Cutting Edge Science
Changes to the Ninth Edition

Part I: The Molecular Basis of Life

The material in this section does not change much with time. However, we have updated this section to make it more friendly to the student. The student is introduced to the pedagogical features that characterize the book here: learning objectives with various levels of cognitive difficulty, scientific thinking figures, and an integrated approach to guide the student through complex material.

In chapter 1, the idea of emergent properties has been clarified, and material added to emphasize the nonequilibrium nature of biology. This will help introduce the student to the fundamental nature of biological systems and prepare them for the rest of the book.

Part II: Biology of the Cell

The overall organization of this section was retained, but material on cell junctions and cell-to-cell interactions was moved from chapter 9 to chapter 4 where it forms a natural conclusion to cell structure. Within chapter 4 microsome/peroxisome biogenesis was clarified to complete the picture of cell structure for students. The nature of trans fats is clarified, a subject students are likely to have been exposed to but not understand. A brief discussion of the distribution of lipids in different membranes was also added.

Chapter 7—The organization of chapter 7 was improved for greater clarity to students. ATP structure and function is introduced earlier, and the opening summary section covering all of respiration was removed. This allows the information to unfold in a way that is easier for the student to digest. A new analogy was added for the mechanism of ATP synthase to make this difficult enzyme more approachable to students.

Chapter 8—The section on bacterial photosynthesis was completely rewritten for clarity and accuracy. In addition to the emphasis we have always had on the experimental history of photosynthesis, the scientific thinking figures for chapters 7 and 8 are complementary and cross referenced to reinforce in students how we accumulate evidence for complex phenomenon such as chemiosmosis.

Chapter 9—The removal of the cell junction material keeps the focus of chapter 9 on signaling through receptors, making this difficult topic more digestible for students. The distribution of G protein coupled receptor genes in humans and mouse was updated.

Chapter 10—the discussion of bacterial cell division was updated again to reflect the enormous change in our view of this field. The organization of the chapter was tightened with mitosis and cytokinesis combined as M phase. Not only is this a consensus view in the field, it simplifies the overall organization for greater clarity for the student.

Part III: Genetic and Molecular Biology

The overall organization of this section remains the same. The splitting of transmission genetics into two chapters has allowed students to first be introduced to general principles, then tie these back to the behavior of chromosomes and the more complex topics related to genetic mapping.

Content changes in the molecular genetics portion of this section are intended to do two things: one to update material that is the most rapidly changing in the entire book, and to introduce the idea that RNA plays a much greater role now than appreciated in the past. The view of RNA has undergone a revolution that is underappreciated in introductory textbooks. This has led to a complete updating of the section in chapter 16 on small RNAs complete with new graphics to go with greatly expanded and reorganized text. This new section should both introduce students to exciting new material, but organize it in such a way as to make it coherent with the rest of the chapter. The new material is put into historical context, and updated to distinguish between siRNA and miRNA, and the mechanisms of RNA silencing. Material on the classical bacterial operons trp and lac was also refined for greater clarity for students.

Material on the eukaryotic replisome in chapter 14 was also updated and the graphics for this refined from the last edition. Archaeal replication proteins are also introduced, although space prevents a detailed discussion. However, this does give the students a more complete view of replication.

The organization of chapter 15 was tightened considerably with an extensive, unneeded introduction removed. The example of sickle cell anemia was moved from chapter 13 to 15 where it fits more naturally in a discussion of how mutations affect gene function.

Chapter 11—The information on meiotic cohesins and protection of cohesins during meiosis I was clarified and updated. This is critical for students to understand how meiosis actually works as opposed to memorizing a series of events.

Chapter 12—The second example of epistasis, which did not have graphical support, was removed. This allows the remaining example to be explored in greater detail. The organization of the explication of Mendel's principles was tightened to improve clarity for students.

Chapter 17—Our goal is to help students apply what they’ve learned about molecular biology to solving important biological questions. This chapter has been revised to balance newer technologies with approaches that continue to be used in both the research and education communities. RNAi applications to diseases like macular degeneration and next generation sequencing technology are introduced by building on what the student already knows about DNA replication, transcription, and PCR.

Chapter 18—Our book is unique in having two chapters on genomes. This first chapter extends the molecular unit to the scale of whole genomes while chapter 24 focuses on comparative genomics after students have learned about evolution. This organization is core to our full integration of evolution throughout the book. Chapter 18 has been revised to demonstrate the broad relevance of genomics, from understanding the evolution of speech to identifying the source of the 2001 anthrax attacks.

Chapter 19—The material on stem cells was completely rewritten and updated. The content was reorganized to put into an even more solid historical context using the idea of nuclear reprogramming, and how this led to both cloning of mammals and embryonic stem cells. New information on induced pluripotent stem cells is included to keep this as current as possible. This topic is one that is of general interest, and is another topic that students are exposed to significant misinformation making clear, well organized information critical.

Part IV: Evolution

The evolution chapters were updated with new examples. A strong emphasis on the role of experimental approaches to studying evolutionary phenomena has been maintained and enhanced.

Chapter 20—discusses the various processes that can lead to evolutionary change within populations. Notably, these processes are not considered in isolation, but how they interact is also explored.

Chapter 21—A state-of-the-art discussion of the power of natural selection to produce evolutionary change and the ever increasing documentation in the fossil record of evolutionary transitions through time. It also discusses a variety of phenomena that only make sense if evolution has occurred, and concludes with a critique of arguments posed against the existence of evolution.

Chapter 22—Considers the process of speciation and evolutionary diversification. It includes current disagreements on how species are identified and how speciation operates.

Chapter 23—An up-to-date discussion of not only how phylogenies are inferred, but of their broad and central role in comparative biology.

Chapter 24—This chapter has been revised to incorporate the rapidly growing number of fully sequenced genomes in a conceptual manner. We have incorporated the paradigm changing findings that non-coding DNA plays a critical role in regulating DNA expression. This chapter and chapter 25 illustrate how we integrate both evolution and molecular biology throughout our text.

Chapter 25—With updated examples we explore the changing perspectives on the evolution of development. Specifically, the field is shifting away from the simplified view that changes in regulatory regions of genes are responsible for the evolution of form.

Part V: Diversity of Life on Earth

In revising the diversity chapters – protist, plants, and fungi – the emphasis was on integrating an evolutionary theme. The fungi chapter was restructured to reflect the current phylogenies while keeping species that are familiar to instructors at the fore. While competitors have two plant diversity chapters, we have one. The reason for this is that we integrate the diversity of flowers and pollination strategies, as well as fruit diversity into the plant unit. It is difficult for students to fully appreciate the morphological diversity before they have learned about plant structure and development.

Chapters 32-34 have been completely overhauled to emphasize the latest understanding, synthesizing molecular and morphological information, on the phylogeny of animals. In addition, these chapters have been refocused to emphasize the differences in major morphological, behavioral, and ecological features that differentiate the major animal groups, with a strong emphasis on understanding the organism in the context of the environment in which it occurs. Chapter 32 is an overview which could be used as a standalone chapter, setting the stage for Chapters 33 on non-coelomate animals and Chapter34 on coelomates.

Chapter 26—This chapter has been updated so instructors have the option of using it as a stand alone diversity of chapter if their syllabus is too crowded to include the extensive coverage of diversity in the unit. Endosymbiosis has been consolidated in this chapter (moving some of the content from chapter 4).

Chapter 27—Material on archaeal viruses was added. This is an area of active research that is often ignored. The approach to HIV drug treatments was completely redone with strategies revised and updated with new graphics. The discussions of prions and viroids were also revised.

Chapter 28—All health statistics in chapter 28 were updated, including TB, HIV and STD's. A section on archaeal photosynthesis was added to the section on microbial metabolism.

Chapter 30—Findings of several plant genome projects informed the revision of the plant chapter. The remarkable desiccation tolerance of moss is emphasized in a scientific thinking figure exploring the genes involved in desiccation tolerance. New findings on correlations between the rate of pollen tube growth and the origins of the angiosperms have been integrated into the chapter.

Chapter 31—Since the last edition, much has been learned about the evolutionary relationships among fungi, fundamentally changing relationships among groups. We have revised the fungal phylogenies in this chapter to conform with the current understanding of fungal evolution, while contextualizing the older taxonomic groupings that may be more familiar to some readers.

Chapter 35 on vertebrates has been revised to incorporate current ideas on vertebrate phylogeny and to emphasize the phylogenetic approach to understanding evolutionary diversification.

Part VI: Plant Form and Function

As with the animal unit we have incorporated an evolutionary theme. In the scientific thinking figures, as well as the text, we challenge the students to combine morophological, developmental, and molecular approaches to asking questions about plants. The goal is to help students integrate their conceptual understanding over multiple levels of organization. In addition, most of the end of the chapter questions are new.

Chapter 36—The section on leaf development has been updated to include a molecular analysis of the role of a key gene, UNIFOLIATA, in compound leaf development.

Chapter 39—Throughout the unit we include relevant examples to illustrate core concepts in plant biology. Here we have added information about the effect of pH on germination and included a scientific thinking figure to more fully engage the student in considering pH effects in an agricultural context. The discussion of elevated CO2 levels and increased temperatures on plant growth have been updated. The very complex interactions affecting carbon and nitrogen content in plants is addressed the level of plant and cell physiology, as well as at the ecosystem level later in the text, for a more coherent presentation of the effects of climate change.

Chapter 41—The section of phytochrome has been reorganized and updated. The emphasis is on guiding as student from the historic examples of morphological responses to different daylengths to a clear, coherent understanding of how red and far red light affect the conformation of phytochrome and the signaling pathway it affects.

Part VII: Animal Form and Function

Several organizational changes were made to this section to improve the enhance the overall coherence for students. The entire section was reinterpreted with the intent of increasing the integration of evolution into all topics. The material on temperature regulation was moved from chapter 50 (8E) to the introductory chapter 43. This both provides an illustrative example to the introduction to homeostasis, and removes a formerly artificial combination of temperature control and osmotic control. Respiration and circulation have been made into separate chapters (49 and 50) allowing greater clarity and removing an overly long chapter that was a barrier to student's understanding.

Chapter 44—The material on synaptic plasticity was rewritten with new graphics added. And in chapter 46 the addition of learning objectives and our integrated pedagogical tools make a complex topic approachable to students. A new scientific thinking figure was added as well.

Chapter 51—The osmotic regulation material in this chapter is more coherent as a separate section without the temperature regulation material.

Chapter 52—Reorganized and restructured to emphasize the existence of innate vs. adaptive immunity. This replaces the replaces the old paradigm of nonspecific vs. specific immunity. This reorganization and new material also emphasizes the evolutionary basis of innate immunity, which exists in invertebrates and vertebrates.

Chapter 54—The material on organizer function was updated. The Scientific Thinking figure uses molecular approaches introduced in part III and a figure that was already in the chapter. This figure is much more pedagogically useful in this repurposing than as a static figure, and illustrates the use of these figures.

Part VIII: Ecology and Behavior

The ecology chapters have been revised with a particular focus on providing up-to-date information on current environmental issues, both in terms of the problems that exist and the potential action that can be taken to ameliorate them.

Chapter 55—Completely revised with a strong emphasis on neuroethological approaches to understanding behavioral patterns. It emphasizes modern molecular approaches to the study of behavior.

Chapter 56—Considers the ecology of individuals and populations and includes up-to-date discussion of human population growth.

Chapter 57—Discusses the ecology of communities and the various ecological processes that mediate interactions between co-occurring species. With updated examples, it illustrates how different processes can interact, as well as emphasizing the experimental approach to the study of ecology.

Chapter 58—Focuses on the dynamics of ecosystems. It has been updated to emphasize current understanding of the how ecosystems function.

Chapter 59—Focuses on the biosphere and current environmental threats. The chapter has been extensively updated to provide the latest information on factors affecting the environment and human health.

Chapter 60—Considers conservation biology, emphasizing the causes of species endangerment and what can be done. Data and examples provide the latest information and thinking on conservation issues.