Introduction

Three decades after the Viking missions, which failed to detect any biorelics, not even a slight trace of organic activity, the question as to Mars having harboured habitable conditions, if not life, has been dramatically reopened. A key ingredient, liquid water, might have covered large fractions of early Mars over sustained periods, as indicated by the ongoing space missions. This chapter presents our understanding of the evolution over time of the Martian water reservoirs.

It took centuries for Mars to evolve (in human minds) from a ‘planet of death’ to a ‘world of life’: its colour no longer referred to blood (thus its being named after the God of war) but to rust; rust: thus water; water: thus life. These later syllogisms have persisted until very recently, translating the transcendental quest of life far beyond the scientific sphere. And yet: is Mars actually covered by ferric material? If so, is liquid water responsible for the oxidation? More importantly still, would that be sufficient for life to have emerged on Mars? Without direct means to address (and possibly answer) such questions, Mars has always been viewed as the closest and most favourable planet to have harboured extraterrestrial life. A variety of similarities between Mars and the Earth could support the ‘plurality of worlds’ that was conceived as the operational dogma.

Introduction

Since the beginning of this century, astronomers have discovered hundreds of exoplanets, almost all of them being giant planets. However, we expect the possibility of detecting relatively smaller exoplanets similar in size to our Earth soon. Among the thousands of exoplanets that will be discovered by the end of this century, some may host life. Obviously the possibility of finding life on another planet is not only a function of the number of discovered planets, but also of the stability of life on those planets: if life is only a glimpse, the search for life will be much harder! We have under our feet a marvellous example demonstrating that one kind of life may be hosted on a planet (Earth) for billions of years. This relative stability of life on Earth seems to be strongly correlated with the stable environmental conditions that have prevailed on the surface of our planet for several billion years (1 Ga = 109 years). This is the reason why this chapter is devoted to deciphering and understanding the ‘stable’ climate conditions on Earth since 3.8 Ga. Observation of our neighbouring planets in the Solar System teaches us that the conditions for the development of life (habitability) and sustainability at the surface of a planet are not widespread – at least in the Solar System. Nowadays, Mars is a very cold desert experiencing dust storms, whereas Venus is a burning hell whose surface is totally hidden by a thick greenhouse-gas atmosphere.

The high stress resistance of the bacterium Deinococcus radiodurans

Deinococcus radiodurans (D. radiodurans), initially isolated in canned meat that had been irradiated at 4000 grays in order to achieve sterility (Anderson et al., 1956), is a bacterium belonging to a bacterial genus characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents, including ionizing radiation, ultraviolet light and desiccation (Battista and Rainey, 2001).

Initially, D. radiodurans was named Micrococcus radiotolerans because of its morphological similarity to members of the genus Micrococcus. Subsequent studies led to its reclassification into a distinct phylum within the domain Bacteria and this bacterium was renamed Deinococcus radiodurans, the Greek adjective deinos meaning strange or unusual. Deinococcaceae were isolated from diverse environments after exposure to high doses of ionizing radiation. Among this family, containing to date more than 20 identified members, D. radiodurans is by far the best characterized. D. radiodurans cells are non-motile, non-spore-forming and are obligate aerobes that grow optimally at 30°C in rich medium. On agar plates, they are pigmented and appear pink-orange. In liquid media, cells divide alternately into two planes, exhibiting pairs or tetrads (Figure 22.1A).

Ionizing radiation, when applied to any living organism, leads to the formation of highly reactive radicals (e.g. hydroxy radicals) and can cause a variety of DNA damage, such as DNA single- and double-strand breaks and base modifications.

Before the Solar System

The formation of the Sun and stars

The Sun is somewhat a late-comer in our Galaxy, the Milky Way. It was born 4.6 Gyr ago (4.5685 Gyr ± 0.5 Myr, to be precise, from the decay of specific radioactive heavy elements in the most primitive meteorites – see below). This is to be compared with the age of the Universe, constrained by the best theoretical fits to the observed spatial fluctuations of the ‘cosmic background radiation’ to be 13.7 Gyr after the Big Bang, within 2%. When galaxies form is less certain, but current estimates give a time lapse of less than 1 Gyr after the Big Bang – implying that our own Galaxy has an age of over 12.7 Gyr and that the Sun was born over 8.1 Gyr later. So at the time the Sun formed, our Galaxy was already sufficiently evolved by successive generations of stars that it presented no major differences with the one we observe today. Therefore, we can safely derive conclusions about the distant birth of the Sun from observations of contemporary young stars.

In a nutshell, from various observations we know that bright nebulae, including some famous ones like Orion, the Eagle or Carina nebulae, are ‘stellar nurseries’ (Figure 8.1), where stars like the Sun form in clusters of thousands of low- to intermediate-mass stars. A few massive stars, like the Orion Trapezium, for which the highest mass is of order 45 Mʘ also form in these stellar nurseries.

Introduction: some conceptual remarks on metabolism

Metabolism is the set of enzymatic reactions that allow living beings to use external energy sources to drive the building of their biochemical components from external chemical sources and also to carry out energy-consuming functions, such as osmotic and mechanical work. The role played by gene-encoded enzymatic catalysts is one of the essential properties of life. Since their stability is finite and there is a need for constant replacement, enzymes are themselves products of metabolism (Cornish-Bowden et al., 2004). Thus, the proteome (i.e. the totality of proteins and their concentrations that exists in a particular cell state) is a product of the metabolome (i.e. the totality of metabolites and their concentrations that exists in a particular metabolic state). This situation gives rise to the ‘metabolic circularity’ or ‘recursivity’; a concept needed for a complete understanding of metabolism (Cornish-Bowden et al., 2007).

Extant metabolic networks are certainly complex, with hundreds or thousands of concatenated enzymatic reactions. Since there is a limited number of coenzymes (i.e. the special reactants that help enzymes to perform their catalytic functions), recurrently used by different enzymes, and some central metabolites are true crossroads between different lines of chemical transformation, complex networks emerge. From a topological perspective, metabolic networks show a power-law distribution of connectivity (Fell and Wagner, 2000). In other words, most metabolites are poorly connected whereas a few of them (coenzymes and metabolic crossroads) support many connections.

Introduction

Human common experience tells us that the individuals of a particular species reproduce among themselves to produce a progeny which tends to resemble their parents. This inheritance of characters from one generation to the following one is known as ‘vertical inheritance’. Although the nature of the physical support of the genetic information transmitted through generations remained mysterious until 1944 when DNA was shown to constitute such support, Gregor Mendel had already described the laws that control this kind of inheritance in plants in the nineteenth century. The vertical inheritance of favourable modifications is one of the pillars of the Darwinian theory of evolution: natural selection can be effective only if the advantageous characters selected can be transmitted to the progeny. This central role of vertical inheritance in evolution was adopted later on in the twentieth century by the neo-Darwinian evolutionists. For example, they proposed the ‘biological species concept’, which states that a species is defined by the capacity of its members to reproduce among themselves, namely, a species concept that, instead of being based on morphological characters as in the classical definitions, was based on the capacity of vertical inheritance. In addition, the vertical transmission of the genetic information with changes due to selection defines evolutionary lineages of organisms that are distinct from the rest of the lineages (for example our own Homo sapiens lineage). As Darwin stated in his The Origin of Species, the evolutionary relationships between those lineages are best represented by a phylogenetic tree.

Introduction

Looking for a definition of life raises various issues, the first being its legitimacy. Does seeking such a definition make sense, in particular to scientists? I will successively refute the different arguments of those who consider that looking for such a definition makes no sense, and then propose good reasons to do just that, but also add some caveats regarding what sort of definition is sought. After considering definitions proposed in the past, I will examine various present-day definitions, what they share and how they differ. I will show that the recent suggestion that viruses are alive makes no sense and obscures discussions about life. Finally, I will emphasize two important recent transformations in the way life is defined.

Philosophical and scientific legitimacy of a definition of life

Two questions immediately emerge. Are we seeking a definition of life or a definition of organisms? And what kind of definition should be sought? Two types of definition are, in fact, traditionally distinguished. A definition may aim to give the essential characteristics that causally explain the existence of the category of objects considered. Or a definition may be of more limited scope: to establish a list of properties that are necessary and sufficient to define this category of objects and to distinguish them from objects belonging to other categories. If one adopts the first kind of definition it will be possible to define life. If one opts for the second, one will look for a definition of organisms.

Introduction to artificial life

Would a theoretical biologist be surprised to be told that computer use and software developments should help him make substantial progress in his discipline? It is doubtful. There is a long tradition of software simulations in theoretical biology to complement pure analytical mathematics which are often limited to reproducing and understanding the self-organization phenomena resulting from non-linear and spatially grounded interactions of the huge number of diverse biological objects. Nevertheless, proponents of artificial life would bet that they could help them further by enabling them to transcend their daily modelling/measuring practice by using software simulations in the first instance and, to a lesser degree, robotics, in order to abstract and elucidate the fundamental mechanisms common to living organisms. They hope to do so by resolutely neglecting much materialistic and quantitative information deemed as not indispensable. They want to focus on the rule-based mechanisms making life possible, supposedly neutral with respect to their underlying material embodiment, and to replicate them in a non-biochemical substrate. In artificial life, the importance of the substrate is purposefully understated for the benefit of the function (software should ‘supervene’ to an infinite variety of possible hardware). Minimal life begins at the intersection of a series of processes that need to be isolated, differentiated and duplicated as such in computers. Only software development and usage make it possible to understand the way these processes are intimately interconnected in order for life to appear at those crossroads.

Characteristics of a habitable planet

What is a habitable planet? There is no formal definition at present, but the term is generally understood to mean a planet that can sustain life in some form. This concept is of limited use in practice since the conditions required to support life are poorly constrained. A narrower definition of a habitable planet is one that shares some characteristics with Earth, and hence one that could support at least some of Earth's inhabitants. A commonly adopted minimum requirement is that a planet can sustain liquid water on its surface for geological periods of time. Earth is the only body in the Solar System that qualifies as habitable in this sense. One advantage of this definition is that it can be used to categorize hypothetical and observable planets in a relatively straightforward manner, and we will use it in the rest of this chapter. However, one should bear in mind that not all life-sustaining environments will be included under this definition. Tidally heated satellites of giant planets, like Europa, are likely to possess oceans of liquid water beneath a layer of ice (Cassen et al., 1979), but these objects would not be ‘habitable’ according to the conventional usage.

Planets that can support liquid water at their surface must have an atmosphere, and surface temperatures and pressures within a certain range. These planets will occupy a particular range of orbital distances from their star that is commonly referred to as the star's habitable zone (HZ).

Introduction

The scope of life models and simulations is as broad as that of biology. It encompasses studies on cell metabolism, intercellular communication, immunology, physiology, development, cognitive processes, molecular evolution, population genetics, epidemiology etc. However, for the purpose of the present book, we will focus on the use of computing and simulation approaches as tools for studying the origins of life. Under the global denomination of ‘automata’, a large number of different frameworks have been used to implement and test models accounting for the emergence of life.

Despite their diversity, these approaches call upon the same fundamental grounding: bottom-up model building. Instead of identifying state variables of the whole system and formulating their relationships by equations, the idea is to start with elementary components and then specify how they interact with one another and with the environment. The whole system behaviour is therefore not an a priori descriptor of the model, but rather emerges from within the system. This kind of reasoning is obviously appropriate for research on the origins of life, where the main question is precisely to find out how a property (life) which is valid for the system (a living being) has emerged out of multiple elements (chemical components), which are not individually endowed with this property.

Introduction

At one end, the Earth, we have complex molecular structures giving rise to life; at the other end, the diffuse interstellar medium (hereinafter ISM), we have atoms floating in an almost empty space. How, when and where did the transition from unbound atoms to complex molecular structures occur? Had it occurred already in the dense molecular-cloud phase of the ISM and/or during the formation and evolution of the protosolar nebula? These are the questions whose answers will help in understanding whether, as the Nobel prizewinner C. De Duve wrote, ‘The building blocks of life form naturally in our galaxy and, most likely, also elsewhere in the cosmos. The chemical seeds of life are universal’ (De Duve, 2005). What we know for sure is that a long process, of a few billions years, brought matter from the diffuse state of the ISM to the condensed state of planets (Earth), comets and meteorites (see Chapter 7 of this volume). We also know that primitive meteorites, the oldest fossils we have from the Solar-System formation aeons, contain the ‘seeds of life’ that De Duve alluded to: amino acids.

In this chapter we will show that the formation process of solar-type stars, while bringing matter from a diffuse to a condensed state, also leads to increasing molecular complexity. Although solar-type star-forming regions are not the only places in the ISM where organic molecules are found, two reasons lead us to focus here on them: (1) they are among the places with the richest harvest of organic molecules; and (2) they are regions similar to our Solar-System progenitor, so that the organic chemistry observed there is directly linked to the possible inheritance of terrestrial life from the ISM.

Naturally occurring physical and chemical constraints of life and the biosphere

Deep-sea and deep-subsurface environments have been recognized to be among the most extreme biotopes potentially placed very close to an interface between the habitable and the uninhabitable terrains for life on Earth. The concept of habitability appears difficult to define, particularly in terms of an astrobiological perspective. Nevertheless, it is widely accepted that the harshest habitats for life, such as deep-sea and deep-subsurface environments in this ‘highly habitable’ planet, the Earth, may be approximated to the most plausible environments for extraterrestrial life in some ‘hardly habitable’ planets and moons of our Solar System. Thus, to understand the limits of life and the biosphere in the deep-sea and deep-subsurface environments of the Earth could be a key for elucidating the potential habitability of extraterrestrial life in the Universe. In this chapter, the possible factors that limit life and the biosphere on the Earth are overviewed and discussed from insights gained from the recent biogeochemical and geomicrobiological explorations in the deep-sea and deep-subsurface biosphere.

In the deep-sea and deep-subsurface environments many physical and chemical parameters limiting the activities of microbial life have been elucidated. The best example is temperature. In the terrestrial and oceanic surface environments, liquid water boils at around 100°C, while with an increasing pressure (hydrostatic), liquid water can be present at up to 373°C for pure water and 407°C for seawater (critical points) (Bischoff and Rosenbauer,1988).

Introduction

Biomineralization is the process by which organisms form minerals; this is a widespread phenomenon and more than 60 minerals of biological origin have been identified up to now (e.g. Lowenstam, 1981; Baeuerlein, 2000; Weiner and Dove, 2003). Particular attention has been paid so far to eukaryotic biominerals, including the siliceous frustules of diatoms (e.g. Poulsen et al., 2003; Sumper and Brunner, 2008), the calcitic tests of foraminifers (e.g. Erez, 2003) and the aragonitic skeleton of modern scleractinian corals (e.g. Cuif and Dauphin, 2005; Meibom et al., 2008; Stolarski, 2003). However, prokaryotes can form minerals as well (Figure 27.1; Boquet et al., 1973; Krumbein, 1979). For instance, stromatolites are carbonate deposits that are usually interpreted as the result of bacterial biomineralization. Interestingly too, some bacteria, called ‘magnetotactic’, can produce intracellular magnetite crystals seemingly aimed at directing their displacements using the local magnetic field (Blakemore, 1982). While eukaryotes obviously synthesize minerals exhibiting very specific structures (although ascertaining quantitatively why it is obvious might be an issue), the biogenicity of prokaryotic biominerals is more difficult to infer. The morphology, the structure (e.g. crystallinity, presence/absence of defects) and the chemistry (including the isotopic composition) of these prokaryote biominerals have, however, frequently been proposed as potential biosignatures (e.g. Konhauser, 1998; Little et al., 2004). Such biosignatures have been used to infer the presence of traces of life not only in ancient terrestrial rocks but also in extraterrestrial rocks such as the Martian meteorite ALH 84001 (McKay et al., 1996).