Introduction to Evolution PDF

Chapter 1 Introduction We are all one with creeping things; And apes and men Blood-brethren. From ‘Drinking Song’ by Thomas Hardy The consensus among the scientific community is that the Earth is a planet orbiting a fairly typical star, one of man...

Chapter 1 Introduction We are all one with creeping things; And apes and men Blood-brethren. From ‘Drinking Song’ by Thomas Hardy The consensus among the scientific community is that the Earth is a planet orbiting a fairly typical star, one of many billions of stars in a galaxy among billions of galaxies in an expanding universe of enormous size, which originated about 14 billion years ago. The Earth itself formed as the result of a process of gravitational condensation of dust and gas, which also generated the Sun and other planets of the solar system, about 4.6 billion years ago. All present-day living organisms are the descendants of self-replicating molecules that were formed by purely chemical means, more than 3.5 billion years ago. The successive forms of life have been produced by the process of ‘descent with modification’, as Darwin called it, and are related to each other by a branching genealogy, the tree of life. We human beings are most closely related to chimpanzees, with whom we shared a common ancestor about 6 million years ago. The mammals, the group to which we belong, shared a common ancestor with living species of reptiles about 300 million years ago. All vertebrates (mammals, birds, reptiles, amphibia, fishes) trace their ancestry back to a small fish-like creature that lacked a backbone, which lived over 500 million years ago. Further back in time, it becomes increasingly difficult to discern the relationships between the major groups of animals, plants, and microbes, but, as we shall see, there are clear signs of common ancestry in their genetic material. Less than 450 years ago, all European scholars believed that the Earth was the centre of a universe of at most a few million miles in extent, and that the planets, Sun, and stars all rotated around this centre. Less than 250 years ago, they believed that the universe was created in essentially its present state about 6,000 years ago, although by then the Earth was known to orbit the Sun like other planets, and a much larger size of the universe was widely accepted. Less than 150 years ago, the view that the present state of the Earth is the product of at least tens of millions of years of geological change was prevalent among scientists, but the special creation by God of living species was still the dominant belief. The relentless application of the scientific method of inference from experiment and observation, without reference to religious or governmental authority, has completely transformed our view of our origins and relation to the universe, in less than 500 years. In addition to the intrinsic fascination of the view of the world opened up by science, this has had an enormous impact on philosophy and religion. The findings of science imply that human beings are the product of impersonal forces, and that the habitable world forms a minute part of a universe of immense size and duration. Whatever the religious or philosophical beliefs of individual scientists, the whole programme of scientific research is founded on the assumption that the universe can be understood on such a basis. Few would dispute that this programme has been spectacularly successful, particularly in the 20th century, which saw such terrible events in human affairs. The influence of science may have indirectly contributed to these events, partly through the social changes triggered by the rise of industrial mass societies, and partly through the undermining of traditional belief systems. Nonetheless, it can be argued that much misery throughout human history could have been avoided by the application of reason, and that the disasters of the 20th century resulted from a failure to be rational rather than a failure of rationality. The wise application of scientific understanding of the world in which we live is the only hope for the future of mankind. The study of evolution has revealed our intimate connections with the other species that inhabit the Earth; if global catastrophe is to be avoided, these connections must be respected. The purpose of this book is to introduce the general reader to some of the most important basic findings, concepts, and procedures of evolutionary biology, as it has developed since the first publications of Darwin and Wallace on the subject, over 150 years ago. Evolution provides a set of unifying principles for the whole of biology; it also illuminates the relation of human beings to the universe and to each other. In addition, many aspects of evolution have practical importance; for instance, pressing medical problems are posed by the rapid evolution of resistance by bacteria to antibiotics and of HIV to antiviral drugs. In this book, we shall first introduce the main causal processes of evolution (Chapter 2). Chapter 3 provides some of the basic biological background, and shows how the similarities between living creatures can be understood in terms of evolution. Chapter 4 describes the evidence for evolution derived from Earth history, and from the patterns of geographical distribution of living species. Chapter 5 is concerned with the evolution of adaptations by natural selection, and Chapter 6 with the evolution of new species and of differences between species. In Chapter 7, we discuss some seemingly difficult problems for the theory of evolution. Chapter 8 provides a brief summary. Chapter 2 The processes of evolution To understand life on Earth, we need to know how animals (including humans), plants, and microbes work, ultimately in terms of the molecular processes that underlie their functioning. This is the ‘how’ question of biology; an enormous amount of research during the last century has produced spectacular progress towards answering this question. This effort has shown that even the simplest organism capable of independent existence, a bacterial cell, is a machine of great complexity, with thousands of different protein molecules that act in a coordinated fashion to fulfil the functions necessary for the cell to survive, and to divide to produce two daughter cells (see Chapter 3). This complexity is even greater in higher organisms such as a fly or human being. These start life as a single cell, formed by the fusion of an egg and a sperm. There is then a delicately controlled series of cell divisions, accompanied by the differentiation of the resulting cells into many distinct types. The process of development eventually produces the adult organism, with its highly organized structure made up of different tissues and organs, and its capacity for elaborate behaviour. Our understanding of the molecular mechanisms that underlie this complexity of structure and function is rapidly expanding. Although there are still many unsolved problems, biologists are convinced that even the most complicated features of living creatures, such as human consciousness, reflect the operation of chemical and physical processes that are accessible to scientific analysis. At all levels, from the structure and function of a single protein molecule, to the organization of the human brain, we see many instances of adaptation: the fit of structure to function that is also apparent in machines designed by people (see Chapter 5). We also see that different species have distinctive characteristics, often clearly reflecting adaptations to the environments in which they live. These observations raise the ‘why’ question of biology, which concerns the processes that have caused organisms to be the way they are. Before the rise of the idea of evolution, most biologists would have answered this question by appealing to a Creator. The term adaptation was introduced by 18th-century British theologians, who argued that the appearance of design in the features of living creatures proves the existence of a supernatural designer. While this argument was shown to be logically flawed by the philosopher David Hume in the middle of the 18th century, it retained its hold on people’s minds as long as no credible alternative had been proposed. Evolutionary ideas provide a set of natural processes that can explain the vast diversity of living species, and the characteristics that make them so well adapted to their environment, without any appeal to a mind that designed them. These explanations extend, of course, to the origin of the human species itself, and this has made biological evolution the most controversial of scientific subjects. If the issues are approached without prejudice, however, the evidence for evolution as a historical process can be seen to be as strong as that for other long-established scientific theories, such as the atomic nature of matter (see Chapters 3 and 4). We also have a set of well-verified ideas about the causes of evolution, although, as in every healthy science, there are unsolved problems, as well as new questions that arise as ever more is understood (see Chapter 7). Biological evolution involves changes over time in the characteristics of populations of living organisms. The time-scale and magnitude of such changes vary enormously. Evolution can be studied during a human lifetime, when changes occur in a single character such as the increase in the frequency of strains of bacteria resistant to penicillin within a few years of the widespread medical use of penicillin to control bacterial infections (as discussed in Chapter 5). At the other extreme, evolution involves events such as the emergence of a major new design of organisms, which may take millions of years and require changes in many different characteristics, as in the transition from reptiles to mammals (see Chapter 4). A key insight of the founders of evolutionary theory, Charles Darwin and Alfred Russel Wallace, was that changes at all levels are likely to involve the same types of processes. Major evolutionary changes largely reflect changes of the same type as more minor events, accumulated over longer time periods (see Chapters 6 and 7). Evolutionary change ultimately relies on the appearance of new variant forms of organisms: mutations. These are caused by stable changes in the genetic material that can be transmitted from parent to offspring. Mutations affecting almost all conceivable characteristics of many different organisms have been studied in the laboratory by experimental geneticists, and medical geneticists have catalogued thousands of mutations in human populations. The effects of mutations on the observable characteristics of an organism vary greatly in their magnitude. Some have no detectable effect, and are known to exist simply because it is now possible to study the structure of the genetic material directly, as we will describe in Chapter 3. Others have relatively small effects on a simple trait, such as a change in eye colour from brown to blue, the acquisition of resistance to an antibiotic by a bacterium, or an alteration of the number of bristles on the side of a fruitfly. Some mutations have drastic effects on development, such as the mutation of the fruitfly Drosophila melanogaster that causes a leg to grow on the fly’s head in place of its antenna. The appearance of any particular kind of new mutation is a very rare event, with a frequency of around one per hundred thousand individuals per generation or even less. An altered state of a character as a result of a mutation, such as antibiotic resistance, initially occurs in a single individual, and is usually restricted to a tiny fraction of a typical population for many generations. To result in evolutionary change, other processes must cause it to increase in frequency within the population. Natural selection is the most important of these processes leading to evolutionary changes in the structure, functioning, and behaviour of organisms (see Chapter 5). In their papers of 1858, published in the Journal of the Proceedings of the Linnaean Society, Darwin and Wallace laid out their theory of evolution by natural selection with the following argument:  Many more individuals of a species are born than can normally live to maturity and breed successfully, so that there is a struggle for existence. There is individual variation in innumerable characteristics of the population, some of which may affect an individual’s ability to survive and reproduce. The successful parents of a given generation may therefore differ from the population as a whole. There is likely to be a hereditary component to much of this variation, so that the characteristics of the offspring of the successful parents will differ from the characteristics of the previous generation, in a similar way to their parents. If this process continues from generation to generation, there will be a gradual transformation of the population, such that the frequencies of characteristics associated with greater survival ability or reproductive success increase over time. These altered characteristics originated by mutation, but mutations affecting a particular trait arise all the time regardless of whether or not they are favoured by selection. Indeed, most mutations either have no effects on the organism, or reduce its ability to survive or reproduce and are eliminated from the population by natural selection against them. It is the process of increase in frequency of variants that improve survival or reproductive success that explains the evolution of adaptive characteristics, since better performance of the individual’s body or behaviour will generally contribute to greater survival or reproductive success. Such a process of change will be especially likely if a population is exposed to a changed environment, where a somewhat different set of characteristics is favoured from those already established by selection. As Darwin wrote in 1858: But let the external conditions of a country alter … Now, can it be doubted, from the struggle each individual has to obtain subsistence, that any minute variation in structure, habits or instincts, adapting that individual better to the new conditions, would tell upon its vigour and health? In the struggle it would have a better chance of surviving; and those of its offspring that inherited the variation, be it ever so slight, would also have a better chance. Yearly more are bred than can survive; the smallest grain in the balance, in the long run, must tell on which death shall fall, and which shall survive. Let this work of selection on the one hand, and death on the other, go on for a thousand generations, who will pretend to affirm that it would produce no effect … There is, however, another important mechanism of evolutionary change, which explains how species can also come to differ with respect to traits with little or no influence on the survival or reproductive success of their possessors, and which are therefore not subject to natural selection. As we shall see in Chapter 6, this is especially likely to be true of the large category of changes in the genetic material which have little or no effect on the organism’s structure or functioning. If there is selectively neutral variability, so that on average there are no differences in survival or fertility among different individuals, it is still possible for the offspring generation to differ slightly from the parental generation. This is because, in the absence of selection, the genes in the population of offspring are a random sample of the genes present in the parental population. Real populations are finite in size, and so the constitution of the offspring population will by chance differ somewhat from that of the parents’ generation, just as we do not expect exactly five heads and five tails when we toss a coin ten times. This process of random change is called genetic drift. Even the biggest biological populations, such as those of bacteria, are finite, so that genetic drift will always operate. The combined effects of mutation, natural selection and the random process of genetic drift cause changes in the composition of a population. Over a sufficiently long period of time, these cumulative effects alter the population’s genetic make-up, and can thus greatly change the species’ characteristics from those of its ancestors. We referred earlier to the diversity of life, reflected in the large number of different species alive today. (A very much larger number have existed over the past history of life, because the eventual fate of nearly all species is extinction, as described in Chapter 4.) The problem of how new species evolve is clearly a crucial one, and is dealt with in Chapter 6. The term ‘species’ is hard to define, and it is sometimes difficult to draw a clear line between populations that are members of the same species, and populations that belong to separate species. In thinking about evolution, it makes sense to consider two populations of sexually reproducing organisms as different species if they cannot interbreed with each other, so that their evolutionary fates are totally independent. Thus, human populations living in different parts of the world are unequivocally members of the same species, since there are no barriers to interbreeding if migrant individuals arrive from another place. Such migration tends to prevent the genetic make-up of different populations of the same species from diverging very much. In contrast, chimpanzees and humans are clearly separate species, since humans and chimpanzees living in the same area cannot interbreed. As we shall describe later on, humans also differ much more from chimpanzees in the make-up of their genetic material than they do from each other. The formation of a new species must involve the evolution of barriers to interbreeding between related populations. Once such barriers form, the populations can diverge under mutation, selection, and genetic drift. This process of divergence ultimately leads to the diversity of life. If we understand how barriers to interbreeding evolve, and how populations subsequently diverge, we will understand the origin of species. An enormous amount of biological data falls into place in the light of these ideas about evolution, which have been put on a firm basis by the development of mathematical theories which can be modelled in detail, just as astronomers and physicists model the behaviour of stars, planets, molecules, and atoms in order to understand them more completely, and to devise detailed tests of their theories. Before describing the mechanisms of evolution in more detail (but omitting the mathematics), the next two chapters will show how many kinds of biological observations make sense in terms of evolution, in contrast with special creation and its appeal to ad hoc explanations. Chapter 3 The evidence for evolution: similarities and differences between organisms The theory of evolution accounts for the diversity of life, with all the well- known differences between different species of animals, plants, and microbes, but it also explains their fundamental similarities. These are often evident at the superficial level of externally visible characters, but extend to the finest details of microscopic structure and biochemical function. We will discuss the diversity of life later in this book (in Chapter 6), and describe how the theory of evolution can account for new forms appearing from ancestral ones, but here we focus on the unity of living species. In addition, we will introduce many basic biological facts on which later chapters build. Similarities between different groups of species Similarities between even widely disparate types of organism exist at every level, from familiar, externally visible resemblances, to profound resemblances in life-cycles and the structure of the genetic material. They are plainly detectable even between creatures as different as ourselves and bacteria. These similarities have a natural and straightforward explanation in the idea that organisms are related through an evolutionary process of descent from common ancestors. We ourselves have obvious similarities to apes, as illustrated in Figure 1, including similarities in internal characters such as our brain structure and organization. There are lesser similarities to monkeys, and even smaller, but still extremely clear, similarities to other mammals, despite all our differences (Figure 1). Mammals have many similarities to other vertebrates, including the basic features of their skeletons, and their digestive, circulatory, and nervous systems. Even more amazing are similarities with creatures such as insects, for example in their segmented body plans, their common need for sleep, the control of their daily rhythms of sleep and waking, and fundamental similarities in how the nerves work in many different kinds of animals, among other features. 1. A. Hands (m) and feet (p) of several primate species, showing the similarities between different species, with differences related to the animals’ way of life, such as the opposable digits of climbing species (Hylobates is a gibbon, Macaca is a Rhesus monkey, Nycticebus and Tarsius are primitive arboreal primates). B. Skeletons of a bat and a bird, showing their similarities and differences. Systems of biological classification have long been based on easily visible structural characteristics. For example, even before the scientific study of biology, insects were treated as a group of similar creatures, clearly distinguishable from other groups of invertebrates, such as molluscs, by their possession of a segmented body, three pairs of jointed legs, a tough external protective covering, and so on. Many of these traits are shared with other types of animal such as crabs and spiders, except for differing numbers of legs (eight, in the case of spiders). These different species are all grouped into one larger division, the arthropods. The arthropods include the insects, and among these flies form one group, characterized by the fact that they all have only one pair of wings, as well as several other shared characters. Butterflies and moths form another insect group, whose members all have fine scales on their two pairs of wings. Among flies we distinguish the houseflies and their relatives from other groups by shared characters, and among these we name individual species, such as the common housefly Musca domestica. Species are essentially groups of similar individuals capable of interbreeding with each other. Similar species are grouped into the same genus, again united by a set of characters not shared with other genera. Biologists identify each recognizable species by two names, the genus name followed by the name of the species itself, for example Homo sapiens; these names are conventionally written in italics. The observation that organisms can be classified hierarchically into groups, which successively share more and more traits that are lacking in other groups, was an important advance in biology. The classification of organisms into species, and the naming system for species, were developed long before Darwin. Before biologists could begin thinking about the evolution of species, it was clearly important to have the concept of species as distinct entities. The simplest and most natural way to account for the hierarchical pattern of similarities is that living organisms evolved over time, starting from ancestral forms that diversified to produce the groups alive today, as well as innumerable extinct organisms (see Chapter 4). As we shall discuss in Chapter 6, it is now possible to discern this inferred pattern of genealogical relationships among groups of organisms by directly studying the information in their genetic material. Another set of facts that strongly supports the theory of evolution is provided by modifications of the same structure in different species. For instance, the bones of bats’ and birds’ wings indicate clearly that they are modified forelimbs, even though they look very different from the forelimbs of other vertebrates (Figure 1B). Similarly, although the flippers of whales look much like fish fins, and are clearly also well adapted for swimming, their internal structure is like the feet of other mammals, except for an increased number of digits. This makes sense, given all the other evidence that whales are modified mammals (for instance, they breathe with lungs, not gills, and suckle their young). Fossil evidence shows that the two pairs of limbs of land vertebrates are derived from the two pairs of fins of the lobe-finned fishes (of which coelacanths are the most famous living representatives, see Chapter 4). Indeed, the earliest land vertebrate fossils had more than five digits on their limbs, just like fishes and whales. Another example is provided by the three small bones in mammals’ ears, which transmit sound from the outside to the organ that transforms sound into nerve signals. These tiny bones develop from rudiments in the embryonic jaw and skull, and in reptiles they enlarge during development to make parts of the head and jaw skeleton. Fossil intermediates that connect reptiles with mammals show successive modifications of these bones in the adults, finally evolving into the ear bones. These examples are just a few of many known cases in which the same basic structure was considerably modified during the course of evolution by the demands imposed by different functions. Embryonic development and vestigial organs Embryonic development provides many other striking examples of similarities between different groups of organisms, clearly suggesting descent from common ancestors. The embryonic forms of different species are often extremely similar, even when the adults are very different. For example, at one stage in mammalian development, structures appear that resemble the developing gill slits of fish embryos (Figure 2). This makes perfect sense if we are descended from fish-like ancestors, but is otherwise inexplicable. Since it is the adult structures that adapt the organism to its environment, they are very likely to be modified by selection. Probably the developing blood vessels require the presence of gill slit rudiments to guide them to form in the correct places, so that these structures are retained, even in animals that never have functional gills. Development can evolve, however. In many other details, mammals develop very differently from fish, so that other embryonic structures, with less profound importance in development, have been lost, and new ones have been gained. 2. Human and dog embryos, illustrating their great similarity at this stage of development. The gill slits, labelled visceral arches (f and g) in the figure, are plainly visible. From Darwin’s The Descent of Man and Selection in Relation to Sex (1871). Similarities are not confined to embryonic stages. Vestigial organs have also long been recognized as remnants of structures that were functional in the ancestors of present-day organisms. This observation is very interesting, because such cases tell us that evolution does not always create and improve structures, but sometimes reduces them. The human appendix, which is a greatly reduced version of a part of the digestive tract that is quite large in orang-utans, is a classic example. The vestigial limbs of legless animals are also well known. Fossils of primitive snakes have been found with almost complete hindlimbs, indicating that snakes evolved from lizard-like ancestors with legs. The body of a present-day snake consists of an elongated thorax (chest), with a large number of vertebrae (more than 300 in pythons). In the python, the change from the body to tail is marked by vertebrae with no ribs, and at this point rudimentary hindlimbs are found. There is a pelvic girdle and a pair of truncated thigh bones whose development follows the normal course for other vertebrates, with expression of the same genes that normally control limb development. A graft of python hindlimb tissue can even promote the formation of an extra digit in chick wings, showing that parts of the hindlimb developmental system still exist in pythons. More advanced types of snakes, however, are completely limbless. Similarities in cells and cellular functions The similarities between different organisms are not confined to visible characteristics. They are profound and extend to the smallest microscopic scale and to the most fundamental aspects of life. A basic feature of all animal, plant, and fungal life is that their tissues are made up of essentially similar units, the cells. Cells are the basis of the bodies of all organisms other than viruses, from unicellular yeasts and bacteria, to multicellular bodies with highly differentiated tissues like those of mammals. In the eukaryotes (all cellular non-bacterial life) the cells are organized into the cytoplasm and the nucleus within it that contains the genetic material (Figure 3). The cytoplasm is not just a liquid inside the cell membrane with the nucleus floating in it; it contains a complex set of tiny pieces of machinery that includes many subcellular structures. Two of the most important of these cellular organelles are the mitochondria that generate cells’ energy, and the chloroplasts in which photosynthesis in green plants’ cells occurs. It is now known that both of these are descended from bacteria that colonized cells and became integrated into them as essential components. Bacteria are also cells (Figure 3), but simpler ones with no nucleus or organelles; they and similar organisms are called prokaryotes. The only non-cellular forms of life, the viruses, are parasites that reproduce inside the cells of other organisms, and consist simply of a protein coat surrounding the genetic material. 3. Prokaryote and eukaryote cells. A. Electron micrograph and drawing of a portion of a cell from the mammalian pancreas, showing the nucleus containing the chromosomes inside the nuclear membrane, the region outside the nucleus containing many mitochondria (these organelles also have membranes enclosing them), and membrane-like structures that are involved in protein synthesis and export, as well as in importing substances into the cell. A mitochondrion is somewhat smaller than a bacterial cell. B. Electron micrograph and drawing of a bacterial cell, showing its simple structure, with a cell wall and DNA which is not enclosed in a nucleus. Cells are ultra-miniaturized and highly complex factories which make the chemicals that organisms need, generate energy from food sources, and produce bodily structures such as the bones of animals. Most of the ‘machines’ and many of the structures in these factories are proteins. Some proteins are enzymes that take a chemical and carry out a procedure on it, for example snipping a chemical compound into two components, like chemical scissors. The enzymes used in biological detergents snip up proteins (such as blood and sweat proteins) into small pieces that can be washed out of dirty clothes; similar enzymes in our gut break molecules in food into smaller pieces that can be taken up by cells. Other proteins in living organisms have storage or transport functions. The haemoglobin in red blood cells carries oxygen, and in the liver a protein called ferritin binds and stores iron. There are also structural proteins, such as the keratin that forms skin, hair, and fingernails. In addition, cells make proteins that communicate information to other cells and to other organs. Hormones are familiar communication proteins, which circulate in the blood and control many bodily functions. Other proteins are located on cell surfaces and are involved in communication with other cells. These interactions include signalling to control cell behaviour during development, communication between eggs and sperm in fertilization, and parasite recognition by the immune system. Like any factory, cells are subject to complex controls. They respond to information from outside (by means of proteins that span the cell membrane, like keyholes which fit molecules from the outside world—see Figure 4). Sensory receptor proteins, such as olfactory receptors and light receptors, are used in communication between cells and their environment. Chemical and light signals from the outside world are transformed into electrical impulses that travel along the nerves to the brain. All animals that have been studied use largely similar proteins in chemical and light perception. To illustrate the similarities that have been discovered in cells of different organisms, a myosin (motor) protein, similar to proteins in muscle cells, is involved in signalling in flies’ eyes and in the ears of humans; one form of deafness is caused by mutations in the gene for this protein. 4. Biosynthetic pathways by which melanin and a yellow pigment are synthesized in mammalian melanocyte cells from their amino acid precursor, tyrosine. Each step in the pathway is catalysed by a different enzyme. Absence of active tyrosinase enzyme results in albino animals. The melanocyte-stimulating hormone receptor determines the relative amounts of black and yellow pigments. Absence of the antagonist to the hormone leads to black pigment synthesis, but presence of the antagonist sets the receptor to ‘off’, leading to yellow pigment formation. This is how the yellow versus black parts of tabby cat and brown mouse hairs come to be formed. Mutations that make the antagonist non-functional cause darker coloration; however, black animals are not usually the result of this, but simply have the receptor set to ‘on’ regardless of the hormone level. Biochemists have catalogued the enzymes in living organisms into many different kinds, and every known enzyme (many thousands in a complex animal like ourselves) has a number in an international numbering system. Because so many enzymes are found in cells of a very wide range of organisms, this system categorizes enzymes by the jobs they perform, not the organism they come from. Some, such as digestive enzymes, snip molecules into pieces, others combine molecules together, while others oxidize chemicals (combine them with oxygen), and so on. The means by which energy is generated by cells from food sources is largely the same for all kinds of cells. In this process, there is an energy source (sugars or fats, in the case of our cells, but other compounds, such as hydrogen sulphide, for some bacteria). A cell takes the initial compound through a series of chemical steps, some of which release energy. Such a metabolic pathway is organized like an assembly line, with a succession of sub-processes. Each sub-process is carried out by its own protein ‘machine’; these are the enzymes for the different steps in the pathway. The same pathways operate in a wide range of organisms, and modern biology textbooks show the important metabolic pathways without needing to specify the organism. For example, when lizards tire after running, this is caused by the build-up of the chemical lactic acid, just as in our muscles. Cells have pathways to make chemicals of many different kinds, as well as to generate energy from foods. For example, some of our cells make hairs, some make bone, some make pigments, others produce hormones, and so on. The metabolic pathway by which the skin pigment melanin is made (Figure 4) is the same in ourselves, in other mammals, in butterflies with black wing pigments, and even in fungi (for instance in black spores), and many of the enzymes involved in this pathway are also used by plants in making lignin, the main chemical constituent of wood. The fundamental similarity of the basic features of metabolic pathways, from bacteria to mammals, is once again readily understandable in terms of evolution. Each of the different proteins for these cell and body functions is specified by one of the organism’s genes, as we will explain more fully later in this chapter. The functioning of each biochemical pathway depends on its enzymes. If any enzyme in a pathway fails to work, the end-product will not be produced, just as a failure in an assembly-line process stops output of the product. For instance, albino mutations result from lack of an enzyme necessary for production of the pigment melanin (Figure 4). Stopping a step in a pathway is a useful means to control the output of the cell machinery, so cells contain inhibitors to carry out such control functions, as in the control of melanin production. As another example, the protein that forms blood clots is present in tissues, but in soluble form, and a clot will develop only when a piece is cut off this precursor molecule. The enzyme that cuts this protein is also present, but is normally inactive; when blood vessels are damaged, factors are released that alter the clotting enzyme, so that it immediately becomes active, leading to clotting of the protein. Proteins are very large molecules made up of strings of dozens to a few hundreds of amino acid subunits, each joined to a neighbouring amino acid, forming a chain (Figure 5A). Each amino acid is a quite complex molecule, with individual chemical properties and sizes. Twenty different amino acids are used in the proteins of living organisms; a particular protein, such as the haemoglobin in our red blood cells, has a characteristic set of amino acids in a particular order. Given the correct sequence of amino acids, the protein chain folds up into the shape of the working protein. The complex three- dimensional structure of a protein is completely determined by the sequence of amino acids in its constituent chain or chains; in turn, this sequence is completely determined by the sequence of chemical units of the DNA (Figure 5B) of the gene that produces the protein, as we will soon explain. 5. A. The three-dimensional structure of the protein myoglobin (a muscle protein similar to the red blood cell protein haemoglobin), showing the individual amino acids in the protein chain, numbered from 1 to 150, and the iron-containing haem molecule that the protein holds. The haem binds oxygen or carbon dioxide, and the protein’s function is to carry these gas molecules. B. The structure of DNA, the molecule that carries the genetic material in most organisms. It consists of two complementary strands, wound around each other in a helix. The backbone of each strand is formed of molecules of the sugar deoxyribose (S), linked to each other through phosphate molecules (P). Each sugar is connected to a type of molecule called a nucleotide; these form the ‘letters’ of the genetic alphabet. There are four types of nucleotide: adenine (A), guanine (G), cytosine (C), and thymine (T). A given nucleotide from one strand is paired with a complementary nucleotide from the other, as indicated by the double lines. The rule for this pairing is that A binds to T and G binds to C. When DNA replicates during cell division, the two strands unwind, and a complementary daughter strand is synthesized from each parental strand according to this pairing rule. In this way, a place where A and T bind to each other in the parental molecule produces a place with A and T in each of the daughter molecules. Studies of the three-dimensional structures of the same enzyme or protein in widely different species show that these are often extremely similar across huge evolutionary distances, such as between bacteria and mammals, even if the sequence of amino acids has changed greatly. An example is the myosin protein that we have already mentioned, which is involved in signalling in flies’ eyes and in mammalian ears. Such fundamental similarities mean that, astonishingly, it is often possible to correct a metabolic defect in yeast cells by introducing a plant or animal gene with the same function. Yeast cells with a mutation causing a defect in ammonium uptake have been ‘cured’ by expressing a human gene in their cells (the gene for the Rhesus blood-group protein, RhGA, which was suspected to have the relevant function). The natural (non-mutant) yeast version of this protein has many amino acid differences from the human RhGA one, yet in this experiment the human protein can function in yeast cells lacking their own normal version. The result of this experiment also tells us that a protein with an altered amino acid sequence can sometimes work quite well. The basis of heredity is common to all organisms The physical basis of inheritance is another fundamental similarity between all eukaryote organisms (animals, plants, and fungi). Our understanding of the mechanism of inheritance, that is the control of individuals’ many different characteristics by physical entities that we now call genes, first came from work by Gregor Mendel on garden peas, but the same rules of inheritance apply to other plants and to animals, including humans. The genes that control the production of metabolic enzymes and other proteins (and thus determine individuals’ characteristics) are stretches of DNA carried in the chromosomes of each cell (Figures 6 and 7). The discovery that the chromosomes carry the organism’s genes in a linear arrangement was first made in the fruitfly, Drosophila melanogaster, but it is equally true for our own genome. The order of genes on the chromosomes can be rearranged during evolution, but changes are infrequent, so that sets of the same genes in the same order can be found in the human genome and in the chromosomes of other mammals such as cats and dogs. A chromosome is essentially a single very long DNA molecule encoding hundreds or thousands of genes. The DNA of a chromosome is combined with protein molecules that help to package it in neat coils inside the cell nucleus (resembling the devices used for keeping computer cables tidy). 6. Diagram of one pair of chromosomes, with a schematic drawing of a small region magnified to show three genes that are located in this chromosome region, and the non-coding DNA in between them. The three different genes are shown as different shades of grey, to indicate that each gene encodes a different protein. In a real cell, only some of the proteins would be produced, while other genes would be turned off so that their proteins would not be formed. 7. A dividing cell of a nematode worm, showing the chromosomes no longer enclosed in the nuclear membrane (A), several stages in the division process (B, C), and finally the two daughter cells, each with a nucleus enclosed in a membrane (D). In higher eukaryotes like ourselves, each cell contains one set of chromosomes derived from the mother through the egg nucleus, and another set derived from the father through the sperm nucleus (Figure 6). In humans, there are 23 different chromosomes in a single maternal or paternal set; in Drosophila melanogaster, which is used for much research in genetics, the chromosome number is five (one of which is tiny). The chromosomes carry the information needed to specify the amino acid sequences of an organism’s proteins, together with the controlling DNA sequences that determine which proteins will be produced by the organism’s cells. What is a gene, and how does it determine the structure of a protein? A gene is a sequence of the four chemical ‘letters’ (Figure 5A) of the genetic code, in which sets of three adjacent letters (triplets) correspond to each amino acid in the protein for which the gene is responsible (Figure 8). The gene sequence is ‘translated’ into the sequence of a protein chain; there are also triplets marking the end of the amino acid chain. A change in the sequence of a gene causes a mutation. Most such changes will lead to a different amino acid being placed in a protein when it is being made (but, because there are 64 possible triplets of DNA letters, and only 20 amino acids used in proteins, some mutations do not change the protein sequence). Across the entire range of living organisms, the genetic code differs only very slightly, strongly suggesting that all life on Earth may have a common ancestor. The genetic code was first studied in bacteria and viruses, but was soon checked and found to be the same in humans. Almost every possible mutation that this code can generate in the sequence of the human red blood cell protein haemoglobin has been observed, but mutations that are impossible with this particular code do not occur. 8. DNA and protein sequences of a part of the gene for the melanocyte- stimulating hormone receptor shown in Figure 4, in humans and several other mammals. The figure shows only 40 amino acids out of the total of 951 in the protein. The human DNA sequences are shown at the top, with spaces between the sets of three DNA letters, and the protein sequence is in the grey bars below this (using a three-letter code for the different amino acids). The other species are shown below. Where the DNA sequences differ from the human one, the letter is printed as a capital letter. Triplets that include a difference from the human sequence, but code for the same amino acid as in humans, are asterisked, while triplets that encode differences from the human protein sequence are highlighted. Many red-haired people have an amino acid variant in triplet 151. In order to produce its protein product, the DNA sequence of a gene is first copied into a ‘message’ made of a related molecule, RNA, whose sequence of ‘letters’ is copied from that of the gene by a copying enzyme. The RNA message interacts with an elaborate piece of cellular machinery, made up of a conglomeration of proteins and other RNA molecules, to translate the message and produce the protein specified by the gene. This process is essentially the same in all cells, although in eukaryotes it occurs in the cytoplasm, and the message must first move out of the nucleus to the translation machinery, which is located outside the nucleus. In between the genes on the chromosomes are stretches of DNA which do not code for proteins; some of this non-coding DNA has the important function of acting as sites for binding proteins that turn the production of the RNA messages of genes on or off as needed. For instance, the genes for haemoglobin are turned on in cells developing into red blood cells, but off in brain cells. Despite the enormous differences in the modes of life of different organisms, ranging from unicellular organisms to bodies composed of billions of cells with highly differentiated tissues, eukaryote cells undergo similar cell division processes. Single-celled organisms such as an amoeba or yeast can reproduce simply by division into two daughter cells. A fertilized egg of a multicellular organism, produced by the fusion of an egg and a sperm, similarly divides into two daughter cells (Figure 7). Many further rounds of cell divisions then take place to produce the many cells and tissue types that form the body of the adult organism. In a mammal, there are over 300 different types of cell in the adult body. Each type has a characteristic structure and produces a specific array of proteins. The arrangement of these cells into tissues and organs during development requires elaborately controlled networks of interactions between the cells of the developing embryo. Genes are turned on and off to ensure that the right kind of cell is produced in the right place at the right time. In some well-studied organisms, such as Drosophila melanogaster, we now know a great deal about how these interactions result in the emergence of the intricate body plan of the fly from the apparently undifferentiated egg cell. Many signalling processes involved in development and differentiation of particular tissues, such as nerves, are found to be shared by all multicellular animals, while land plants use a rather different set, as might be expected from the fact that the fossil record shows that multicellular animals and plants have separate evolutionary origins (see Chapter 4). When a cell divides, the DNA of the chromosomes is first replicated, so that there are two copies of each chromosome. Cell division is a process with tight controls to ensure that the newly copied DNA sequence undergoes ‘proof-reading’ for errors. Cells have enzymes that, using certain properties of the way DNA is replicated, can distinguish new DNA from the old ‘template’ DNA. This enables most errors in copying to be detected and corrected, ensuring that the template has been faithfully copied before the cell is allowed to proceed to the next step, division of the cell itself. The machinery of cell division ensures that each daughter cell receives a complete copy of the set of chromosomes that was present in the parent cell (Figure 7). Most prokaryotes’ genes (including those of many viruses) are also sequences of DNA which are organized only slightly differently from those carried in eukaryote chromosomes. Many bacteria have just one circular DNA molecule as their genetic material. Some viruses, however, such as those responsible for influenza and AIDS, have genes made of RNA. The proof-reading that occurs in DNA replication does not happen when RNA is copied, and so these viruses have extremely high mutation rates, and can evolve very rapidly within the host’s body. As we will describe in Chapter 5, this means that it is difficult to develop vaccines against them. Eukaryotes and prokaryotes differ greatly in their amounts of non-coding DNA. The bacterium Escherichia coli (a normally harmless species that lives in our intestines) has about 4,300 genes, and the stretches that code for protein sequences form about 86% of this species’ DNA. In contrast, less than 2% of the DNA in the human genome codes for protein sequences. Other organisms lie between these extremes. The fruitfly, Drosophila melanogaster, has about 14,000 genes in about 120 million ‘letters’ of DNA, and about 20% of the DNA is made up of coding sequences. The number of different genes in the human genome is still not precisely known. The current best count comes from the sequencing of the complete genome. This allows geneticists to recognize sequences that are probably genes, based on what we know from genes that had previously been studied. It is a difficult task to find these sequences in the huge amount of DNA that makes up the genome of any species, particularly for our own genome, which has a very large DNA content (25 times as much as the fruitfly). The number of genes in humans is about 20,000, much smaller than had been guessed from the number of cell and tissue types with different functions. The number of proteins a human can make is probably considerably larger than this, because very small genes, or unconventional ones, may be missed (for example, genes that lie within other genes, which exist in several organisms). It is not yet known how much of the non-coding DNA is important for the life of the organism. Although much of it is made up of viruses and other parasitic entities that live in chromosomes, some of it has important functions. As we have already mentioned, there are DNA sequences outside genes that can bind proteins controlling which genes in a cell are ‘turned on’. The control of gene activity must be much more important in multicellular creatures than in bacteria. In addition to the discovery that widely different organisms have DNA as their genetic material, modern biology has also uncovered profound similarities in the life-cycles of eukaryotes, despite their diversity, which ranges from unicellular fungi such as yeasts, to annual plants and animals, to long-lived (though not immortal) creatures like ourselves and many trees. Many, though not all, eukaryotes have a sexual stage in each generation, in which the maternal and paternal genomes of the uniting egg and sperm (each made up of a set of some number n of different chromosomes, characteristic of the species in question) combine to make an individual with 2n chromosomes. When an animal makes new eggs or sperm, the n condition is restored by a special kind of cell division. Here, each pair of maternal and paternal chromosomes lines up, and (after exchanging material to form chromosomes that are patchworks partly of paternal and partly of maternal DNA) the chromosome pairs separate from each other in a similar way to the separation of newly replicated chromosomes in other cell divisions. At the end of the process, the number of chromosomes in each egg or sperm cell nucleus is therefore halved, but each egg or sperm has one complete set of the organism’s genes. The double set will be restored on the union of egg and sperm nuclei at fertilization. The basic features of sexual reproduction must have evolved long before the evolution of multicellular animals and plants, which are latecomers on the evolutionary scene. This is clear from the common features displayed in the reproduction of sexual unicellular and multicellular organisms, and the similar genes and proteins that have been discovered to be involved in the control of cell division and chromosome behaviour in groups as distant as yeast and mammals. In most single-celled eukaryotes, the 2n cell produced by fusion of a pair of cells, each with n chromosomes, divides immediately to produce cells with n chromosomes, just as described above for germ cell production in multicellular animals. In plants, the reduction of chromosome number from 2n to n happens before egg and sperm formation, but the same kind of special cell division is again involved; in mosses, for instance, there is a prolonged life-cycle stage with chromosome number n that forms the moss plant, on which the small 2n parasitic stage develops after eggs and sperm are made and fertilization has occurred. The complications of such sexual processes are absent from some multicellular organisms. In such ‘asexual’ species, mothers produce daughters without a reduction of chromosome number from 2n during egg production. Nevertheless, all multicellular asexual organisms show clear signs of being descended from sexual ancestors. For example, common dandelions are asexual; their seeds form without the need for pollen to be brought to the flowers, as is required for most plants to reproduce. This is an advantage to a weedy species like the common dandelion, which speedily generates large numbers of seeds, as anyone who has a lawn can see for themselves. Other dandelion species reproduce by normal matings between individuals, and common dandelions are so closely related to these that they still make pollen that can fertilize the flowers of the sexual species. Mutations and their effects Despite the proof-reading mechanisms that correct errors when DNA is copied during cell division, mistakes do occur, and these are the source of mutations. If a mutation results in a change in the amino acid sequence of a protein, the protein may malfunction; for example, it may not fold up correctly and so may be unable to do its job properly. If it is an enzyme, this can cause the metabolic pathway to which it belongs to run slowly, or not at all, as in the case of the albino mutations already mentioned. Mutations in structural or communication proteins may impair cell functions or the organism’s development. Many diseases in humans are caused by such mutations. For instance, mutations in genes involved in controlling cell division increase the risk of cancer developing. As already mentioned, cells have exquisite control systems to ensure that they divide only when everything is in order (proof-reading for mutations must be complete, the cell must show no signs of infection or other damage, and so on). Mutations affecting these control systems can result in uncontrolled cell division, and malignant growth of the cell lineage. Luckily, it is unusual for both members of a pair of genes in a cell to be mutant, and one non-mutant member of the pair is often enough for correct cell functioning. A cell lineage also usually requires other adaptations to become a successful cancer, so malignancy is uncommon. (A blood supply is needed for tumours, and the cells’ abnormal characteristics must evade detection by the body.) Nevertheless, understanding cell division and its control is a major part of cancer research. The process is so similar in cells of different eukaryote organisms that the 2001 Nobel prizes in medicine were given for research on cell division in yeast, which showed that a gene involved in the control system of yeast cells is mutated in some human familial cancers. Mutations that give a predisposition to cancer are rare, as are most other disease-causing mutations. The most common genetic disorder in northern European human populations is cystic fibrosis, but even in this case the non- mutant sequence of the gene involved represents more than 98% of copies of the gene in the population. Mutations that cause failure of an important enzyme or protein may lower the survival or fertility of affected individuals. The gene sequence that leads to the non-functional enzyme will thus be under-represented in the next generation, and will eventually be eliminated from the population. A major role of natural selection is to keep the proteins and other enzymes of most individuals working well. We will revisit this idea in Chapter 5. One important type of mutation leads to a protein not being produced in sufficient amounts by its gene. This could happen because of a problem in the normal control system for that gene, which either does not switch it on when it should do so, does not produce it in the right quantities, or stops production of the protein before it is finished. Other mutations may not abolish an enzyme’s production, but the enzyme may be faulty, just as a production line can be hindered or stopped if one of the necessary tools or machines is defective in some way. If one or more of the component amino acids are missing, the protein may not function correctly, and the same can happen if a different amino acid appears at a particular position in the chain, even if all the rest are correct. Mutations causing loss of function can contribute to evolution when selection no longer acts to eliminate them (see Chapters 2 and 6 for how selectively neutral mutations can spread). About 65% of human olfactory receptor genes are ‘vestigial genes’ that do not produce working receptor proteins, so we have many fewer olfactory functions than mice or dogs (not surprisingly, given the importance of smell in their daily lives and social interactions, compared with its minor role in ours). There are also many differences between normal individuals in a species. For instance, individuals in human populations differ in their ability to taste or smell certain chemicals, or to break down some chemicals used as anaesthetics. People who lack an enzyme that breaks down an anaesthetic may suffer a bad reaction to it, but the lack of the enzyme would otherwise not matter. Similar differences in the ability to deal with other drugs, and sometimes foods, are an important aspect of variability in humans, and knowledge of these differences is necessary for modern medicine, in which strong drugs are often used. Mutations in the enzyme glucose-6-phosphate dehydrogenase (an enzyme for an early step in the pathway by which cells derive energy from glucose) illustrate some of these kinds of differences. Individuals entirely missing this gene cannot survive (because the pathway in which it functions is vital in controlling the levels of toxic chemicals produced as a by-product of cellular energy generation). In human populations, there are at least 34 different normal variants of the protein that are not only compatible with healthy life, but are actually protective against malaria parasites. Each of these differs by one or a few amino acids from the protein’s most common normal sequence. Several of these variants are widespread in Africa and the Mediterranean regions, and in some malarial populations variant individuals are frequent. However, some of the variants cause a form of anaemia when a type of bean is eaten, or when certain anti-malarial drugs are given. The well known ABO and other blood-groups are another example of normal variability within the human population; they are due to variation in the sequences of proteins that control details of the surfaces of red blood cells. Variation in the receptor protein for melanocyte-stimulating hormone, which is important in the production of the skin pigment melanin (see Figure 4), can cause hair colour differences; in many red-haired people, this protein has an altered amino acid sequence. As we shall discuss in Chapter 5, genetic variability is the essential raw material on which natural selection acts to produce evolutionary changes. Biological classification and DNA and protein sequences A new and important set of data providing clear evidence that organisms are related to one another through evolution comes from the letters in their DNA, which can now be ‘read’ by the chemical procedure of DNA sequencing. Systems of biological classification based on visible characteristics, which were developed over the past three centuries of study of plants and animals, are now supported by recent work comparing DNA and protein sequences among different species. Measuring the similarity of DNA sequences makes it possible to have an objective concept of relationship among species. We will describe this in more detail in Chapter 6. For the moment we need only understand that the DNA sequences of a given gene will be most similar for more closely related species, while those of more distantly related species are more different (Figure 8). The amount of difference increases roughly proportionally to the amount of time separating two sequences being compared. This property of molecular evolution allows evolutionary biologists to estimate times of events that cannot be studied in fossils, using a molecular clock. For instance, we have already mentioned changes in the order of an organism’s genes on its chromosomes. A molecular clock can be used to estimate the rate of such chromosomal rearrangements. Consistent with the evolutionary viewpoint, species that we believe to be close relatives, such as humans and rhesus monkeys, have chromosomes that differ by fewer rearrangements than humans and New World primates such as the woolly monkey. In the next chapter, we will explain the evidence for evolution based on fossil data, and from data on the geographical distribution of living species. These observations complement those described here, in showing that the theory of evolution provides a natural explanation for a wide range of biological phenomena.