UNCG Biology 105 Study Guide, Part III

This outline of topics is designed to help students in Dr. O’Hara’s section of Biology 105 follow the main points made in the class. It is not a comprehensive presentation of all the course material; instead it is an outline that will help you keep the course structure and main points in mind. In studying for exams you should study your lecture notes, the syllabus, the poems-of-the-week, the assigned parts of the texts (including the Peabody Park website), and the species particularly described in class.

This section of the study guide (Part III) covers the final third of the course. The third exam will have 50 questions; 5 will be drawn from the material in the first two-thirds of the course, while the remaining 45 will come from material in this final third. (In other words, 10% of the exam will be cumulative.) Remember that 5% of your final grade for the whole course will be based on your writing down from memory the Darwin paragraph we have been practicing at the beginning of class all term. That will be part of the third exam.

Poems-of-the-Week

• Richard Eberhart, “The Groundhog”
• Robert Frost, “Design”
• Emily Dickinson, “How many flowers fail in wood”
• Alfred Tennyson, In Memoriam (part)
• Edgar Allan Poe, “To Science”
• George Wither, “When I behold the havocke and the spoyle”

Decomposition

The earth is a natural recycling system. It has to be, because it is a closed matter system. No new matter is being added to the earth, so any new things (such as organisms) must be made from matter already here, including carbon, oxygen, hydrogen, nitrogen, phosphorus, calcium, potassium, and other chemical elements. (Recall that there are about 100 different chemical elements in nature; they combine to form molecules. A water molecule, for example, is made up of two atoms of the element hydrogen (H) and one atom of the element oxygen (O). Living things are mostly made up of only a dozen or so of these elements, with very tiny amounts of a few others.) Energy from the sun is new every day and drives living things, but the matter is all old and must be continually recycled. Although it is a closed matter system, the earth is thus an open energy system. Where are the dinosaurs today? Where are all the living things that have ever existed? In a manner of speaking, they are all still here: they have just been disassembled. Assembly is growth. Disassembly is decomposition.

Soil is where much of this decomposition takes place. When an organism dies, its parts get recycled into the soil and from there they may be assembled into parts of new organisms. (Someone once defined “soil” as “the temporary repository for the atoms of decomposed plants and animals.”) Components of the air and water also are incorporated into the bodies of living things: the carbon in plants, for example, comes from carbon dioxide in the air.

Some organisms are producers: mainly the green plants, which produce their own food through the direct use of the sun’s energy. Other organisms are consumers: mainly animals, which do not produce their own food, but have to consume the bodies of other organisms to get energy. Still other organisms are decomposers: primarily the fungi and bacteria, which chemically break down the bodies of organisms and derive their food that way. (You can think of them as consumers of dead bodies.)

Fungi are very diverse and are found throughout the world, and are one of the principal agents of decomposition. Many familiar types can be found on campus: gilled mushrooms, pore mushrooms, bracket fungi, puffballs, and others. Fungi are neither plants nor animals; they are a distinct group that reproduce by means of dustlike spores.

A “mushroom” is just the reproductive structure of a fungus. The body of the fungus is made up of a diffuse network of tissue called mycelium that typically grows under ground or in the body of a decaying organism (a dead tree trunk for example). If you peel back the bark of a rotting log you may see a cottony, white material growing there—that is the mycelium of a fungus. The mycelium is made up of many individual strands or hyphae (singular, hypha) twined together like a net. The hyphae grow into the decaying material, secrete digestive chemicals, and absorb nutrients directly.

Mycorrhizal fungi have special symbiotic relationships with the roots of living trees, whereby the fungal hyphae provide nutrition to the tree, and vice versa.

In addition to fungi, the soil contains millions of bacteria which are also essential to chemical decomposition.

When deciduous trees drop their leaves in the fall, the process of leaf decomposition begins on the forest floor. The leaves of different species decompose at different rates depending upon their chemical composition. Eventually the atoms making up the leaves are returned to the soil: nitrogen, phosphorus, potassium, calcium, and others important to life.

Soil is produced very slowly; perhaps one inch per 100 years. Soil has been badly eroded in many parts of the world. The “dustbowl” of the 1930s in the United States was caused by soil erosion from plowed fields. Loss of soil and soil nutrients is a serious problem for agriculture around the world.

Many species of small animals live in the soil, and contribute especially to mechanical decomposition (as well as chemical decomposition through digestion). Among these are slugs and snails (which are mollusks), earthworms, isopods, millipedes, centipedes, spiders and mites, ants and termites, roundworms, and many others.

It is possible to trace any particular chemical nutrient (such as carbon) as it cycles through the environment, and we traced the carbon cycle in class from carbon in the air, to the green plants that take it up, to the animals that consume the green plants, to the decomposers that may release it again into the air. Some of the chemical components of organisms may get locked away under ground for a very long time, however, and are essentially removed from this routine recycling system. Carbon from the air that is incorporated into a plant may become buried and fossilized for millions of years; that is what coal and oil are. When we burn those “fossil fuels” we are releasing back into the atmosphere carbon that has been locked away for millions of years. Since the industrial revolution in the 1800s humans have released millions of years of stored carbon into the atmosphere, and global carbon dioxide levels in the atmosphere have risen significantly.

Adaptation

Adaptation is a central concept in natural history and it has played an important role in many biological fields, including systematics and ecology. By “adaptation” we mean the fit of living things to each other and to the environment: the fast-growing plant with a plumed seed that can disperse quickly to new locations; the woodpecker with a skull that allows it to pound its head all day long into a tree and not be hurt; the green caterpillar camouflaged on a green leaf; the brown moth on the brown tree trunk; the flower that blooms in March so it will be able to get sunlight before the tree canopy closes. Naturalists observe adaptation throughout the living world. A major question in the history of natural history has been, “How did this adaptation come about?”

Up through the mid-1800s the standard answer was that living things are adapted to each other and to their environments because they were designed that way by an intelligent designer (God). The fit of organisms to their environments can’t possibly be the result of chance; the only way it could have happened is through intelligent design. Indeed, the fact that organisms are adapted to their environments has long been seen by many people as evidence that God (or a god of some kind) must exist, because the adaptation we see in nature could not have occurred any other way. This viewpoint was common in science from at least the 1600s through the mid-1800s. Its advocates were commonly called “natural theologians” and their school of thought “natural theology.” (Bryant’s “Forest Hymn” is a literary expression of the world view of natural theology.)

“The argument from design” is an argument that says God must exist because there is no other way that the design (adaptation) we see in nature could have arisen. The argument from design has featured prominently in Western philosophy for centuries. One of the most famous versions of it was William Paley’s story of the watch on the moors, written about 1800. Paley asks us to imagine finding a watch on the open ground. How did the watch come to be? He says either (1) it assembled itself from random things blowing around in the environment, or (2) a watchmaker made it. In the case of watches, we know (2) is correct and (1) is silly. Then Paley asks us to look at a flower or other organism and ask how it came to be. The same two choices are offered: (1) it randomly assembled itself, or (2) an intelligent being made it. Paley, and most others of his time, chose (2) because they saw the complexity in nature as evidence that there must be a God.

(Remember some of the terminology that is commonly used in science and scholarship generally. By “argument” we mean an ordered collection of reasons for believing something is true; this is the same meaning you see in law court when a judge says, “The court will now hear arguments in the matter of Jones. vs. Smith.” Scientists and other scholars make observations of things they can see in the world, and then draw inferences about things they can’t see. Adaptation is something we can see. From the observation of adaptation, many naturalists inferred that an intelligent designer must have been the cause of that adaptation. Science proceeds by making observations, drawing inferences about things that may be out there but not yet seen, and then going out and looking some more to see if more evidence can be found to support or contradict the inference.)

In the mid-1800s, Charles Darwin (and also Alfred Russel Wallace) proposed another explanation for adaptation. They argued that even though organisms look like they were designed, they in fact were not. Darwin’s argument was that there is a process working in nature which he called “natural selection.” This process adapts living things to each other and to their environments over many generations in such a way that they appear to have been designed. We will learn more about natural selection shortly.

Species and Essentialism

Another fundamental observation about nature is that living things are arranged into species: basic “kinds” that are made up of individuals that breed with each other but not with members of other species. Members of a species all look alike, but they don’t look exactly alike: every species has individual variation within it. The human species is a perfect example: it is easy to recognize another organism as a human or not a human, but we also know that every human looks different. The important questions that naturalists have asked about this subject for centuries are: What causes the individual variation? Why don’t all the individuals in a species look the same? (By the mid 1800s geologists had shown that species have come and gone throughout the history of the earth.)

The early view on this subject, contemporary with natural theology, was the notion that every species has some kind of permanent and fixed form, and that individual variation is “error” caused by the effects of the environment during development. If you get too much food, or too little food, or not enough space, or bad sunlight, etc., you will deviate a bit from the “ideal form” of your species. This view of individual variation is called “essentialism” or “typology”—the true, permanent, fixed form of every species is its “essence” or “type,” and it never changes, even though individual variation occurs around it (some bigger than the type, some smaller, some lighter, some darker).

The view of species that Charles Darwin and Alfred Russel Wallace developed in the mid-1800s turns this picture upside down. In their view, there is no “essence” or “type” holding a species together; there are only all the interbreeding individuals with all their individual variations. The “type” is an abstract average, it exerts no “force” on the species that draws individuals back toward it in some mysterious way. Wallace titled one of his papers, “On the tendency of varieties to depart indefinitely from the original type.” The key phrase is “depart indefinitely.” For an essentialist, variation is always temporary error, and the species will “snap back” to the original type once external pressure from the environment is removed. For Wallace, varieties can “depart indefinitely”—there is nothing holding them to any original “type” at all, and they can just keep changing and changing and changing according to whatever local conditions they encounter. As things have turned out, no one has ever been able to find an unchanging “essence” within a species—there isn’t any material thing there to be found. There might have been, but as it turns out there just isn’t; that’s the way the world is, and essentialism as applied to species turns out to be false.

Reproduction and Inheritance

Another fundamental fact of the living world is that organisms reproduce. Inanimate objects don’t do that. Furthermore, offspring tend to resemble their parents. You know that to be true from observations of people: while children do not look exactly like their parents, they do tend to resemble them in a general way (tall people have tall children, short people have short children, and so on). This is just as true for all other organisms as it is for people, and it has been the basis of selective breeding in agriculture for centuries. The deep questions here are: How does this work? What is the basis of inheritance? What causes offspring to look like their parents?

In early natural history there were two basic ideas on how inheritance works: the blending model and the particulate model. The blending model saw inheritance as being a process like blending buckets of paint: the father’s traits were poured together with the mother’s traits and the offspring was a blend of both. Some traits, like skin color in humans, do seem to work this way. The particulate model thought of traits as being carried in little packages or particles (what they were no one knew), and that combining them was like mixing marbles rather than liquid paint: they retained their individual identity and didn’t blend together, and offspring got one type of “particle” or the other. Some traits, like eye color in humans, seem to work this way: they don’t blend together. Many people struggled with this problem all through the 1800s and it was a source of great controversy. Charles Darwin tried to answer it with an idea he called “pangenesis”: there are particles in the blood, he said, that are passed on to offspring (he called the particles “pangenes”). This turned out to be completely wrong, but it shows that many people were struggling to answer the question of how inheritance actually works.

The experiments of Gregor Mendel solved this problem in the 1860s, although it took almost 100 years to recognize that he was completely right. Mendel did careful studies with garden peas, which vary in a number of characteristics. Their flowers, for example, may be purple or white; their seeds may be green or yellow. Mendel took true-breeding purple peas and crossed them with true-breeding white peas, and saw that their offspring were all purple. That seems to go against the blending model. But he carried the experiments much further. He crossed these purple offspring with each other, and found that the next generation contained three purple peas for every one white pea. The white trait reappeared, and there was a consistent numerical ratio between purple and white.

From his many experiments, Mendel constructed a detailed model of how he thought inheritance works. He proposed that it was particulate, and not only that, but that each adult organism contains two copies of each inheritance “particle.” The sex cells (egg and sperm) contain only one copy of each particle, and when they combine to make a new individual, that new individual has two copies again. The true-breeding purple peas have two copies of the purple “particle” and the true-breeding white peas have two copies of the white “particle”; their offspring, however, have one copy of each particle. In that case, said Mendel, the purple particle masked (was dominant to) the white particle. The white particle was still there, it was just hidden, and could reappear when it was combined with another white particle in the next generation.

Mendel’s model turned out to be completely right, but it took almost 100 years to work out all the details. About 1900 several biologists rediscovered Mendel’s work (which had been forgotten), and they confirmed his results with other species. In the early 1900s it was also noticed that certain structures inside cells that were called “chromosomes” (“colored bodies”) seemed to be present in two copies in adults, but only in single copies in the sex cells. Could they be the inheritance “particles” that people had been talking about for centuries? These chromosomes were made up of two substances: protein and nucleic acid. James Watson and Francis Crick in the 1950s determined that the nucleic acids have a ladder-like structure, and that the rungs of the ladder can be read like letters in an alphabet: there are millions of them in every cell, and they store all the information needed to make an organism. The egg and sperm cells get a complete copy of this sequence of letters, and every offspring thus has one set from its mother and one set from its father.

Overproduction

Yet another fundamental observation about nature is that every species produces far more offspring than the environment can support. The seeds produced by a single tree, if they all survived, grew, and produced seeds themselves, would fill the earth within a few hundred years. This observation was applied to human beings in 1798 by Thomas Malthus in his Essay on the Principle of Population and it led Malthus to conclude that human society would always suffer from poverty, famine, war, and lots of other bad things because we will always produce more children than we can support.

Both Charles Darwin and Alfred Russel Wallace read Malthus, and it was from Malthus that they got the last piece of the puzzle they needed to explain how it is that species change and adapt to their environments. As Wallace said, “It occurred to me to ask, ‘Why do some die and some live?’”

Natural Selection

Natural selection is a simple idea, but it brings together a variety of observations and so can be a bit confusing. But you have already seen all the parts above. Here’s a summary of how adaptation is produced by natural selection; much of it should now be familiar.

(1) Within every species there is individual variation. This can be seen in our own species as well as in other species. This individual variation is produced randomly—some individuals are larger, some are smaller, some lighter, some darker, some faster, some slower, and so on, for almost any trait you can think of.

(2) Living things reproduce and exhibit inheritance. Reproduction just means that individuals do not last forever; they are replaced over time by their descendants, who are then replaced by their descendants, and so on from generation to generation. Inheritance simply means that offspring tend to resemble their parents more than they resemble a random member of the population. Offspring do not exactly resemble their parents, because there is individual variation (as we know), but in general, offspring tend to resemble their parents, and traits that the parents possess are commonly passed on to their offspring.

(3) The members of every species produce far more offspring than can possibly survive. This is “the doctrine of Malthus” as Darwin called it. Because all species over-produce offspring, there is therefore a “struggle for existence” during which most individuals die.

(4) Although individual variation is generated randomly, individual organisms do not die randomly in the struggle for existence. Those individuals that happen to have randomly-generated variations that are favorable in the local environment are less likely to die, and those individuals that happen to have randomly-generated variations that are unfavorable in the local environment are more likely to die and leave few or no offspring. The individuals that happen to have favorable variations will be “naturally selected” by the local environment, and the next generation will be made up disproportionately of their offspring. The favorable trait, therefore, will (because of inheritance) be more common in the next generation. Over a series of generations, the favorable trait will increase in frequency in the population, and the unfavorable trait will decrease.

(5) Environments change over time. We know this from geology, as well as from direct observation. Because environments are constantly changing (although they may be changing slowly), the meaning of “favorable” and “unfavorable” is also changing, because what is favorable in one environment may no longer be favorable as the environment changes. (In a forest that is drying up and becoming a desert it may at first be advantageous to be green for camouflage, but in a desert it is more advantageous to be beige for camouflage.) Natural selection, which is continually operating, will over a series of generations adapt a population to the local environment and will cause the population to “track” the environment from one generation to the next as the environment changes.

Note that natural selection causes populations to adapt over time to an environment by selecting individuals with locally favorable traits and allowing them to reproduce. Individual organisms are not changing over the course of their lives; they are dying and being replaced by other individual organisms.

Note also that natural selection isn’t making species “better” in some universal sense; it is just adapting each population to the local conditions which may vary from place to place and from time to time. “All evolution is local.” This is a fundamental concept you must understand.

And note further that this is a two-step process: randomly-generated variation arises in a population first, and then selection (which is non-random) occurs, allowing some variants to survive and reproduce and other variants to die, depending upon what is favorable or unfavorable in the local environment.

A Scientist’s Picture of the World

All the things we have talked about this semester can be put together into a scientist’s picture of what the world is like, a picture that has been worked out over the last 150 years. Nothing like this picture has ever existed before. The background to this picture is the “discovery of time” that shows the earth is about 4.6 billion years old:

“Elaborately constructed forms.” The similarities and differences among species are intricate and complex, and have been the subject of comparative study for hundreds of years, both on a large scale (gross anatomy) and on a small scale (biochemistry).

“Dependent on each other in so complex a manner.” Organisms fit together with each other and their environments in great detail. This is the ancient phenomenon of adaptation, but it will get a new explanation here.

“Growth with reproduction.” The genes control organismal development (growth) as well as inheritance.

“Inheritance.” We now understand (as of the 1950s) the mechanism of inheritance: all the inherited information is passed on in the DNA “alphabet” and each individual cell has about six billion letters. Reproduction is the act of combining two sets of these letters, then shuffling and separating them out again. Every individual organism is a wholly new combination that has never existed before. Essentialism turns out to be false: there is no one human genome, there are as many human genomes as there are humans.

“A ratio of increase so high as to lead to a struggle for life.” Malthus showed how powerful overproduction of offspring could be, and how it leads to unhappy consequences. Humans are not immune: in 1650 the world population of humans was about 500 million; in 1930, about 1 billion; in 2000, about 6 billion. This is going to catch up with us eventually, as this rate of growth cannot continue indefinitely.

“And as a consequence to natural selection.” Natural selection is the process that fits populations to their local environments over many generations, and it has produced the spectacular diversity of the natural world. This spectacular diversity is the result of the cumulative effects of natural selection acting for millions of years on local populations in varying local environments. “All evolution is local.”

Many people have found this view disturbing. The section from Tennyson’s In Memoriam is a famous example of such a reaction. But from a scientist’s perspective:

“There is grandeur in this view of life.” It makes each of us a unique but connected part of a complex history that has been going on for billions of years “whilst this planet has gone cycling on according to the fixed laws of gravity,” and during which “endless forms, most beautiful and most wonderful, have been, and are being, evolved.”