Four basic observations

Progress in cosmology in the past few decades has also led to new insights into the global question of the emergence of intelligent life in the universe. I am referring not to discoveries that are related to very localized regions, such as the detection of 200 extrasolar planetary systems (at the time of writing), but rather to properties of the universe at large.

In order to set the stage properly for the topics that follow, I would like to start by presenting four observations with which essentially all astronomers agree. These four observations define the cosmological context of our universe and form the basis for any theoretical discussion.

1. Ever since the observations of Vesto Slipher in 1912–22 (Slipher, 1917) and Edwin Hubble (1929), we have known that the spectra of distant galaxies are red shifted.

2. Observations with the Cosmic Background Explorer (COBE) have shown that, to a precision of better than 10−4, the cosmic microwave background (CMB) is thermal, with a temperature of 2.73 K (Mather et al., 1994).

3. Light elements, such as deuterium and helium, have been synthesized in a high-temperature phase in the past (see, for example, Gamow, 1946; Alpher et al., 1948; Hoyle and Tayler, 1964; Peebles, 1966; Wagoner et al., 1967).

4. Deep observations, such as the Hubble Deep Field, and the Hubble Ultra Deep Field, have shown that galaxies in the distant universe look younger. Specifically, they are smaller (see, for example, Roche et al., 1996; Ferguson et al., 2004), and they have a higher fraction of irregular morphologies (see, for example, Abraham et al., 1996). This is what one would expect from a higher rate of interactions and from the “building blocks” of today's galaxies.

In 1913, long after Charles Darwin had argued for the fitness of organisms for their environment, the Harvard chemist Lawrence J. Henderson pointed out that the organisms would not exist at all except for the fitness of the environment itself. “Fitness there must be, in environment as well as in organism,” he declared near the outset of his classic work, The Fitness of the Environment (1913, p. 6). While most of Henderson's contemporaries ignored the philosophical implications of this work, as John Barrow and Frank Tipler have noted, it “still comprises the foundation of the Anthropic Principle as applied to biochemical systems” (1986, p. 143).

Henderson pointed out the uniqueness of hydrogen, carbon, and oxygen in the chemistry of living organisms. Another two decades would pass before astronomers would establish that these were three of the four most abundant elements in the cosmos; but Henderson was at least aware that these atoms were commonly found in the stars and planets. In his treatise, he began with the properties of water, just as William Whewell had done eight decades earlier in his far more teleologically oriented Bridgewater Treatise (1833).

Henderson grouped the notable qualities of water under two headings: (1) thermal properties and (2) interaction with other substances. As far as he was concerned, these were empirical, observed properties with minimal theoretical explanation. (Remember that Rutherford's nuclear atom was still a future concept, while quantum mechanics and the nature of the hydrogen bond lay many more years ahead.)

Introduction

It is now believed that our universe was created around 13.8 billion years ago. Our planet earth came into existence around 4.5 billion years ago. For nearly a billion years or so after it was formed, the earth was stark and bereft of life. The matter contained on earth was inorganic with relatively small molecules. There were endless rock formations, oceans, and an atmosphere.

And then there was life.

The problem of how life was created is a fascinating one. Our focus is on looking at life on earth and asking how it works. The lessons we learn provide hints to the answer to the deep and fundamental question pondered by our ancients: Was life on earth inevitable? Then there are the questions posed by Henderson [1]: Is the nature of our physical world biocentric? Is there a need for fine-tuning in biochemistry to provide for the fitness of life in the cosmos – or, even less ambitiously, for life here on earth? Surprisingly, as we will show, a physics approach turns out to be valuable for thinking about these questions.

All living organisms have a genetic map consisting of a one-dimensional string of information encoded in the DNA molecule. An essential question that one seeks to answer is how an organism converts that information into a three-dimensional living being.

Life has many common patterns. All living cells follow certain simple “universal” themes.

Introduction

Life as we know it today completely depends on water. Without water, life would be either impossible or totally different. Thus, a deep understanding of the relationship between water and other simple building blocks of life is crucial to gain insight into how prebiotic life forms could have originated and evolved and whether the physical laws of this universe are in any way predisposed to the emergence of life (Henderson, 1913, 1917; Eisenberg and Kauzmann, 1985; Ball, 2001).

It is unlikely that under prebiotic conditions the complex and sophisticated biomacromolecules commonplace in modern biochemistry would have existed. Thus, research into the origin of life is intimately associated with the search for plausible systems that are much simpler than those we see today. However, it is also plausible that these simple building blocks of life might have been amphiphilic molecules in which water could have had an enormous influence on their prebiotic molecular selection and evolution, because water can either form clathrate structures or drive these simplest molecules together (Ball, 2001).

Structure of water

Water is both simple and complex. It is simple because it consists of only one oxygen atom and two hydrogen atoms (see Figure 20.1). But at the same time it exhibits highly complex molecular behavior (far exceeding the multibody problem in mathematics, planetary science, and astrophysics) wherever numerous water molecules interact dynamically (Eisenberg and Kauzmann, 1985; Ball, 2001).

Introduction

If we inspect our surroundings on earth, we will see a myriad of materials, objects, natural and artificial constructions (many resulting from the activities of the human species), and, of course, an enormous variety of living organisms, from the simplest bacteria to the most complex animals. We can also inspect the sky and observe other planets, stars, galaxies, and clusters of galaxies far away in our expanding universe, leaving us wondering whether life can also be found elsewhere. Is it all an inevitable product of such a finely tuned construct as the universe seems to be, given appropriate local conditions? At a very basic level, it must be. We are an evolved species co-existing with many other simpler species on which we depend. All are made of the same chemical elements resulting from that fine-tuning that allowed their kinetically controlled formation in big stars and created our planet and the fields to which all life is exposed. Life must be a possibility included in a finely tuned cosmos – we sense it in our minds. We also know that it has evolved and diversified here on earth, although the reasons for this – that is, the factors that determined evolution – are not so obvious. This question has intrigued philosophers and scientists through the ages, and it reached public awareness toward the end of the eighteenth century.

This book is part of a two-part program focused on the broad theme of “biochemistry and fine-tuning.” Fitness of the Cosmos for Life began with a symposium held at Harvard University in October 2003 in honor of the 90th anniversary of the publication of Lawrence J. Henderson's The Fitness of the Environment. The symposium was an interdisciplinary, exploratory research meeting of scientists and other scholars that served as a stimulus for the creative thinking process used in developing the content of this book. The chapters in this volume were developed following the symposium and take advantage of the rich technical and interdisciplinary exchange of ideas that occurred during the in-person discussions.

The Fitness of the Cosmos program has provided a high-level forum in which innovative research leaders could present their ideas. In the spirit of multidisciplinarity, the fields represented by the meeting participants and book contributors are diverse. From the sciences, the fields of physics, astronomy, astrophysics, cosmology, organic and inorganic chemistry, biology, biochemistry, earth science, medicine, and biomedical engineering are represented; the humanistic disciplines represented include the history of science, philosophy, and theology.

This volume explores in greater depth issues around which the 2003 meeting was convened. It addresses the broad inquiry Is the cosmos “biocentric” and “fitted” for life? Keeping this question in mind, the authors presented their thoughts in the context of their own research and knowledge of others' writings on topics of “fitness” and “fine-tuning.” This work pays tribute to the groundbreaking inquiry of L. J. Henderson.

Introduction

The Earth is certainly, so far, the most interesting planetary body for astrobiology since it is still the only one where we are sure that life is present. However, there are many other bodies of astrobiological interest in the Solar System. There are planetary bodies where extraterrestrial life (extinct or extant) may be present, and which thus would offer the possibility of discovering a second genesis, the nature and properties of these extraterrestrial living systems, and the environmental conditions which allowed its development and persistence. Mars and Europa seem to be the best places for such a quest. On the other hand, there are planetary bodies where a complex organic chemistry is going on. The study of such chemistry can help us to better understand the general chemical evolution in the Universe and more precisely the prebiotic chemical evolution on the primitive Earth. Comets are probably the best example, especially considering that their organic content may have also been involved in the prebiotic chemistry on the primitive Earth.

Titan, which is the largest satellite of Saturn, may cover these two complementary aspects and is thus an interesting body for astrobiological research. Moreover, with an environment very rich in organics, it is one of the best targets on which to look for prebiotic chemistry at a full planetary scale. This is particularly important when considering that Titan's environment presents many analogies with the Earth.

Introduction

A glance at a bacterium, and a humpback whale, will reveal not only two immensely complex organisms, but also two very different life forms. Each is, in its respective way, constrained by a whole series of physical and chemical factors. One of the most obvious aspects is the fluid environment in which they live, albeit at scales that in being separated by about eight orders of magnitude are determinative of radically different behaviors. The bacterium's world is submillimetric, and accordingly it is dominated by constraints of viscosity. Motion involves the remarkable method of flagellar propulsion (the nearest thing to a wheel in biology; see, for example, Berg, 2003). When its flagella stop beating, the bacterium ceases its movement in a distance equivalent to the diameter of a hydrogen atom. The humpback whale, by contrast, occupies a liquid environment with which we are somewhat more familiar, although our swimming ability is feeble compared with the whale's oceanic travel range of thousands of kilometers. Fully aquatic, the humpback occupies a world that to us is both alien, with its complex system of echolocation, and familiar, with its ability to communicate – which includes singing.

Despite such wide divergences, the basic point of commonality is that both bacteria and whales live in environments where the physical controls imposed by the physico-chemical properties of water – be they viscosity or acoustic transmission – predetermine what is biologically possible. To this simple example could be added many other physical and chemical constraints.

Introduction

A famous metaphor in integrative biology refers to the relationship between environmental constraint and evolutionary change as “the ecological theater and the evolutionary play” (Hutchinson, 1965). In the forty years since the penning of that phrase, the relationship between play and stage has been a matter of vigorous and fascinating debate. The issues have profound implications, not only for our scientific account of the evolutionary process, but also for our expectation of what life might look like on other planets and, indeed, for our philosophical and theological understandings of what it might mean on this one.

The controversy involves differing conclusions about the roles of contingency and constraint in evolutionary history, including, among other things, the way in which fundamental regularities of the physico-chemical environment, or “stage,” influence the unfolding of the evolutionary drama. On the one hand, many prevalent expositions of the evolutionary play suggest that the fundamental or ultimate actors are genes, not organismic (much less mental) agents (Dawkins, 1976, 1998; Dennett, 1995). The drama itself is a theater of the absurd, a plotless improvisation using whatever props are contingently provided by the environment (Gould, 1989, 1996). Contingency is held to exert determinative influence on history, and, according to Stephen Gould's widely cited metaphor, “we would probably never arise again even if life's tape could be replayed a thousand times” (1989, p. 234).

Introduction

In his great classic The Fitness of the Environment (1913), Lawrence J. Henderson examined the fitness of the basic chemical constituents and chemical processes used by living organisms on earth and of the general environment, including the hydrosphere and atmosphere of the earth, and argued that the laws of nature and the properties of matter appear uniquely and maximally fit for life as it exists on earth.

The inspiration for this book arises from the creation of the Origins Institute (OI) at McMaster University, which formally started operating in July 2004. Many of the greatest questions that face twenty-first century scientists are interrelated in fundamental ways. The OI was established to address several of these major interdisciplinary questions from within a broad framework of ‘origins’ themes: space-time, elements, structure in the cosmos, life, species, and humanity.

The origin of life has a privileged position in this great sweep of scientific endeavour and ideas. It addresses, arguably, the most surprising and most fundamental transition to have arisen during the entire evolution of the universe, namely, the transformation of collections of molecules from the inanimate to animate realm. Substantial progress in solving this great problem has been achieved relatively recently but may be traced back to ideas first proposed by Darwin. The great excitement in our era is the realization that physical properties of planetary systems play an important role in setting the stage for life, and that microbial life, on Earth at least, is incredibly robust and has adapted itself to surprisingly ‘extreme’ conditions. Progress can be traced to four scientific revolutions that have occurred over the last two decades:

1. the discovery, since 1995, of over 200 extrasolar planets (one which is only 7.5 times more massive than the Earth) around other stars and the possibility that at least a few of these systems may harbour life-sustaining planets;

2. the discovery of extremophile microorganisms on Earth that have adapted to conditions of extreme temperatures, acidity, salinity, etc., which considerably broadens the range of habitats where we might hope to find life on other planets in our solar system and other planetary systems;

3. […]

Introduction

The remnants of ancient life on Earth are extremely rare and difficult to interpret, since they have been modified by billions of years of subsequent geological history. Therefore, any understanding of the evolution of Earth's biosphere will heavily rely on the study of extant organisms for which complete genome sequences are already available or will eventually be established. A central point is the phylogenetic inference of the tree of life from such genomic data. Serving as a unifying framework, this tree will allow the disparate and often incomplete pieces of information gathered by various disciplines to be collected and structured. In the first half of this chapter, we will briefly explain the principles of phylogenetic inference and the major artefacts affecting phylogenetic reconstruction. Then we will introduce phylogenomics, starting with a theoretical presentation before illustrating the explained concepts through a case study centred on animal evolution. In the second half, we will review our present understanding of eukaryotic evolution and show how recent knowledge suggests that secondary simplification is an important mode of evolution that has been too long overlooked. We will also summarize the current views about the root and the shape of the tree of life. Finally, we will attempt to debunk two common hypotheses about the early evolution of life, i.e., a cell fusion at the origin of eukaryotes and a hyperthermophilic origin of life.

Introduction

Darwin was obsessed with origins. The book with which he distinguished himself as among the greatest thinkers ever to have walked on Earth, The Origin of Species by Means of Natural Selection or, The Preservation of Favoured Races in the Struggle for Life, was intended as only an abstract to a ‘big species book’ (Gould, 2002) about organisms and their environments and how they interact to elicit change over time. In a letter to Hooker (Darwin, 1871), Darwin speculated on how life, itself, might have originated, including the now infamous notion that it started in a ‘warm little pond’. As Einstein would do for physics with space and time less than a half-century later (Minkowski, 1952), Darwin, in his magnum opus and personal correspondence, accomplished for biology: ecology and evolution were inextricably linked forevermore.

But origins posed problems for Darwin, even concerning particular groups, such as metazoans (i.e., animals): ‘[t]here is another and allied difficulty, which is much graver. I allude to the manner in which numbers of species of the same group, suddenly appear in the lowest known fossiliferous rocks’ (Darwin, 1859; in the section titled ‘On the Imperfection of the Geological Record’).

In this chapter, we consider the origin of metazoans as a model for the origin of life. Considering only a group within the tree of life offers us three advantages in demonstrating our thesis (which is described in the subsequent paragraph).