Outline and Chapter notes to accompany chapter 4 EVOLUTION AND CLASSIFICATION Jan., 2001 A. THE DARWINIAN PARADIGM REORGANIZED BIOLOGICAL THOUGHT PRE-DARWINIAN THOUGHT: THE SCALE OF BEING (Scala Naturae): Originally a non-evolutionary hierarchy of static, unchanging perfection People were on top, animals below them, plants below animals; theological versions had angels above people. Among people, racist, sexist, and class-based ideologies put Europeans above other races, men above women, masters above slaves (as in Aristotle), and upper castes or classes above lower ones. People who were listed at lower levels were taught to accept their position as "natural" and unchangeable. Continuity of the scale was stressed, e.g., by Alexander Pope. Discoveries of the Renaissance and later centuries seemed to confirm the continuum because all newly discovered species could be made to fit into it somewhere. Gaps were explained by saying that new discoveries would fill them in. LAMARCK: Made the chain of being into a moving escalator which he called Nature's Parade (La Marche de la Nature). The lowest forms of life, such as bacteria, would form by spontaneous generation from lifeless matter, and each species would slowly change (i.e., evolve) into the next higher species on the scale, culminating in humans. In order to account for local adaptation to the environment, Lamarck added as a secondary mechanism the Use and Disuse hypothesis: use would strengthen and enlarge any organ, while disuse would weaken an organ and allow it to atrophy. Lamarck did not realize that such ACQUIRED CHARACTERISTICS would not be inherited (it was commonly assumed in his day that they would be; non-inheritance of acquired characteristics was demonstrated in the 1870s by Weismann). Whenever ADAPTATION was discovered, Lamarck attributed it to the effects of use and disuse under each individual's voluntary control. Other French writers (Geoffroy, de Maupertius, Buffon) also stressed local adaptation to the environment, though sometimes by different mechanisms. WILLIAM PALEY AND NATURAL THEOLOGY: A British clergyman, Rev. William Paley, attributed all ADAPTATIONS to divine benevolence. He even used the intricacy of adaptations as evidence that they had been consciously designed by a mind more powerful than our own: "design must have a designer, that designer must [be] ... God." Paley's ideas were the dominant theory in England during the early nineteenth century. THE DEVELOPMENT OF DARWIN'S IDEAS Darwin's ideas were formulated principally during the voyage of H.M.S. Beagle. Darwin saw many tropical habitats much richer in species than those he knew. He noticed that the same habitat often produced different species on different continents: the savannahs (grasslands) of East Africa and the pampas (grasslands) of Argentina have almost no species in common. This is contrary to Lamarck's and similar theories of environmental determinism. He also noticed that the closest relatives of animals were often found elsewhere on the same continent but in different habitats: the same group of South American rodents (the Caviomorpha, or guinea pig group) inhabited South American forests (but not African forests), South American plains, South American mountain regions, and so on. In other words, geography was more important than habitat in determining relationships (Fig. 4.1). He noticed that islands (like the Galapagos) always had inhabitants whose nearest relatives were on the nearest continent. For example, the Galapagos Islands had birds and plants related to those of South America, while the Cape Verde Islands (volcanic, geologically similar to the Galapagos) had species related to those of Africa and unlike those of the Galapagos. Also, nearby islands often had distinct but related species, as if they were descendants of a few original colonists (Fig. 4.2). He noticed the absence of frogs and other amphibians on oceanic islands. In a few places, where humans had introduced them, amphibians flourished, meaning that the habitat was quite suited to them. Neither Lamarck's theory nor Paley's could explain why the environment (Lamarck) or God (Paley) had not produced amphibians on these islands, but Darwin said that they could never arrive as colonists across salt water. NATURAL SELECTION: Upon return to England, Darwin began studying the methods of animal breeders who had changed many domesticated species in the preceding 100 years or so. They had done so by always selecting the best of their flocks or breeds, a practice called ARTIFICIAL SELECTION. Darwin also read the works of the economist Malthus, who convinced Darwin that populations tend to overreproduce and overreach the available resources, only to be held in check by starvation, predation, and similar forces. From these ideas, he concluded that a continual "struggle for existence" (metaphorical) always exists in nature, not usually including actual combat, but, "what is more important, success in leaving progeny". Darwin concluded that the struggle for existence brings about NATURAL SELECTION by a process similar to artificial selection among domestic species. Natural variation occurs in both natural and domesticated species. Variations that lessen the ability to survive and reproduce will not be passed on to future generations; variations that increase the ability to survive and reproduce will be passed on; this difference in the contributions to future generations is called NATURAL SELECTION. NATURAL SELECTION DEFINED: Consistent differences in the relative contribution of different genotypes to future generations. Agents of selection can include predators, diseases, environmental extremes, ability to obtain food, and potential mates (of the opposite sex). Selection by potential mates is called SEXUAL SELECTION. FITNESS DEFINED: The relative number of viable offspring left by each genotype. Natural selection can explain MIMICRY while earlier theories could not: many species survive because they resemble other, unrelated species that predators avoid. Selection by the predators perpetuates the best mimics and eliminates the less effective ones (Fig. 4.3). Example: Industrial melanism among moths demonstrates natural selection at work (Fig. 4.4): The frequency of dark-colored moths varies geographically with levels of soot pollution. Experiments with bird predators confirms that predators eat the non-camouflaged moths much more often than those which resemble their background. Darwin's theory became accepted because it explained the available evidence better than any previous theory. BRANCHING DESCENT WITH MODIFICATION Darwin's was not the first evolutionary theory, but it was the first that emphasized BRANCHING descent (in treelike patterns), which Darwin called "descent with modification". Descent with modification explained the facts of geographic distribution much better than any previous theory. The theory also explained HOMOLOGIES (Fig. 4.5), structures which resembled one another in their construction among related species, despite differences in adaptive use in many cases; earlier theories could not explain homologies so well. Some homologies include embryonic characters, others include functionless VESTIGIAL organs. Descent with modification also explained why classifications should consist of "groups within groups": families of related species, orders and classes made of related families, etc. (Fig. 4.6). Darwin's theory also explained CONVERGENT resemblances reflecting similar adaptations (ANALOGIES). Again, Darwin's theory was accepted because it explained the known facts better than all previous theories. The Darwinian paradigm was very productive of other research. For example, it stimulated Haeckel's theory of RECAPITULATION, which claimed a resemblance between embryos and ancestors. Although most of this theory was later rejected, it did stimulate many decades of careful research in embryology. FOSSILS AND THE FOSSIL RECORD The fossil record was poorly known in Darwin's time. Fossils discovered since Darwin wrote have in most cases fit well into branching patterns of descent with modification. The ages of fossils are determined by both relative and absolute dating methods (Figs. 4.7, 4.8). As an example: mollusks of the class Cephalopoda (squids, octopus, extinct ammonites, etc.) all fit into a pattern of branching descent shown in Box 4.1, and their shared adaptations and anatomical features are all consistent with this pattern of descent. B. CREATIONISTS CHALLENGE EVOLUTIONARY THOUGHT CREATIONISM AND DARWIN'S RESPONSE Most scientists before Darwin's time were devout (many were clergymen) and most believed that living species had been created by God. The many scientific allies of Rev. William Paley believed in the theory of SPECIAL CREATION, under which each species was the result of a separate ("special") divine act of creation. Rev. Paley and his supporters all used scientific methods, not biblical quotations, to support their claims. Foremost among their claims were adaptations so perfect in every detail that they said only God could have made them. Darwin and his supporters argued against Paley's theory by showing: * Adaptations seemingly limited by inherited patterns; such patterns would not constrain an omnipotent God. * Geographic distributions limited by opportunity to migrate; an omnipotent God would not be subject to such limitations. * Mimicry, a form of deceptive resemblance that always imitated a species living in the same area but never far away. EARLY TWENTIETH CENTURY CREATIONISM Afraid that the teaching of evolution was eroding people's faith in divine creation and in religious faith generally, a creationist movement sought to outlaw the teaching of evolution in many parts of the United States. Most supporters of this creationist movement were U.S. Protestants who called themselves Fundamentalists. In 1925, John Scopes was convicted in a Tennessee court for teaching evolution in violation of a state law. The law remained on the books until many decades later. CREATIONISM TODAY Since about 1960, creationists have changed tactics by insisting only that creationism be taught side by side with evolution and be given "equal time". Religious concepts and quotations from the Bible pervade their writings. Leading creationist writers have proclaimed the Bible to be an infallible guide that is not subject to falsification. Arkansas public law 590, providing "Balanced Treatment" for "Evolution Science" and "Creation Science", was declared unconstitutional in 1981, as was a similar Louisiana law a few years later. C. SPECIES ARE CENTRAL TO THE MODERN EVOLUTIONARY PARADIGM POPULATIONS AND SPECIES A POPULATION consists of all members of a species inhabiting a given location. A population can also be defined as all individuals that freely interbreed with one another in nature. SPECIES are defined as reproductively isolated groups of naturally interbreeding populations. REPRODUCTIVE ISOLATION consists of all biological mechanisms (not mere geographical separation) that prevent the interbreeding of natural populations. REPRODUCTIVE ISOLATING MECHANISMS (Box 4.2) can act either before or after mating. Premating isolating mechanisms include isolation by differences in ecology, differences in mating seasons, differences in behavior, and differences which prevent sexual parts from fitting together. Postmating mechanisms include the inviability of gametes, of fertilized eggs, of embryos or larval stages, or hybrid inviability, hybrid sterility, or F2 breakdown. HOW NEW SPECIES ORIGINATE Most new species originate after a period of geographic separation by an extrinsic barrier. If the barrier lasts long enough for the populations on either side to diverge, then one or more reproductive isolating mechanisms will result (Fig. 4.9). Evidence to support the geographic theory of speciation comes from many cases where intermediate stages in the process can be observed, and especially from cases of incomplete speciation in which once disconnected populations were brought back together before reproductive isolation between them had been completed (Fig. 4.10). Plants sometimes undergo speciation by POLYPLOIDY, a sudden change in chromosome number, which results in speciation when it reproductively isolates them. Other mechanisms of speciation are controversial, and even their supporters concede that these other mechanisms cover only a small fraction of cases. HIGHER TAXA Grouping organisms in formal ways based on data is called CLASSIFICATION. Any of the groupings are called TAXA, and the hypothesis testing which includes the defining of these taxa is called TAXONOMY. Related species are grouped into GENERA (singular: genus), related genera into FAMILIES, related families into ORDERS, related orders into CLASSES, related classes into PHYLA, and related phyla into KINGDOMS. Any one of these groups is called a TAXON. Additional levels are occasionally used, e.g.: subphylum, suborder, and superfamily. Levels among higher taxa are based on interpretations of data and are thus somewhat arbitrary: what one expert calls a class may be only a subclass to another expert. D. LIFE ORIGINATED ON EARTH BY NATURAL PROCESSES OPARIN AND MILLER Louis Pasteur demonstrated that bacteria did not originate by spontaneous generation. Alexander Oparin hypothesized that life originated on the early Earth under a REDUCING ATMOSPHERE containing ammonia, methane, water vapor, and hydrogen. Stanley Miller tested Oparin's ideas experimentally and showed that organic compounds could originate under sterile conditions from Oparin's mix of gases (Fig. 4.11). Subsequent experiments have showed that many other gas mixtures will also work. We now think that organic matter originated in this way, and that simple, self-replicating systems originated when organic matter reached a certain level of complexity. EVIDENCE OF EARLY LIFE ON EARTH Meteorites contain many organic chemicals that we believe were formed without life by processes similar to those in Miller's experiment. The earliest known rocks on Earth show evidence that they were formed under a reducing atmosphere in which no oxygen was present. Many of these early rocks contain fossils. Petroleum deposits and other chemical fossils include the breakdown products of complex molecules like chlorophyll. Chlorophyll breakdown products were absent in the earliest rocks, but accumulated gradually over the time during which the atmosphere changed. We now believe that our present oxygen-rich atmosphere was built up slowly by photosynthetic action over a period of about half a billion years. Both the atmosphere and the process of photosynthesis have evolved along with life itself. PROCARYOTIC AND EUCARYOTIC CELLS The earliest cells were PROCARYOTIC, resembling those of present- day simple bacteria (Box 4.3). Bacterial and other procaryotic cells have only a single unpaired chromosome (containing DNA but no protein) and no internal membrane-limited ORGANELLES. The chromosomal DNA of procaryotic cells is not enclosed in a well-defined nucleus. EUCARYOTIC CELLS contain protein in their chromosomes, which are usually multiple in number and diploid during at least some portion of the life cycle. They also contain large numbers of membrane-limited ORGANELLES: mitochondria, endoplasmic reticulum, golgi apparatus, vacuoles, lysosomes, and (in plants) plastids. The chromosomes of eucaryotic cells are contained in a well-defined nucleus which is enclosed in a nuclear envelope. In 1970, Lynn Margulis proposed a theory of the origin of eucaryotic cells by ENDOSYMBIOSIS: large procaryotic cells became eucaryotic by engulfing smaller procaryotic cells and maintaining them inside without digesting them. The smaller procaryotes became organelles, bounded by membranes which were originally plasma membranes of the smaller cells. Evidence for this theory includes the fact that both chloroplasts and mitochondria contain their own DNA that resembles procaryotic DNA and differs from the DNA in the nuclei of eucaryotic cells. KINGDOMS OF ORGANISMS (See also Classification on Web site) Since 1970, most biologists have recognized these five kingdoms of organisms: EUBACTERIA: Bacteria and blue-green Cyanobacteria (procaryotic) PROTISTA: Simple eucaryotic organisms such as Protozoa (eucaryotic) MYCOTA: Fungi, characterized by absorptive nutrition (eucaryotic) PLANTAE: Plants, containing plastids (eucaryotic) ANIMALIA: Animals, usually containing motile, multicellular life stages (eucaryotic). The discovery of ARCHAEBACTERIA, a very primitive group of procaryotic organisms, has added a sixth kingdom. Boundaries between these kingdoms, especially between plants and protists, are drawn differently by different experts, depending on their different interpretations of the available data. E. EUCARYOTIC DIVERSITY DOMINATES LIFE TODAY KINGDOM PROTISTA Includes single-celled eucaryotic organisms that lack the specializations of other eucaryotic kingdoms. Different Protista are distinguished by their means of locomotion and in some cases by their means of reproduction. Some experts include algae among the Protista. KINGDOM PLANTAE Includes photosynthetic organisms possessing plastids. Subkingdom Thallophyta includes simple plants (algae) lacking differentiated organs and having eggs not protected by nonreproductive cells. Most algae are aquatic. Subkingdom Embryophyta includes plants whose eggs are surrounded by nonreproductive cells, forming an embryo. Most live on land. Bryophyta includes mosses and liverworts, which lack vascular tissues capable of efficiently transporting materials. Tracheophyta or vascular plants are those possessing vascular tissues capable of efficiently transporting materials from one part of the plant to another, thus allowing different parts of the plant to specialize into different organs. The simplest vascular plants do not possess seeds. Seeds are reproductive structures in which the plant embryo and some food reserves are enclosed in several protective layers. The most advanced vascular plants are he flowering plants or angiosperms (division Anthophyta). KINGDOM MYCOTA Includes fungi, characterized by absorptive nutrition. Most fungi have threadlike filaments called hyphae, and most reproduce using spores. KINGDOM ANIMALIA Includes multicellular organisms that develop from a hollow ball of cells called a blastula. Most animals are motile at some life stage. Sponges (phylum Porifera) are simple animals without tissues. Most animals are differentiated into tissues, consisting in the simplest cases of an outer layer (ectoderm) and an inner layer (endoderm). Many animals also have a middle layer (mesoderm). Phylum Cnidaria contains jellyfish and other animals with just two tissue layers (ectoderm and endoderm). Phylum Platyhelminthes (flatworms) contains animals with three tissue layers (ectoderm, mesoderm, and endoderm) but no body cavities. Animals more complex than the Platyhelminthes all possess body cavities. A body cavity surrounded entirely by mesoderm is called a coelom. A body cavity containing other tissue layers in its lining is called a pseudocoel. Most animals with body cavities also have a digestive system with an entrance (mouth) at one end and an exit (anus) at the other end. Annelid worms (phylum Annelida) and arthropods (phylum Arthropoda) have bodies divided into a series of segments. The Arthropoda, including the shrimp, lobsters, spiders, mites, and insects, are the largest phylum by far, including over three fourths of the whole animal kingdom. The phylum Chordata, to which we belong, is characterized by a stiff notochord, gill slits, and a dorsal, hollow nerve cord at some stage of development. Most Chordata also have a backbone and are called vertebrates. Vertebrates include fishes, amphibians, reptiles, birds, and mammals. F. HUMANS ARE PRODUCTS OF EVOLUTION Humans all belong to the kingdom Animalia, the phylum Chordata, and the class Mammalia. Mammals maintain a steady internal body temperatures (usually above that of their surroundings) with the help of insulation (usually hair or fur). All mammals provide parental care and nurse their young with milk. Among the mammals, humans, apes, monkeys, and lemurs belong to the order Primates. Primates show many anatomical and behavioral adaptations to life in trees, such as grasping hands and feet, good depth perception, and a prolonged period of spatial learning associated with high intelligence and extensive parental care. Among primates, humans are distinguisted from apes by upright locomotion (bipedal walking). THE GENUS AUSTRALOPITHECUS Most fossils of Australopithecus come from South Africa or East Africa. A few specimens come from elsewhere, including Java (in Indonesia). Both large and small Australopithecus are known. Small, early species include A. anamensis, A. afarensis, and Ardipithecus ramidus (now put in a genus by itself). The best-known small species is the late-appearing A. africanus of South Africa. Larger ("robust") species include A. robustus in South Africa and A. boisei in East Africa. Anatomical study of the feet, pelvis, and lower vertebral column shows that Australopithecus walked erect and bipedally. Footprints at Laetoli, Kenya confirm this. Stone tools and many more tools made of bones and teeth were fashioned by hand. Many tools were used as weapons. Hunting seems to have been cooperative, which implies some language or communication. THE GENUS HOMO Homo habilis was a contemporary of later Australopithecus. It was small, but it brain was proportionately larger than that of a comparably sized Australopithecus would have been. Homo erectus was widespread across Africa, Asia, and much of Europe. Its brain size was larger than that of Australopithecus. There is evidence of the use of fire. Homo sapiens came after (and evolved from) Homo erectus. Homo sapiens had larger brains than Homo erectus, especially in the vertical dimension. Stone tools were mounted on shafts to make spears, and larger animals were hunted. Cave paintings show artistic sophistication and religious rituals. EVOLUTION AS AN ONGOING PROCESS CONTINUING EVOLUTION WITHIN SPECIES There is good evidence that evolution continues to take place. Natural selection brings about seasonal fluctuations in the characteristics of fruit flies and Galapagos finches. CULTURAL CHANGE AND BIOLOGICAL EVOLUTION Agriculture presented humans with new selection forces: new foods, new needs, new diseases (and an increase in many old ones). Malaria, tuberculosis, and many other infectious diseases were able to spread more rapidly in larger, settled populations than they did when populations were sparse. Industrial society presents new hazards and thus new forces of natural selection: motor vehicle accidents and industrial accidents, greater availability of alcohol and other drugs, pollution hazards, etc. Migrations across great distances often brings populations into contact that had been adapted to different environments. This prevents speciation and enriches our pool of genes. CONTINUED BIOLOGICAL EVOLUTION IN HUMANS Evolution continues to take place wherever natural selection occurs, meaning whenever mortality differs according to genotype or phenotype. Examples include: higher mortality among low birth weight babies (even with good hospitals), higher susceptibility of certain blood groups to epidemic diseases, higher incidence of certain cancers in people with certain genotypes, and so on. People continue to die from genetically controlled diseases. Even many traits that allow people to live a life of many decades may result in decreased fitness: diabetics and chondrodystrophic dwarfs leave fewer offspring (on average) than their non-affected siblings. INTERACTION BETWEEN CULTURAL AND BIOLOGICAL EVOLUTION: Cultural evolution often modifies biological evolution. Some biological abilities are less crucial for survival than they once were: poor eyesight can be corrected with glasses, for instance. The ability to survive starvation periods is now less important in most parts of the world, and may even predispose people to diabetes. Other abilities have become more important in survival: the ability to read danger signs, to drive safely, or to avoid excessive alcohol and other drugs. ---------------------------------- Jan., 2001