Guttman/Biology

Preface

This book has grown out of a personal journey of discovery. I have been trying for many years to understand biology as a coherent science with organizing principles, and Johns Hopkins and I have tried for most of our professional lives to help students develop their personal understanding of often complicated biological concepts. (Here I must explain that this book developed as a long-term collaboration with Johns W. Hopkins III, and it bears much of his contributions and influence. Johns's untimely illness took him out of the project as it was coming to a climax, but I must write this preface with a mixture of "we" and "I" to reflect our collaboration.) Pedagogically, the book relies on many years of teaching introductory biology to a wide variety of students in many contexts.

This project began long ago as an exploration in theoretical biology, a search for general principles in biology and general ways to understand organisms, but it soon became a project in pedagogy, based on the conviction that students can learn biology more effectively if the myriad details of the science are developed in a strong conceptual framework. When the project was pursued by the team at WCB/McGraw-Hill, the critical comments of nearly 100 reviewers told us that the book was indeed on the right track, with unique features that would make it welcome even in a crowded market. This preface explains the background to this project and the features that make Biology unique, innovative, and worthy to teach and learn from.

The trouble with biology is that it is full of facts. An unimaginable number of factual statements could be made about the few million species of organisms on earth. Someone once published an example of a college zoology exam from the pre-Darwinian era that required only the recitation of endless anatomical facts; the Darwinian paradigm changed that, and for a long time, biology was taught primarily as a collection of these facts organized around the principle of natural selection and the fact of evolution. Of course, students of biology must still learn many facts about the natural world, often fascinating facts that motivate them to continue their personal explorations. But as the science of biology matures, it should increasingly subsume facts under general principles and develop coherent general concepts. As our knowledge of molecular, cellular, and physiological processes has grown, that foundation emerges from the genetic conception of an organism: a structure that operates on the basis of information in its genome.

The beginnings of this foundation emerged with Norman Horowitz's (1959) conception of an organism as a structure that can reproduce itself and mutate. For a long time, I used this as a foundation for thinking about biology. But its emphasis gradually shifted as I realized that the definition was too limited-for instance, there are perfectly good organisms that for one reason or another cannot reproduce. A more satisfactory foundational statement is this: An organism is a structure whose organization and operation are governed by the information in a genome.

Fortuitously, this conception is consonant with the thinking of a computer age, since everyone now knows that a computer is a hardware device that operates on the basis of particular software instructions; biological theory was therefore strengthened by John von Neumann's (1951) theoretical demonstration that it is possible to create a self-reproducing automaton that would operate on the basis of its instruction tape and produce an identical automaton. As such automata reproduce, occasional errors (mutations) will creep into copies of the genome. It is then obvious that such systems, operating within an ecological framework where resources are necessarily limited, will undergo evolution through natural selection (Guttman, 1966). Thus, the entire Darwinian paradigm emerges from the genetic conception of an organism.

Biology is still full of facts, and students can only understand the science by learning many of them. This book, however, is based on the conviction that students of biology will benefit far more from an emphasis on concepts and principles developed within this genetic-evolutionary-ecological framework, as explained more fully below.

Four Unifying Conceptual Themes

This book is tied together by four primary themes. This conceptual framework gives students something solid on which to hang virtually all the specific facts and more limited principles we develop. Let's examine these ideas carefully.

1. Organisms are genetic systems. They operate and reproduce themselves on the basis of instructions encoded in their genomes. As I pointed out above, populations of organisms will experience mutation and evolution through natural selection, so the entire Darwinian framework that traditionally forms such an important foundation for biology emerges from this broader genetic framework. The genetic theme also makes sense of the principal cellular activities of synthesizing molecular structure under genetic instructions, using materials and energy derived from other phases of metabolism. The book's genetics theme, and the central importance of inheritance with variation, is symbolized by the cover photo of this book kindly contributed by Tony Griffiths of the University of British Columbia. Tony is also co-author of the first genetics book to stress a secondary theme of the present book-the use of genetic analysis to dissect biological process. For a few places where this theme is emphasized, look at:

-Sections 2.7 and 2.8, for basic concepts about organisms
-Section 12.1, about how a genome instructs cells to operate
-Sections 15.6 to 15.8, about how a genome determines development

2. Organisms live in ecosystems, where they are adapted to particular ways of life and engage in complex interrelationships with other organisms and the environment. From the beginning, the genetic framework is immersed in an indispensable ecological framework. The book emphasizes the triumvirate of selection, adaptation, and ecological niche, which describes how organisms live, how they come to have their particular features, and how they interact with one another. For places where this theme is emphasized, look at:

-Section 2.9a, for basic ideas about ecosystems
-Section 7.10, about energy in ecosystems
-Section 11.7, for chemical communication among organisms in a community

3. Evolution, operating primarily through the process of natural selection, has produced the enormous variety of life and continues to operate today. This cornerstone of modern biology needs no explanation. However, instructors commonly complain that the theme gets lip-service by being relegated to an introductory chapter and a few later chapters specifically about evolution. I have tried to integrate the theme more consistently throughout the book, and the reader can judge how successful the integration has been by examining some representative sections such as:

-Section 2.9, about the concept of natural selection
-Section 4.13, about the evolution of proteins
-Section 14.5, which shows how cellular processes restrict evolution

4. Organisms function through molecular interactions. This theme emphasizes the basic fact that organisms are molecular machines and that they operate through molecular interactions. Scientific explanation is a matter of showing how phenomena fit into the causal structure of the universe, and much of the explanatory structure of biology shows how molecules push and pull on one another. I establish the concept early on that biomolecules are structures with unique shapes that interact with one another in unique ways, and then we keep returning to this general way of thinking through many examples.

Now a general biology course is obviously no place to discuss the molecular details covered in a biochemistry course with students who understand organic reaction mechanisms. So this idea is developed almost entirely through pictorial examples. Thus, the book emphasizes molecular explanation without being strongly chemical. Although this sounds self-contradictory, it is basically simple. I continually stress the concept of biomolecules having specific, complementary shapes, and this is demonstrated through pictures that are little more than artists' conceptions, requiring little or no understanding of organic chemistry. For places where this theme is emphasized, look at:

-Section 8.6, about the structure of membranes
-Sections 8.12 and 8.13, about how membranes move molecules
-Sections 11.7 to 11.10, about proteins of the cytoskeleton

Three General and Pedagogical Themes

In addition to these conceptual themes, I have worked hard to develop certain features of pedagogical importance to students.

Science as stories of living history. Scientists know that our subject is a dynamic structure based on the investigations of many people. The facts and principles we teach were not handed down from some mystical source, yet they are often presented as if humans had nothing to do with their discovery. But students should know at least some history of discovery and should think of science as an ongoing human enterprise. If only there were room to tell all the great stories! But there isn't, and I have confined myself to some of the best. In any case, you will find many names of contemporary investigators in the text, and Section 1.5 explains why their biographies are not given.

Learning through exercises. Exercises interspersed throughout allow students to test their comprehension of ideas immediately after they have been presented and to go beyond mere memorization by applying concepts to new situations. Students need to check their understanding as soon as possible, to be sure they can understand the ideas to be developed next. These exercises emphasize the skill of problem-solving; many are quantitative and are used to develop a conception of sizes and rates in the biological world.

Telling students what they need to know when they need to know it. Teachers have realized for themselves that there is a time to explain concepts and a time to hold back. But many authors seem to believe that students can and should learn everything the instructor knows about a topic as soon as the topic is introduced. However, understanding develops slowly, with repetition, and it is easy to create an informational overload that just confuses students. Accordingly, I have tried to follow the principle that concepts and information should only be introduced at the time when students can use it, not before.

Chapter 4, for example, introduces the general principle of polymeric structure and explains the structures of polysaccharides, nucleic acids, and proteins; but this is not the time to start developing complicated concepts about the role of nucleic acids in the genetic apparatus. Let the first idea sink in and develop a bit. The genetic ideas will come in good time. (I know from experience that introducing the functions of different kinds of RNA at this point is useless to students because they have no basis for assimilating the information.) Along with the major polymers, I introduce lipids briefly, but lipids are not polymers. They just aren't. And talking about them as if they were confuses the issue of biological structure. Furthermore, students don't have to know about lipids until they encounter membranes in Chapter 8, so I delay most of the information about them until I can introduce it in a more meaningful biological context.

Intended Audience

This book is designed for the typical majors biology course taken by college students in their first or second year. It assumes relatively little prerequisite knowledge-principally that students have become aware of many natural phenomena during 18 years or so of living, including some experience with the world of organisms. It does make the assumption that students can think as well as memorize, so they are able to work out some ideas through exercises rather than just being told every point dogmatically. Since science is quantitative, students must know elementary algebraic manipulations and must be able to work with scientific notation (powers of 10), although this is explained in Appendix A. The book explains elementary chemical concepts as needed. Although a lot of organic molecules are displayed in the book for the sake of reference and concreteness, I actually treat most chemical structures as little more than unique shapes that interact with other unique shapes, so no knowledge of organic chemistry is required beyond the simple structural ideas in Chapter 3.

Unique Chapters and the Placement of Ideas

Organisms as Genetic Systems that Evolve within Ecosystems
Several specific features of the chapters set this book off from traditional books. First, please pay attention to Chapter 2. Although the book generally follows the now-traditional "micro-to-macro" approach, Chapter 2 provides the broad genetic-ecological- evolutionary context for the whole book. It defines an organism(and a virus) and provides some of the language for thinking about all the details and the specific concepts to be developed in the rest of the book, before we can deal with genetics, ecology, and evolution more extensively. The information comes too fast here, too condensed-of course, it does, and I don't expect students to really understand it all during a first go-around. But it sets a tone, an orientation. It says to students that they should start to look at organisms as genetic systems that evolve within ecosystems.

Understanding Basic Chemical Structure
To return to the treatment of biomolecular structure in Chapter 4, beginning students have trouble understanding the basic chemical structure of organisms. The key is understanding the principle of polymeric structure and learning the structures of the principal monomers and their polymers (polysaccharides, nucleic acids, and proteins). This principle is not usually emphasized enough. I discuss polysaccharides in some detail, because they won't be discussed in much detail elsewhere, and nucleic acids in outline.

Chapters 4 and 5 then devote a lot of time to proteins, and throughout the book we relentlessly emphasize proteins, proteins, proteins. The biological reality is that virtually everything an organism is or does depends upon its particular protein composition, and it is hard to emphasize enough that an organism is made of thousands of different proteins, each with its own function. I point out that amino acids and proteins have charges, because students should understand this and because it is necessary to understand electrophoresis, one of the most important modern techniques for analyzing structure. The story of protein structure is then developed through Sanger's work on insulin, Kendrew and Perutz's work on myoglobin and hemoglobin, and Anfinsen's work on ribonuclease. This story makes some critical points about protein structure; understanding biology depends upon the point that each protein consists of a specific sequence of amino acids with a unique shape. And it is best, I think, to make the point by telling how these discoveries were made.

Chapter 4 ends with a return to the genetic and evolutionary themes. Even though I have only sketched the genetic conception in general terms so far, I want to continue building on it at every opportunity; I want students to start thinking about the genetic reason that proteins have their particular structures, rather than simply thinking that proteins exist, that they come to be in some obscure or magical way. And I want to emphasize the importance of evolutionary thinking at every opportunity.

Let me emphasize another point here: As I introduce the idea of mutation as a basis for evolution, it is easy to say that most mutations are likely to be disadvantageous rather than advantageous. But the principle of polymeric construction gives us new insight here by showing that a mutation may only replace one amino acid in a protein out of hundreds, and in some cases the mutation might only replace a few atoms out of thousands. Thus, polymeric construction makes for great subtlety in evolutionary change. When I emphasize that evolution occurs through a kind of editing process, I show that it can be a very subtle editing.

Introduction to Enzymes
Chapter 5 introduces enzymes as classic examples of proteins and develops another general principle that will pervade the whole book: That proteins bind to ligands through weak interactions. The chapter introduces the idea of saturable (Michaelis-Menten) kinetics-not the mathematics, but rather the idea that M-M kinetics implies that proteins have a discrete number of binding sites. The idea is used later in discussing myoglobin and hemoglobin, and it will be used again in Chapter 8 to distinguish simple diffusion from facilitated diffusion. Chapter 5 also introduces the general idea of allostery, which will, of course, be used throughout the book.

Survey of Cell Structure
Chapter 6 is a traditional survey of cell structure, but not quite traditional. I think it is a mistake to try to tell students everything about each cellular organelle when they aren't prepared to understand the information. So this is only a light survey, emphasizing the overall organization of a cell and the size relationships of cellular components (especially by means of two special boxes). The details come in later chapters, when students can integrate information about the functions of each structure one by one into their developing conceptual framework.

General Concepts of Regulation
Chapter 11, The Dynamic Cell, introduces some important concepts that I return to several times later, especially general concepts of regulation. Here we meet the ideas of feedback, steady state, homeostasis, informational transduction, receptor proteins, signal ligands (the various "-mones"), and the general signal transduction pathway that includes G-proteins and protein kinases.

Mitosis and Meiosis as Distinct Processes
Biologists have long been divided into two armed theological camps on the mitosis-meiosis issue; I strongly believe they should be discussed at different times. The conceptual reason is that mitosis and meiosis are distinct processes with entirely different functions. Mitosis is a phase of the cell cycle, and it should be understood in that context along with cell growth and DNA replication; meiosis is a phase of the sexual cycle, and it should be understand in that context as part of the life cycles of most eucaryotic organisms. The pedagogical reason is that the processes are too similar, and trying to discuss them together would be like trying to teach a child about football and soccer simultaneously.

I think it is important for a modern biology book to put mitosis into its proper place in the cell cycle. Until recently, mitosis was all we knew about; the rest of the cycle was relegated to the anonymity of interphase. But now that so much is known about the cycle as a whole and its regulation, our view should be corrected. Students come from high school biology thinking that mitosis is the cell cycle, and in my own teaching I have to reverse the emphasis and put all the events in perspective. My students have asked why the modern textbooks we use fail to do this, and I don't have a good answer.

In introducing the general sexual cycle, I use the convenient terms haplontic, diplontic, and haplodiplontic. They replace a multiplicity of more complicated terms that have been used for certain taxonomic groups, and they are easy to grasp.

Instructors have conflicting ideas about how Mendelian genetics should be developed, but I feel strongly that it should be done after developing a clear view of meiosis and the sexual cycle. Then it is easy to show how Mendel's laws follow from the events of meiosis and random fertilization. Furthermore, I believe it is important that students should already have a conception of what genes are for, so the entire DNA-RNA-protein story comes first (Chapters 12-14).

Introduction to Plants and Animals
Chapter 32 is a unique introduction to plants and animals. Many classic biology textbooks of an older era treated the general functions of plants and animals together, and many instructors still prefer this approach. I believe plants and animals are different enough to justify the now-current separate approach, but it is still valuable to discuss their commonalities. Here we can consider general body form, water relationships, exchange of oxygen, nitrogen, and carbon dioxide, and some general considerations of size.

Home Page