The cell
Part 4. Complex Cells
by Ian Magrath
- A hydrothermal ocean vent, known as Champagne, emitting liquid carbon dioxide (socalled “white smokers”) and minerals such as barium, calcium and silicon as well as acetyl thioesters, which, along with the heat, can form organic molecules – a potential location for the origin of Life. Picture from the U.S. National Oceanic and Atmospheric Administration
Life on Earth is a dynamical system that, since its origin in self-replicating molecules approximately four billion years ago, has continued to evolve through a process of adaptation to the ever-changing environment – which is both modified by and includes Life itself. The most rapid evolution has taken place in the last two billion years, creating in the process ever more complex systems known in the field of biology as biomes or ecosystems – the sum total of living organisms in a specific habitat. All existing biomes, which are interconnected, together comprise the biosphere.
Complexity implies an increase in the number of interacting component parts of a system or in the number of component parts in each element of the system (which in the case of Life may be systems in their own right), or both. Eukaryotic cells are only comparatively more complex than prokaryotic cells – the development of which was the point at which Part 3 of this series of articles describing the evolution of cells ended. In reality, prokaryotic cells are immensely complex and there is much that remains to be discovered about them. But eukaryotic cells are enormously more diverse in their structure and functions and also able to cooperate in the formation of the complex multicellular systems that we refer to as animals, plants and fungi, and which comprise the elements of the next higher level of biological organization. Moreover, each organism is an ecosystem in its own right, such that Life consists of ecosystems within ecosystems (the human body, for example, contains ten times as many microbial cells, known as its microbiome, as human cells) and Life is probably the most complex system in the universe. There can be little doubt that had eukaryotic cells not evolved, Life on Earth would still consist of “simple cells” rather than the present rich profusion of multicellular organisms. The more complex among the latter have developed awareness, and in the case of humans, rational thought. Had this not been the case, and unless there is Life beyond Earth, the Universe itself would in effect, have never existed, for what is existence without the perception of existence?
The Emergence of Eukaryotic Cells
There is a great deal of debate regarding both the processes that led to the formation of eukaryotic cells, and precisely when, on an evolutionary time-scale, the first eukaryotic cells emerged.
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Volume 10, Numbers 1 and 2
December 2010 - March 2011
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The most generally accepted hypothesis, supported by a considerable amount of scientific data as well as the fossil record, is that eukaryotic cells arose from the fusion of many small prokaryotes with a much larger prokaryotic cell, approximately 1.6 to 2 billion years ago, close to 2 billion years after the emergence of prokaryotic cells (a date that is also uncertain but likely to be in excess of 3.5 billion years ago). The conditions required for the development of eukaryotic cells can only be hypothesized, but it is highly probable that two events were of critical importance: the evolution of oxygen photosynthesis, making oxygen available from water molecules, and the development by some prokaryotes of metabolic pathways enabling them to use oxygen as a source of energy. Aerobic respiration, the process of obtaining energy from intracellular chemical reactions involving oxygen, is much more efficient than anaerobic respiration or fermentation, thereby permitting the emergence of greater complexity. Organisms could develop alternative, active means of obtaining food, including preying upon, or becoming the parasites of other life-forms. Initially, single eukaryotic cells (Protista) were able to prey upon prokaryotes, but as Life evolved, the possibilities expanded enormously, and photosynthesis ensured that the high levels of energy required could be obtained from the sun, by at least some life-forms, and passed on to others by processes such as parasitism or predation.
The advent of molecular genetic analysis led Carl Woese and George Fox, in 1977, to subdivide prokaryotic cells, on the basis of differences in their ribosomal RNA, into two types, the Archaebacteria, subsequently referred to as archea and the Eubacteria or “true” bacteria. Although it is now believed that these subgroups are no closer to each other at a genetic level than each is to the Eukarya (i.e., all of the organisms whose cells are eukaryotic), both are still prokaryotes, since this term refers to the absence of a true cell nucleus; prokaryote comes from the Greek meaning “prior to the presence of a nucleus (actually, nut or kernel).” Presumably both bacteria and archea evolved from a single precursor, and some (notably Carl Woese) favor the hypothesis that this precursor may also have given rise to the eukaryotes, hence Woese’s three “domains” of life, Bacteria, Archea and Eukaryota, in which case, eukaryotes could be of more ancient lineage than proposed. An early date for the evolution of eukaryotic cells, however, seems unlikely if, indeed, their development required the ability to use oxygen in order to obtain sufficient energy for their needs, for the evidence suggests that oxygen did not become available for use by prokaryotes, at least in significant quantities, until perhaps 2.5 billion years ago.
- Figure 1. Diagrammatic representation of endosymbiosis which is thought to have led, through endosymbiont evolution, to the presence of mitochondria (aerobic bacteria) and chloroplasts (cyanobacteria) in eukaryotic cells.
Evolution by Fusion
Molecular analysis has led to the recognition that eukaryotes more closely resemble archeons with respect to their DNA and genetic machinery (e.g., the enzymes involved in transcription and translation), although they contain mitochondria - membranous organelles that closely resemble bacteria in several respects. This strongly supports the hypothesis that it was a fusion event that gave rise to the eukaryotic cell, as proposed by Lynn Margulis - probably between an archeon and several smaller prokaryotic cells with which it was interdependent (symbiotic). Perhaps the prokaryotes that underwent fusion had previously contributed to each other’s metabolic processes, as occurs today in bacteria which produce acetic acid, from which archeons, which would otherwise have access only to longer chain fatty acids, are able to produce methane. Regardless of the mechanism, and whether one or many episodes of fusion took place, stable cells with an endosymbiotic relationship arose, i.e., the bacteria were able to survive, indeed, benefit from their location in the cytoplasm of a much larger archeon, while the latter similarly benefited from the presence of the bacteria (Figure 1). This must have entailed the replication of the bacteria becoming synchronized with the archeon chromosome (DNA), a process which may already have existed since it is known that prokaryotes are able to transfer DNA to each other through a process known as conjugation. The transferred extrachromosomal DNA, which may contain a gene, for example one that confers antibiotic resistance (bacteria themselves make antibiotics which have a role in regulating mixed bacterial populations, such as those in the gastrointestinal tracts of animals), is passed from one prokaryotic cell to another and retained over generations. Extrachromosomal DNA, often in the form of circular DNA molecules, known as plasmids, can also be incorporated into (or removed from) the bacterial chromosome, in effect, adding one or more genes to the latter. Almost certainly, some of the genes of the endosymbiotic bacteria were transferred to the nuclear genome of the archeon, at the time of the creation of the eukaryotic cell, although genes involved in the production of proteins involved in energy production and some other cellular processes remained in the bacterial chromosome, and persist today in the mitochondria of eukaryotic cells, which are the main source of adenosine triphosphate (ATP), the molecule in which energy is stored in all life forms. Mitochondria resemble, in many ways, the bacteria from which they are believed to have originated – they use, for example, a variant genetic code that is also used by the group of diverse bacterial genera known as Proteobacteria, and in particular, the Rickettsia.
Photo synthesis
How the first cells obtained the energy required to form the carbon polymers from which they were constructed is unknown. At least some of the essential chemical reactions may have been driven by the very inefficient process of using heat from the Earth’s core, available at volcanic hydrothermal vents under the sea. The earliest cells were probably hetero-trophs, i.e., they used available organic molecules present in the sea around them as a source of raw materials and energy. Heterotrophs, which include modern animals, fungi, most protists and prokaryocytes, are unable to "fix" carbon, i.e., use carbon dioxide for the production of the carbon polymers essential to life. An important step towards both the development of eukaryotic cells and the expansion of the habitats that could support life was the development of autotrophs - cells able to create their own complex carbon compounds (essentially, food) from carbon fixed from carbon dioxide present at high levels in the atmosphere and dissolved in the sea. Although little is known of the details of the chemical pathways, they may have involved a primitive form of photosynthesis, in which the necessary electron donors were inorganic molecules such as sulphur, metal ions, methane or hydrogen, which could be used to fix carbon by reducing carbon dioxide, leading to the synthesis of sugars and other organic molecules with the production of energy (ATP).
- Figure 2. A large bloom of modern cyanobacteria (also often referred to as blue-green algae) on Lake Atitlán, Guatemala. The filamentous strands are clearly visible in the lake, which is surrounded by forest and cultivated fields. Sewage agricultural run-off is thought to have caused the bacterial growth. Picture from NASA Earth Observatory.
These processes were probably available to prokaryotic cells some 3.5 billion years ago, and their relative inefficiency could have imposed an upper limit on the size and complexity of prokaryotic cells, except perhaps in exceptional circumstances. Some 2.8 billion years ago, perhaps as much as 3.5 billion years ago, the cyanobacteria emerged (Figure 2). It was probably much later – 2.3 to 2.4 billion years ago – that cyanobacteria developed photosynthetic pathways in which water was the electron donor and energy was derived from the sun. Little is known about the evolution of chlorophyll, a green pigmented protein located in the cell membrane of cyanobacteria, and able to absorb energy from light, particularly from the blue and red parts of the electromagnetic spectrum, but this, in its several forms, has probably been the major photochemical pigment for at least 2-2.5 billion years. Less efficient light-absorbing pigments may have preceded chlorophyll. Chlorophyll never developed in the Archea, although some are able to use another pigment, retinal, which is able to absorb green light that can then be used for carbon fixation and carbohydrate production.
The Oxygen Catastrophe
- Figure 3. Chloroplasts in lamina cells of Plagiomnium affine, a plant that grows in close proximity to water. Photograph by Kristian Peters.
A problem for the cyanobacteria, and, subsequently other prokaryotes, was that photosynthesis in which water is used as the electron donor produces oxygen as a waste product. Oxygen entered the surrounding sea water and was trapped by the large quantities of dissolved minerals, particularly ferrous iron, which precipitated out as ferric oxides that can still be seen in “banded iron formations” in sediments in Minnesota. It may have been another billion and a half years before most of the oxygen-trapping minerals were “rusted” or oxidized (creating, incidentally, a major diversification of minerals in the Earth’s crust), such that oxygen could build up in the atmosphere - a process believed to have begun approximately 900 million years after the evolution of oxygen photosynthesis. This triggered the mass extinction of anaerobic prokaryotic cells, but some were able to develop mechanisms not only for protecting themselves against free oxygen radicals, but also for using oxygen as a means of generating energy through oxidation of glucose (glycolysis). A major metabolic pathway, namely, the citric acid or Krebs cycle, which is universally present in living organisms, is central to this process, although it participates in many other reactions such that even anaerobic (non-oxygen - using) organisms make use of it. The Krebs cycle is so important that it has even been suggested that it evolved prior to the evolution of nucleic acids and genes. Whether or not this is correct, the development of oxygen photosynthesis increased the ability of living organisms to produce energy via oxygen-based (aerobic) metabolism, which is estimated to produce 30 ATP molecules per molecule of glucose reduced, as opposed to 2 ATPs per molecule of glucose in anaerobic respiration. This very large increase in the efficiency of energy production from organic molecules may have been an essential requirement for the emergence and evolution of eukaryotic cells.
Another factor may have been the onset of one of the periods known as snowball Earth, for atmospheric methane would have been oxidized. Methane is a powerful greenhouse gas which had been trapping heat, preventing its loss into space, and its elimination produced a period of cooling of the Earth, and the formation of the so-called Huronian glaciations, which essentially covered the Earth some 2.1 to 2.4 billion years ago, giving rise to one of the longest ice ages (300-400 million years). When it eventually subsided, the melting of the glaciers led to glacial sediments that contained increased levels of nutrients and phosphorus, an environment favorable to the cyanobacteria, thus raising even more rapidly the oxygen levels in the atmosphere and favoring the rapid evolution of eukaryotic cells.
At some point in their evolution, some eukaryotic cells developed an endosymbiotic relationship with cyanobacteria, which, presumably as a consequence of mutations, became able to survive in their cytoplasm and evolved into chloroplasts (Figure 3). This theory is supported by the fact that chloroplasts, like mitochondria, still contain their own DNA, separate from the nuclear DNA, which genetically resembles the DNA of cyanobacteria. Chloroplasts also contain ribosomes and are capable of synthesizing proteins that are involved in the reactions involved in photosynthesis. Eukaryotes (algae) that contained chloroplasts and were eventually to give rise to plants, also contributed to the addition of oxygen to the Earth’s early atmosphere.
Multicellularity
- Figure 4. A simplified classification of Life. Eukaryote: red, archea: green, bacteria: blue. Based on whole genome sequencing. Protozoa are Protists.
Eukaryotes still account for only a small proportion of all life-forms (Figure 4), but although there are many phyla (perhaps 30 or 40) of single-celled eukaryotes (Protista), which sometimes form colonies, eukaryotic cells have also given rise to all forms of truly multicellular life – i.e., complex biological systems in which the component cells undergo a process known as differentiation, primarily during the process of development of the multicellular organism from the germ-cells which gave rise to it, a process known as embryogenesis. Some would refer to colonies, such as the large colonies of bacteria that formed the earliest known fossils, stromatolites, perhaps as much as 3.5 - 3.8 million years ago, - as multicellular, but within such colonies there is minimal differentiation, although differences in gene expression may occur in the outermost compared to innermost parts of the colony. True multicellularity is extremely rare in prokaryotes, and even when it does occur, it is limited in its potential. For example, in Myxobacteria, a simple form of multicellularity involving the formation of a fruiting body, rather like that of the eukaryotic slime-molds, occurs. With these rare exceptions, essentially all multicellular organisms have evolved from eukaryotic cells - and in a remarkably brief period on an evolutionary time scale - emphasizing the enormous differences in the potential for prokaryotic versus eukaryotic cells to evolve into multicellular organisms. It has also been postulated that the rapidity of eukaryotic evolution was due to a similar period of glaciations to the Huronian period, perhaps precipitated by environmental factors that led to a further rapid rise in atmospheric oxygen and a second snowball Earth episode some 650 million years ago, “triggering” the development of multicellular organisms from eukaryotic cells and subsequently the Cambrian explosion in which essentially all animal groups (phyla) emerged in the course of a mere 10 million years (figure 4). The melting of the glaciers, as before, may well have caused a population explosion in cyanobacteria, as well, on this occasion, of protists and a further increase in the level of oxygen in the atmosphere (and hence seas), providing a second major leap in the availability of the energy required for evolution and the number of organisms neaded to ensure the necessary mutations.
Characteristics of Eukaryotic Cells
The Nucleus
- Figure 5. Diagrammatic depiction of the endomembrane system of eukaryotic cells. Not all of these structures are discussed in the text. Plasma membrane is an alternative term for the cell membrane. Created by Mariana Ruiz Villarreal.
The defining element of eukaryotic cells, which tend to be much larger than prokaryotic cells, perhaps because of their larger genomes and cell organelles, is the presence of lipoprotein membranes within the cell (Figure 5). The most important of these is the double membrane that surrounds the nucleus (it is the wellformed, or true nucleus, eu-karyon, from the Greek, which gives the cell type its name). The membrane is pierced by large numbers of “pores” that regulate the traffic of proteins in and out of the nucleus, and their access to DNA. Many of these proteins are involved in the regulation of the expression of genes. Large differences exist in the arrangement of the DNA, for the much greater number of genes need to be accessible when needed - this applies particularly to multicellular organisms where the gene expression in different tissues may need to be entirely different.
Eukaryotic DNA is divided into several chromosomes, and the meter or so of DNA (the quantity varies greatly among different species) is packaged around histone proteins to form a linked chain of nucleosomes. The coiling of DNA around histones reduces the length of the DNA molecule by a factor of seven; further reduction is achieved by secondary coiling to create a shorter, thicker fiber, referred to, because of its diameter, as a 30 nanometer fiber. The precisely packaged DNA is held in place by links to the inner nuclear membrane, thus positionally stabilizing the packaged DNA and ensuring that DNA replication and transcription is carried out in a highly organized and reproducible fashion. In contrast, the prokaryotic cell generally has only a single DNA strand, or chromosome (occasionally up to four, which may be linear or circular), located in a region known as the nucleoid, which is in continuity with the cytoplasm. Prokaryotic DNA is supercoiled but not packaged around histones, although archeons do contain histones and form nucleosomes.
The processes of transcription and RNA processing occur within the nucleus in eukaryotic cells. Translation takes place in the endoplasmic reticulum, which is a system of interconnected vesicles and cisternae (sac-like structures) connected to the outer layer of the nuclear membrane and held together by the fibrous proteins that make up the cell's cytoskeleton. The rough endoplasmic reticulum is the major site of translation of messenger RNAs into protein and the smooth endoplasmic reticulum, the location of the synthesis of lipids and steroids. The endoplasmic reticulum is also the site of protein folding, and modification, e.g., by the addition of sugar molecules (glycosylation). Proteins destined for transportation to other parts of the cell, including, for example, the cell nucleus, are packaged in vesicles and contain specific sequences that function as “addresses” to ensure that they are correctly distributed. Further processing and packaging, especially of large molecules for export from the cell (e.g., hormones and other molecules that influence the behavior of adjacent or distant cells), take place in the somewhat similarly structured Golgi apparatus, named after its discoverer, which also secretes the proteoglycans that comprise a major part of the intercellular matrix in multicellular organisms.
These complex but highly efficient mechanisms for regulating the transcription, translation, processing and transportation of proteins must have evolved in concert with the complexities of form and physiology that emerged during the evolution of multicellular organisms, which range from simple sponges and Cnidaria, such as the hydra, to the intricacies of highly evolved animals, such as primates, including humans. It is important to recognize that in the truly multicellular metazoans, the vast range of differentiated cells must all arise from a single cell during the process of embryogenesis. Each cell contains the entire cellular genome, and programmed within its DNA must be the information required to regulate gene expression in such a way that only necessary genes are expressed at various stages of its development (e.g., larva, pupa, imago in insects), in different tissues, or during responses to internal or external conditions that the cell encounters. It must be able to sense these changes via a range of cell surface and cytoplasmic receptors.
The number of protein-coding genes (which in many organisms comprise only a few percent of the entire genome) is less important (assuming that a required threshold is exceeded) than the way in which the contained information is retrieved and processed – as evidenced by the fact that sea-urchin cells contain a similar number of genes to human cells (20-25,000), and flies and nematode worms about half the number. This is probably because a set of some tens of thousands of genes can give rise to a variable, but potentially enormous range of functional attributes, not only through the production of specific proteins, but via their modification, e.g., glycosylation and phosphorylation, their assembly into a wide variety of protein complexes, that may contain large numbers of subunits, and the interactions that occur in protein networks. Thus, the genome, transcriptome and proteome work together in a complex threedimensional dance that must take account of the precise role that the eukaryotic cell subserves in a broad range of environments orders of magnitude more complex in organisms such as animals, plants and fungi than in simple prokaryotic cells.
Gene expression is governed by a broad array of mechanisms that include chemical changes in the chromatin, which governs physical access to genes, or chemical modification (e.g. methylation) without sequence changes to DNA, and the binding of proteins and protein complexes to the sequences that act as promoters and enhancers of the expression of specific genes. Yet the genetic dance does not end with the synthesis of messenger RNA. Such messages are also subject to regulation, and their lifespan, and whether or not they are translated, are governed by various small untranslated RNA molecules. These processes are much less developed in prokaryotes, although there is evidence of an ancient RNA interference system that may have had, as its major function, protection against foreign RNAs, e.g., derived from viruses.
This level of genomic complexity and the evolution of efficient mechanisms for the use of the information contained in the genome, took millions, if not billions of years to evolve, and consumes a considerable amount of energy. This may account for the flowering of the eukaryotic cell only after the evolution of oxygen photosynthesis and aerobic metabolism.
Building a Genome and a Transcriptome
A major difference between the DNA of eukaryotic cells and prokaryotic cells is the much greater frequency of introns, or intragenic sequences, which are interspersed among the coding sequences of genes. Introns permit such phenomena as differential splicing whereby different cassettes of coding sequences, known as exons, can be expressed in a protein, such that, in effect, genes can be superimposed upon one another in the genome, or give rise to proteins that differ with respect to the presence or absence of certain domains according to which exons were transcribed, thereby modifying their folding, their location in cells (which is governed by specific sequences within the protein), or adding (or subtracting) specific functions to proteins or protein networks. Introns and other non-coding DNA sequences are also the site of various regulatory elements that govern the expression of genes, whether or not they are translated into proteins. The origin of introns remains obscure, but they may have arisen early in eukaryotic cell evolution.
There are various ways in which introns can be created, but the likeliest possibility is that they were inserted into the genome. This phenomenon is well known and is responsible for a considerable amount of the non-coding DNA that makes up the bulk of the human genome (perhaps as much as 98%). For example, transposons, which comprise some 45% of human DNA, also often referred to as “jumping genes” (such as Alu or LINE sequences) because of their ability to copy themselves from one location in the genome to another, and retroviruses are well known to insert themselves into genomes. Retroviruses comprise some 8% of the human genome. Another mechanism involves the breakage of the DNA, e.g., under the influence of enzymes (endonucleases) followed by the repair of the broken strands but with the addition of many more nucleotides to the gap. Whatever their origin, introns must contain specific DNA sequences which delineate the intron/exon border, so that they can be cut out of the gene during transcription, for introns, necessarily, are not present in the messenger RNA copy of the gene that will be translated into protein. The complexity of regulatory mechanisms is much more important than the absolute amount of DNA per cell, as evidenced by the observation that some simple organisms, such as the amoeba, Polychaos dubium, have approximately 200 times the amount of DNA per cell than humans!
The breaking up of genes into exons, or coding regions separated by introns, also has many advantages. Exons, for example, can be duplicated and incorporated into other genes in the course of evolution, creating possibilities, via additional structural changes to the genes which encode them, for modifying the function of proteins, their location in the cell, or creating a new member of a family of proteins. Similarly, whole genes or segments of chromosomes containing multiple genes can be duplicated. Such duplicated genes may not initially be functional, or they may, in the course of time, perhaps millions of years, undergo various degrees of modification to create related genes with slightly different functions, or proteins that can form dimers or other types of complex compounds which may create new functional possibilities (a good example is the alpha and beta globin genes, believed to have arisen from the duplication of a single globin gene half a million years ago in a jawless fish related to the lamprey). Rarely, the wholesale incorporation of new genes into the cell genome may occur as a result of cellular fusion, as is believed to have happened at the time of creation of eukaryotic cells. The possibility that genes are also derived from intracellular parasites, or via the fusion of single-celled eukaryotes, cannot be excluded. Whatever its origin, DNA added to the genome forms the raw materials from which additional genes can be constructed.
Genetic Reshuff ling via Sexual Reproduction
The evolution of multicellular organisms made possible yet another method of genetic variability, although precisely when, or how it evolved remains unknown. Sexual reproduction is of vital importance to both the maintenance of genetic integrity, and reshuffling of genes derived from males and females among daughter cells. Most animals and plants practice sexual reproduction, but asexual reproduction does occur, particularly in plants, while parthenogenesis in animals, in which the female gamete, (germ cell) is not fertilized by a male gamete also occurs, although usually as a temporary phenomenon.
Meiosis
- Figure 6. Diagrammatic depiction of meiosis. Chromosomes or regions of chromosomes of different color are from different parents. For simplicity, only one pair of homologous chromosomes is shown here. Image from National Institutes of Health.
The chromosomal complement of germ cells, which pass the genome on to the next generation in multicellular animals is derived from both parents, such that there are generally two copies of each chromosome and a double complement of genes (the socalled “diploid” state, comprising two haploid sets, one derived from each parent), although polyploidy (e.g., three, four or more copies of the haploid number of chromosomes) is also found naturally in nature, especially in plants. In general, polyploid plants can only reproduce with polyploid plants, such that although they may resemble their diploid cousins very closely (e.g., the Silver Birch tree, Betula pendula is diploid, its almost indistinguishable cousin, the Downy or White Birch, Betula pubescens, tetraploid), they are, by definition, separate species.
The presence of two copies of each chromosome in diploid species provides additional possibilities for the genetic reshuffling of genes, and has an important role in ensuring that organisms become increasingly adapted to their environment (or, alternatively, fail to survive or reproduce). This is because of a process known as meiosis (from the Greek, meaning “lessening”). Meiosis, unlike the standard mode of DNA and cell replication, called mitosis, is unique to germ cells and requires two cell divisions (meiosis I and meiosis II). Immediately after the replication of DNA, homologous chromosomes (i.e., equivalent chromosomes, but of male and female origin), each having been replicated, such that each chromosome in the pair now consists of two chromatids, undergo a process known as crossing over, whereby variably sized homologous fragments of the chromosomes are exchanged by the paired chromatids of male and female origin. The replicated chromosomes (chromatids), each of which now constitute a mixture of genes of male and female origin, are drawn into the daughter cells-to-be and a subsequent cell division results (in males, at least) in four daughter cells, each containing a different mixture of genes from maternal and paternal origin (in females, three of the resultant cells usually undergo degeneration and form small polar bodies) (Figure 6).
This form of genetic variation, exclusively available to eukaryotes, can be seen to occur at the level of groups of genes rather than single genes. It is also confined to a single individual, capable, through sexual reproduction and the process of meiosis, to mix his or her genes with those of other adult individuals, producing offspring that differ genetically from their parents and from each other (except in the case of uniovulate twins). Meiosis creates much greater genetic variety in the offspring (the parents die after a variable period of time) than would otherwise be the case, permitting adaptive evolution to occur at a much faster rate. Crossing over randomly mixes many genes derived from different individuals that usually differ only slightly from each other (as a consequence of point mutations that may develop during replication, or as a consequence of environmental mutagens). Some of the offspring may prove to be better adapted to the environment, or more likely, for other reasons, to make attractive mates. But many offspring fail to survive as a result of inheritance of multiple mutations that have a negative effect on survival. Although a major problem for human societies, meiotic crossing over can be seen as a mechanism for a population to rid itself of individuals with mutated genes that have negative survival value while at the same time, producing at least some individuals with advantageous gene mixtures.
We are only now beginning to identify gene combinations that mutations may predispose to certain illnesses in humans, for although some may strongly predispose to diseases, including cancer, most diseases are polygenic, in which many genes each exert only a small positive or negative effect, such that their influence on the selection process – positive, negative or neutral – depends very much upon the genetic company in which they find themselves (and, of course, the environment).
Mitochondria
Mitochondria are present in most eukaryotic cells and it is here that most of the ATP (and hence energy) of the cell is produced via the Krebs cycle. Mitochondria can be transferred from one part of the cell to another (or to daughter cells), rather like mobile generators, such that the changing energy needs of different regions of the cell can be met as needed. This is made possible by proteins known as kinesins, which function as engines that take mitochondria in tow, and transport them via the cytoskeleton – that can function as tracks which guide the mitochondrion to its destination. The circular (intron-free) DNA molecules of mitochondria, that can occur in several copies (sometime varying from one tissue to another in the same organism), encode for only a small number of genes in a particular species, but perhaps a few thousand across species. In addition, they encode a small number of ribosomal RNAs (which are structurally similar to those of bacterial ribosomal RNAs) and the 22 transfer RNAs.
They also play an important role in apoptosis (programmed cell death), a process that does not exist in prokaryotes, although proteins bearing varying degrees of homology with the apoptotic pathways of multicellular organisms have been found in bacteria (although not archea). It is possible that ancient vestiges of these pathways were present in prokaryotes, but had a very different function at that time – e.g., involvement in signaling pathways, possibly related to stress reactions. Certainly it is difficult to envisage a mechanism whereby apoptosis could evolve via natural selection in single cells! Apoptosis, is, however, of considerable importance to multicellular organisms, since it is a means by which the organism can be precisely sculpted during embryogenesis, ensuring that various structures are correctly shaped and of appropriate size. It is also set in motion in cells in which errors occur during differentiation, or which are damaged for other reasons (e.g., invasion by microorganisms or genetic damage caused by external or internal factors). This is crucially important to the integrity of the organism, since some defects may be potentially carcinogenic, i.e., cause the cells in which they reside to fail to respond to the signals that control their location(s) and functions in the context of the organism). Thus, apoptosis is vital to multicellularity and its evolution by natural selection is easily comprehensible in multicellular organisms.
Animals and Plants
- Figure 7. Edicarian fossil resembling an Echinoderm.
The earliest known, bizarre (by modern standards) multicellular organisms were first discovered in the Ediacara Hills in Australia (under water at the time of the emergence of the earliest fossils) and have since been found in many other sites across the world (Figure 7). They have been dated to the 40 million years before the Cambrian Period, some 635-542 million years ago, interestingly, again, just after a major ice age.
Animals and Plants
- Figure 8. The first Anomalocaris (a shrimp-like animal) found in Walcott Quarry, part of the Burgess shale. Photograph by Keith Schengili-Roberts.
This implies that the first metazoans arose some time before 635 million years ago – perhaps several million years before. The Ediacaran fossils bear little relationship to modern fauna, although brave palaeobiologists have attempted to liken some to the members of modern phyla. In contrast, by the mid-Cambrian period, animals that show strong resemblances to animals in most of the modern phyla had appeared, and can be found in regions in which conditions were such that soft-bodied as well as shelled animals could be preserved, such as the Burgess Shale Formation in the Rocky Mountains of British Columbia, whose fossils date to over 500 million years ago (Figure 8). The animals in such deposits must be considered as remnants of the much broader range of animals that existed at the time, and even earlier, but which were not preserved in the fossil record because the conditions in which they lived were not suitable for their preservation. Thus, it is not unreasonable to surmise that soft-bodied multicellular organisms arose sometime in the first quarter of the last billion years, perhaps a billion years after the emergence of the eukaryotic cell. Those which bore chloroplasts became algae, from which plants evolved, while the remainder evolved into animals or fungi. Many eventually colonized the land, although some time after the prokaryotes, which “paved the way” as it were, by providing both oxygen and a source of food for the earliest land organisms.
Life as a Complex System
Life functions in many ways as a unit, albeit as an extremely complex system in which some elements (particularly the most recent additions, such as humans) are expendable. Indeed, our concept of an evolutionary hierarchy may well be erroneous. Without prokaryotes, Life as we know it would presumably never have existed. Prokaryotes, which still comprise the bulk of the biomass of Earth, might be seen as the substrate on which all else is built - they represent, in many senses, the biochemists who created the basic genetic mechanisms (the construction of a genome and its transcription and translation) and metabolic pathways (e.g., photosynthesis and aerobic respiration) that are still used in all organisms. Eukaryotes, particularly multicellular organisms, could be seen as a superstructure, built by the fusion of prokaryotic cells which then, through their transformation into mitochondria, became the engines of the generation of diversity. Having much more available energy, the genomes of eukaryotic cells could be much more rapidly and dramatically modified, while they also provided a host of new habitats for both prokaryotes and eukaryotes, thereby dramatically increasing the range and quantity of life-forms that can be borne by the planet.
One thing is certain. Humans, regardless of their ability to reason and imagine, could not survive in the absence of the prokaryotes that inhabit their bodies – indeed, prokaryotes remain critical to the survival of all organisms derived from eukaryotic cells. But whether the human characteristics of reason and imagination will be of value to Life in general, or will cause the extinction, not only of humans, but of many other life-forms – a process already well underway - remains to be seen. Humans, or their descendents, could eventually populate the Universe, but equally, they could return their planet to a condition resembling that of hundreds of millions or even several billion years ago. The evolution of the eukaryotic cell, and hence of consciousness, a process that has required approximately half of the lifespan of the solar system, has given us the ability to observe, and partially to understand, the miracles of Life on Earth and of the greater universe; this is a privilege of inestimable worth, but also one that carries the seeds of destruction of Life itself. Nevertheless, whatever Life’s origins, or its destiny, it has permitted the Universe, after 13.7 billion years of existence, to observe itself, at least briefly; to open its eyes and to wonder, even if it then slips quietly back into its deep and dreamless sleep.
