ocean, lagoons, surfaces of various minerals, thin layers of organic compounds, the gaseous phase of the atmosphere, or submarine hydrothermal vents. Different prebiotic processes proposed in the literature are placed in different conditions.

The origin of life on Earth might have not been a singular event. There is no reason to assume that our cells’ metabolism represents the only possible type of metabolic process; there could have been multiple origins of life. The evidence suggests that all known life comes from a single ancestor (see below), which implies that if there were multiple origins of life, only one lineage succeeded and survived, proliferating into all known forms of life. This LUCA—the last universal common ancestor of all organisms (Penny and Poole, 1999; Delaye et al., 2005)—was most likely a population of cells resulting from previous prebiotic, and earliest biological, evolution and selection.

It is not impossible that origin-of-life processes are still occurring, although they are far less likely to occur in the modern oxidized environment. Further, on a planet already inhabited it would be extremely difficult for any other form of metabolism to grow well enough to compete with “our type” of life. No effective biogenesis processes have been observed to date (Delaye and Lazcano, 2005).

Research into the sequence of events that led to the origin of life has focused on three essential aspects of modern life: metabolic networks, self-replicating genetic systems, and compartmentalization of the metabolites. Individual researchers tend to focus on the origin of one of these three features as the most essential event in the origin of life, but these debates are influenced by differences in each author's implied definition of life (see Chapter 2). In particular, origin-of-life research is often characterized as a debate between the RNA-first model and the metabolism-first model; the RNA-first model proposes the origin of self-replicating genetic systems before the metabolic networks, and the metabolism-first model proposes the origin of metabolism before the rise of genetic systems.

Debates arise when authors ascribe the status of “life” to one of these systems but not the other. Nevertheless, it is clear that both metabolic networks and self-replicating genetic systems must have been integrated and encapsulated within a compartment before the evolution of the first modern living cell could have started.

3.3.6.1. Metabolic networks

One of the most fundamental observations in biology is that all forms of life share the same core metabolic pathways and biochemical building blocks. This profound fact of life, known as the “unity of biochemistry,” implies that the core metabolism must be ancient and date back to LUCA (see Chapter 4).

Historically, research into the origins of metabolism has been structured in terms of the “organic soup” model that was inspired by the famous Miller-Urey experiment (Miller, 1953) as well as Darwin's vision of a “warm little pond.” Investigators have employed theoretical models, some quite mathematically sophisticated (Kauffman, 1993), to attempt to explain how a shallow pool full of organic compounds could react with each other in such a way that their interactions as well as their chemical compositions increase in complexity until a primitive metabolism is achieved. Little experimental evidence exists, however, for an organic soup that leads to reactions resembling a metabolic network.

The “organic soup” model implies present-day metabolism was a subset of a nearly infinite array of reactions among a random collection of many different kinds of starting materials. Alternatively, it is possible that the steps that led to proto-metabolic networks were more constrained (Morowitz and Smith, 2007). In this view, present-day metabolism is a direct consequence of prebiotic chemistry, rather than an accidental by-product, and the origin of RNA and DNA is intimately linked with these proto-metabolic reactions (Copley et al.,2007).

Support for the constrained network model is also derived from recent studies of the links between metals and the catalytic properties of enzymes in modern metabolic pathways. Carbon fixation pathways, in particular, appear to be ancient and involve a remarkable number of enzymes that require metal cofactors in their catalytic centers. Experimental studies have shown that the metals alone, without any organic components, can catalyze many of the reactions that constitute modern carbon fixation pathways (Huber and Wächtershäuser, 1997; Cody et al., 2000, 2004). Furthermore, the metals involved in these reactions are typically found in abundance at hydrothermal vent systems. The similarities between naturally occurring minerals and carbon fixation enzymes are unlikely to be coincidences, and an emerging model is that the first biochemical pathways evolved based on already operating geochemical reactions (Cody and Scott, 2007; Nitschke et al., 2013; Russell et al., 2013, Sousa et al., 2013).

Peptide-based metabolic networks have also been studied (Goldman et al., 2012). Recent evidence suggests that small, prebiotically plausible peptides could have been catalyzing nucleic acid synthesis and peptide synthesis before the origin of protein catalysts (Li et al., 2000; Gorlero et al., 2009; Wieczorek et al., 2012; Adamala and Szostak, 2013a). For example, the simple dipeptide catalyst seryl-histidine (Ser-His) can drive vesicle growth through the catalytic synthesis of a hydrophobic dipeptide, N-acetyl-l-phenylalanine leucinamide (AcPheLeuNH 2 ), which localizes to the membrane of model protocells and drives competitive vesicle growth in a manner similar to that previously demonstrated for phospholipids. Ser-His has previously been shown to catalyze the formation of peptide bonds between amino acids and between peptide nucleic acid (PNA) monomers (Gorlero et al., 2009). Although Ser-His is a very inefficient and nonspecific catalyst, Ser-His generates higher yields of peptide product in the presence of fatty acid vesicles. As a result, vesicles containing the catalyst generate sufficient reaction product to exhibit enhanced fitness, as measured by competitive growth, relative to those lacking the catalyst. It is therefore possible to observe how a simple catalyst causes changes in the composition of the membrane of protocell vesicles and enables the origin of selection and competition between protocells (Adamala and Szostak, 2013a).

3.3.6.2. Genetic systems

The traditional central dogma of molecular biology states that genetic information always flows one way from DNA through RNA to protein. DNA acts as information storage. RNA acts as messenger. Protein carries out catalytic functions. The elucidation of the central dogma immediately created a difficult “chicken and egg” problem for the origin of life. If DNA originated first, how did it replicate itself without proteins? But if proteins originated first, how was their informational content encoded?

The RNA World model (Gilbert, 1986) for the origin of life is extremely popular because of its elegant solution to this quandary: RNA acted as both a genetic information–storing molecule and a catalytic molecule. Today, RNA serves as the sole genetic molecule in many viruses, and the number of reactions catalyzed by RNA enzymes (“ribozymes”) is ever increasing (Doudna and Cech, 2002; Chen et al., 2007). Therefore, one can envision a primitive cell in which genetic information is encoded by RNA and functions are carried out by ribozymes.

According to the RNA World hypothesis of the origin of life on Earth, all reactions in protocells were catalyzed by nucleic acid enzymes before the origin of protein-based catalysis known from modern biology (Gilbert, 1986; Szostak, 2012). The RNA enzymes can catalyze a wide variety of reactions, encompassing all types of transformations necessary for the protocell activity (Doherty and Doudna, 2001; Lilley, 2003). It is unclear, however, how the very first ribozymes came into existence in the absence of catalysts capable of synthesizing long, functional RNA.

Non-enzymatic RNA polymerization allows synthesis of short RNA oligonucleotides under prebiotic conditions (Joyce et al., 1984; Adamala and Szostak, 2013b). In this reaction, the growing RNA primer strand is elongated by addition of RNA nucleotides activated with a good leaving group, for example, an imidazole or imidazole derivatives (Hey and Göel, 2005; Szostak, 2012). This reaction, while giving a prebiotically plausible route to RNA oligos on early Earth, is not efficient enough to allow for high-yield synthesis of long, active RNA enzymes (Fig. 12).

FIG. 12. Non-enzymatic template-directed RNA synthesis (Joyce et al., 1984). The incoming base (green), activated with 2-methylimidazole (red), binds to the template region (blue).

The RNA World hypothesis states that RNA must have served important genetic and catalytic roles in life's early stages. On the other hand, some authors stress that a complex and unstable molecule like RNA could not have existed on its own without a supporting metabolic network composed of simpler molecules. Indeed, the intricate and universal relationship between RNA and amino acids that led to the genetic code seems likely to have been a very early development in the evolution of life (e.g., Copley et al., 2005).

While the RNA World hypothesis remains very popular with many astrobiologists, some experiments suggest that earliest synthesis and catalytic activity of RNA could have been supported, or supplemented, by different molecules. Other models for the origin of the first genetic system include systems based on peptides (Rode, 1999) or clay minerals (Cairns-Smith and Hartman, 1986).

The prebiotic replication of RNA could have occurred non-enzymatically inside protocells via chemically activated nucleotides (Joyce et al., 1984; Mansy et al., 2008; Adamala and Szostak, 2013b). The coupling of lipid membrane compartmentation (see Section 3.3.6.3) with the possibility of RNA activity and replication, and the division of the protocell compartment, provides a scenario for the possible origin of the interaction between the RNA World and protocell compartments, leading to the formation of the first evolving protocell.

3.3.6.3. Encapsulation

All living cells are encapsulated by lipid membranes that serve essential biological functions including transport, communication, and energy conservation. For example, all organisms today conserve energy for metabolism by establishing a chemiosmotic gradient across their lipid membranes. The prebiotic origin of the lipid membrane is still not fully explained. The open question about the nature of the membrane in LUCA leaves many possible routes to the origin of lipid membranes during the earliest stages of protobiological evolution.

In modern cells, apart from compartmentation, membranes perform several other functions, including energy transduction and transport of organic and inorganic compounds, and provide a docking site for many enzymes. Presumably, the very first role of the membranes was simple encapsulation—isolation of the reaction cycles (i.e., genetic materials or enzymatic peptides) from the environment. This could be done by the simplest amphiphiles, possibly available under the prebiotic conditions: medium-sized (up to C10) chain carboxylic acids.

The main building blocks of modern cell membranes are phospholipids and sterols. Phospholipid glycerol esters and sterols are too complex to be synthesized under abiotic conditions. However, all these compounds can be derived from simple building blocks—sterols from isoprene units, and lipid derivatives from simple unsaturated carboxylic acids. Compounds based on these simplest units could have formed the first membranes that encapsulated biochemical cycles of the protocell (Walde, 1999).

In water, the simplest amphiphiles spontaneously self-organize into bipolar membrane sheets that close into spherical structures known as vesicles (Apel et al., 2002). Lipids in solution form vesicles spontaneously because of their amphiphilic nature; that is, they have one hydrophobic end and one hydrophilic end (Pohorille and Deamer, 2009). Vesicles are commonly accepted as an approximation of the compartments of the earliest protocells (Walde, 2006). Amphiphilic molecules collected from the Murchison meteorite spontaneously form vesicles when placed in aqueous solution (Deamer and Pashley, 1989). The ease with which vesicles form causes many researchers to assume encapsulation occurred almost immediately after lipids became available, either via extraterrestrial delivery or abiotic synthesis (Pohorille and Deamer, 2009). Encapsulation may have strongly affected the dynamics of prebiotic chemistry by segregating molecules and reactions, increasing local concentrations, promoting coevolution of biochemicals, allowing selective permeability, and creating membrane gradients. It is not clear how large biochemicals would have become encapsulated initially, but several models have been proposed (Deamer et al., 2002).

As with the origins of metabolic networks, many researchers view encapsulation as mimicry of geochemical reactions that were already occurring on early Earth. Russell and Martin, for example, developed a highly detailed model in which the origin of life occurs within the iron-sulfide bubbles of hydrothermal vent chimneys (Russell and Martin, 2004). Clays are also known to accelerate the formation of vesicles (Szostak, 2001). Vesicle structures can grow (Chen and Szostak, 2004), divide (Hanczyc et al., 2003), and selectively take up compounds from the environment (Chen et al., 2004). Therefore, investigating properties of the different vesicle systems can give insight into possible routes to the origin of protobiological compartmentalization. The origin of a selective membrane transport system was crucial for the origin of the living cell's homeostasis. Self-sustaining dynamic equilibrium between the cell's interior and the external environment required simultaneous development of two elements: the cell membrane and channels to control the permeability of the membrane. Most known natural ionophores are peptides; therefore, the prebiotic synthesis of peptide-based ion channels and pores may have been an important stage in the earliest, chemical evolution of life.

3.3.7. What are the different approaches to studying the origins of life?

The debate about the origin of life is ongoing, and this continues to be an area of active research. Recently, the field of synthetic biology (creating artificial biological systems) has provided novel insights into the possibilities of different origin-of-life and evolution scenarios. The so-called “bottom up” synthetic biology approaches give insights into the possible routes of assembly of complex biological systems from simpler precursors. These include information about variations in the structure of our genetic material, the way genetic information is interpreted and used by cells, the incorporation of self-replicating genetic molecules within lipid vesicles, the linking of energy generation to vesicle formation, the evolutionary journey from vesicles to “protocells,” and the possibility of creating new artificial life-forms in the laboratory (Chen and Szostak, 2004; Bayer, 2010; Chen and Walde, 2010; Rothschild, 2010; Gibson et al., 2011; Yang et al., 2011; Adamala and Szostak, 2013a). Finding one complete, probable, and experimentally verifiable scenario of the origin of a living cell will also help set boundary conditions for prebiotic evolution, even if this is not the exact scenario that unfolded for the origins of life on Earth. Establishing a working scenario will significantly help the search for possible habitable worlds elsewhere in the Solar System and beyond.

Chapter 4. How Have Earth and Its Biosphere Evolved?

4.1. What does the tree of life tell us about how life has evolved?

4.1.1. What is a phylogenetic tree, and how is it constructed?

The “tree of life,” a diagram that organizes all living biological organisms, is designed in a way that allows us to understand the evolutionary relationship and shared features of those organisms (Gaucher et al., 2010). It demonstrates that all known life has evolved from a single origin, which could have been a single organism or a group of interacting organisms (Woese, 1998).

The tree of life is an example of a phylogenetic tree, which is a diagrammatic representation of how closely related genetic sequences are to each other. Any gene can be used to make a phylogenetic tree, and trees can be made by using DNA, RNA, or amino acid sequences. Different methods for calculating relatedness may be used and can give different resulting trees (see below). Different organisms have different types of genes, so the choice of which gene to use determines which organisms can be included in the tree; any organism that does not possess the relevant gene cannot be included in the tree. For the tree of life, which is intended to cover all life on Earth, the small subunit ribosomal RNA (ssu rRNA) gene is used to make the tree, as this is a gene that is essential to cellular processes, so there is very good reason to believe that all cells possess it (see Section 4.1.2). The degree of relatedness of the ssu rRNA gene is used to define taxonomic groups, which are groups of organisms that are more closely related to each other than to organisms outside the group at different levels. For example, for microbes, 97% identical is generally considered equivalent to a single species, while 95% identical is considered equivalent to a single genus, although no exact percentage is currently agreed upon to define lower-level taxonomic positions. The ssu rRNA tree is therefore commonly considered to demonstrate relationships not just between a single gene but between different organisms as well. One important caveat to this is that, due to horizontal gene transfer (see Sections 2.3 and 4.1.3), it is possible that all the genes in an organism may not have the same evolutionary history. Viruses are not cells, do not contain the ssu rRNA gene or an equivalent, universally conserved genetic feature, and so are not included in the ssu rRNA tree, and there is no consensus as to whether they should be considered alive (see Sections 2.3 and 4.1.2).

To make a phylogenetic tree, genetic sequences are compared; organisms with closely related sequences are located in close proximity, and organisms with distantly related sequences are located far apart on the tree (Fig. 13). A phylogenetic tree therefore provides information about the progress of evolution by showing the relative order in which the DNA sequence of a gene has changed over time. Prior to the advent of genetics, the relatedness between two different organisms was determined by comparing physiological characteristics and physical appearance. However, organisms with similar characteristics (such as similarly shaped beaks for birds) may not have a common ancestor if they obtained those features from convergent evolution instead of divergent evolution. In divergent evolution, the organisms inherited the characteristic from a common ancestor, and it changed into slightly different forms in each descendent branch. In convergent evolution, two different groups of organisms evolved the same characteristic completely independently. Phylogenetic trees can tell us whether organisms with shared physiological characteristics have a common ancestor or whether those traits evolved independently. However, it is important to understand that the vast majority of sequences on a tree come from organisms that are currently alive (although extinct organisms can be included if DNA is available from them); these are the tips of the branches of the tree. Historical information about how the gene sequence has changed is deduced from the structure of the tree—including where the nodes, or branch points, are—which is dependent on the method used to construct it (Fig. 13). Different methods include the rectangular phylogram, the rooted rectangular cladogram, and the bifurcating unrooted tree. The first two of these have a root, which specifies the most evolutionarily ancient branch. The difference between these two is that branch lengths on the phylogram are proportional to evolutionary distance, whereas all branches are equal in length on the cladogram. The third tree shown here—the bifurcating unrooted tree—is unrooted and used when it is not clear which branch is the most ancient.

FIG. 13. Nodes and branches compose a phylogenetic tree. Taxonomic units are represented by modern organisms located at the tips/leaves of branches. Nodes are the connection points before the divergence and represent common ancestors before bifurcation of two species. Branches can be flipped freely about the nodes; therefore the determination of which taxon appears in which branch of the node is arbitrary. There are various visual representations of trees; shown here are the (a) rooted “rectangular phylogram,” (b) rooted “rectangular cladogram,” 