All organisms on Earth are connected by an evolutionary journey spanning more than 3 billion years. The diversity of life we see around us is the sum of a limitless number of mutations, changes in genetic information that are usually subtle but sometimes dramatic. When Charles Darwin proposed that natural selection acts on variation in populations, he had no knowledge of the mechanisms that give rise to that variation. Such mechanisms lie at the heart of modern molecular biology.

Almost anyone can distinguish a living organism from an inanimate object. However, a rigorous scientific description of life is harder to achieve. Life differs from nonlife in identifiable ways, as summarized in Figure 1-1. Organisms move, reproduce, grow, and alter their environment in ways that inanimate objects cannot. But such characteristics alone provide an unsatisfying definition of life, particularly when a few of them may be shared by inanimate substances. In 1994, the United States National Aeronautics and Space Administration (NASA) convened a panel to consider the question, “What is life?” A simple definition resulted: Life is a chemical system capable of Darwinian evolution. The importance of evolutionary theory to all biological sciences gains full expression in this concise statement.

Every living system we know about has several requirements for its existence. Two of these—raw materials and energy—are supplied by a home planet endowed with an abundance of both. Molecules in Earth’s life forms are made up largely of the elements hydrogen, oxygen, nitrogen, and carbon. These are the smallest and most abundant atoms that can make, respectively, one, two, three, and four covalent bonds with other atoms. The molecules formed by these elements tend to be quite stable and can be very complex. The energy required for life is derived from the sun. Plants and photosynthetic microorganisms collect and store the energy derived from sunlight in the chemical bonds of complex biomolecules.

A third requirement for a living system is an envelope, creating a barrier between the living and inanimate worlds and establishing a means of selective interaction between a cell and its environment. The work of Jack Szostak, chronicled in this chapter’s Moment of Discovery, may be replicating some key evolutionary moments that led to enveloped living systems (Figure 1-2).

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The final two requirements—catalysis and biological information—are particularly important, truly distinguishing a living organism from an inanimate object. These requirements are the domain of molecular biology. The energy transactions that support homeostasis (the maintenance of parameters such as pH and biomolecule concentrations within the narrow range needed to support life) and enable the transmission of genetic information from one generation to the next are initiated by powerful catalysts called enzymes. Enzymes are highly specific, and each enzyme accelerates only one or a small number of chemical reactions. Most enzymes are proteins, although a few catalytic RNA molecules play important roles in cells. The catalysts that a particular organism possesses define which reactions can occur in that organism. Enzymes determine what a cell takes in for nourishment, how fast the cell grows, how it discards wastes, how it constructs its cellular membranes, how it responds to other cells, and how it reproduces.

The presence of enzymes in a cell depends on the faithful transmission of the genetic information that encodes them from one generation to the next. Enzymes, as well as the myriad other proteins and RNA molecules that regulate their synthesis and function, are the actual molecular targets of evolution. When a cell acquires a new function, it generally reflects the presence of a new enzyme or set of enzymes, or an alteration in the regulation or function of an existing enzyme or process. The new functions arise through changes in genes—changes that are shaped by evolutionary processes. In the biosphere of today, DNA is the standard macromolecule for the long-term storage and transmission of biological information. It is exquisitely adapted to that function (Figure 1-3). However, as we shall see, there were probably stages in the evolution of life when DNA did not serve as the primary genetic library in living systems.

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In 1973, the geneticist Theodosius Dobzhansky published an article in the professional journal The American Biology Teacher entitled “Nothing in Biology Makes Sense Except in the Light of Evolution.” This sentiment has special meaning in molecular biology, because the pathways and processes in living systems give rise to the genetic variation on which natural selection acts (Figure 1-4). They also inform the ongoing investigations into how life arose on Earth.

Evolution relies on spontaneous and generally random changes in an organism’s genomic material, called mutations. In spite of the elaborate cellular mechanisms we consider in this book, all of which help ensure accurate transmission of genetic information from one generation to the next, mutations regularly occur. Mutations can be as simple as a change in a single base pair of DNA or base of RNA or as substantial as the inversion, deletion, or insertion of large segments of genetic material. As we will be discussing in detail, errors can arise during replication (Chapter 11), and DNA damage can lead to permanent mutation when repair systems (Chapter 12) go awry. Larger chromosomal changes can arise from recombination (Chapter 13) or transposition (Chapter 14). Some mutations affect genes directly; others affect the ways in which DNA is transcribed into RNA or RNA is processed or translated (Chapters 15, 16, 17 and 18). Relatively minor changes in genes involved in regulatory processes (Chapters 19, 20, 21 and 22) can give rise to dramatic changes in the organism; this realization has created a new field, essentially a modern merger of the fields of evolutionary and developmental biology, dubbed “evo-devo” (described in Chapter 22). All the processes that contribute to information transfer are highly, but not perfectly, accurate, and the slow accumulation of alterations is inevitable. Many organisms even have mechanisms to speed up the pace of mutational change, which they draw upon in times of stress.

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An understanding of these processes has also given us insights into the origins of life and the process of evolution. Continuing explorations of RNA structure (Chapter 6) and metabolism (Chapters 15 and 16) have informed new theories of prebiotic evolution. The genetic code (Chapter 17) provides a particularly vivid look at the shared history of every organism on Earth.

Molecular biology has provided the enzymes that make most of the methods of biotechnology possible (Chapter 7). These increasingly powerful methods for studying the genes of many different organisms allow us to trace their evolution. Through modern genomics (Chapter 8), molecular biology is opening a window onto evolution that Charles Darwin would marvel at.

The interrelationship of molecular biology and evolution is of more than academic interest. Human beings exist in a world where every organism continues to evolve. Microorganisms, with their short life cycles, evolve most rapidly (Highlight 1-1). Of special concern are human pathogens, as well as the microorganisms, fungi, insects, and other organisms that affect our food crops, livestock, and water supply. Molecular biology provides essential tools for use in tracking pandemics, investigating new microbial pathogens, identifying the genes underlying human genetic diseases, solving crimes, tracing the origin of diseases, treating cancer, and engineering microorganisms for new purposes in bioremediation and bioenergy. All of these efforts rely heavily on the concepts of evolutionary biology. Indeed, modern society relies on countless innovations in medicine and agriculture that would not exist but for Darwin’s great insight.

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About 4.6 billion years ago, the sun and Earth and the other planets and asteroids of our solar system were formed. Within the first billion years of our planet’s existence, life appeared on its surface. How did this happen, and how likely is it that this has happened on other, similar worlds? Modern geologists, paleontologists, and molecular biologists are slowly piecing together the history of life on Earth from the rich trove of clues in the geologic, fossil, and genomic records. A plausible sequence emerges, providing a wide range of hypotheses that can be tested using modern chemical and physical methods.

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The first few hundred million years were a time of prebiotic chemistry (Figure 1-5). No life was present, but chemical reactions were happening everywhere. The atmosphere contained primarily water, methane, ammonia, hydrogen, nitrogen, and carbon dioxide. Reactions driven by the constant stream of energy coming from the sun were slowly yielding more complex molecules such as simple sugars, amino acids, and nucleotide bases. And the accumulation of organic material was supplemented by materials from a multitude of collisions between early Earth and meteors laden with organic matter. Prebiotic chemistry is being studied by a large community of researchers. A small sampling of their work is presented in the How We Know section at the end of this chapter.

Over a period of millions of years, the accumulation of reaction products yielded a soup containing molecules and polymers. As they grew increasingly complex, particular polymers acquired the capacity to duplicate themselves. The first self-replicating polymer, possessing two of the key requirements for life—catalysis and biological information—might be considered the first life form.

We do not know what this first “living” polymer was. However, modern molecular biology has given us many reasons to think that RNA either was the first self-replicator or arose as a much-improved descendant of that first self-replicator. RNA differs from DNA only in that it uses ribose instead of deoxyribose in its backbone. That single additional hydroxyl group in each monomeric unit of the polymer allows RNA to take up a plethora of complex structures that are inaccessible to DNA. The structural malleability of RNA gives it a capacity for both catalysis and information storage that has made it indispensable for life, from its beginnings to the present time.

The RNA world hypothesis was first proposed as a stage in evolution by molecular biologists Carl Woese, Francis Crick, and Leslie Orgel, in separate papers published in the late 1960s. The hypothesis describes a living system (or set of living systems) based on RNA. In this system, a variety of RNA enzymes could catalyze all of the reactions needed to synthesize the molecules required for life from simpler molecules available in the environment. The RNA enzymes would include replicators to duplicate all of the RNA catalysts. The “RNA organism,” out of equilibrium with its surroundings, would have to be defined by a boundary. The experiments of Szostak and colleagues show one way in which lipid-enclosed RNA systems can arise (see the How We Know section at the end of this chapter).

Four more-recent lines of evidence have added much breadth and depth to the RNA world proposal. The first was the discovery by Thomas Cech and Sidney Altman, in the early 1980s, of catalytic RNAs, or ribozymes—enzymes that are made of RNA instead of protein. Thus we learned that some extant RNA molecules catalyze reactions and so possess both of the key conditions for life—biological information and catalysis. In modern organisms, ribozymes catalyze a relatively narrow range of reactions, such as the cleavage and ligation of other RNA molecules—a range insufficient to support an RNA world.

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What is the real catalytic potential of RNA? The second line of supportive research demonstrated that RNA molecules generated in the laboratory can catalyze almost any imaginable reaction needed in a living system—certainly a range of reactions much broader than those attributable to ribozymes existing today. Early RNA molecules could clearly have catalyzed all of the reactions required to set up a primordial cellular metabolism.

The third and fourth discoveries have further broadened our perspectives on RNA function. We now know that in ribosomes, the large ribonucleoprotein complexes that translate RNA into protein, the RNA is the active component with the capacity to catalyze protein synthesis (Figure 1-6; see also the Moment of Discovery for Chapter 18). Finally, and most recently, RNA sequences capable of simple forms of self-replication have been discovered (discussed in Chapter 16).

Ongoing research thus makes it possible to visualize a highly plausible sequence of events unfolding on the pathway from prebiotic soup to living systems. Arising from a myriad random primordial polymers, an RNA world came into being and gradually became more complex. An RNA capable of reliable self-replication may have been the first living entity. Self-replicators would have diversified to synthesize other ribozymes, leading to an RNA-based metabolism capable of providing a greater supply of needed RNA precursors. Ribozyme groupings became enclosed within lipid membranes. Particular groupings were successful, resulting in the first cells and a capacity to maintain a metabolic state out of equilibrium with the surroundings. As the RNA molecules in those cells increased in size and structural complexity, a need for stabilization and auxiliary functions arose. Peptides (proteins) were synthesized to neutralize the negative charges of the phosphates in the RNA backbone, to stabilize RNA structure in other ways, and to augment early metabolism. As more peptides were synthesized, some with catalytic activities arose. Proteins gradually supplanted RNA as catalysts, because the greater catalytic potential of proteins yielded an advantage. The protein world emerged, but not without retaining important vestiges of the RNA world (ribosomes and some other RNA catalysts), as we find them today.

Countless nascent life forms probably arose from the primordial soup, along with many biological advances that improved their fitness. Successful combinations of RNA catalysts gave way to systems based on protein catalysts. Improvements in catalytic efficiency appeared, along with systematized genetic codes to link genetic information in RNA and DNA to protein sequences. Additional changes facilitated cellular metabolism and reproduction. Protein synthesis was systematized through the evolution of an efficient ribosome machine. RNA became more specialized for information storage and transmission. Cell membranes became more structured and specialized, eventually including mechanisms to selectively transport materials into and out of the cell as needed. And some processes became regulated. In this way, a variety of primitive cells may have evolved—each of them a viable living system. Organisms living today exhibit shared properties, telling us that one of these early experimental cells won out over the others. This cell, sometimes called LUCA (last universal common ancestor) (Figure 1-7), ultimately gave rise to all life now present on Earth.

LUCA is a special source of fascination for molecular biologists. Although LUCA probably lived more than 3 billion years ago, our speculation about what this cell was like is informed by experiment. One approach is to determine the minimum protein and genetic requirements for life. Attempts to create a minimal life form, either by reconstituting basic components or by taking bacteria and tsripping them of all unnecessary parts, are underway in laboratories around the world. These experiments are not only defining properties that must have been present in LUCA; they are also setting the stage for the laboratory generation of engineered bacterial cells that can be used to manufacture chemicals for bioenergy, agriculture, and medicine.

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Another approach to understanding LUCA is to survey all types of living systems on Earth to determine which genes or characteristics are universal. The only genes that are truly universal in living systems are those encoding the cellular machinery for protein synthesis and some components of RNA transcription. All organisms also share (with very minor modifications discussed in Chapter 17) the same genetic code. That same code must have been present in LUCA. To support protein synthesis and RNA synthesis, a simple metabolism must have been present that allowed the uptake of chemical energy and its use to synthesize amino acids, nucleotides, and whatever lipids existed in the cell membrane from precursors available in the environment. The study of LUCA is described in more detail in Chapter 8.

The appearance of LUCA signaled the beginning of biological evolution on Earth. New types of cells gradually appeared, and new environments were exploited. The first cells were capable of taking up organic molecules from their surroundings and converting them to the molecules needed to support protein and RNA synthesis. Cellular complexity resulted in ever-increasing requirements for cellular genomic information. DNA, with a more uniform structure and some stability advantages relative to RNA, may first have appeared in viruses. It then gradually supplanted RNA as the most stable platform for the long-term storage and transmission of genetic information, and DNA replication and systems for the segregation of replicated DNA chromosomes into daughter cells evolved.

The early single-celled organisms derived from LUCA diversified to inhabit all niches in the ecosystem of this early Earth. The diversification eventually generated the three major groups of organisms that we recognize today: bacteria, archaea, and eukaryotes (Figure 1-8).

Many additional events helped shape the life we see around us. Notably, photosynthesis appeared about 2.5 billion years ago, as evidenced by the sudden rise in the concentration of atmospheric oxygen documented in the geologic record. As cells engulfed other cells, some endosymbiotic relationships developed and became permanent. The engulfed cells became organelles within their hosts more than 1 billion years ago, and we see these organelles today as chloroplasts and mitochondria. Loose clusters of unicellular organisms led to cell specialization, and more permanent assemblies produced multicellular organisms. Diversification of body plans became more rapid about 600 million years ago, eventually generating all the major types of organisms we observe today.

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Charles Darwin (1809–1882) was one of the most influential thinkers in history, and his name is forever associated with the concept of evolution. In his book On the Origin of Species, published in 1859, Darwin developed several general observations and ideas, laying out the evidence he had collected during and after his now famous voyage on the Beagle. He documented the variation among individuals in a population and inheritance of the variations by offspring. He noted that individuals in a population compete for resources. He argued that those individuals best adapted to exploit the prevailing resources are the ones most likely to survive and reproduce. These ideas together constitute a mechanism for evolution that can be described by the term natural selection.

The Origin of Species had a tremendous and immediate influence on scientific thought, due in part to the huge volume of work it described and in part to the story it told. Darwin contributed a detailed body of evidence to support a range of interconnected ideas—some his own, some borrowed from his predecessors and contemporaries (see the How We Know section at the end of this chapter). Darwin’s study of finches and other organisms introduced the idea of branching evolution (Figure 1-9), which ultimately led to the idea that all life on Earth has a common ancestor. For natural selection to work, evolution must be gradual, with no discontinuities. All of these ideas coalesced, in The Origin of Species, into an internally consistent and compelling story describing the development of life in its many forms. Darwin’s definition of the mechanism by which all of this occurred—natural selection—was the crowning achievement.

Natural selection depends on two characteristics of a population: variation and competition (Figure 1-10). However, the source of a population’s variation eluded Darwin. The genetic program that exists in every organism was unknown to him, as were the mechanisms by which it is handed down from one generation to the next. Darwin was unaware that the work that would eventually reveal these mechanisms had been begun by one of his contemporaries, Gregor Mendel (see Chapter 2). Mendel’s work was little appreciated during his lifetime.

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Darwin’s ideas have been expanded and developed into a modern synthesis of the theory of evolution, a direct outgrowth of the development of genetics in the early twentieth century—a time when Mendel’s work was rediscovered, giving rise to the term Mendelian genetics. The concept of the gene was developed by influential geneticists such as Thomas Hunt Morgan, J. B. S. Haldane, and Theodosius Dobzhansky, providing the necessary mechanism of inheritance. As our understanding of genetic mechanisms emerged and matured, the concept of organismal variation as observed by Darwin and Mendel slowly evolved into the modern concept of mutation—a chemically definable change in a gene. By the 1950s, the theory of evolution could be stated in more detail and was bolstered by more evidence on mechanisms than was conceivable in Darwin’s day. Populations, as we now know, contain inherent genetic variation generated by random mutation and genetic recombination. The frequency of different forms of genes in a population changes from generation to generation as a result of several processes (discussed in Chapters 8 and 14). Organismal changes can occur as the result of inherited mutations in a gene. Whether the change remains in a population depends to a large degree on whether the change confers an advantage to the organism. If the advantage is small or nonexistent, random genetic drift—changes in the frequency of a particular form of a gene—can occur, especially in small, isolated populations. Organisms can also acquire new genes through gene flow from other species in a process called horizontal gene transfer. Several mechanisms by which horizontal gene transfer can occur in bacteria are outlined in Figure 1-11 (see Chapters 8 and 14).

Darwin’s theory of natural selection provides a mechanism that responds directly to the environment. Most of the genetic changes that do not kill an organism produce only small changes in protein function or expression, resulting in a small change in the whole organism. As a result, evolutionary change is usually gradual. Sufficient diversification leads to new species and, with time, to new genera and phyla.

On the most practical level, our connectivity with other species through the tree of life has a critical effect on the study of molecular biology: we can learn about ourselves by studying other organisms (as described in detail in the Model Organisms Appendix). Even the simplest organisms have much to teach us about the inner workings of our own cells. As we will see throughout this book, the processes involved in the flow of biological information, though common to all organisms, are often much more complex in eukaryotes than in bacteria. Much of our understanding of these processes is due to groundbreaking research on bacteria or yeast, followed by further research on more complex model organisms such as worms, insects, or mice (Figure 1-12). In this way, the elucidation of gene functions in a relatively simple organism such as yeast can lead to cures for human disease. Discoveries made in bacteria can generate improvements in agriculture. Fruit flies instruct us about the intricacies of human cognition and the complexities of fetal development. Pandemics of the future can be predicted and tamed by studying the pathogens of the past. Each investigation into the molecular biology of an organism is made more valuable by the fact that all species are related through a shared evolutionary history.

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As Darwin remarked in The Origin of Species, “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”