Biology as a Whole

2 BIOLOGY AS A WHOLE In this chapter we provide an overview of the broad topic of biology. Much of biological science, as well as the chapters of this book, is reductionist. That is, systems are studied by focusing on their component parts. However, in this chapter we examine biology holistically, stepping back and looking at concepts that connect all of its disparate components. The most basic concept, which forms the foundation of the entire structure of biology, is the definition of life. A ‘‘vertical’’ view of the structure generates a hierarchy of scale from biochemical reactions to the ecosystem. A ‘‘horizontal’’ view displays the classifications of living things, the pigeonholes that biologists use to group organisms into species, families, and so on. Connecting the parts of the structure is the theory of evolution, the grand organizing principle that gives the structure resilience, explaining why things are as they are. Finally, stepping back a bit, one can examine the two-way interactions between the structure and its surroundings, the environment. 2.1 WHAT IS LIFE? First, we must define our subject. Biology is the study of living things. What, then, is the definition of life? For the most part, none of us would have trouble distinguishing living from nonliving things. Therefore, we will make our definition to include everything we consider to be alive and to exclude the nonliving things. This must be done carefully because we can sometimes find counterexamples to particular rules. Doesn’t a crystal grow and possess order? Have you ever seen a polymer solution climbing out of a glass (motility)? Aren’t there computer programs that reproduce and evolve? What about virus particles? Viruses are crystalline particles that must take over the cell of an 16 WHAT IS LIFE? 17 ordinary organism in order to reproduce. Should we make our definition include them? Even if we do, it turns out that there are infectious agents, viroids and prions, which are even simpler in structure, possibly even single molecules. It should be obvious that this is one of those somewhat arbitrary questions that often arise in biology. Recognizing this, and also that there may be alternative definitions, let’s go ahead and make our definition as best we can: A living thing is a discrete entity, or organism, that has the following characteristics:
It can capture useful energy from its surroundings.
It can extract materials from its surroundings for growth and maintenance of its structure.
It is responsive—it reacts to its surroundings, using energy and material to move or grow.
It reproduces—it generates other organisms like itself, preserving its own characteristics by passing them on to succeeding generations.
It adapts and evolves—successive generations can change as the environment changes; individuals exhibit adaptations, that is, they are specialized for a particular function in a particular environment. Other characteristics sometimes mentioned are that life is orderly and complex; that it is capable of motility, or movement, which is a type of response; that it exhibits development, in which its complexity increases progressively; and that it has heredity, in which its characteristics are passed to its offspring as it reproduces. So, is a virus alive? It is capable of evolution and reproduction, but it clearly fails in the first two of the criteria above. Strictly adhering to the criteria, the answer would be no. However, this might not be satisfying to some, who feel intuitively that they should be included. It may be that the best answer would be just to say that ‘‘viruses have several of the characteristics of living things’’ and leave it at that. To press the question further may be meaningless. Certainly, the topic of viruses belongs in a book on biology. On the other hand, the line may be drawn to definitively exclude viroids and prions. These may be considered to be chemical substances with infectious behavior. Textbooks often do not mention at this point in the discussion another criterion for life that is commonly used by biologists:
All living things are composed of cells. A cell is the smallest entity completely surrounded by a membrane and containing a nuclear region, which stores the hereditary information used for growth and reproduction, and cytoplasm, which is a gel-like substance between the membrane and the nuclear region. With this additional criterion, viruses are clearly excluded, since they lack a membrane and cytoplasm. Life may also be described in thermodynamic terms. The molecules in any isolated system (a system whose boundaries are sealed to both matter and energy) tend to rearrange themselves by random processes. For such systems of even moderate complexity, of all the possible random arrangements the ‘‘orderly’’ ones are extremely rare. Thus, such systems tend to rearrange into ‘‘disordered’’ systems. This behavior is described by the second law of thermodymics, which states that entropy, a measure of disorder, tends to increase in isolated systems. 18 BIOLOGY AS A WHOLE But Earth is not an isolated system. It receives energy in the form of visible and ultraviolet light and emits the same amount of energy to space in the lower-grade form of infrared radiation. As this energy passes through the living world, part of it is used to do the work of countering the increase in entropy on Earth. In fact, living things use energy to cause a local decrease in entropy. The infrared emission to space results in an even greater increase in entropy outside the Earth, so that the total entropy of the universe still is found to increase. Erwin Schrödinger (1956), developer of the quantum wave equation, described these ideas in a book entitled ‘‘What Is Life?’’: Thus a living organism continually increases its entropy—or, as you may say, produces positive entropy—and thus tends to approach the dangerous state of maximum entropy, which is death. It can only keep aloof from it, i.e. alive, by continually drawing from its environment negative entropy—which is something very positive as we shall immediately see. What an organism feeds on is negative entropy. Or, to put it less paradoxically, the essential thing in metabolism is that the organism succeeds in freeing itself from all the entropy it cannot help producing while alive. Later, he continues: Hence the awkward expression ‘‘negative entropy’’ can be replaced by a better one: entropy, taken with the negative sign, is itself a measure of order. Thus the device by which an organism maintains itself stationary at a fairly high level of orderliness (¼ fairly low level of entropy) really consists in continually sucking orderliness from its environment. . .. After utilizing it they return it in a very much degraded form—not entirely degraded, however, for plants can still make use of it. (These, of course, have their most powerful supply of ‘‘negative entropy’’ in the sunlight.) This ‘‘negative entropy’’ can be identified with the thermodynamic concept of Gibbs free energy, described in Section 5.1.1. 2.2 THE HIERARCHY OF LIFE One way to examine living things is to look at them with different degrees of magnification, as it were, from the atomic level to cells, to organisms, to standing back and looking at Earth as a whole. The following lists the levels of detail in this hierarchy: Metabolism Organelle Cell Tissue Organ Organ system All of the chemical reactions within an organism that sustain life. Subcellular structures within cells that carry out specialized functions. The basic unit of life, a structure completely surrounded by a membrane, containing a nuclear region and cytoplasm; the smallest structure capable of having all of the characteristics of life. A group of similar cells having the same function in a multicellular organism. A single structure of two or more tissues that performs one or more functions in an organism. A group of organs that carry out related functions. THE HIERARCHY OF LIFE Organism Population Community Ecosystem 19 An individual entity that has all of the characteristics of life described above and possessing the same hereditary information in all its cells. A group of individuals of the same species living in the same environment and actively interbreeding. A group of interacting populations occupying the same environment. The combination of a community and its environment. To understand the last several items, it is necessary in addition to define environment: the physical and chemical surroundings in which individuals live. Strictly speaking, the environment does not have boundaries. In practice, of course, it is common to restrict the discussion to a particular region, such as a single forest, a particular glen within that forest, or just the soil in a glen in a forest. The first half of this book is organized roughly along the lines of the hierarchy. A more detailed description of the items in the hierarchy follows. Metabolism This is the view of life at the chemical level. The study of chemical reactions in organisms is called biochemistry. The reactions can be classified into (1) energy conversion reactions, (2) synthesis and breakdown of cell material, and (3) reactions associated with specific functions such as reproduction or motility. The energy conversion reactions include those that capture energy from sunlight (photosynthesis) and convert it into food or that convert food energy into a simple form that is available for other reactions (respiration, fermentation). The synthesis reactions include production of the components of the major constituents of cells, such as proteins, carbohydrates, and lipids (which include fats), or minor ones (in terms of mass), such as nucleic acids, hormones, and vitamins. Reactions that break molecules down into simpler forms may facilitate the removal of waste products. All of the metabolic reactions are connected to each other by a web of metabolic pathways, which consists of sequences of biochemical reactions. A particular compound can often participate in several reactions, thus becoming a link between those pathways. Organelles Some of the specialized functions carried out by these substructures include protein synthesis, photosynthesis (the conversion of light energy to chemical energy), and respiration (the release of chemical energy into a form usable by cells). The organelles that perform these functions are the ribosomes, the chloroplasts, and the mitochondria, respectively. There are many other organelles, especially in higher organisms. Not all cells have all types of organelles. Cells All living things are made of cells. Some are composed of a single cell and are called unicellular. Organisms made of more than one cell are called multicellular. A key structure of all cells is the plasma membrane. This separates the cell contents from its environment and forms the boundary of many of the cell’s organelles. There are two primary types of cells. The prokaryote is the simpler of the two. It has no internal membrane structures, and the only organelle is the ribosome. Bacteria are typical prokaryotes. The other type is the eukaryote, which has internal membrane-bound structures such as mitochondria and chloroplasts. All the plants and animals are eukaryotic organisms, as are some single-celled organisms such as protozoans and algae. 20 BIOLOGY AS A WHOLE Tissues These are present only in multicellular organisms, of course. Examples include muscle tissue, bone tissue, or nerve tissue. Tissues should not be confused with organs. Although they may be composed predominantly of one type of tissue, organs may also be formed from a variety of tissues. Organs This is a complete unit such as an entire muscle, a bone, or the brain. Many organs serve a single function. Others organs have multiple functions, such as the pancreas and the adrenal gland. Both of these glands produce more than one hormone, which have unrelated functions. Organ Systems Some organs work in concert with each other and form a system. Examples are the nervous system, the circulatory system, the respiratory system, the skeletal system, and the endocrine system. Organism An organism is a living thing with a single genome (the set of hereditary information contained in all its cells’ nuclear regions), which exists, for at least part of its life cycle, in the environment and separately from others of its kind. Some organisms, such as the algae and the fungi in lichens, must live together, but they have different genomes. Others live in colonies but exist separately at an earlier stage of their lives. An example of the latter is the jellyfish, which is really a colony of organisms that started out as free-swimming larvae. The individual cells of a jellyfish may come from different parents, yet it is difficult not to think of a jellyfish as a single organism. This is another example of the difficulty in making distinctions in biology. Population Examples of populations include all of the striped bass that breed in the Hudson River (although they spend most of their lives in the Atlantic Ocean), and the Nitrosomonas europaea bacteria in a biological wastewater treatment plant. Sometimes the definition of population is extended to any group of organisms sharing a characteristic, such as the population of invertebrates (animals lacking an internal skeleton) in the soil, or the population of deer ticks that carry the Lyme disease bacteria. Thus, in this usage, a population may either incorporate more than one species or may be a subset of a species. Although such usage is common, it should be avoided. It would be more proper to label multiple-species groups as populations (note the plural) and to call the subset of a species a subpopulation. Community Strictly speaking, a community comprises all of the organisms in a region. Thus, an earthworm may be considered a member of a number of communities, depending on the region defined: It may be a member of the soil community, the forest community, or the community of organisms on a particular island in a lake. The word community is sometimes used in a looser sense, similar to the second usage of the word population described above. For example, some may speak of the community of soil bacteria when they are concerned about the interactions among those members, even though there are other species in the same environment. Again, it would be more precise to use the term populations. Ecosystem The ecosystem is the most inclusive unit studied in biology. Again, the term may be restricted to local systems, such as a particular lake, or an island and nearby waters. Strictly speaking, since all of these systems are interconnected, there is really EVOLUTION 21 only one known ecosystem—the Earth’s. This all-inclusive ecosystem is also known as the biosphere. 2.3 EVOLUTION Evolution is the process of genetic change by which species adapt to their environment or develop new ways of coping with environmental stress. The theory of evolution is the most fundamental organizing principle in biology. It can be invoked to explain the origin of almost any feature of living things. By the early nineteenth century enough geological and fossil evidence had accumulated to challenge the prevailing idea that Earth and the life on it were unchanging. Jean-Baptiste Lamarck then proposed the ultimately rejected theory that species evolved by passing on new characteristics that were acquired by changes during their lifetime. For example, it was suggested incorrectly that early giraffes stretched their necks by reaching for leaves from high branches and that their offspring retained this change. Two English naturalists then developed a better explanation for evolution. From 1831 to 1836, Charles Darwin served on the round-the-world voyage of HMS Beagle. His observations in South America, especially in the Galápagos Islands off Ecuador, led him to form the modern theory of evolution. Darwin wrote a summary of the theory in 1842 but did not publish it immediately. Independently, and several years later, Alfred Russell Wallace developed the same ideas, even using the same term, natural selection. After Wallace published several papers he sent one to Darwin, asking him to forward it to the Linnean Society for publication, which Darwin did. Darwin then rushed his own life’s work into print in 1859 (giving proper credit to Wallace) in the form of the book The Origin of Species. Our modern understanding of evolution is based on genetic theory. However, its original development preceded that knowledge. Here a detailed discussion of heredity and genetics is deferred to Chapter 6. Evolution can be described based on the understanding that individuals in a population vary in numerous traits (observable characteristics) that can be inherited by their offspring. The traits may be of various types, such as morphological (related to structure, such as height or shape of the eyes), biochemical (such as the ability to produce their own vitamin C), or even behavioral (e.g., aggressiveness in dogs). The theory of evolution can be reduced to two mechanisms that act in combination: 1. Random variation. The sources of the variation in traits within a population are random mutations in the genetic code, and sorting and recombination of genetic material that occurs during meiosis, a type of cell reproduction. Only a minority of genetic changes may confer an advantage on an individual. In fact, most changes are probably fatal and are not passed on to future generations. Mutations are caused by errors in the biochemical processes of reproduction in which the genetic material is copied for progeny, or by damage from chemical or physical agents such as ionizing radiation. 2. Natural selection. Because organisms have an inherent reproductive growth rate that would cause the population to exceed the ability of the environment to support it, not all individuals survive to reproduce. Individuals with heritable traits that do confer an advantage tend to leave more offspring than those without such traits. Consequently, those traits become more common in succeeding generations. 22 BIOLOGY AS A WHOLE These cause the traits held by a population to tend to change with time either because novel traits are developed randomly that confer an advantage in the current environment, or because different traits are selected for when the environment changes, such as by climate change, introduction of new competing species to the area, or various forms of human intervention. Favorable traits, which increase the fitness of a population to an environment, are called adaptations. The Galápagos Islands, which have become a field laboratory for evolution, furnish an example. In 1977 a drought wiped out 85% of a species of finch. Studies showed that the survivors were mostly birds with larger beaks. It was found that this was because during the drought there were fewer herbs and grasses that produced small seeds. The birds with small beaks were unable to eat the larger seeds that remained, and they did not survive to pass on their characteristics. Prior to our modern understanding of genetic theory and molecular biology, the theory of evolution could be supported by three types of evidence: the fossil record, comparisons between the structure and function of different species, and by an analysis of the geographic distribution of existing species. The fossil record shows that (1) different organisms lived at different times, (2) different organisms lived in the past than are in existence today, (3) fossils found in adjacent sedimentary layers (and therefore relatively close to each other on a geological time scale) are similar, (4) intermediate forms of species are sometimes found, and (5) older rocks tend to have simpler forms. Comparison of species falls into three categories: comparative anatomy, comparative embryology, and comparative biochemistry. Comparative anatomy shows that similar organisms have similar structures, but structures that serve different functions. For example, the same bones that a human has in the forearm are found in the flipper of a whale and the wing of a bat. It was easier for nature to modify existing structures of these mammals than to develop completely new, specialized structures. Sometimes a structure loses its function altogether, forming a vestigial organ. For example, whales and snakes retain the pelvis (hipbone) and femur (thighbone). Comparative embryology finds that similar organisms have similar embryos (the earliest multicellular form of an individual). For example, all vertebrate embryos, including humans, have gill slits, even if the adult does not. Evolution accounts for this by explaining that those features are retained from ancestral forms. In an example of comparative biochemistry, techniques of molecular biology have shown that similar species have similar genetic material. It is possible to compare species based on the degree of similarity between their DNA (the chemical in the nuclei of cells that stores the hereditary information). This has shown definitively that species that are similar on an evolutionary scale (based on other evidence) are also similar genetically. Furthermore, the code that converts DNA into proteins is the same in all living things from bacteria to humans (see Table 6.2). There is no fundamental reason that this should be so unless all these organisms developed from a common ancestor. The third line of evidence is from biogeography, the study of geographic distribution of living things. This type of evidence was particularly striking to Darwin. He observed many unique species in the Galápagos, off South America, and in the Cape Verde Islands, off Africa. Although the two island groups have similar geology and climate, their species are more similar, although not identical, to those on the nearby mainland than to each other. This suggested that the islands were colonized from the nearby mainland by organisms swimming, flying, or rafting on floating vegetation, and that evolution continued through their subsequent isolation. At the same time, unrelated organisms of the two island chains had similar characteristics, suggesting that evolution formed similar structures in response to similar requirements. EVOLUTION 23 The study of evolution has helped to understand changes in populations other than the formation of new species. Random changes in traits can occur in a population, resulting in what is called genetic drift. This is seen when a population becomes divided by some circumstance, such as the formation of an island from a peninsula by rising water levels. If two populations are isolated from each other long enough, they can diverge to form distinct species, even if both are in similar environments. This is called divergent evolution. The differences between Galápagos species and the mainland species with which they share ancestry is an example. Another form of genetic drift is called the bottleneck effect. This occurs if some catastrophe destroys a large portion of a population. As a result, only those traits carried by the survivors are found in future generations. Many of the less common traits will disappear, and some rare ones may become common (see Figure 2.1). The bottleneck effect is also seen when a small number of a species are introduced to a new ecosystem and flourish there. The descendents share a few recent ancestors and limited genotypes. Environmental stresses can cause changes in the genetic makeup of a population by favoring organisms with certain alleles more than others. This is, in fact, the normal way that populations can adapt rapidly to changes in their environment without mutations being required to produce new adaptations. It is also the reason why populations with genetic diversity are more likely to survive in the face of change. However, there is another side of this phenomenon related to human impacts on populations. Toxins added to the environment exert selection pressure for individuals that are more tolerant of the toxins. One negative impact of this is that it can reduce the genetic diversity of a population, making it vulnerable to further stresses. Another problem occurs if the organism is a pest and the toxicant is an agent such as a pesticide or antibiotic. As a result of the selection pressure, the population seems to develop tolerance or resistance to the agent, which then becomes less effective. Original population contains many rare alleles. Aa Oo cc Dd ww Ss rr Jj Bb Gg kk A disaster destroys 80% of the population. Ss rr rr SS rr Ss rr ss rr Ss Ss rr ss rr Ss rr Ss rr ss rr SS rr Recovered population has lost many of the rare alleles, and a few rare alleles become common. Figure 2.1 Bottleneck effect. (Based on Wallace et al., 1986.) 24 BIOLOGY AS A WHOLE Sometimes very different species develop similar characteristics in response to similar environmental conditions. This is called convergent evolution. Because of this it is not always possible to consider species to be related evolutionarily because of superficial similarities. For example, most of Australia’s original mammals are marsupials, which nurture their fetuses in pouches; whereas North America is dominated by placental mammals, whose fetuses grow internally in the uterus until ready to live independently. Despite their being very different groups, similar species have arisen on both continents, such as marsupial analogs to the wolf, mouse, and even the flying squirrel. The Pace of Evolution The traditional view of evolution has been that it proceeds by the accumulation of small increments of change. This view is called gradualism. Some fossil evidence supports this. For example, fossils have shown a series of species leading from a small, dog-sized animal, to the modern horse. However, the fossil record is more compatible with the view that species remained stable for millions of years before suddenly disappearing and being replaced by new ones. An alternative view, called punctuated equilibrium, was proposed in 1972 by Niles Eldredge and Stephen Jay Gould. This predicts that evolutionary changes occur rapidly over short periods, forming new species in small populations. These stay relatively unchanged for millions of years until they become extinct. Gould suggests that the rapid changes could be caused by small, yet influential genetic modifications. For example, radical changes in the body plan of an organisms could be mediated by a small number of mutations. The theory of punctuated equilibrium answers the criticisms directed at evolution theory for the absence of ‘‘missing links’’ in the fossil record. However, gradualism also explains some of the features observed in the living world. The structure of the eye has been cited as being so complex as to defy explanation in terms of development from simpler forms. However, four different species of mollusk illustrate stages of a continuum in eye development (see Figure 2.2). Extinction Extinction is the elimination of a species from Earth. The term is also used to describe elimination of a species from a particular area or ecosystem. Today, there is serious concern because human activities are causing the extinction of numerous species each year. Activities that destroy ecosystems or even just reduce their size cause loss of species. Some biologists estimate that human population pressure on natural ecosystems could eliminate 20% of Earth’s species over the next 25 or 30 years. The term biodiversity describes the taxonomic variation on Earth or in an ecosystem. The loss of species due to human activities eliminates adaptive information created by nature over eons. Many hope to protect against loss of biodiversity. Besides the moral motivation, there is also the utilitarian concern that lost species might have been useful, such as for drug development or to help control biological pests. Extinctions also occur naturally, of course. A species may become extinct because of competition or increased predation from another species. This could occur if the other species is one that is newly evolved or that has invaded the ecosystem from other locations. Such invasions are caused by geological and/or climatic changes such as land bridges that form between major islands and continents due to fluctuation sea levels, or elimination of a climatic barrier between, say, ecosystems separated by mountains or desert. Human importation of exotic species, intentional or not, produces a similar effect. The fossil record shows that a number of mass extinctions have occurred in the past. At the end of the Permian Period, some 250 million years ago, 96% of species, such as EVOLUTION 25 Figure 2.2 Development of the eye in mollusks: limpet, nautilus, scallop, octopus. (From Postlethwait and Hopson, 1995.) the trilobite, disappeared from the fossil record. Some 65 million years ago, at the end of the Cretaceous Period, known as the K-T boundary, as much as 76% of species disappear, including the dinosaurs. Recently, geologic evidence has established that this mass extinction was caused by a large meteorite or comet striking Earth at the Yucatan Peninsula in what today is Mexico. Shock waves traveling through Earth’s crust seem to have focused on the opposite point of the globe, southwest of India, causing massive volcanic outpourings. The impact plus the volcanism are thought to have sent dust and smoke into the atmosphere, darkening the sun, directly wiping out many ecosystems and reducing the primary productivity of the Earth (Chapter 14), starving many species into extinction. 26 BIOLOGY AS A WHOLE Mass extinctions seem to be followed by a period of accelerated evolution of new species. The elimination of dinosaurs, for example, paved the way for the further development of mammals. Human activities are currently being blamed for causing the extinction of great numbers of species, mostly by encroaching on their habitats. 2.4 TAXONOMY There are an estimated 50 million species on Earth. Of the 1.5 million species that have been named, about 5% are single-celled organisms (prokaryotes and eukaryotes), and plants and fungi make up about 22%. About 70% of the known species are animals. Most of these are invertebrates, especially insects, of which there are about 1 million known species.The earliest and, until this century, the most dominant activity in biology has been the classification of species. Aristotle was concerned with it. Even Charles Darwin, who started developing his theory of evolution while on the famous round-the-world voyage of the Beagle, was occupied primarily with collecting and categorizing new species of organisms. Why should environmental engineers and scientists study taxonomy? One reason is so they won’t be at a loss to see how any particular organism fits in with others. Does that worm always live where it is, or will it someday metamorphose into an insect and fly away, perhaps carrying biological or chemical contamination with it? At a more fundamental level, classification is a prerequisite to the identification of patterns, which leads to generalizations or hypotheses, and ultimately to tests of hypotheses by experiment or further observations. Thus, classification can be seen as a basis for the scientific method. The generalizations came later to biology than they did to physics and chemistry, perhaps owing to the dazzling variety of life and the inherent complexity of the underlying mechanisms. Taxonomy is the science of classification of organisms. Taxonomy (except for microorganisms) was a fairly settled area until recently. Now, genetic techniques are reopening old questions and revealing new things. The possibility that humans are causing a new mass extinction lends a new urgency to knowing the organisms that now exist on Earth. This loss in the diversity of life would have several potential consequences. From a utilitarian point of view, destruction of species results in a loss of genetic material that may include useful traits, such as production of chemicals that may have medical uses, or traits that may be useful for invigorating agricultural plants or animals. Ecological relationships may link the survival of one species to many others. Finally, it may be argued from several ethical viewpoints that we have a moral imperative to preserve Earth’s biological heritage regardless of actual or potential utility. Two ways to classify organisms are to group them (1) by structure and function or (2) by closeness of evolutionary descent. The two approaches often produce similar results, but not always. Convergent evolution can make dissimilar evolutionary branches form similar characteristics, whereas divergent evolution does the opposite. Barnacles and limpets both live in shells glued to rocks in the sea, but barnacles are arthropods, like crabs, whereas limpets are mollusks, like clams. The use of evolutionary descent was constrained in the past due to the incompleteness of the fossil record, resulting in ambiguity in classifying existing organisms. Recently, however, the development of genetic engineering techniques has led to quantitative measures of genetic similarity. These have settled old classification questions and even led to increased detail in classification by TAXONOMY 27 dividing old groups, forming new ones, and producing new species, phyla, and even kingdoms (see below). Biologists use the Linnaean system to classify organisms, which consists of a hierarchy of groupings and a naming convention. The lowest level of the hierarchy is the species. Similar species are grouped into a genus. The naming convention, called binomial nomenclature, assigns to each species a two-word name. The first word, which must be capitalized, is the name of the genus, and the second, which is uncapitalized, is the name of the species. For example, modern humans are in the genus Homo and the species sapiens; thus, they’re called Homo sapiens. Other species in our genus are extinct, such as Homo habilis. Genus and species names are either italicized or underlined when written, and the genus name may be abbreviated by a capitalized first initial once it has already been written out in full: H. sapiens. In increasing degrees of generality, the other classifications are family, order, class, phylum or division (in plants and fungi), kingdom, and domain. Each of these may sometimes be subdivided: for example, subkingdom, subphylum, or subspecies. The following phrase is a memory trick for the sequence from kingdom to species: King Kingdom Phillip Phylum came Class over from Order Family Greece Genus Saturday: Species The highest-level category is the domain. It is based on the type of cell comprising the organism, of which there are three: the bacteria, the archaeans, and the eukarya. Each domain is subdivided into kingdoms. Some biologists consider the archeans and the bacteria each to consist of only one kingdom. However, microbiologists note that molecular biology methods have shown that different groups of bacteria, for example, are more distinct from each other genetically than plants are from animals. Therefore, archaea have been divided into three kingdoms, bacteria into 15, and eukarya into four. Although this method of classification has not yet become universal among biologists, in this book we adopt this approach. One domain is that of the bacteria, also sometimes called eubacteria. Their cell type is the prokaryote, which is a simple type lacking any internal membrane structures. Their size is typically 0.2 to 2.0 micrometers (mm). Based on morphology (physical structure) and biochemical characteristics, the bacteria have classically been organized into 19 groups. Examples are Pseudomonas, a common soil bacterium that is also exploited in wastewater treatment processes; and the Cyanobacteria, or blue-green bacteria, important in the environment because they convert atmospheric nitrogen into a useful nutrient. Based on genetic techniques, new groups have been found and some of the older ones combined; one current classification system now has 15 high-level groupings. Another prokaryotic domain is that of the archaea, which includes three kingdoms. Archaea includes the methanogenic bacteria that produce methane gas in a wastewater treatment plant’s anaerobic digester. Archaeons were once considered to be bacteria. However, unsuccessful attempts to transfer genes from eubacteria to archaebacteria led to the discovery that their membranes, although structurally similar to the other domains, are chemically distinct. Many of the archaea are notable for the harsh chemical and physical environments in which they thrive. Because of this it is thought that archeons may be relics of the earliest forms of life that still exist today. The third domain is that of the eukarya, which comprises four kingdoms, including the familiar plants and animals. The cells of this domain are called eukaryotic. This is a more 28 BIOLOGY AS A WHOLE Domain Eukarya EUKARYOTES KINGDOM PLANTAE KINGDOM FUNGI KINGDOM ANIMALIA Dicots Monocots Ascomycota Gymnosperms Basidiomycota Seedless vascular plants Bryophytes Deuteromycota Multicellular algae Vertebrates Arthropods Annelids Molluscs Echinoderms Nematodes Flatworms Cnidarians Sponges Zygomycota KINGDOM PROTISTA Slime Molds Unicellular Algae Domain Bacteria FIFTEEN KINGDOMS Protozoans Domain Archaea THREE KINGDOMS PROKARYOTES Figure 2.3 The six kingdoms, according to one taxonomic approach. complex cell type that is characterized by internal membrane structures and membranebased organelles. Eukaryotic cells are much larger than prokaryotes; animal cells are typically about 20 mm across, and plant cells are about 35 mm. The next level of classification below kingdom is phylum (in animals) or division (in plants and fungi). Figure 2.3 summarizes the variety of life at the domain and kingdom level and shows some of the major phyla and divisions. Table 2.1 shows how several TABLE 2.1 Classification of Several Familiar Eukaryotes Kingdom Phylum Subphylum Class Order Family Genus Species Common name Animalia Chordata Vertebrata Mammalia Primates Pongidae Homo H. sapiens Human Animalia Chordata Vertebrata Mammalia Cetacea Mysticeti Balenoptera B. musculus Blue whale Animalia Arthropoda Uniramia Insecta Orthoptera Tettigoniidae Scudderia S. furcata Katydid Kingdom Division Subdivision Class Order Family Genus Species Common name Plantae Anthophyta Dicotyledones Sapindales Aceraceae Acer A. rubrum Red maple TAXONOMY 29 familiar organisms are classified according to this system. Biology does not have a central authority for determining how to organize animals into phyla. The classifications gain currency by general usage and adoption in textbooks. Species may be further subdivided into subspecies, strain (especially in prokaryotes), or cultivar (in crop plants). Formerly, the eukaryotic domain was considered to consist of only two kingdoms, plants and animals. Now it has been further subdivided to include fungi and protists. Several of these kingdoms are characterized based on their source of carbon. Autotrophs obtain their carbon from the inorganic form, in particular carbon dioxide. Heterotrophs are organisms that must obtain their carbon in the form of organic chemicals such as sugars, fats, or proteins. The fungi kingdom is defined to include the plantlike, mostly multicellular heterotrophic organisms lacking the green pigment chlorophyll. Fungal cells are surrounded by a rigid capsule called a cell wall. Fungal cell walls are made of a polymer called chitin. Fungi have a major ecological role in breaking down dead organisms and making their nutrients available to other organisms. Four divisions have been recognized: the ascomycetes include yeast, mildew, and the prized edibles morels and truffles; basidiomycetes include most of the common mushrooms; deuteromycetes include the mold that produces penicillin; zygomycetes include common black bread mold. Plants are multicellular photoautotrophs that reproduce sexually to form embryos (an early stage of multicellular development). Photoautotrophs are autotrophs that get their energy from light (as opposed to chemical sources of energy). Plant cells usually contain chloroplasts, which are organelles containing the chlorophyll. The cells of plants are surrounded by a cell wall composed largely of cellulose fibers. The major ecological role is the capture of light energy from the sun to fix atmospheric carbon dioxide and produce oxygen in the process called photosynthesis. This provides food for other organisms and oxygen for their respiration, the biochemical oxidation of organic matter to produce energy that is the opposite reaction to photosynthesis. The plant kingdom consists of 12 divisions: the bryophytes (mosses and relatives), four seedless vascular plants divisions (e.g., ferns), gymnosperms (including conifers), and anthophyta (also referred to as angiosperms, the flowering plants). Like the fungi, animals, are multicellular heterotrophic eukaryotes. In addition, they reproduce primarily by sexual reproduction, are motile in some part of their life cycle, and their cells lack a cell wall. There are 33 animal phyla, including several marine organisms, such as sponges, corals, and jellyfish; several phyla containing wormlike organisms; mollusks; arthropods (which include crustaceans and insects); and the chordates. The latter include the vertebrates, which are the organisms with an internal skeleton. Thus, we humans are chordates. All of the other animal phyla, plus a small group within the chordates, are called invertebrates. The remaining kingdom in domain eukarya is that of the protists. This kingdom somewhat arbitrarily combines single-celled eukaryotes that would otherwise be part of either the fungi, plant, or animal kingdoms. Thus, they are classified into three groups: animallike protists, or protozoans, which have four phyla, including those with paramecium and the amoeba; plantlike protists, with six divisions, euglena, dinoflagellates, diatoms, red algae, brown algae, and green algae; and funguslike protists, with three divisions, including slime molds. Each of these groups function ecologically in ways that are similar to their analogous multicellular kingdom. 30 BIOLOGY AS A WHOLE The six divisions of the plantlike protists are also called algae. Three of these divisions, the red algae, brown algae, and green algae, are dominated by multicellular forms. For example, kelp is a brown algae and sea lettuce is a green algae. For this reason, some textbooks place them in the plant kingdom. However, these divisions also include many unicellular forms. Many phytoplankton are green algae, including Chlamydomonas and a family called the desmids. In this book we adopt the convention of keeping them with the other algae in kingdom Protista, although in Chapter 10 their modern taxonomy is examined more closely. Plankton are very small aquatic or marine plants, animals or algae. Plant and algal plankton are referred to as phytoplankton, and animal plankton or animal-like protists are called zooplankton. Viruses, viroids, and prions are infectious agents not considered to be members of a living kingdom. They do not have a cytoplasm or cell membrane and are not capable of any metabolic reactions within their own structure. They reproduce by infecting living cells and causing them to produce more of the infectious particles. The resulting damage is responsible for many diseases. They may be more properly considered to be chemical agents. Viruses are the largest and most complex, being a geometrical particle of DNA or RNA (the chemical agents of heredity), and surrounded by protein. They may be 1/1000 to 1/10,000 the size of prokaryotic cells. An important medical distinction between viruses and bacteria, which also cause disease in humans, is that since viruses do not metabolize, virus diseases cannot be treated by antibiotics, which act by killing or otherwise preventing the reproduction of microbes. However, viruses can often be prevented by vaccines, which stimulate the human immune system to destroy the virus particles within the body. Viroids are even simpler than viruses, consisting of a single RNA molecule. They have been found to cause some crop diseases. Prions are similar in that they consist of a single molecule; however, in this case the molecule is a protein. They are poorly understood. Prions are suspected causes of several serious neurological diseases in humans and animals, including scrapie in sheep, bovine spongiform encephalopathy in cows (mad cow disease), and Creutzfeldt–Jakob disease and kuru in humans. They are remarkable in that they may be the only biological agent that reproduces yet does not have DNA or RNA, the chemical basis of heredity. 2.5 INTERACTION OF LIVING THINGS WITH THE ENVIRONMENT Living things don’t just live in the environment: To a great extent they create it. Photosynthetic plants and microorganisms are responsible for our atmosphere consisting of 21% oxygen and having only trace levels of carbon dioxide. Without them the atmosphere would more closely resemble that of the primitive Earth, which was composed of carbon dioxide, nitrogen, water vapor, hydrogen sulfide, and traces of methane and ammonia. It is not only chemical changes that are wrought, but also physical ones, from the temperature of Earth to the form of our landscape. The temperature of Earth’s surface is strongly affected by plants’ ability to remove carbon dioxide, a greenhouse gas that prevents radiation of heat energy from Earth into space. Bacteria in the gut of termites have been found to be responsible for the release of methane gas, another greenhouse gas, into our atmosphere. Trees, grasses, and other plants reduce soil erosion, affecting the shape of the landscape. INTERACTION OF LIVING THINGS WITH THE ENVIRONMENT 31 The two-way relationship between the all the living things on Earth and the physical environment has been recognized in the Gaia hypothesis, put forward by the English scientist James Lovelock (1987). His statement of the hypothesis is: ‘‘The biosphere is a self-regulating entity with the capacity to keep our planet healthy by controlling the chemical and physical environment.’’ Lovelock is also known for another important contribution to environmental protection. He is the inventor of the electron capture detector, used in gas chromatographs to analyze for organics containing halogens or oxygen with exceptional sensitivity. By revealing the fate and transport of minute chemical quantities such as pesticides, this device can take some credit for stimulating the environmental revolution. Lovelock illustrated the Gaia hypothesis with a computer model that demonstrated how organisms could control the environment to their advantage. In a model he called Daisyworld, he postulates a planet like Earth receiving energy from the sun and covered with two species of daisy, one light-colored and the other dark (see Figure 2.4). Both species had an optimum temperature for growth, with the light daisy’s optimum higher than that of the dark daisies. He then simulated the system and varied the amount of energy radiated by the sun. The simulation showed that when the energy input increased, raising the temperature, the population of light daisies would increase and the dark would decrease. This increases the planet’s albedo, the fraction of incident energy that is reflected back into space. By reflecting more energy, the temperature of the surface is prevented from increasing as much as it would otherwise. At lower incident radiation, the cooler temperatures would favor dark daisies that decrease the albedo. Without the organisms, the surface temperature increases smoothly as radiation increases. With the daisies present, as radiation is increased, the temperature first increases, then forms a plateau within which the organisms stabilize the system. As evidence for the Gaia hypothesis, Lovelock cites the fact that Earth’s atmosphere is far from equilibrium. Without organisms to maintain it, he says that the nitrogen and oxygen would eventually combine to form nitrates, which would dissolve in the oceans, leaving an atmosphere consisting mostly of CO2, like that of Mars. More light daisies More dark daisies Temperature Optimum temperature for light daisies Optimum temperature for dark daisies Stabilized temperature range Intensity of solar radiation Figure 2.4 Temperature vs. radiation intensity for Daisyworld. The dashed line shows the global temperature in the absence of the two daisy populations. The solid line shows how temperature would vary with their influence included. 32 BIOLOGY AS A WHOLE Individual organisms employ control mechanisms to regulate their internal environments, such as body temperature or blood chemistry in mammals. Because of this similarity, some have extended the Gaia concept to mean that Earth itself is a living organism, rather than saying that it is like one. This has created controversy for the hypothesis, but it is not part of Lovelock’s conception. Although suggestive, Daisyworld is not proof of the Gaia hypothesis. Proof awaits stronger evidence that such feedback mechanisms actually operate on Earth. Although the self-regulating nature of Earth’s ecosystem as a whole remains to be proven, there are many examples of environmental conditions that are caused by biological activity, some of which involve self-regulation. Some examples include the cycling of minerals and elements in the environment, the formation of soil, and the control of pH in anaerobic digestion. Biogeochemical cycles describe the various reservoirs for an element, and the reactions and transformations that convert the matter from one reservoir to another. For example, the major reservoirs for carbon are atmospheric CO2, aquatic or marine CO2, the biosphere (in the form of living or dead biological material), and the lithosphere (solid minerals, i.e., rocks or soil) as carbonate rocks or as fossil carbon (coal, oil, or natural gas). The cycles can be described quantitatively in terms of the amount in each reservoir and the rate of each reaction. Look ahead to Figure 14.5 to see that most of Earth’s carbon is stored in carbonate rocks such as those that form the Rocky Mountains. It is interesting to realize that the Rockies and similar mountain chains worldwide are formed entirely from biological activity, by the gradual accumulation of the skeletons of microscopic plants in sediments on the ocean floor, followed by geological upheavals. Biogeochemical cycles are a starting point for the analysis of the effect of humans on the environment. Since the heat-trapping effect of atmospheric CO2 and methane are a serious concern, it is important to understand the rate of anthropogenic (human-caused) emissions of these gases and the rates at which they are naturally removed. Such an analysis has led to the conclusion that half of the CO2 released by combustion of fossil fuel since the beginning of the Industrial Revolution remains in the atmosphere. It is thought that the ocean has absorbed the remainder. The details of biogeochemical cycles are discussed in Chapter 13 and Section 14.2. Soils may be formed abiotically, but the result is very different when mediated by living things. First, the rate at which rocks are broken down into soil can be accelerated by the action of acids produced by lichens (an association of fungus and algae) and by mechanical effects of the roots of plants, which can widen cracks in rocks, exposing more surface area to weathering. Plants prevent the soil from eroding by absorbing moisture and by the action of their root structure. Dead plant matter is degraded by fungi and bacteria to form humic substances. These are complex polymeric phenolic compounds that resist further biodegradation. Their presence enhances soil water–holding capability and makes it more friable (easy to crumble), which makes it easier for roots to penetrate. Humic substances also enhance the ability of soils to adsorb organic pollutants. Insects and other invertebrates, especially earthworms, aerate and mix the upper soil. Charles Darwin’s major preoccupation in the years after he published The Origin of Species was a detailed study of how earthworms affect the soil, especially by moving soil continually from the depths to the surface. Microorganisms in the soil and associated with the roots of plants convert atmospheric nitrogen to a form available to plants, effectively producing a fertilizer in place. These changes are both caused by organisms and benefit them. BRIEF HISTORY OF LIFE 33 Anaerobic digestion, an environmental engineering process used to biodegrade concentrated slurries of biomass, provides another good example of organism–environment interaction. Here, the pH is controlled by a delicate balance between two populations of microorganisms. The acidogens break down organics into simple volatile fatty acids such as acetic and propionic acids. This consumes alkalinity. The methanogens use the acids to make methane, restoring the alkalinity. The methanogens are more sensitive to environmental changes, including pH, than the eubacterial acidogens. Should some disturbance affect the methanogens adversely, the acid generation can cause a pH drop, further slowing acid destruction and causing a cessation of methane formation from which it is difficult for the system to recover. This is similar to Daisyworld, where the organisms control their environment until conditions are forced outside the range in which control can occur, and the system becomes unstable. 2.6 BRIEF HISTORY OF LIFE With the overview of the types of living things and the mechanisms by which they evolve, as given above, let us take a brief look at the changes that have occurred in the biology of Earth. One of the biggest questions is: How did life originate from prebiotic conditions? After the formation of Earth and the cooling of its crust, the atmosphere consisted mostly of water vapor, carbon dioxide, carbon monoxide, and N2. The dominant theory derives from the ideas of Haldane and Oparin, early twentieth-century biochemists. It holds that energy from sunlight, lightning, and volcanic action gradually formed simple organic molecules from these precursors. In the 1950s, Urey and Miller conducted famous experiments that proved that this could occur. They passed spark discharges through similar TABLE 2.2 Timeline for Life on Earth Million Years Ago 4,600 3,800 3,000 1,000 570 405 225 135 65 40 4 2 Years Ago 30,000 5,000 146 52 8 Event Earth forms. Life begins. Prokaryotes appear. Eukaryotes appear. Algae and marine invertebrates (e.g., trilobites) dominate. Terrestrial plants and vertebrates appear. Dinosaurs appear. Flowering plants appear. Mass extinction, including dinosaurs and up to 70% of all animal species. Mammals begin to dominate. Primates appear. Hominids appear. Genus Homo appears. Homo sapiens neanderthalis disappears. H. sapiens sapiens appears. Development of agriculture. Publication of The Origin of Species (1859). Discovery of DNA structure (1953). Cloning of mammals (1997). 34 BIOLOGY AS A WHOLE primitive atmospheres in a sealed glass apparatus and produced aldehydes, carboxylic acids, and most important, amino acids, the building blocks of proteins. In the absense of life on early Earth, these compounds could accumulate until the seas consisted of primordial soup. These compounds could be further concentrated in drying coastal ponds or at hot springs. Experiments have shown that under realistic conditions, polymeric macromolecules could be formed. Other steps along the way to a viable self-replicating cell have been reproduced, but many critical steps have not. Overall, the process is still a mystery. However the origin occurred, the fossil record shows that life developed in complexity continuously (Table 2.2). Humans are a very recent addition. Notice how long the dinosaurs were on Earth relative to our tenure here. PROBLEMS 2.1. Consider a toxic pollutant such as gasoline, the dry-cleaning solvent perchloroethylene, the heavy metal mercury, or the pesticide DDT. Can you think of ways in which the pollutant might have some effect at each level of the biological hierarchy from metabolism to ecosystem? 2.2. How are ecosystem and environment distinguished from each other? Note that these two terms are often confused by the public. 2.3. How could anthropogenic effects change the course of evolution? 2.4. Can you think of some pollutants that have different effects on different biological kingdoms? How will these effects differ from each other? 2.5. All of the following have been used for biological waste treatment: bacteria, cyanobacter, green algae, fungi, green aquatic plants, earthworms. Try to think of how each could be used, and for what type of waste each would be applicable. 2.6. Think about how you would create a model like Daisyworld. What laws and relationships would you use? 2.7. Assuming that the Gaia hypothesis were true, which of the criteria for life does Earth’s ecosystem as a whole satisfy, and which does it not satisfy?