Saturday, February 22, 2014



So we are now into the autumn of our one-year history of the Universe. The year is more than three-quarters gone and only now have we seen life get a toehold on the planet Earth. It has begun the process of replication, subjecting it to natural selection and evolutionary change. Its next great development will be the formation and evolution of cellular life. The cell is the basic structural unit of all living things on this planet. Its evolution, which was perhaps concomitant with the first replicating organic polymers, was a momentous step in the history of the prehistoric world—and our story as well.

Ideas About the Evolution of the Protocell and the Cell Membrane

Cells are surrounded by a membrane, a semi-permeable structure that allows for the influx of nutrients, the expulsion of waste products, and other forms of chemical and physical interaction with the outside world. The membrane maintains a physical barrier between the cytoplasm within a cell and the environment in which the cell exists. A membrane consists of both lipids and proteins. The fundamental structural feature of the membrane is the phospholipid bilayer, which simply means two layers of fatty compounds that contain phosphate groups and glycerol. The complex structure and physiology of membranes suggest that they are evolutionary descendants of much more basic structures, and that cells themselves were at one time of the utmost simplicity. In the previous chapter we encountered the protocell. How did such primitive cells evolve?

The formation of droplets or bubbles seems to be a basic feature of self-organization in liquid environments. Recent research has revealed that nucleotides and basic kinds of peptides (sequences of amino acids) can accumulate in small droplets in water, and that these small droplets, or microdroplets, are stable even in environments with variable temperatures and salinity. Additionally, these microdroplets exhibit a variety of chemical activities and can assemble important chemical structures.1 Such simple enclosures may have self-organized in the Earth’s early biochemical environment and become the first true protocells. The early types of membrane-like structures surrounding these protocells are often referred to as lipid vesicles, a vesicle here meaning a simple sac-like object. Lynn Margulis and Dorian Sagan point out that lipids tend to spontaneously form drops when in water, much in the same way oil does. Experimentation has shown that these lipids can combine with proteins, and that these lipid-based drops could have contained carbon-based chemicals in the early Earth’s environment. Therefore, it is possible that cell-like structures predate life itself.2

From such primitive cells the more biologically sophisticated and complex membranes gradually evolved, but there is as yet no consensus about how this occurred. Some researchers contend that the earliest kind of membranes were much more permeable than later forms. In their hypothesis, these early types of membrane represented a transition between life forms that had no structural boundaries and the “tight” membranes that now tend to be the rule. Protocells with such relatively porous membranes, they contend, would have undergone a great deal of gene-swapping and enzyme sharing in a horizontal manner, prompted by their ability to encompass proteins and nucleotides favorable for such activities. They say it is possible (although speculative) that these gene-sharing cells formed consortiums with other cells in a network-like fashion, allowing them to contribute metabolites to a common pool. These consortiums would have been subject to selection, based on the ability of the consortium’s members to occupy empty, inorganic bubbles of the kind that form near hydrothermal vents.3 This hypothesis will need extensive experimental support, however, before it is widely accepted.

Among the many, many areas of research on the evolution of cell membranes is the study of the evolution of ion channels, complexes of proteins on a membrane surface that make it possible for charged particles to cross through the membrane. The phospholipid bilayers themselves are evolved to form a barrier to water-friendly, charged molecules. Ion channels, in effect, are a kind of insulation for charged particles, giving them a pathway through otherwise hostile territory. Not everything about their structure is yet understood, but five different kinds of them have been identified.4  In 2005 a team of researchers argued that the evolution of simple kinds of ion channels that could carry out complex functions may have occurred early in the history of cellular life, and that there are proteins associated with the construction of ion channels common to all three domains of living things. They argue that the different kinds of ion channels have enough “universal” features that they could have readily adapted themselves to a number of different functions during the course of evolution.5  The evolution of the complex cell membrane has not yet been fully elucidated, but there are many researchers working on it, and promising avenues of research are being opened.

The Emergence of Archaea and Bacteria; The Variety and Pervasiveness of Prokaryotes

As we saw in the previous chapter, all life forms belong to one of three domains, Archaea, Bacteria, or Eukarya. (The identification of the archaea as a distinct domain of life is generally credited to Dr. Carl Woese and his associates at the University of Illinois.) Archaea and Bacteria are generally thought to be the oldest, but it is not yet clear which domain of life evolved from the Last Universal Common Ancestor first. Some researchers contend that the Archaea, due to the ability of many varieties within the domain to survive in extreme environments, may have been the first. (There is, however, evidence of many archaeans evolving in more moderate conditions.6) Although there is some evidence that archaean life existed as early as 3.4 billion ybp, this has not yet been confirmed. Archaea shares features with both Bacteria and Eukarya. For example, the way in which archaeans replicate their DNA has strong similarities to the way in which eukaryotes carry out this key function, but the way in which chromosomes are arranged in archaeans is very similar to the way in which they are arranged in bacteria. There are also features archaeans possess that are unique to them, such as the chemical structure of the phospholipids in their membranes.7 Additionally, we do not yet know the true relationship between the archaeans and the eukaryotes. Did the two evolve from a common source, or did the eukaryotes evolve directly from the archaeans? This is one of the thorniest issues in evolutionary biology, and the best we can say is that research in this area is on-going.8

The archaeans come in a wide variety of types, and are generally classified into two broad phyla, the Euryarchaeota and the Crenarchaeota (although a third phylum has been proposed). The first group contains microbes that produce methane, microbes called halophiles that live in highly saline environments, and microbes that thrive in hot, highly acidic environments. The second group contains the hyperthermophiles, microbes that thrive in very high temperatures, microbes that comprise a large share of the world’s plankton, and microbes that perform the critically important function of converting ammonias into nitrates, a function they perform both on land and in the world ocean.9

In classifying bacteria microbiologists start by separating them broadly into two categories, depending on how their cell walls react to a dyeing technique called the Gram stain.  The bacteria that retain the dye are called Gram-positive. Among their numbers are the Firmicutes, a diverse category that includes the microbes that cause anthrax, tetanus, or botulism, the microbes that are considered common soil bacteria, the bacteria that convert milk into cheese and other dairy products, the microbes that cause staph infections, and many others. Other Gram-positive bacteria are the Actinobacteria, which play an active role in the decomposition of dead organic matter and which are a major source of antibiotics, and the Mycobacteria and Corynebacteria, a group that causes tuberculosis, leprosy, and diphtheria. In the Gram-negative category there are the Proteobacteria, a huge category the members of which range from the various microbes that cause typhus, meningitis, gonorrhea, whooping cough, cholera, cystic fibrosis, and bubonic plague, among other maladies to the purple sulfur bacteria, the nitrosomonas bacteria that help plants utilize nitrogen, the Escherichia coli that populate the human colon (in most cases harmlessly), and the myxobacteria that assist in the decay of dead organic matter, among others. Other Gram-negative bacteria are Bacteroidetes that are a major component of human waste (and which actually aid in digestion), the Spirochetes that cause syphilis and Lyme disease, the Chlamydiae which, as their name suggests, cause chlamydia, and the Cyanobacteria, often referred to as blue-green algae, which have played an enormously significant role in the development of life on this planet, as we will see below.10

The bacteria, of course, have seen tremendous evolutionary changes over the billions of years of their existence. Not all species of bacteria have existed from the start. It would appear, for example, that Escherichia coli is a species that evolved out of older kinds of proteobacteria, a determination made by comparing its genetic content with the estimated gene content of ancestral proteobacterial forms.11 But many of the earliest kinds of bacteria still exist, and phyla like Actinobacteria are so ancient that it is hard for scientists to trace their origins. The exploration of the bacterial genomes is still in a relatively early stage, but new DNA sequencing techniques are being employed in this field now, and we will, perhaps in the near future, have a fuller picture of the taxonomic relationships among bacteria than we have now.

The bacteria can be said to be absolutely ubiquitous on the surface of this planet. The number of bacterial species is unknown, with estimates ranging up into the millions, but in 2009 it was estimated that more than 19 different phyla of them are found just on the skin of humans, quite apart from the varieties thought to live in the human gut.12

The number of prokaryotes alive at any given time is thought to be utterly enormous. In 1998, three scientists from the University of Georgia estimated the number of prokaryotes at between 4 and 6 x 1030,  and further estimated that prokaryotes contain the vast majority of the carbon, phosphorus, and nitrogen found in living organisms.13

The Evolution of the Nucleus, the Evolution of the Eukaryotes

Since humans are part of the domain of the Eukarya, the evolution of eukaryotes is a subject of particular interest to us. The evolution of the cell nucleus is, obviously, the crucial development in the story of the eukaryotes.

In 2010, three researchers in Germany examined the ways the nucleus may have evolved by investigating the features of the chromatin—the material that comprises the nucleus—and the amount of non-coding DNA, that is to say DNA that is not used to make proteins, found in the typical nucleus. They also examined the tendency of the nucleus to compartmentalize its functions, and the way in which such compartmentalization might have arisen. On the basis of their research, they contend that the domain of the Archaea is an evolutionary offshoot of Bacteria, and that the earliest eukaryote—what they refer to as the eukaryotic root—is a separate offshoot from the bacterial line. They emphasize that the identity of the eukaryotic root is still a matter of debate, but that there is little doubt that the eukaryotes share a common evolutionary ancestor. Although they consider the possibility that the nucleus is an endosymbiont, that is an independent cell that was engulfed by another cell (see below), it appears much more likely that the nucleus evolved from a structure in the cell known as the endoplasmic reticulum. Their research has revealed characteristics that are conserved across all eukaryotic cells, and that the variations we see in the nuclei of some organisms are evolutionary changes that happened later and not ancestral to the line from which these organisms evolved. Finally, they argue that the nucleus itself has undergone “major adaptive changes as a result of environmental triggers.”14

Another microbiologist speculates that the cell nucleus evolved because certain prokaryotic cells were more mobile, and an internal membrane evolved to encompass and protect the fragile strands of DNA from the stresses of the cell’s movement. (In my view, this mobility might constitute a selection pressure.)15  This encompassing of the DNA may have arisen from DNA clinging to the interior of the membrane and being progressively more surrounded by an invagination (structural infolding) of the cell wall known as a mesosome. This process produced a membrane that sheltered DNA while still allowing access to the cytoplasm.16 This biologist further points out that the process by which the various kinds of RNA carry out transcription and translation (see previous chapter) is made more efficient by separating these functions in both space and time. Prokaryotic cells carry out these functions concurrently. Eukaryotic cells carry them out sequentially, in a compartmentalized fashion, thereby allowing a greater variety of proteins to be produced.17 The complexity and sophistication of which the first true eukaryotes were capable was to have enormous consequences.

When did the Eukarya evolve? Organic microfossils larger than 50 micrometers in size and of uncertain relationship to other organisms are called acritarchs. Eukaryotic acritarchs approximately 1.8 billion years old have been discovered in China, and were previously believed to be the oldest ones in existence. However, we now have interesting evidence from South Africa of acritarchs 3.2 billion years old which may be of eukaryotic origin. The cell walls of these fossils certainly hint strongly of this. If confirmed, this will lead the study of the evolution of eukaryotes in new directions.18

It is time for us to now examine what might have been the most significant of all the changes to the Earth’s surface brought about by one-celled organisms—the establishment of the conditions that made it possible for more complex life forms to evolve. From this has stemmed the entire multicellular part of the biosphere—and, of course, us. This change was…

The Evolution of Photosynthesis

The surface of the Earth is luxuriant with plant life, a phenomenon we will later examine in some detail. (See The Plant World in a subsequent volume.) Animal life on this planet is utterly dependent on this vegetation. From where did it emerge? And more specifically, why are plants phototrophs—literally, “sunlight eaters”? It was the evolution of photosynthesis in single-celled organisms that accounts for all of this. Photosynthesis captured the diffuse energy radiated to the outer crust of this planet by our local star, chemically altered it, and truly brought the whole surface of this world to life for the first time.

Photosynthesis is the ability of an organism to use sunlight to facilitate the manufacture of organic compounds. Modern plants require sunlight, carbon dioxide (CO2), and water for this process. Photons strike the pigmentation of the chloroplasts in the plant cells, causing an excitation of the electrons in the pigment. Through various electron carriers, this energy is transduced (converted to a different form). The products of this are carbohydrates, the sugars glucose and sucrose, which the plant can store for later use.  In this process, the hydrogen in water is split away from the water’s oxygen, releasing the oxygen into the atmosphere as a waste product. It is the waste product of these plants that is our most vital necessity. 

The early Earth, as we saw, was an anaerobic (oxygen-deprived) environment. The earliest atmosphere of the Earth may have been overwhelmingly hydrogen. A later atmosphere may have been heavy in CO2. There is no evidence of the presence of significant atmospheric oxygen during the Hadean Eon, the earliest era of Earth’s history. Anoxygenic (non-oxygen producing) photosynthesis must have preceded the oxygenic variety, and it may have emerged very early in the history of life. Anoxygenic photosynthesis splits hydrogen sulfide rather than water and releases sulfur instead of oxygen. Biologist Carl Bauer and his team analyzed the phylogeny of various photosynthetic genes found in all branches of photosynthetic microorganisms. They determined that purple bacteria represent the oldest lineage of photosynthetic microbes, and that anoxygenic photosynthesis probably evolved as one of the first metabolic processes in microorganisms.19 The ancient lines of bacteria that evolved photosynthesis to begin with had no chloroplasts, and must have used light energy through simple surface pigmentation.

As we saw in the previous chapter, there may have been oxygenating photosynthetic cells in the biosphere, the cyanobacteria, as early as 3,465,000,000 years ago. The cyanobacteria whose remnants may have been uncovered in Australia are the forebears of the Plant Kingdom. Cyanobacteria are thought to have evolved in the water. It is thought that the Oreleased by the cyanobacteria reacted with the iron found in the ocean, and was not, for a very long period, exuded into the air. This reactive or ferrous iron was pretty much depleted by about 2 billion ybp, and this facilitated the oxygenation of the Earth’s atmosphere.20

Cyanobacteria contain a kind of pigmentation known as chlorophyll a, the most widespread variety. The chlorophyll is located inside complexes of proteins, and it is this arrangement that allows the cyanobacteria to absorb sunlight and channel it into those areas of the bacterium that convert it into useful chemical energy. The evolution of this capability was biologically revolutionary. But this evolution must have taken considerable time:

The complexity of the photosynthetic machinery leaves no doubt that its origin and subsequent evolution must have occurred in multiple steps under constant selective pressure. This selective pressure could come from at least two key factors: the necessity for the cells to gain energy and to reduce the damaging effects of solar UV, which was orders-of-magnitude stronger in the absence of the ozone shield than it is now.21

Interestingly, since non-oxygenic photosynthesizing bacteria generally faced less severe selection pressures, current microorganisms of this kind probably still preserve the basic features of their microbial forebears. Their oxygenic photosynthesizing cousins faced a much tougher environment, and presumably were sorted out with the usual remorseless indifference of natural selection. As a result, many cyanobacteria are remarkably flexible. In an environment rich with sulfides, they can survive and engage in anoxygenic photosynthesis. But return them to a more oxygen-rich environment, and they revert to their normal function.

In some parts of the world’s aquatic environment, anoxygenic phototrophs can still be found. But the eventual domination of the living world by oxygenic photosynthesis was of enormous significance. Sulfur World could never have produced us. Oxygen World, which enormously expanded the extent of Carbon World, could.

It is thought by many researchers that the cyanobacteria oxygenated the Earth’s atmosphere over an enormously long period of time, making the Earth suitable for the evolution of larger and more complex life forms. There was a concomitant oxygenation of the world ocean, but that process appears to have taken much longer. However, some scientists give primacy to chlorophytes (green algae) in the oxygenation of the Earth’s air and water, pointing out that only when green algae evolved and became widespread did oxygen in the atmosphere reach significant levels. They argue that while cyanobacteria may have been the original oxygenating phototrophs, the ones that started the process of atmospheric oxygenation, it was the eukaryotic green algae, incorporating cyanobacteria into themselves, that accelerated it. There is also some pretty serious debate about just how long the oxygenation of the atmosphere may have taken, with estimates ranging from several hundred million years to well over 1 billion years for oxygen concentrations to reach a level that facilitated the evolution of eukaryotes. There is some pretty solid evidence that the process was at least under way by around 2.5 billion ybp, but the O2 level in the first period of oxygenation would not have supported the kind of animal life that exists today. Further, evidence appears to show that the concentration of oxygen in the atmosphere has fluctuated quite severely over the eons, sometimes because of extensive volcanic activity.

The processes of photosynthesis have been handed down to and preserved by the descendants of the early cyanobacteria, and are one of the most crucial aspects of life on this planet. The significance of this cannot be overstated: 

When our biosphere developed photosynthesis, it developed an energy resource orders of magnitude larger than that available from oxidation-reduction reactions associated with weathering and hydrothermal activity. The significance of this innovation can be illustrated quantitatively for modern Earth…Global thermal fluxes were greater in the distant geologic past, but the onset of oxygenic photosynthesis most probably increased global organic productivity by at least two to three orders of magnitude. [Emphasis added.] This enormous productivity resulted principally from the ability of oxygenic photosynthetic bacteria to capture hydrogen for organic biosynthesis by cleaving water. This virtually unlimited supply of hydrogen freed life from its sole dependence upon abiotic chemical sources of reducing power, such as hydrothermal sources and weathering. Communities sustained by oxygenic photosynthesis could thrive wherever supplies of sunlight, moisture, and nutrients were sufficient.22

Life on this planet, in other words, was enormously expanded by photosynthesis’s evolution, becoming 100 to one thousand times more widespread than it could ever have been when the production of organic carbon was reliant on water heated by the Earth alone. The opportunity for oxygenic photosynthesis to evolve may have come about because of the major reduction in thermal activity on the Earth between 4 billion and 3 billion ybp.23

The chloroplast, that part of eukaryotic plant cells in which the photosynthetic process takes place, is a modified cyanobacterium living in the cell itself. By 1.2 billion ybp at the latest,24 through a process known as endosymbiosis, (see below) cyanobacteria began embedding themselves in certain eukaryotic cells, nourishing them in return for shelter. (In endosymbiosis, one of the partners in the symbiotic relationship actually lives within the body of the other partner.) Mitochondria embedded themselves in cells in the same manner.

Cyanobacteria sometimes create structures known as stromatolites, dome-shaped, layered assemblages built by the tendency of mats of cyanobacteria located in shallow waters to trap sediments—a dramatic example of self-organization. Stromatolites build up through the accretion caused by this sediment trapping and the precipitation of the trapped minerals. Eventually a “community” of microorganisms of many species contributes to the building up of these structures. These communities contain some of the very oldest fossil records that exist, and stromatolites may be the oldest organically-produced structures of any kind.25

Photosynthesis established one of the greatest regular energy-matter exchange cycles on Earth, the exchange of carbon dioxide and oxygen. This exchange eventually made possible the greening of the landmasses of Earth. (Even Antarctica once harbored abundant plant life.) It established the foundation of the food chain that made the evolution of the Animal Kingdom’s metazoans possible. It established the “lungs” of the planet Earth, the plant life that continuously cleans the atmosphere and replenishes the oxygen supply. With the evolution of this process, the planet Earth was able to utilize the solar energy flooding down on it in such a way as to transform the entire outer crust of the planet. With the evolution of photosynthesis, a form of radiant energy was transformed into a more tangible entity for the first time, and by this transformation, the Earth became a world in which the emergence of consciousness was possible—not inevitable—but possible. Without oxygenic photosynthesis, we would not exist. It’s that simple.

Symbiosis and Endosymbiosis

In symbiosis organisms live together in a relationship that benefits at least one of the organisms involved, but not necessarily both. Sometimes the relationship is mutually beneficial, sometimes only one organism benefits and the other organism is unaffected, and sometimes one of the organisms is harmed because the other is engaged in parasitism (which is what viruses are engaged in, as we will see). We saw that cyanobacteria were incorporated into eukaryotic cells, and we briefly noted that mitochondria had done the same. As we noted, these are examples of endosymbiosis, a mutually beneficial form of symbiosis in which one of the organisms lives within the body of the other. How did this happen, and what evidence do we have that it did? Moreover, what is the significance of the mitochondrion in a cell?

The mitochondrion, since it is common to animals, plants, and most fungi and protists, is of particular interest to us. The mitochondrion’s role in a eukaryotic cell is absolutely crucial. It extracts energy from oxygen and drives the metabolic process in eukaryotes. It oxidizes food molecules and produces adenosine triphosphate, or ATP, the fuel that the mitochondria and the cells they inhabit both use. The waste products from this process are water and carbon dioxide. Where did the mitochondria we have in our cells originate? The evidence is clear that the mitochondria were, at one point, independent organisms. The mitochondria have their own DNA, their own messenger RNA (mRNA), their own transfer RNA (tRNA), and their own ribosomes. They have a sensitivity to antibiotics virtually identical to that of bacteria. They split in two to reproduce, just as the bacteria do. They are, without doubt, endosymbionts. Lynn Margulis hypothesizes that they are the descendants of bacteria that preyed on other bacteria. This predatory ancestral bacterium was oxygen-breathing, in an era in which oxygen was a deadly poison gas to many organisms (and in which oxygen levels were rising, thanks to the cyanobacteria). In this scenario, the ancestors of the modern mitochondria invaded other cells, reproducing within them. Only those that evolved a cooperative arrangement with their hosts survived. Natural selection weeded out the killers, the ones who destroyed their own hosts. Natural selection also blindly conferred advantages to cells that could resist the oxygen-breathing predators to some degree, facilitating the development of the symbiotic relationship. In this manner, Margulis believes, did the mitochondria found in our cells come to be part of us.26

The number of mitochondria in individual human cells varies according to the type of cell, but can number more than a thousand. They are a direct link between us and the early world of living things. As Margulis puts it, “[t]he descendants of the bacteria that swam in primeval seas breathing oxygen three billion years ago exist now in our bodies as mitochondria”.27 So once again we are reminded of the unity of all life, and the tremendous antiquity of so many of the traits that characterize us.

We turn now to the crucial distinction that evolved between the animals and the plants—the source of their nutrients.

Autotrophs, Heterotrophs, and Mixotrophs 

Organisms that exclusively use photosynthesis for their energy needs are by definition autotrophic, which is to say they do not need to derive energy from any other organism to facilitate their survival. Animals, by definition, are heterotrophic, as are a great many bacteria and archaea. They must acquire energy from the consumption of other organisms. They must eat, and in so doing, they must kill something else to survive, or else rely on something to do their killing for them, as in the case of scavengers or animals living in a symbiotic relationship that allows them to feed on the organic matter that clings to another organism. When put this bluntly, it brings many characteristics of the world into sharp focus. Animals need to kill either plants or other animals, or both, in order to live. The entire world of grazing, and the continuous war between those who eat other animals and the animals who are eaten, stem from this brutally simple fact. How did heterotrophic organisms arise?

Some researchers are convinced that heterotrophy emerged from the fact that the first complex organic polymers needed to “ingest” pre-formed nutrients and enzymes from the environment, but it is not entirely clear whether the first true organisms were autotrophs, some of which lost their ability to use photosynthesis and evolved heterotrophy over the course of their species’ existence, or whether some of the earliest bacteria preyed on other bacteria for their nutrients, and autotrophic forms evolved from them.28  J. William Schopf is convinced that autotrophy preceded heterotrophy, as autotrophs established conditions conducive to the spread of heterotrophs. He cites the rise of the cyanobacteria, for example, as the event that made possible the spread of prokaryotic heterotrophs that required the presence of oxygen.29 Complicating all of this was (and is) the presence of mixotrophs. Mixotrophic organisms employ both autotrophic and heterotrophic strategies to sustain themselves. While this makes them less efficient in certain ways, since maintaining a dual system for acquiring nutrients requires a larger expenditure of energy, it gives them obvious advantages, especially in highly variable environments. Mixotrophy has ancient evolutionary roots and is very widespread in aquatic settings, where mixotrophs can have a significant impact on their habitats There are both single-celled and multi-celled mixotrophs.30

Autotrophs are the basis of the world’s food chain (along with certain aquatic mixotrophs). These autotrophs are either land plants or phytoplankton, many of which are plants while others are bacteria or protists. The spread of plant life over the planet Earth arose, as we saw, from photosynthetic bacteria. The drama of predator and prey on this planet also began in the world of single-celled organisms, as certain bacteria devoured  other bacteria in the relentless struggle for survival. The entire multi-billion-year epic that is the history of the recycling of energy-matter through the life forms of this world can therefore be traced to the humble prokaryotes that represented the first life to be enclosed in membranes. It was from their unconscious ability to acquire energy for metabolism that the world we have come to know arose.


The existence of viruses presents a special challenge to the life sciences. In their basic state they appear to be non-living. They are incapable of reproduction until they invade a living cell and capture its reproductive functions. However, after they have effected such a capture, their numbers can proliferate wildly. Viruses also show the capacity to mutate and evolve, which is one of our potential criteria for life forms. (See previous chapter.) So are they living or non-living entities? From where did they arise, and how do they evolve?

Viruses are parasites by definition, symbionts that harm their symbiotic “partners”. They are also totally pervasive in the biosphere, the most widespread organic entities on Earth. Viruses are capable of infecting any kind of life form, including bacteria, the viral parasites of which are known as bacteriophages. (Most viruses are shielded by protein sheaths known as capsids, which themselves are subject to selection, and which not only provide protection to a virus’s genetic material, but also assist the viruses in their infiltration of cells.31) Viruses do not, in the view of many virologists, appear to have a single point of origin. Virologist Ed Rybicki explains that many viruses are strands of nucleic acid that have “escaped” from cells. The simplest ones are just bits of RNA, so basic that they may be no more than “rogue” messenger RNA (mRNA). Viruses therefore, he believes, have probably evolved many times in the history of life. There is evidence that certain viruses are extremely ancient, having evolved before eukaryotes did, while others are of much more recent origin. Their complexity varies widely, and some of the DNA viruses have more than 1 million base pairs in their genomes. The viruses with the most base pairs, in fact, may be the most ancient of all, perhaps having evolved very soon after the first lines of organisms emerged from the last universal common ancestor. The impact of these ancient viruses may be very, very significant indeed, as Rybicki explains:

However, their actual origin could be in an even more complex interaction with early cellular life forms, given that viruses may well be responsible for very significant episodes of evolutionary change in cellular life, all the way from the origin of eukaryotes through to the much more recent evolution of placental mammals.  In fact, there is informed speculation as to the possibility of viruses having significantly influenced the evolution of eukaryotes as a cognate group of organisms.32

There are researchers who contend that all viruses are evolved from a very ancient pool of genes that emerged early in the history of life, and which has retained its distinct nature throughout the eons. These scientists point out that many key proteins found in a wide range of viruses are completely absent from ordinary one-celled organisms. It is their view that the first genetic elements on Earth gave rise to both cells and viruses, with RNA viruses evolving first, then retroviruses (see below), and then DNA viruses. They hypothesize that “selfish” genetic elements ancestral to viruses evolved even before cells did. Once bacteria and archaeans evolved, very simple viruses began living through parasitism. In their view, as eukaryotes evolved, they provided a setting in which new varieties of virus could evolve. They see the evolution of eukaryotic cells as a fusion of archaeal and bacterial elements. These researchers call the history of this viral genetic material that takes a multiplicity of forms and yet retains its essential character the Virus World.  As they put it, “the Virus World appears to be a spatial-temporal continuum that transcends the entire history of life on this planet.”33  The authors of this study are careful to call their views conjectural, and there are no doubt many virologists who would question their hypothesis. But very often it is through such speculation that important discoveries are made. 

In the history of life, the evolution of retroviruses has been of major significance. A retrovirus is an RNA virus that engages in reverse transcription, which means that it has an enzyme that allows it to convert RNA into DNA instead of the usual sequence (DNA to RNA to proteins). It inserts this DNA into the target cell’s genome, altering it.34 There are 11 known genera of them, and they have the capacity to do grave harm. They are implicated in certain kinds of cancer, for example, and of course the human immunodeficiency virus is a retrovirus. They are also implicated in certain kinds of paralysis, in ataxia, in arthritis, in dementia, and neuropathy, among others35 A careful analysis of the human genome has revealed something utterly surprising: a full eight per cent of our genetic makeup is composed of disabled retroviruses. As an author writing about the people who study retroviruses has put it,

They are called endogenous retroviruses, because once they infect the DNA of a species they become part of that species. One by one, though, after molecular battles that raged for thousands of generations, they have been defeated by evolution. Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years.36

Astonishingly, retroviruses may have played a role in the evolution of placental mammals. Biologists have found a protein called syncytin in the placental tissue of several types of mammal, including humans. Syncytin is critical in the process of fusing cells in order to form the placenta. It uses the same method to do this that retroviruses use to attach themselves to cells they are attacking. Moreover, the placentas of the different mammals who were studied all had retroviruses on the layer of tissue that separates mother and fetus, and yet all of the subject animals were healthy. Moreover, an embryo itself acts in a parasitic fashion. It is possible that more than 200 million years ago a retrovirus invaded a mammal of that time, which was probably of the egg-laying variety, and in the process of changing the DNA of its target (and being resisted by it in turn) set off a chain of subtle changes that ultimately resulted in the rise of mammals that bear their young alive and outside of an egg.37 (See pp. 286-289 for another view.)

Viruses have been the mortal enemies of humans throughout our time on this planet, killing people by the millions through epidemics of influenza, racking up huge numbers of victims through smallpox, wiping out millions through AIDS, and crippling untold others through polio, to cite the more prominent examples. Our bodies have waged war against them, in turn, and in so doing we have been modified, in ways we do not yet fully understand. Viruses can be thought of as a selection pressure on humans, predators that force us to adapt. Their origin in the world of the one-celled organisms has had the most profound consequences for the human genus. In our DNA, we find the remains of the ones we have absorbed and conquered—but the war is far from over.

The Origin of Sex

The earliest one-celled organisms reproduced by means of mitosis, asexual reproduction, and of course an enormous number of unicellular life forms still do. Mitosis is carried out in a series of five steps, the end result of which is a cell that is a duplicate of the original. (Of course, this process is subject to errors.) But in the Mesoproterozoic Era, between 1.0 and 1.6 billion years ago, the processes of meiosis—sexual reproduction—evolved in eukaryotic cells. In meiosis reproduction is achieved by combining half of the genetic material of two different organisms rather than duplicating the genetic material of one. There is still a strong debate among biologists about why sexual reproduction evolved and what the advantages it conferred were. Moreover, the evolution of meiosis is one of the most challenging issues in the life sciences.

One team of researchers, through careful analysis of the genes of a simple eukaryotic organism, a protist named Giardia intestinalis, have determined that meiosis must have evolved very early in the history of the Eukarya. [This would naturally place this event toward the beginning of the Mesoproterozoic, or perhaps even before it.] Giardia has several known meiotic genes, and there can be little doubt that it was capable of sexual reproduction in ancient times. Moreover, meiosis must have existed prior to Giardia breaking off in its own direction from the main eukaryotic line, but the advent of meiosis in the Eukarya has not yet been ascertained.38

A pair of researchers writing in the journal Genetics in 2009 came to these conclusions:

1.   An understanding of the early environment in which eukaryotic cells lived is crucial to our understanding of the selection pressures that made eukaryotes evolve in the direction of meiosis.

2.  The initial development of meiosis from mitosis required only a single innovation, homolog synapsis, the lining up of similar chromosomes in pairs to allow their combination to occur.

3.  This capacity may have arisen from the need to avoid genetic abnormalities during the recombination process by making sure that the proper gene sequences were being recombined.

Finally, these researchers make the following key points:

Our hypothesis in no way contradicts the idea that meiosis serves to promote intergenic recombination, thereby providing new variation for selection to act upon. Indeed, one of us has proposed that the advantages of increased intergenic recombination were important in the early establishment of eukaryotic cells competing for niches with prokaryotic cells We argue here, however, that this benefit of meiosis did not provide the initial selective pressure for its origins. Although our idea differs from traditional thinking about the advantages of meiosis, it is consistent with the known facts, and its central premise—that recombination has to be limited in extent to ensure the fidelity of the transmission of the genetic complement—is testable.39

It will take much further research to elucidate all the details surrounding the evolution of sex. If we seek the deep origins of our own sexuality, we must begin with an understanding of the emergence of meiosis. From its humble beginnings among the early eukaryotes, sex evolved and took myriad, fantastically elaborated forms, both shaping the contours of animal life and being shaped by it. The competition for survival within the animal kingdom is defined by an animal’s ability to kill or scavenge enough material to feed its metabolic processes, and its ability to have its genetic material sexually reproduced. To do these things it must learn to survive in a world filled with other animals trying to do exactly the same things. We can see clearly that the roots of this ceaseless drama lie in the realm of the one-celled organisms, who mindlessly went about the business of establishing the future of the living world, a world in which consciousness was now a more distinct possibility.

Geological and Climatic Conditions During the Period of One-Celled Organism

Most geologists are agreed that plate tectonics, the horizontal and vertical movements of sections of the Earth’s crust against each other, probably did not begin during the Hadean Eon, owing to the lack of crustal rigidity at that time. (There are those who dissent from this view.) However, by the Archean, evidence indicates that the process was definitely underway. (We will examine the specific operation of plate tectonics in a chapter called The Motions of the Earth, in a subsequent volume.) There seems to be good evidence of tectonic activity dating back to 3.1 billion ybp, in the Precambrian Era, which coincides (approximately) with the entire period from the origin of the Earth to the evolution and wide distribution of multicellular life forms. Additionally, paleomagnetic evidence has allowed geologists to estimate the approximate positions of certain landmasses on the Earth’s surface as far back as 2.68 billion ybp.40  The long period in which single-celled life forms were dominant saw vast changes in the emergence or submergence of landmasses and the position of various landmasses relative to each other. There is a great deal of evidence to support the contention that the Earth’s landmasses have, from time to time, aggregated themselves into supercontinents, which then, over huge expanses of time broke up, eventually to aggregate themselves into yet another supercontinent. Geologic processes in the Earth’s mantle, such as the convection of its heat, disturb and shift the segmented pieces of the Earth’s crust, driving this process.41

Researchers working in Canada have uncovered evidence of what might be called a protocontinent, a major landmass that may have formed 4 billion ybp as part of a very ancient supercontinent. Of course, the question of how such a landmass formed without plate tectonics is a challenging one.42 Other researchers have estimated that a supercontinent may have formed somewhere around 2.7 billion ybp, based on the known formation of crust at that time.43  About 1.1 billion years ago, in the latter part of the period we have been discussing, a supercontinent named Rodinia began to form, a process which took about 100 million years. Rodinia did not incorporate all of the Earth’s land, however, and by 800-750 million ybp it had begun to fragment, losing Australia and part of Antarctica, among other territories.44

During the long period of unicellular life’s dominance, the Earth’s climate went through a great many fluctuations, not all of which are fully understood, by any means. A good hypothesis in regard to climate changes on this planet is related to the action of plate tectonics. The collision of plates can force some of the crustal material downward, toward the mantle, causing it to become molten. This phenomenon is called subduction. The instability resulting from this process can manifest itself in volcanism. Extensive volcanism can throw huge amounts of sulfur gases (which convert to sulfate aerosols), and ash particles into the atmosphere, altering the ability of solar radiation to penetrate to the Earth’s surface. The result is planetary-wide cooling at the surface, but a heating of the stratosphere. The effects of volcanic eruptions on both the surface and the stratosphere vary according to latitude. Counter-intuitively, perhaps, an eruption can also cause winter warming in northern latitudes.45

We need to consider as well the fact that the physical position of landmasses on the surface of the Earth has a major impact on climate. When land is concentrated near the polar regions, and covered with ice and snow, it reflects a great deal of solar radiation back out into space. (The relative amount of light that is reflected in a given region is known as the region’s albedo.) When land is concentrated near the equator, much more solar energy is absorbed. Where solar radiation falls on the ocean is also of major importance. These differences are manifested in wind patterns, the movement of ocean currents, patterns of rainfall, and wide swings in temperature. Further, tectonic activity, in raising or submerging land, can have a significant effect on sea level. Changing patterns of oceanic fault lines and underwater ridges, caused by tectonic movements, help bring these changes about. Finally, the formation of mountains in various regions by tectonic plate activity also alters the pattern of world climate.46 Therefore, in the three billion years between the emergence of life and the evolution of multicelled animals, the Earth’s climate underwent sweeping changes, and these changes must have had a profound impact on the single-celled life forms that dominated and defined its biosphere. Richard Fortey has expressed it this way:

The least ambiguous record of climatic events is probably preserved in sediment cores recovered from the deep sea, where the gentle rain of microscopic fossils continued unabated even as ice sheets grew and shrunk on land. Various species of planktonic animals  moved back and forth, north or south, in sympathy with the fluctuations in the climate.47

There was a time in the Earth’s geological history, near the end of the one-celled organisms’ dominance, known as the Cryogenian Period. This was an era that lasted from about 850 million to about 650 million ybp, characterized by periods of severe and extensive glaciation, what some researchers call “Snowball Earth”. Some scientists believe that around 716 million ybp, glaciation actually reached the Earth’s equatorial regions, encompassing the entire planet in ice. A major disruption in the Earth’s carbon cycle, evident in sediments and ancient organic material, lends support to this view.48 Other researchers, however, have raised doubts. They argue that had the Earth been entirely wrapped in ice, its ability to thaw itself out would have come into question, as most solar radiation would have been reflected rather than absorbed. Further, they contend, such glaciation would have had a catastrophic effect on life, completely altering the path of evolution.49 The resolution of this issue is important, because humans in our era face critical questions about possible climate change, and the mechanisms by which this happens need to be understood.

The Advent of Multicelled Life Forms

Single-celled organisms were, and are, spectacularly successful life forms. They are found in every ecological niche on the surface of this planet, in numbers we cannot begin to comprehend. Some of their lines can be traced back to the very beginning of the Tree of Life itself. Their importance in the living world is immense. So we might reasonably ask: what evolutionary advantage did multicelled life forms have? How did such a momentous change in the organization of life come about?

The evolution of multicellularity gave life options and opportunities that it would not otherwise have had. By associating with each other, cells could ensure their mutual survival. Very often, in effect, they had a better chance working as a team than they did going it alone. The eventual specialization of cell function allowed life forms to attain greater complexity and considerable, even enormous size. It allowed them to occupy and sometimes dominate a particular ecological niche. At the very least, it enabled sufficient members of their population to reach reproductive maturity. It wasn’t a method that produced the most organisms, and the sexual mode of reproduction that the vast majority of multicelled life forms employed wasn’t necessarily superior to the mitosis employed by the one-celled organisms. It was simply a way of life that worked, and biologically, that was all that was necessary.50

The origin of multicelled organisms lies in the tendency of many one-celled life forms to assemble into colonies with other cells of their kind. Certain kinds of bacteria, for example, have been observed to “pool their resources” for tasks such as breaking down organic matter, even assembling themselves into tight units to help each other survive when food is in short supply. Cyanobacteria have been observed to form into chains more than a meter long, with certain members of the group taking on specialized tasks. Members of a eukaryotic flagellated species of algae have been observed to travel in “packs”, all members of the group heading in the same direction. Members of another species of eukaryotic algae have been observed to form themselves into the shape of a hollow sphere, some 50,000 cells all linked together to do so. There is even a simple division of labor in such spherical colonies. In short, we can actually observe contemporary examples of cell colonies that contain cells engaged in specialized activities.51 There is nothing mysterious, therefore, about the fact that cells, both prokaryotic and eukaryotic, engage in these behaviors. Doing so enhances their survival odds, and thus they are reinforced, yet another example of non-conscious natural selection.

Scientists who are researching the evolution of multicellularity are quick to point out that many aspects of this phenomenon are unknown, and that animals have genetic traits that are not found in the single-celled organisms that are their closest biological relatives. However, researchers comparing a certain form of algae (Volvox) to its closest single-celled relative (Chlamydomonas) have found that the change from the single-celled organism to the multi-celled one did not require any major change in the kinds of proteins found in the ancestral line. The algae appear to have expanded the role of proteins already present rather than evolving completely new types.52 Research such as this is broadening our understanding of the ways in which multicellularity may have emerged.

Single celled organisms evolved methods of adhering to other cells, and multicelled organisms are the inheritors of this. Cells can secrete cellulose or proteins to act as binding agents. The complete network of such substances in a set of cells is called the extracellular matrix, and in many cases it is this matrix rather than the cells themselves that bears the physical stresses to which an organism may be subjected. Another major way in which cells can be bound together is by means of epithelial tissue, which binds cells together into sheets known as epithelia. Cells in the epithelia are bound together directly by strong threads of protein that attach one membrane to the other at junctions evolved for that purpose.53 Research has begun to elucidate the evolution of epithelial-type cells, and it would appear that they evolved early in the development of metazoans, or multi-celled heterotrophs—animals, in other words. The same kinds of mechanisms appear to generate epithelia across the animal kingdom. Proteins governing the making of epithelia are found in animals as diverse as the Cnidaria (which includes the corals and jellyfish), mammals, and fruit flies, all of which suggests an ancient evolutionary origin.54 Cells, in short, evolved the ability to bind themselves with other cells, and it was this ability that aided the transition from one-celled to multi-celled life forms. Eventually, complex networks of genetic feedback loops evolved in aggregations of cells, which allowed for the phenomenon of selective gene expression to emerge. (Gene expression is carried out through the transcription and translation processes described in the previous chapter.) Differential gene expression is what allows cells to become “specialists”, and it was instrumental in the rise and evolution of complex multicellular life forms. We will focus on this phenomenon in more detail in the next chapter.

The Earliest Multicelled Organism Yet Discovered

For approximately 2 billion years single-celled microorganisms were the only life forms on the Earth.55 In terms of our chronology, that period would be from about 29 September to around 20 November. The first evidence we have that things were changing is the presence of Grypania spiralis, a eukaryotic algae, possibly—possibly—the first multicelled life form. G. spiralis has been discovered in the United States, China, and India. The examples of Grypania spiralis found in India have been dated to about 1.6 billion ybp. This would be in the early Mesoproterozoic. The unearthed organisms have been found in coils, the length of which are between 0.75 and 6.5 centimeters.56 The evolution of this very humble life form may have been revolutionary. It is the first known instance of a colony of cells joining together to form an organism, a harbinger of profoundly important events to come.

Humans are the product of many inheritances, ranging from the nucleosynthesis of the first elements in the early Universe to the first metabolic processes that may have given rise to life itself. The inheritance we have received from the world of one-celled life forms is in many ways just as significant. Humans are collections of cells, which means our basic physical structure originated in this world. The one-celled life forms evolved heterotrophy, which is how we acquire our “fuel”. One-celled life forms evolved sexual reproduction, which is how we replenish our numbers. Certain one-celled life forms generated oxygen, which is our priority need. The bacteria at the base of the Tree of Life have affected us in ways that  range from helpful to brutally destructive. One-celled organisms gave rise to viruses, which have assaulted us and shaped us. Everywhere we turn, we see the effects of the life forms that evolved in the protocells that first sheltered organic material. From the ability of one-celled organisms to form mutually-supporting colonies came the world of plants and the animal kingdom of which we are an intrinsic part. The one-celled life forms dominated our planet for billions of years—and they may just be the last life forms that survive until the Earth’s final days. Our lives, in other words, might merely be an interruption of their inconceivably long reign. 

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