The Earliest Life on Earth

THE EARLIEST LIFE ON EARTH

PERHAPS AS EARLY AS ABOUT 18 SEPTEMBER; ABOUT 715,000 METERS UP THE LINE

The world of living things we know today is the product of an inconceivably long, complex, and varied process of organic evolution. But how and when did this evolutionary process start? How did life arise from non-life, and is it possible for us to know with any degree of certainty how this happened? And there is a more fundamental question: what is life, in the biological sense of the word? What definitions make the most sense and possess the greatest empirical support? And when we look for the deep origins of life on the Earth, to see how the biosphere of which we are now a part came into being, what exactly are we looking for?

Credible Definitions of Life

As we saw in the previous chapter, the early Earth developed conditions favorable for the emergence of life. But defining the line between the living and the non-living is more difficult than it looks at first. There are self-organizing patterns that appear spontaneously throughout nature, as we have seen, patterns brought about by the passage of energy through a set of particles or other units of matter. If by such a process a pattern grows and develops, such as formations of crystals, would we say that such a pattern is alive? I think we would be hard-pressed to do so. So what is the fundamental defining characteristic of life? Many of us would probably say that it is the potential for self-reproduction. A living thing reproduces by gathering energy from the environment. It does this in order to maintain both its own physical equilibrium and to produce a new living entity with characteristics similar to its own. So it would seem, at first, that the ability to reproduce is the rock-bottom, absolute defining characteristic of living things.

And yet, viruses live in the shadowlands between the living and the non-living. They are incapable of self-reproduction, but by seizing a portion of a living object they can indeed reproduce prodigiously. Are they alive, or are they merely potentially alive? And what of living things that cannot reproduce during their lives? Are they not alive, after all? What is the specific set of properties all living things share in common that distinguish them from the non-living?

Biologist William Schopf points out that all living things in the world today share a common chemical heritage. Living things are primarily constructed out of hydrogen, oxygen, nitrogen, and carbon, all very simple elements, very ordinary stuff. Living beings may have other elements in them, such as sulfur and phosphorous, but these four essential elements (what Schopf simply calls CHON) make up an astounding 99.9% of all living systems.¹ So perhaps this is where our search for a definition of life can begin. Is life simply that which possesses a specific kind of chemical composition?

Obviously, it is not enough to simply know the chemical composition of life. What do living things characteristically and uniquely do? In the early 1940s Erwin Schrödinger said that living things, above all, are entities that gather energy to temporarily stave off the effects of entropy. Entropy in this instance is understood as total physical equilibrium—in biological terms, death.² Schrödinger said that the organization and structure produced by life were distinctive in the physical realm, different from the behavior of any other thing, and yet the behavior of life and its tendency to resist disorder were fully consistent with the known laws of physics.³ So is the defining characteristic of life the ability to temporarily stave off the effects of entropy?

In 1944 Oswald Avery discovered DNA, and in 1953 James Watson and Francis Crick, assisted by Rosalind Franklin, elucidated DNA’s structure. It was now clear that DNA was the “molecule of life”. DNA is the polymer (complex molecule) that, in conjunction with ribonucleic acid, RNA, holds the “instructions” by which structure and organization in living things are brought about. So can we argue that living things are physical objects that by definition possess nucleic acids? Certainly every living thing or potentially living thing in the world today does. But is there more to living things than the mere possession of the requisite nucleic acids? After all, living things are active participants in the environment, entities which perform a variety of functions and which are affected by multitudinous events. How can we make our criteria more rigorous? 

Hungarian biologist Tibor Gánti, in a 1971 work, laid out a very convincing set of criteria by which life can be defined. He distinguishes between the absolute criteria of life and the potential criteria. The absolute criteria, in his view, are the following:

1. Living systems are individual units which have properties in combination that the individual components that comprise the system do not possess in isolation. [In my view, Gánti is saying that living entities are essentially synergistic.]

2.  Living systems are engaged in metabolism. Metabolism is the use, by a living entity, of energy-matter ingested or absorbed from the environment, energy-matter which is changed into forms the living thing can use to maintain its life functions. Certain forms of dormant life, such as seeds, may, however, be possible exceptions to this criterion.

3. A living system displays a degree of stability. Changes in its surroundings do not change its basic functions. [Of course, Gánti is discussing environmental changes that fall within a living thing’s survival parameters. Obviously environmental disruptions can kill something off.]  Living things display both the capacity for homeostasis [the maintenance of internal stability through the operation of internal feedback mechanisms] and excitability [the ability to respond to stimuli].

4. Living systems carry information within themselves that is necessary for their construction, development and functioning. This information is contained in subsystems within the living thing, and this information is acted on by other subsystems capable of “reading” and using it.

5.  Living things possess internal processes that need regulation. These internal processes must be regulated so that the living thing can go on living. Even a living entity that is not reproducing requires such regulated systems.

Gánti then describes the criteria that define the potential properties of life:

1.  Living systems have the potential for reproduction. Not all members of a group of living things possess this ability, nor do all cells in an animal body, but at least some individual entities in each instance must have this capacity if the group or individual animal is to survive.

2. A living system must have the capacity for hereditary change and evolution. Obviously, since an individual organism does not evolve, this criterion applies only at the group or population level.

3.  Living systems tend to be mortal. This is not an absolute criterion because it is thought that certain cells (such as cancer cells) and some kinds of bacteria may be immortal. But in general, living things die, and it is definitely one of their potential traits.⁴

I think these criteria are as rational and complete as any I have seen, and I think them a reasonable basis on which to proceed. They incorporate much of the thinking of other biologists as well. So in looking for the origin of life, we will be looking for physical entities that were the chemical precursors of the first objects to display these criteria, and then finally the first objects that actually exhibited such characteristics themselves.

Hypotheses About the Origins of Life

By the end of the 19^th century the advent of evolutionary ideas in biology and the advances made in the studies of chemistry and geology had made it evident to most scientifically-educated people that the Earth was very old, that life forms had changed over time, and that the stories handed down by the various religions about the origins of the Universe and humanity were nothing more than creation myths, the products of particular cultures and their narrative literary traditions. These myths, frequently allegorical in nature, were colorful and of literary and historical interest, but they were of no scientific value whatsoever. (See the chapter Myths: Biological in Origin, Cultural in Dissemination in a later volume)

As the decades of the 20^th century passed, evidence about the natures of the Universe, the Earth, and life poured in from every science. Evolutionary concepts deepened, augmented by the tremendous discoveries being made in genetics, which ultimately led to what is known as the Neo-Darwinian synthesis. But one intractable problem remained: how had life itself originated?

The search for a fully naturalistic solution to this problem has been underway for many decades. The Russian biochemist Alexander Oparin began writing about this issue in the 1920s. Oparin originally was seeking to refute vitalism, the view that living things consist, in part, of non-material or ultimately mysterious features. Oparin wanted a fully materialistic explanation of life. He ultimately concluded that the early Earth must have had a non-oxygenated atmosphere, and that the crucial processes that brought about life on Earth had begun in the ocean. He hypothesized that the coagulation of organic compounds in that setting led to the formation of droplets that displayed rudimentary metabolic functions. It was by this process, Oparin believed, that the transition from non-life to life had begun.⁵ British biologist J. B. S. Haldane also thought that the early Earth had had a non-oxygenic atmosphere, and he conjectured that the earliest life was actually a viral-like entity, half-way between life and non-life, that displayed primitive gene-like properties. Ultimately there emerged the Oparin-Haldane hypothesis. It rejected vitalism completely and asserted that life had a totally materialistic basis. It assumed the early Earth had a strongly reducing atmosphere and this atmosphere, in conjunction with a “primordial soup” of elements in the ocean and inputs of electrical energy, had produced first organic monomers (simple molecules) and then organic polymers.⁶

As we saw, the ultimate organic polymers are DNA and RNA. We have come to understand that DNA and RNA are so complex that both must have appeared only after an extensive process of chemical evolution. To explain how life really began, it is therefore necessary to find the chemical processes and precursors from which nucleic acids evolved. Gradually, as our knowledge of nucleic acids has grown, the issues surrounding the beginning of life on this planet have come into sharper focus. It is now clear that the challenges are greater than the first investigators into life’s origins had imagined. Consequently, it now appears that the following questions must be answered in order to determine how life originated:

1. How did amino acids and nucleotides (a chemical base, a sugar group, and a phosphate group) come to exist?

2. How were amino acids and nucleotides assembled into macromolecules like proteins and nucleic acids, a process which requires the presence of catalysts?

3. How were these macromolecules able to reproduce themselves?

4. How were these reproducing macromolecules assembled into systems which had boundaries that separated them from their environments (in the manner of cells)?7

If we begin to consider these questions solely by looking at modern life forms, we run into a thorny issue immediately:

The essential problem is that in modern living systems, chemical reactions in cells are mediated by protein catalysts called enzymes. The information encoded in the nucleic acids DNA and RNA is required to make the proteins; yet the proteins are required to make the nucleic acids. Furthermore, both proteins and nucleic acids are large molecules consisting of strings of small component molecules whose synthesis is supervised by proteins and nucleic acids. We have two chickens, two eggs, and no answer to the old problem of which came first.⁸

In response to such difficulties, certain researchers have argued that life did not originate on this planet at all, but rather was brought here by objects from space that crashed into the Earth, objects which contained organic molecules. This hypothesis is known as panspermia, although its current advocates say that it should be understood more broadly. It can be traced back to a Swedish chemist named Svante Arrhenius, who in the early 20^th century hypothesized that microorganisms from extraterrestrial worlds had drifted to Earth and seeded this planet with its first living things. But panspermia’s most ardent defenders have been the late Fred Hoyle, a noteworthy astronomer who argued comets were the chief source of our planet’s earliest life, and one of his former students (and a prominent scientist in his own right) Chandra Wickramasinghe. (Hoyle, as we have already seen, made major contributions to the study of stellar nucleosynthesis; see The First Stars) Unfortunately, in promoting panspermia, these two researchers published a series of increasingly tendentious scientific papers in the 1970s and 1980s. These papers made claims so shaky and so open to criticism by other scientists that some researchers concluded sadly that Hoyle’s convictions had become a kind of “cometary religion.”⁹

There are major objections to the panspermia hypothesis, notable among them the observation that it merely pushes the questions about the rise of life back to an unknown extraterrestrial location without explaining how life arose there. And if life can originate beyond the Earth, and survive journeys of enormous distances through inconceivably inhospitable environments, why would the Earth itself not be a suitable environment for life’s origins, given the Earth’s many advantages? Although its advocates are adamant in their contention that they have accounted for the presence of life on this planet, and although their studies of what are known as extremophiles (life forms that can exist in extremely harsh conditions, such as conditions found in interplanetary or interstellar space) demonstrate the possibility of panspermia, most researchers believe that there is no need to look beyond our own world for an explanation of terrestrial life. Yes, many researchers think extraterrestrial organic compounds may have augmented or complemented the development of life on the Earth, but these same scientists contend that these compounds were not the origin of terrestrial life. Additionally, advocates of panspermia sometimes have the unfortunate habit of asserting that if a prominent scientist states that some life forms could have arrived from space then these same scientists are, in effect, saying that they must have done so, and that these scientists have therefore “endorsed” panspermia.¹⁰ This is a deliberate twisting of the facts, and it only makes panspermia’s claims to be objectively scientific more dubious.

If we assume a terrestrial origin for life on this planet, there must have been some simple and direct way by which pre-organic monomers, the simplest kinds of molecules, were formed. In order to understand how such monomers must have been produced, we need a credible picture of conditions on the early Earth. The first real experiments on the origin of life in fact tried to replicate such conditions, based on certain assumptions about the early Earth’s atmosphere, primarily those of the Oparin-Haldane hypothesis. These experiments were conducted in the 1950s by a University of Chicago graduate student, Stanley Miller, and U. of C. Professor Harold Urey. Miller and Urey used an apparatus that employed water, methane, ammonia, and hydrogen gas. Electrical energy was passed through the apparatus periodically. The water represented the early ocean. The methane, ammonia, and hydrogen represented the postulated early atmosphere. The electrical discharges represented the lightning that was assumed to be commonplace on the early Earth. The two investigators reasoned that among the chemical compounds produced in this process there might very well be organic ones. The net results of these experiments were, however, ambiguous. Certain amino acids were produced, but only two of them are significant in the production of proteins. Moreover, Miller and Urey’s assumption that the early atmosphere was dominated by methane and ammonia is no longer thought to be valid. So although there were indeed intriguing results from these experiments, they do not appear to lead us in the right direction.¹¹

Among origin-of-life researchers there is a fundamental divide which seems to exist between those who argue that metabolic-like processes, through the harnessing of catalyzing chemicals, must have preceded replication, and those who argue that replication itself must be given primacy. There are eloquent arguments in favor of each position. In assessing these viewpoints, we must consider hypotheses about self-organizing tendencies in the physical world, the nature of the early Earth’s atmosphere, the role of the primitive world ocean, the surface conditions prevalent on the Earth in its first several hundred million years, the nature of molecular evolution in general and the evolution of enzymes in particular, the effects on nascent life forms of hostile environmental factors such as intense radiation, the ability of membranes to form and in so doing to encompass small quantities of liquid (the origin of protocells), and a variety of other factors, all of which must be considered. Most significantly, hypotheses about life’s origins must be tested through the use of the most rigorous experimentation. What are some of the scenarios that have emerged, therefore, since the days of the Oparin-Haldane hypothesis and the Miller-Urey experiments?

Natural selection, as we will see in more detail below, is the process by which organisms flourish or decline based on their reproductive success in a given environment. It is usually thought of only in association with life forms. Manfred Eigen, a Nobel laureate who has devoted much of his career to studying the origin of life, has argued that natural selection, rather than being the result of the existence of living things, brought about the emergence of living things by acting on non-living, but self-replicating molecules. Natural selection, he says, is a physical principle that operates in defined situations. When non-living entities begin to replicate, he believes, natural selection will begin to work.¹² Eigen contends that the prebiotic world was chemically diverse enough to allow for the emergence of a cycle where very short sequences of RNA and very basic kinds of enzymes evolved and in effect drove each other’s development in a reciprocal manner.  However, Eigen’s critics claim that he has not adequately accounted for the emergence of his postulated short RNA sequences, and that the production of proteins by these simple kinds of replicators would be difficult. So while Eigen has given us valuable insight into how a system can evolve once nucleic acids exist and the genetic process has begun, his postulated scenario may not have occurred.¹³

The emergence of RNA was a crucial event in the evolution of complex life forms. In 1986 Harvard biochemist Walter Gilbert coined the phrase The RNA World in an essay. Gilbert hypothesized that RNA could have been self-organizing and self-catalyzing, and indeed ribonucleic acid has the interesting property of being able to both store information, as DNA is able to, and catalyze reactions, as proteins are able to. But the production of full-fledged RNA from a prebiotic environment is simply too unlikely, given the extreme difficulties inherent in constructing nucleotides. The generation of ribose, a simple sugar, from a non-organic setting seems to be particularly problematic as well. Further, nucleotides display chirality, or “handedness”.  They come in forms that mirror each other but which cannot be superimposed on each other. (Through the application of specific tests, chemists assign a designation of left-handed or right-handed to particular molecules.) If the building blocks of nucleic acids are nucleotides, and if they can produce chains that have both left-handed and right-handed varieties, this presents a problem. RNA can be built from either variety (although in our cells it is entirely of the right-handed kind) but it cannot grow from a mixture of left- and right-handed varieties. This has led many scientists to abandon the idea that RNA was the original molecule of life. They are instead looking for prebiotic molecules that are nonchiral, ones which can be readily synthesized and which can form polymers. Important progress has been made in this area of research, and it is now thought that RNA replaced its antecedents and began functioning independently.¹⁴

In an article published in American Scientist in 2009, physicist James Trefil, biologist Harold J. Morowitz, and physicist Eric Smith laid out a hypothesis about the origin of life that does not require the presence of RNA or DNA in its earliest steps, and may not require the presence of even a rudimentary cell. Their hypothesis is an example of the metabolism first viewpoint. The three scientists postulate that the process that led to life may have begun with basic, simple chemical reactions taking place in porous varieties of minerals. These reactions would not have required the presence of complex enzymes. Small molecules, arranged in simple networks in certain minerals, would have served as catalysts for these reactions. If a network of small, simple molecules generated its own constituent parts, it would be the core of a recursive chemical system, a system these researchers call self-amplifying. [I would call it synergistic.] These scientists hypothesize:

that such a system arose and that much of that early core remains as the universal part of modern biochemistry, the reaction sequences shared by all living beings. Further elaborations would have been added to it as cells formed and came under RNA control, and as organisms specialized as participants in more complex ecosystems.¹⁵

Feedback mechanisms that would eliminate side reactions, mechanisms these researchers call “self-pruning” features, would be absolutely essential. They would concentrate reacting molecules to a limited series of pathways in the same way metabolism does, and advocates of metabolism first are seeking these mechanisms.

And why must these initial chemical steps on the path toward life be of the most basic kind? To eliminate the need for highly improbable random events, such as the appearance of complex nucleic acids out of a prebiotic environment. In the metabolic process today, we can see preserved the actions of simple networks of small molecules. Why, the authors ask, did the non-living world bring forth such reactions to begin with? It may have been something as simple as the fact that the laws of physics tend to “prefer” low states of energy to high ones. Just as water seeks the lowest point in whatever area it is found in, moving from a high energy state to a lower one by forming and flowing in channels down the side of a hill, so chemical channels were created on the early Earth. The researchers contend that “reservoirs of energy” accumulated in the non-living world of our planet’s first eon, masses of electrons and certain other ions “seeking” to release their energy. The earliest chemical reactions that led in the direction of life facilitated the release of this energy by establishing biochemical channels acting in concert with each other.

The authors point out that in metabolism as seen in the modern world the citric acid cycle, or Krebs cycle, breaks down organic molecules into carbon dioxide and water. Oxygen is used to effect this break-down, and the outcome is energy. Organic molecules are, in a sense, being “burned” as fuel. But the cycle can work in reverse, taking in high-energy electrons from carbon dioxide and water and using them to construct large molecules out of smaller ones. Trefil and his colleagues maintain that this reverse-cycle, known as the reductive mode of energy transfer, must have operated on the early Earth since the earliest atmosphere was non-oxygenated. (This reductive process still operates in certain anaerobic organisms.) The reductive mode gives electrons a method of lowering their energy content and allows for the efficient organization of molecular networks operating in a cyclic fashion. This simple cycle can then interact with other chemical cycles. The process that produces the essential oils that are used in the construction of cell membranes is a pathway that starts through such interaction.

These simple chemical reaction systems are an early manifestation of order (or in my view, emergence). This order, the authors believe, existed prior to the onset of replicating molecules. The three researchers argue that there logically must have been a stage during which these primitive systems evolved in the direction of molecules with replicative abilities. It was these early replicating molecules that allowed for the processes of natural selection (see below for a discussion of this process) to begin operation.

The authors believe that research along these lines, looking for the rise of chemical and biological complexity by examining the most basic form of metabolism, will show us the true pathway to life. They conclude:

If this notion turns out to be true, it will have important implications for a deep philosophical question: whether we should understand the history of life in terms of the working out of predictable physical principles or of the agency of chance. We are, in fact, arguing that life will appear on any planet that reproduces the environmental and geological conditions that appeared on the early Earth, and that it will appear in order to solve precisely the sort of “stranded electron” problem [electrons that are unable to lower their energy state] discussed above. [Emphasis added]¹⁶

One of the most arresting hypotheses about the origin of life comes from chemist A. G. Cairns-Smith. The title of his 1982 study Genetic takeover and the mineral origins of life tells us that he approaches this subject from a unique perspective. He begins his study by reviewing the various hypotheses that had been offered up to that time about the origin of organic polymers, and pointing out their implausible aspects.¹⁷ Cairns-Smith argues that the essence of the origin of life problem is a genetic one: “What would have been the easiest way that hereditary machinery could have formed on the primitive Earth?”¹⁸ He believes that the genetic mechanisms we see in operation today are the advanced replacements for the first, ultra-simple hereditary mechanisms.¹⁹  It is his contention that these ultra-simple systems first emerged as crystals in clays, forming what he calls “inorganic genes”.²⁰  He argues that crystals can store information (through structural defects of various kinds) and replicate structures.²¹ Remarkably, he further contends that these clay structures were subject to natural selection and began self-propagating. Later, he argues, as carbon and nitrogen became incorporated into such systems, energy from sunlight (a primitive form of photosynthesis) helped form chemical structures that ultimately permitted the formation of amino acids, which began the road to nucleotides and true organic evolution.²² (By the way, the rather advanced chemistry in this text forces a layperson like me to depend heavily on the sections which summarize the evidence.)

It is a remarkable contention: the first living things were replicating minerals, clays which possessed crystalline genes. Many observers have examined this hypothesis, but it must be said that very few of them have agreed with it. Cairns-Smith himself has always hoped that experiment can produce (or discover) clay-based life, but for now his ideas must be considered simply interesting conjectures, without any major empirical support.

Could life have emerged around the hydrothermal vents of the deep oceans? Geneticist Paul Lurquin has examined the issue in some detail.  Hydrothermal vents are formed when cracks in the Earth’s crust, which is considerably thinner under the oceans, bring water in contact with magma. The water becomes superheated, but because of the immense pressures at those depths it does not boil. Rather, underwater “chimneys”, the hydrothermal vents, form. These vents are frequently the homes of distinct ecosystems. Lurquin points out that the combination of high pressure and heat can produce chemical conditions in which the production of every amino acid and the formation of small proteins is possible. Experiments which replicate the conditions surrounding hydrothermal vents have been done, and, in Lurquin’s words they have found that,

a whole catalog of organic molecules, including amino acids and pyruvic acid (an important metabolite ubiquitous in living cells) could be formed at high pressure and temperature from H²S, [hydrogen sulfide] CO, and CO², as well as ammonia (from nitrate) and nitrogenated hydrocarbons. Interestingly, iron sulfide (FeS) was absolutely necessary to catalyze these reactions, to generate hydrogen for reduction reactions, and to concentrate and stabilize the reaction products. This mineral is abundant in the earth’s crust in the form of pyrrhotite. Although the formation of nitrogenous bases as found in RNA and DNA has not been reported, hydrothermal vent chemistry seems to be much more than just paper chemistry [a hypothesis without supporting evidence].²³

So perhaps it is possible that chemical evolution began in the depths of the world ocean, a product of the geological conditions of the Hadean Eon. The evidence is indeed intriguing, and research along these lines is promising.

There is a debate among biologists and other scientists over the issue of autocatalysis, the ability of molecules to manufacture their own catalysts. Stuart Kauffman, whom we encountered earlier, in our discussion of self-organizing systems, has contended that once particular kinds of pre-biotic polymers reach a critical stage of complexity their interactions will become autocatalytic. Because of this tendency, in Kauffman’s view, life is an expected phenomenon in such a chemical setting as the Earth. Kauffman’s hypothesis has come under serious criticism, and even if such autocatalytic systems did emerge their exact nature and function have still to be determined. Moreover, if they existed they may have been much simpler than Kauffman originally proposed. However, the contention that some sort of autocatalytic molecules were a necessary (but not wholly sufficient) condition for the emergence of life on this planet seems to be gaining support. Indeed, it is difficult to see how pre-organic molecules could have begun to evolve without the ability to utilize energy from the surrounding environment to sustain their reactions.²⁴

Origin of life research continues unabated. As evidence about the nature of the early Earth continues to accumulate, as research into hydrothermal vents expands, as increasingly sophisticated tools of mathematical analysis are used more and more extensively to evaluate such issues as the reproductive capacity of autocatalytic sets, and as all the diverse aspects of this problem are probed, more progress will be made. Most crucially, as the scientific community’s members continue to review and question each other’s work, suggesting avenues of research, asking hard questions, demanding rigorously-conducted experimentation, and expanding lines of communication among various disciplines, the likelihood grows that a definite, empirically-demonstrable explanation of the origin of life on Earth will be discovered at some point in the 21^st century. Such a discovery is not a certainty, because as this very brief survey of hypotheses has shown (and I have omitted several others), the problems surrounding this issue are as difficult as any faced by the sciences. But if we do discover the processes of chemical evolution that led to the emergence of the universal common ancestors of all living beings in the world today, it will be an event as momentous as any in human intellectual history.

Evidence of the Earliest Life on Earth

In trying to determine when life emerged on this planet, we are constrained by the fact, as noted in the previous chapter, that the geological record of the Hadean Eon is very sketchy. Schopf contends that the bombardment of the early Earth by extraterrestrial bodies precludes an origin of life, at least as we know it now, any earlier than 3.9 billion ybp. He points out that violent bombardments by such bodies as meteorites would have sterilized the surface of the Earth, wiping out any life forms that had managed to emerge.²⁵ Therefore, it appears that the earliest forms of life could have evolved no sooner than the last era of the Hadean Eon, and in fact may not have appeared until after the onset of the Archean (sometimes Archaean) Eon, a period of time beginning anywhere (according to various estimates) from 4.0 to 3.8 billion ybp and waning by 2.5 billion ybp. And as we have seen, the earliest replicating beings were probably no more than organic molecules, the result of pre-existing metabolic processes at the microscopic level, none of which could have left any physical trace. This has made the search for the first signs of life challenging, to say the least. But there are hard data beginning to emerge from this search.

In a paper published in Nature in 1996, six researchers argued that carbonaceous structures (carbon-based and exhibiting carbon isotopes consistent with life-forms) found in sediments from western Greenland indicate that life forms may have been there more than 3.8 billion, and perhaps earlier than 3.85 billion ybp. These scientists argue that the structural complexity of the first known microfossils indicates that there must have been simpler life forms that existed prior to their evolution, and that even though the Earth may still have been under periodic bombardment by extraterrestrial objects 3.8 billion ybp, such bombardment did not eliminate these particular structures and possible early life forms²⁶ But these results have been challenged by other researchers on geological grounds, and there is by no means any consensus of opinion supporting the conclusions of these six scientists. There is, however, more solid evidence that has been found in Greenland of organic activity dating back to 3.7 billion ybp, so perhaps Greenland’s place in life’s origins was indeed primary. Evidence gathered from Australia tells us there may have been photosynthesizing microorganisms, known as cyanobacteria, present on the Earth as early as 3.465 billion ybp but the evidence that they were indeed cyanobacteria has been challenged (see below). There are also carbonaceous microstructures in South Africa dated from around 3.4 billion ybp.²⁷

The purported Australian microorganisms were discovered in the Apex Chert of western Australia and may, if fully confirmed, turn out to be the oldest fossils yet discovered. In the early 1980s Schopf and a team of his colleagues began work on physical evidence from this region, and in 1993 Schopf was confident enough to announce their findings in a scientific paper. In his view, there appear to be 11 different species in the sample, and Schopf believes that at least six of these ancient samples are kinds of cyanobacteria, the first living things to engage in oxygenating photosynthesis (a key point). At the very least their structure appears to resemble that of cyanobacteria. Schopf has presented detailed evidence demonstrating, to his satisfaction, that these samples are indeed kinds of bacteria and, judging from the age of the rocks in which they are embedded, are at least 3.465 billion years old, plus or minus 5 million. (The date, determined in this instance by measuring the rate of decay from ²³⁸Uranium to ²⁰⁶Lead in the Apex Chert sample, is remarkably precise in the field of radiometric dating.)²⁸

Schopf’s contention that the Apex Chert finds are true fossils has been seriously contested. In a response to Schopf’s work published in Nature in 2002, eight researchers, including a number of geologists, contended that the structures Schopf interpreted to be microfossils can be explained as purely geological phenomena, the result of hydrothermal activity. They argue that before these finds can be labeled as organic that all other alternative explanations must be explored. These scientists are not completely rejecting the possibility that rock formations such as the Apex Chert could hold evidence of biological activity. But they are saying that this particular case has not been proved.²⁹  In the same issue, Schopf and several of his colleagues vigorously defended their hypothesis, contending that the most advanced spectroscopic evidence supports the contention that these samples are organic in nature.³⁰  Research published in 2011 strikes something of a middle position, questioning the biological interpretation of the Apex Chert finds while pointing out that the chert itself contains carbonaceous structures consistent with the presence of microbial life.³¹  Suffice it to say that the debate is on-going and as of this writing has not been resolved.

It remains to be seen if any fossils older than 3.5 billion years old can be uncovered. Perhaps they will be unearthed in one of the promising regions of Australia, South Africa, or Greenland. But the odds are not good, inasmuch as the structures that preceded these bacteria may not have had cell walls that lent themselves to fossilization. And fossilization itself is rare. After its death, over 99.9% of all living matter is ultimately recycled into other living matter. Fossils are drawn from the less than 0.1% that has not been recycled.³² In all probability we will have to rely on indirect evidence to piece together the story of life from its earliest origins.

Looking for the LUCA

All life on Earth is thought to belong to one of three domains. These domains include the eukaryotes (living things composed of cells which possess a nucleus and various substructures, all of which are known as organelles), bacteria (single-celled microorganisms that possess neither a nucleus nor organelles, and which are therefore kinds of prokaryotes), and archaea (the smallest of all microbes, prokaryotic cells with genetic characteristics different from those of bacteria, and which are often found in the harshest and most extreme environments). There was discussion at the time of this writing that there may a fourth domain of life, consisting of microscopic life forms so genetically unusual that they seem only distantly related to other living things, but as yet no consensus of opinion supports this hypothesis.³³ All domains are thought to be evolutionary offshoots of the Last Universal Common Ancestor, known by the shorthand designation LUCA. In tracing the history of life on our planet from the LUCA, scientists have devised an organizational scheme commonly referred to as the Tree of Life. There are scientists, such as J. Craig Venter (who led the key project that helped elucidate the human genome) who consider the Tree of Life to be an outdated metaphor, preferring to think of the “tree” as more of a bush-like structure with many very small branches. But Venter, contrary to the assertions of some who are seeking to undermine evolutionary theory, still points out that even the most exotic, unique, and rare sets of genes that have been discovered, a group of 12 out of the approximately 60 million that have been studied, are DNA-based. Venter readily accepts the notion that life has a shared, common ancestry, and postulates that the earliest split-off from the last common ancestor took place about 3.5 billion years ago, when the archaea and the bacteria began evolving in their own separate directions.³⁴

Recent evidence has confirmed that all life on this planet is indeed derived from a common source. The most convincing argument yet presented in support of this contention has come from biochemist Douglas Theobald of Brandeis University. In a paper published in 2010, Theobald first laid out the chief general supports in favor of common ancestry, and in support of organic evolution in general. They are as follows:

1.    The evolutionary development of various life forms over time, their phylogeny, is reflected in the distribution of life forms over the surface of the Earth, a distribution known as biogeography. In other words, life forms tend to be where   we might logically expect them to be based on their evolutionary history.

2.    The paleontological record strongly agrees with the phylogenetic record.

3.    There are many transitional fossils that demonstrate the kinds of changes that life forms have undergone over time.

4.    The analysis of morphological characteristics allows us to construct a consistent  hierarchical relationship among various life forms.

5.     Similar life forms contain many homologies, that is to say similar physical  structures performing similar kinds of functions.

6.     Molecular phylogenies confirm phylogenies based on morphology.³⁵

Theobald then notes some critically important points. First, the existence of a universal common ancestor does not rule out the possibility that life had several separate origins. But it does mean that if multiple origins did occur, one of two things must have happened: A. Only one line of life forms survived and all the others were driven to extinction, or B. The various life forms that had emerged genetically converged into a single species.  Second, Theobald explains that the universal common ancestor was not necessarily, nor even probably, a single organism. As he states:

[the idea that the UCA was not necessarily a single life form is] in accord with the traditional evolutionary view that common ancestors of species are groups, not individuals. Rather, the last universal common ancestor may have comprised a population of organisms with different genotypes that lived in different places at different times.³⁶

Theobald analyzed similarities among various proteins found in each domain, taking into account the effects of possible horizontal gene transfer (the spread of genetic material among life forms other than by means of parental transfer). In his analysis, Theobald found that the odds against these proteins being the product of separate, independently evolving lineages were 10²⁸⁶⁰ to 1 against. (By way of comparison, the number of subatomic particles thought to exist in the known Universe is somewhere between 10⁸⁵ and 10⁸⁷.) In fact, Theobald demonstrates that no model of multiple surviving lineages holds up against the probability of a UCA, even when the most stringent statistical methods are applied.³⁷

What kind of environment did the LUCA evolve in? Since the fossil evidence of the earliest life forms is sketchy and subject to varying interpretations, existing genomes have been analyzed to discover whether ancestral life forms left clues about the world in which they lived. In studying them we have acquired evidence regarding their thermal environment. It was at first inferred that the most ancient bacteria were thermophilic—heat loving—because resurrected proteins seem to indicate that the ancestors of modern bacteria were thermophilic. But analysis of ribosomal RNA indicates that the true LUCA may have originally evolved to adapt to environments of moderate temperature, and that the lines that descended from it became adapted to higher environmental temperatures later on in life’s development.³⁸ This matters because temperature has been shown to affect the rate of evolutionary development.

It must be stressed that the LUCA was not the first life form to exist on Earth. When we say it was the last common ancestor, we are not ignoring the fact that the LUCA itself was the product of a long evolutionary process. So it may have been more complex than most people would imagine. A recent study by two biologists has, in fact, postulated the following about the LUCA and its development:

1.    The diversification of life from the LUCA (not the beginning of it) began about 2.9 billion ybp.

2.    The LUCA had, in the words of the study, “advanced metabolic capabilities”.

3.    It was rich in the kind of enzymes needed to metabolize nucleotides.

4.    It had the capacity to synthesize membranes.

5.    It had some capacity to synthesize proteins.

6.    It could not communicate with other cells.

7.    It could not produce enzymes necessary for DNA synthesis.

8.  All in all it was a simple organism with “a rather complex set of modern molecular functions”.³⁹

As science elucidates the nature of the Last Universal Common Ancestor to a greater and greater degree, we will gain important insights into the roots of the Tree of Life—and the evolutionary processes by which it has grown and flourished over the eons, producing one particular branch in the tree’s higher regions—the genus Homo.

The Reality of Organic Evolution (A Necessary Digression)

Since one of the crucial aspects of living systems is that they have the capacity to evolve, an understanding of the basic processes of evolution itself is necessary. Few subjects are more crucial to our understanding of the world, and few subjects require greater clarification. There is a great deal of confusion surrounding the concept of evolution. Because of the resistance of religious authorities (and certain others who are mistrustful of science) in many parts of the world, or because many people simply lack an education in the sciences, there are many humans who do not accept the tenets of evolutionary thought. Many of these people are outrightly dismissive of the idea itself, saying that organic evolution is “just a theory”, unmindful of the fact that the words hypothesis and theory are not synonyms. As we will see in Science, in a later volume, a theory is a set of interrelated propositions that, taken together, describe the characteristics and processes of a given phenomenon. All such propositions are based on either empirical or deductive evidence, or both, and are, by definition, facts in the human frame of reference. Quantum mechanics, relativity, plate tectonics, and heliocentrism are all theories. Organic evolution is an established fact, as fully proven and as completely demonstrated as the fact that the Earth orbits the Sun. Although scientists sometimes disagree about the details of this process, virtually all scientists (with extremely few exceptions) agree that the process itself is real, and is supported by massive amounts of evidence. It is by means of organic evolution that the earliest life forms ultimately gave rise, after an inconceivable number of steps and an incomprehensible length of time, to the genus Homo. We cannot assume, however, that the “objective” of organic evolution was the bringing forth of the human species.

The genetic make-up of an organism is known as its genotype. The physical traits of an organism, its structure, physiology, and biochemical composition, are known as its phenotype and are the product of its genotype. Evolution changes the distribution of genotypes present in a population of organisms. These changes, over time, are expressed as phenotypic changes. The change in a population’s genotypes affects its ability to successfully reproduce. So bearing these basic facts in mind, what are the chief methods by which evolution proceeds?

Natural Selection. The core of evolutionary ideas. Natural selection is concerned with those conditions which lead a species to be either reproductively successful or unsuccessful. What do we mean by reproductive success? In order to be reproductively successful, the members of a species must survive long enough in a given environment to reach reproductive maturity, and when they do, they must reproduce and give rise to fertile offspring similarly capable of surviving. Not all members of a population need to reproduce, but a certain number of them obviously must do so. Two factors above all drive the outcome of this process:

1.   The DNA which determines the physical traits of a species, when reproduced, does not always reproduce with total accuracy. Errors in reproduction, or recombination, are known as mutations. (See below.) Such errors can have only three possible outcomes. First, a mutation may be neutral, and have no effect on the reproductive success of the species. Second, the mutation can be harmful, meaning it lessens the ability of the species to reproduce. Third, the mutation may be beneficial, meaning it enhances the ability of the species to reproduce. (To be perfectly accurate, there are mutations which appear to have negative consequences but which act more broadly to ensure reproductive success.) And how can we judge whether a mutation is neutral, harmful, or beneficial? We have to consider the species in the context of its environment.

2.   All species exist in a particular physical environment. If that environment undergoes significant changes, it will affect the ability of animals or plants to survive long enough to reproduce, and will make certain mutations crucially important.  An example which was of particular importance to us was the rapidity with which the forest environments of our tree-dwelling ancestors changed. Mutations which would be neutral in a stable environment, such as a gene for color vision, would become beneficial in an environment in which new and deadly predators were now common. If color vision gives an animal the ability to detect such predators and take action to evade them, the chances of the animal surviving to reproductive maturity are significantly improved—as are the odds that the gene for color vision will be reproduced. This is the essence of natural selection. What is being “selected” (unconsciously) is genetic material. Natural selection alters the genetic characteristics of a given population when those alterations prove to be beneficial to the reproductive success of that species. If the genetic characteristics of the species do not change rapidly enough to deal with extreme environmental changes, the outcome is grim: extinction. The vast majority, more than 99%, of all species that have ever lived on the Earth are now extinct, but many of them have left modern day descendants. The earliest mammals and primates are all gone, but we are their inheritors.

Natural selection is therefore a deeply interactive process involving all of the variables that affect a population’s genetic composition and the environment in which the population lives. It is not “random” in the sense that it follows no rules, because the rules that govern this process have largely been elucidated, but it is random in the sense that changes in genetic material or the physical environment in which that material exists cannot be predicted. The process of natural selection is driven by…

Selection pressures. Selection pressures (sometimes called selective pressures) are those aspects of the natural environment that, unconsciously and without direction, tend to demand of those animal and plant species living in that environment the ability to conform themselves to the conditions of the environment. In regard to this, a key principle needs to be emphasized once again: if an environment changes extremely rapidly, the results are usually disastrous for those species that have evolved a high degree of specialization for that environment. On the other hand, species having, for whatever reason, greater biological “flexibility”, stand to gain. The massive reptilians that dominated the Earth until 65 million years ago were excellently adapted to a comparatively warm (although perhaps already cooling) environment. When that environment changed with jarring suddenness, their highly specialized adaptations were no longer suitable. The selection pressures, in other words, had radically changed. The mammalians, smaller but more adaptable, were given a tremendous competitive boost from the wiping out of the large dinosaurs. Selection pressures, therefore, are aspects of the natural environment that favor animals and plants that can meet them—and which mercilessly eliminate those that can’t. The forest environment in which our primate ancestors evolved was filled with particularly sharp selection pressures, ones which tested their abilities to the utmost, and winnowed out those who failed the test.  

A great many variables, therefore, influence natural selection. The net result of this phenomenon is life forms that come in an amazing array of sizes, colors, shapes, internal structures, and configurations, living in an astonishing range of habitats. The changes that brought these life forms about are examples of the inherent gradualism of evolution.⁴⁰ This is not to say that all evolutionary change occurs at one, rigidly determined pace, nor is it to say that there cannot be long periods of relatively little change followed by periods of relatively greater change. But it does indicate that large evolutionary change is brought about by the accumulation of small changes, yet another example of emergence in nature.⁴¹

In one perspective, life forms can be thought of as packages that carry genes, genes whose “job” it is to see that they are reproduced. This job can be accomplished in a tremendous variety of different ways. I call the process of natural selection driven by selection pressures by a simple and stark name: The Law of Whatever Works. Whatever works does not have to be especially efficient, attractive, or appealing. As long as some of the life forms in a population succeed in perpetuating their genetic material, that’s all that is required. The life form may be lethal to other animals (as are the Anopheles mosquitoes that transmit malaria), it may be one that (to human eyes) is disgusting or repellent in appearance, it may use methods of reproduction that are very inefficient and time-consuming (such as the reproductive cycle of penguins), it may exist in environments that to humans appear harsh or extreme. None of this is important. There is only one criterion of biological “success”. The species must continue in some way. Nothing else matters.

Adaptation. An adaptation is a physical characteristic of a life form that helps it thrive in a particular environment. It can be thought of, in a sense, as a biological “solution” to an environmental challenge. It is the end result of the natural selection process. Adaptations (for a time) enhance the reproductive prospects of a population of life forms. Evolution by natural selection is therefore also referred to as adaptive evolution. Adaptations are not just external physical traits. They can also be biochemical features, such as the evolution of different varieties of hemoglobin (the molecule that carries oxygen to cells).⁴² Are adaptations always perfect or elegant? Not at all. Natural selection, in “looking” unconsciously for whatever works, uses the available materials and does with them what it can, all without direction or purposefulness. If an adaptation helps ensure an animal or plant’s reproductive success, it gets reproduced more and more consistently. If the environment changes, the adaptation may rapidly become useless—or worse.

DNA Replication, Mutation. Although it is somewhat of an oversimplification, it can be said that bodies are built out of proteins. Proteins also regulate and maintain bodies. Different kinds of protein are used to build different kinds of structures in an animal’s body, and distinct kinds of protein perform the various regulatory functions as well. Gene expression is also regulated by proteins. There are 20 amino acids in life forms, and specific kinds of proteins are built out of specific sequences and arrangements of amino acids. (Not all amino acids can be synthesized in the body; some must be ingested.) The “instructions” for building a protein are found in genes, which are simply segments of DNA located along the bodies of chromosomes, found within cells. Some proteins require several genes to assemble them. Conversely, certain single genes can produce several different kinds of protein. A sequence of nucleotides in a gene assembles a specific sequence of amino acids in a protein.⁴³  

As you know, a DNA molecule consists of nitrogenous bases linked in pairs, with a surrounding structure of phosphate and sugar groups, all arranged in a double helical shape. The base adenine always links with thymine, and the base cytosine always links with guanine. (In RNA thymine is replaced by uracil.) A triplet of bases, called a codon, carries the “instructions” for the building of a particular amino acid. The DNA code for an amino acid is copied and the copy is a molecule known as messenger RNA, or simply mRNA. The copying process is known as transcription, and in eukaryotes takes place in the cell nucleus. The “information” carried by the mRNA is taken out of the nucleus to structures known as ribosomes. Ribosomes, which are constructed out of a different kind of RNA, (rRNA) are where the actual proteins are assembled by yet other forms of RNA (tRNAs). This second phase of the construction process is called translation.⁴⁴ As long as the DNA of a cell reproduces properly, everything goes well within this process, and proteins are assembled according to plan.

But sometimes, there are problems. When a DNA molecule replicates, there are errors of copying that pop up from time to time, Most of these errors are corrected by enzymes that detect and repair these errors. But some of the errors slip through. These errors are the mutations mentioned in the description of natural selection above. The mutation can alter the coding of a protein, which results in the production of a different kind of protein altogether. Point mutations change a base in the DNA sequence to another kind of base. Certain kinds of point mutations change amino acids, and hence protein production. A more drastic kind of mutation, known as a frameshift mutation, inserts a base into a DNA sequence, knocking the whole sequence of base pairs out of position and producing a useless, non-functioning protein. Mutations can also involve a process known as transposition, in which a section of DNA can copy itself and insert itself into an existing gene, altering its function. Finally, whole chromosomes can become entangled with each other, causing a phenomenon called translocation. In translocation, chromosomes which have crossed each other’s path can swap genetic information equally or one can do all or most of the exchanging. In discussing evolution, it is the mutations that occur in gametes—sex cells—that are most crucial. These mutations, if they are of the right kind, can have phenotypic consequences. They can bring forth a new variation of a living thing, one not seen before.⁴⁵ Mutations, therefore, are of crucial significance in evolution. The deep basis of natural selection is found in the process by which the genome of an individual is reproduced. It is the variability of genetic material that gives natural selection something from which to select. 

Genetic Drift. A very precise definition of evolution is that it is “a change in the proportion of alleles (different forms of a gene) in a population.”⁴⁶ In a relatively small population, with a great deal of intergroup mating, certain alleles can be lost over time simply by random chance, and certain other alleles can rise to 100% frequency. This is a less powerful form of evolution, one that cannot produce complex adaptations. In fact, it can be disastrous, leading to high incidences of genetic disorders in isolated populations.⁴⁷ There is a variation of the genetic drift theory known as the Neutral Drift Hypothesis. In the 1960s a Japanese biologist, Motoo Kimura, argued that random genetic changes take place with great frequency, and are not usually driven by natural selection. The overwhelming majority of such changes, according to Kimura, are neutral, and changes in the genetic characteristics of a given population can occur entirely by chance. Kimura is not rejecting the idea of natural selection at the levels of form and function. He is arguing that at the molecular level, however, the majority of mutations result purely from stochastic processes. Nor is he saying that such changes occur at a regular, constant rate. He does not exclude selection as one of the factors in molecular change. He is, however, saying that selection-driven changes at the molecular level are in the minority. Kimura’s work has been widely debated, and it is not universally accepted by any means, but he has definitely influenced the examination of genetic change.⁴⁸

Synergy and Evolution. In the chapter Synergy and Feedback Loops we examined the way in which evolutionary development is driven by synergistic processes, as successful innovations make possible the greater and more widespread expression of these innovations. We examined the proposition that only when all the conditions necessary for the evolutionary development of a species are working in concert with each other can true novelty emerge. So evolution may properly be thought of as a natural process that by bringing together a host of variables produces an outcome that none of those variables operating in isolation can produce.

Speciation. A species can be chiefly understood as a population whose members can successfully reproduce only with other members of the population. (There are indistinct boundaries between species that sometimes allow genetic flow to occur.)  By successfully reproduce, as we noted above, we mean give rise to fertile offspring who will be able to continue the process. Speciation occurs when a population has become genetically distinct from other populations descended from the same ancestral group. If a population has, through natural selection and genetic drift, lost “genetic contact” with another population over the centuries, it may lose the ability to produce fertile offspring with that population, or even to produce any offspring at all. Speciation is usually caused by populations living in distinct environments that call for distinct adaptations. Different physical features have different adaptational advantages in such environments. What “works” reproductively in one place might not “work” in another. Various species of baboon have evolved, for example, to adapt to widely divergent environments in Africa. Speciation may also be driven by the action of speciation genes, genes that contribute to reproductive isolation. Such genes are thought to vary in a purely stochastic (by random chance) manner and if favored by natural selection, to drive the process of speciation forward. This process is still not fully understood, but it is now being studied intensely.⁴⁹

Convergence. Convergent evolution occurs when varieties of animals of different species, or even different classes or orders, become similar in appearance due to selection for certain traits that are advantageous in a given environment. The most spectacular example of convergence we have is found in the cetaceans, the mammalian order that includes whales, dolphins, and porpoises. Through relentless selection pressures, the successful members of the order have acquired extremely hydrodynamic bodies similar in key ways to those of the vertebrate fishes. But an examination of a cetacean skeleton will reveal a surprising fact: in their wonderfully effective fins there are vestigial limbs and digits, the remnants of their terrestrial ancestors.⁵⁰

Parallelism. This is more properly called parallelophyly. As described by the eminent evolutionary biologist Ernst Mayr, this is “the independent emergence of the same character in two related lineages descended from the nearest common ancestor.”⁵¹ This phenomenon is seen clearly in the evolution of birds. It should be noted that every step in the parallel evolution of various species is not going to be identical, nor does it need to be. But the phenomenon has been carefully traced, and it is the process which is complementary to convergence.⁵²

Stasis.  There are particular environments, such as areas of the world ocean, that are so isolated and stable that certain species of animals can occasionally survive in them essentially unchanged over many centuries. The discovery in 1938 of a coelacanth, a fish once thought to have died out with the dinosaurs, illustrates this phenomenon. Such environments are characterized by a lack of selection pressures. For example, there may be no predators in the region. Similarly, the region occupied by a species may be thermally stable or out of the migratory patterns of potentially disruptive animals. But for whatever reasons, certain areas of the Earth harbor these biological remnants of earlier eras.

There are many, many more aspects of evolution that we will touch on as we have need to, but these will suffice for now. Now it’s time for us to examine…

Misconceptions About Evolution

Misconceptions about evolution abound. There is great misunderstanding about the term “survival of the fittest”. Fittest does not necessarily mean biggest and strongest. Fitness in this context refers to reproductive success. Most dinosaurs were huge and tremendously strong; the mosquitoes that existed along with them were small and easily crushed. Which one was more fit? The various mosquito species have an unconscious reproductive “strategy”. They reproduce in such vast numbers that even if 95% of their members die, they have plenty left to continue the lineage. In fact, as Jerry Coyne has pointed out, the “solutions” devised by natural selection aren’t ideal ones, so perhaps we should think in terms of survival of the fitter.⁵³

Further, many people say that “I didn’t descend from monkeys”. Well, if those people are referring to the modern day prosimians, monkeys, and apes, they’re right. They didn’t. All of the modern primates, including humans, are descended from common ancestors, the founders of the primate order some 65,000,000 years ago (or perhaps longer). The ancestral primate groups evolved many branches, and eventually gave rise to the approximately 200 varieties of primate which exist in the modern world, one of which is us. As we will see in more detail later, the lines that were to become the modern chimpanzees and humans split from each other somewhere around 5-6 million ybp, and genetic information can be used to confirm this.

There are those who think the scientific community is deeply divided about whether evolution is a fact. Such is absolutely not the case. The vast majority of scientists are thoroughly convinced by the massive evidence in favor of evolution.⁵⁴ And there are people who believe that the evidence for the reality of evolution is thin. Nothing could be farther from the truth. Virtually every area of the sciences gives irrefutable evidence for its major propositions and supports our estimates of the time frames in which it occurred. Here are just some examples:

-- In outer space, the Wilkinson Microwave Anisotropy Probe (WMAP) has examined the cosmic microwave background radiation, the aftermath of the Big Bang. This examination has allowed us to make an estimate of the age of the Universe, 13.83 billion years, that is accurate to within 1%.⁵⁵ This utterly demolishes the preposterous arguments of those who contend the Universe is only a few thousand years old, and demonstrates that there was an enormous amount of time for nucleosynthesis to have occurred.

--Radiometric dating, based on the known decay rate of radioisotopes, has established reliable absolute dates for many, many samples of the Earth and the life forms fossilized within it. For example, Potassium-Argon dating (⁴⁰K-⁴⁰Ar) is used to reliably date fossil remains embedded in layers of solidified volcanic ash. G. Brent Dalrymple, perhaps the world’s foremost authority on the age of the Earth, has thoroughly explained why radiometric dating is accurate and has completely refuted the ludicrous contentions of “Young Earth Creationists” and their insistence that a “great flood” laid down all the layers of sedimentary rock in the geologic column:

There is also no doubt that the rocks now exposed on the surface of the Earth or accessible to scientists by drilling were deposited and emplaced over the geologic epochs, starting in the earliest Precambrian more than 3.8 billion years ago. There are more than 100,000 radiometric ages in the scientific literature that date rock formations and geologic events ranging in age from Holocene to earliest Precambrian. These data and all the accumulated knowledge from the science of geology show conclusively that the Earth we now see is the result of natural processes operating over vast periods and not the product of one or two worldwide catastrophic events.⁵⁶

--Molecular evolutionists can measure the genetic “distance” between and among various kinds of organisms through an analysis of the sequences of nucleotides or amino acids in key macromolecules:

For example, in humans and chimpanzees the protein molecule called cytochrome-c, which serves a vital function in respiration within cells, consists of the same 104 amino acids in exactly the same order. [Emphasis added.] It differs, however, from the cytochrome-c of rhesus monkeys by 1 amino acid, from that of horses by 11 amino acids, and from that of tuna by 21 additional amino acids.⁵⁷

The calculation of reliable genetic “distances” by such methods has allowed scientists to trace the phylogenies of numerous species. It has allowed geneticists to explain when various lines of animals diverged from one another as life forms evolved from the LUCA (although the existence of fossil evidence is often used to calibrate such measurements). And for those who deny any relationship between humans and chimpanzees: what are the odds that the amino acids in the cytochrome-c molecule of humans and chimpanzees ended up being identical to each other purely by coincidence?

--Paleontologists have uncovered a huge number of fossils which demonstrate transitions over time from one kind of animal to another. This documentation is very strong in the record of dinosaurs, and many transitional examples have been uncovered. Further, there are many examples of animals in the fossil record which suggest a biological relationship between reptilians and birds.⁵⁸ 

--In relation to transitional forms, in 2004 a fossil species named by scientists Tiktaalik roseae was discovered in the Canadian Arctic. Anatomically, it is absolutely a mixture of fish and tetrapod (four-legged animal), exhibiting traits found in both groups, and it is almost exactly the age—375 million years old—that those who were looking for it predicted it would be.⁵⁹ (We will examine this find further in the chapter The Animal Kingdom Begins to Colonize the Land.) This helps bury the absurd creationist argument that there are “no transitional varieties in the fossil record” even deeper than it already was. Even if Tiktaalik does not turn out to be the defining transitional animal, it gives us an excellent idea of what that animal was like.

And as far as assertions of “divine” or “intelligent” design go, anatomists and physiologists have uncovered numerous “design flaws” in the human body, and a great many features of our anatomy that are ancient in origin and which have been conserved across many species through time. (We will look at the various suboptimal “design” features of humans in a subsequent chapter.)

Few propositions in scientific history have been more thoroughly demonstrated than organic evolution. It is evolution that has driven life forward ever since the appearance of the first life forms, and it has produced the various life forms that permeate the surface of the Earth and the world ocean. And it is evolution that continues to operate in every corner of the biosphere, mindlessly hurling out the challenge it always has: adapt, reproduce, or die out. By its processes, it ultimately produced a life form that can study it and understand it. And the interesting thing is that were the process to start all over again from the beginning, there is no guarantee that that life form would ever come into existence again.

Life, as we have observed, is something that energy-matter is capable of doing in the right circumstances. When elements are arranged in a particular manner, they exhibit the properties we associate with life. It was the capacity of living things to undergo change that ultimately led to the emergence, from the fantastically complicated web of life, of our genus. The story of life’s emergence and evolution is still being pieced together, painstakingly and systematically. Not all questions have been resolved, by any means. But we must resist the temptation to assert that these questions cannot be answered, or that they can only be answered by invoking supernatural intervention. The appearance of life on our planet was, obviously, of the most central importance to us. And yet, in the scope of the Universe, it was not a particularly noteworthy or unique development. The advanced, consciousness-possessing life forms of the planet Earth may yet make their mark on the broader Universe, but as of yet they have not done so. They are, in fact, still struggling with their own incomplete understanding of themselves, and their failures to deal with their own tendencies and limitations may yet bring about their downfall.

So now we turn to the specific steps that led from the appearance of life on this planet to the period in which the human experience began to be permanently recorded. We begin by noting the enormous period of time when our planet’s most advanced life-forms consisted of one-celled organisms. This era of prehistory brought about the eventual rise of all the “complex” life forms that pervade the surface of this planet and its ocean. One of the life forms that was a consequence of this era not only carries the inheritance of those times in its cellular structure—it tries to understand itself. Only with the greatest difficulty have the bearers of consciousness been able to prise the secrets out of that remote time—and the effort has still not been completed.

1.   Schopf, J. William. Cradle of Life: The Discovery of Earth’s Earliest Fossils, p. 107

2.   Schrödinger, Erwin, What is Life?, pp. 69-71

3.   Schrödinger, pp. 76-82

4.   The Principles of Life (Summary of Tibor Gánti’s work) located here:  http://home.planet.nl/~gkorthof/korthof66.htm

5.   Fry, Iris. The Emergence of Life on Earth: A Historical and Scientific Overview, pp. 66-71

6.   Fry, pp. 71-77

7.   Kimball’s Biology Pages

8.   Trefil, James Harold J. Morowitz, and Eric Smith. “The Origin of Life” in American Scientist, May-June 2009.

9.    Shapiro, Robert. Origins: a Skeptic’s Guide to the Creation of Life on Earth, pp. 224-247

10.  Introduction: More Than Panspermia, located at: http://www.panspermia.org/intro.htm

11.  Shapiro, pp. 98-106

12.  Fry, 104-105

13.  Fry, pp. 107-111

14.  Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth, pp. 76-80

15.  Trefil, et al.

16.  Trefil, et al.

17.  Cairns-Smith, A. G. Genetic takeover and the mineral origins of life, pp.  45-60

18.  Cairns-Smith, p.  70

19.  Cairns-Smith, p. 120

20.  Cairns-Smith, pp. 160; 257-258

21.  Cairns-Smith, pp.  264-273

22.  Cairns-Smith, pp. 357-365

23.  Lurquin, Paul F. The Origins of Life and the Universe, pp. 102-104 

24.  Wim Hordik, Jotun Hein, and Mike Steel, “Autocatalytic Sets and the Origin of Life”, from Entropy,  2010; Hordik, Kauffman, and Steel, “Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems” in International Journal of Molecular Sciences, 2011.

25.  Schopf, pp. 166-167

26.  S. J. Mojzsis, G. Arrhenius, K. D. McKeegan, T. M. Harrison, A. P. Nutman, and C. R. L. Friend,

“Evidence for life on Earth before 3,800 million years ago”, in Nature 384, 55 - 59 (07 November 1996); doi:10.1038/384055a0

27.  Knoll, pp. 64-71

28.  Schopf, pp. 75-99

29.  Brasier, et al,  “Questioning the Evidence for Earth’s Oldest Fossils” in Nature, March 2002.

30.  Schopf, et al, “Laser--Raman imagery of Earth's earliest fossils” in Nature, March 2002

31.  Marshall, et al, “Haematite pseudomicrofossils present in the 3.5-billion-year-old Apex Chert” in Nature Geoscience, February 2011.

32.  Schopf, p. 72

33.  Colin Barras, “Biology's 'dark matter' hints at fourth domain of life” in New Scientist, 18 March 2011

34.  “Dueling Scientists and the Tree of Life:  Analyzing the ID Response” in The BioLogos Forum,

March 14, 2011

35.  Theobald, Douglas. “A formal test of the theory of common ancestry” in Nature, 13 May 2010

36.  Theobald

37.  Theobald

38.  Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, and Manolo Gouy, “Parallel adaptations to high temperatures in the Archaean eon”, in Nature 456, 942-945, Published online 26 November 2008

39.  Kyung Mo Kim and Gustavo Caetano-Anollés,  “The proteomic complexity and rise of the primordial ancestor of diversified life” in BMC Evolutionary Biology, 2011; 11: 140. Published online 2011 May 25

40.  Coyne, Why Evolution is True, p. 4

41.  Dawkins, The Blind Watchmaker, pp. 43-74

42.  Travis, Joseph, and David. N Reznick, “Adaptation” in Evolution: The First Four Billion Years, pp. 105-109

43.  Mark Ridley, Evolution, pp. 23-25

44.  Ridley, p. 25

45.  Ridley, pp. 27-30

46.  Coyne, p. 122

47.  Coyne, 122-124

48.  Kimura, Motoo, The Neutral Theory of Molecular Evolution, passim.

49.  Nosil, Patrik, and Schluter, Dolph, “The genes underlying the process of speciation” in Trends in Ecology and Evolution, 2011.

50.  Whale and Dolphin Evolution, American Museum of Natural History, located here: http://www.amnh.org/science/papers/spaulding_whales_2009.php

51.  Mayr, What Evolution Is, pp. 225-226

52.  Coyne, p. 13.

53. Some years ago, in the United States, the National Center for Science Education began a project, somewhat tongue-in-cheek, to deflate claims by creationists that there were many scientists who are creationists. Called Project Steve, it has shown that there are more pro-evolution scientists named Steve than there are creationists of all names put together in the scientific community. And only about 1% of all scientists are named Steve (or some variation of that name, like Stephen).

54. Wilkinson Microwave Anisotropy Probe, NASA, located here:  http://map.gsfc.nasa.gov/

55.  G. Brent Dalrymple, How Old is the Earth: A Response to “Scientific” Creationism, in Talk Origins Archive, located here: http://www.talkorigins.org/faqs/dalrymple/summary.html#h48 

56.  Francisco J. Ayala, “Molecular Evolution” in Evolution: The First Four Billion Years, p. 136.

57.  Donald R. Prothero, Evolution: What the Fossils Say and Why It Matters, pp. 249-268.

58.  Coyne, 35-37