Cover

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Title Page, Copyright, Dedication

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pp. i-vi

Contents

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pp. vii-viii

List of Figures

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pp. ix-xii

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Acknowledgments

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pp. xiii-xvi

...Anybody pretending that a book like this is written in a vacuum would be disingenuous. Scientists are nowadays embedded in a dense network of professional interactions, and it is sometimes difficult to discern where one’s ideas begin and another’s ideas...

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1. Introduction

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pp. 1-12

...Living things are unimaginably complex, yet they have withstood a withering assault of harmful influences over several billion years. These influences include cataclysmic changes in the environment, as well as a constant barrage of internal...

PART I: ROBUSTNESS BELOW THE GENE LEVEL

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2. The Genetic Alphabet

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pp. 15-24

...Why does the genetic material have four letters, and why are they exactly the four letters we know: A, T(U), C, and G? One might think that there is no other way to ensure...

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3. The Genetic Code

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pp. 25-38

...The genetic code is responsible for translating a sequence of nucleotide triplets (codons) into a protein’s amino acid sequence. The vast majority of extant organisms use the code shown in Figure 3.1. Ever since this “universal” genetic code was discovered...

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4. RNA Structure

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pp. 39-61

...The currently most explicit and deepest analyses of mutational robustness regard the structure of RNA. These analyses not only show that RNA structures can be very robust to changes in individual RNA nucleotides, they also characterize...

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5. Proteins and Point Mutations

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pp. 62-77

...The main factor hindering the experimental analysis of robustness in RNA structure is the difficulty of determining this structure experimentally. Powerful computational techniques for RNA structure prediction have alleviated this...

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6. Proteins and Recombination

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pp. 78-90

...Recombination is a much more drastic genetic change than the point mutations in individual nucleotides and amino acids I have discussed thus far. It can replace multiple contiguous amino acids in a protein. On a larger scale, it can lead...

PART II: ROBUSTNESS ABOVE THE GENE LEVEL

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7. Regulatory DNA Regions and Their Reorganization in Evolution

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pp. 93-103

...As I discussed in chapter 1, two main approaches can provide information on a biological system’s robustness. The first consists of many experimental perturbations of the system’s parts. An example is the generation of thousands of amino...

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8. Metabolic Pathways

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pp. 104-119

...In diploid organisms, null mutations—mutations in which a gene loses its function—at one out of its two alleles often have no or little phenotypic effect. This observation encapsulates the phenomenon of dominance. Dominance is the facet...

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9. Metabolic Networks

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pp. 120-142

...The metabolic pathways of the previous chapters are but figments of the complex chemical reaction networks sustaining life. To understand robustness of metabolism ultimately requires understanding such larger metabolic networks. Metabolic...

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10. Drosophila Segmentation and Other Gene Regulatory Networks

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pp. 143-160

...This chapter illustrates how one can make educated guesses about the robustness of a genetic network, even when hobbled by incomplete information. The chapter uses one main example (571), the network responsible for subdividing...

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11. Phenotypic Traits, Cryptic Variation, and Human Diseases

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pp. 161-174

...This chapter focuses on robustness in the developmental processes that produce macroscopic characters such as eyes and wings. Specifically, it discusses evidence that many phenotypic characters vary little, despite much variation in the genes...

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12. The Many Ways of Building the Same Body

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pp. 175-192

...This chapter deals with a level of biological organization far removed from DNA: many-celled organisms and their embryonic development. It makes two central observations. First, there are many and sometimes radically different ways to...

PART III: COMMON PRINCIPLES

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13. Neutral Spaces

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pp. 195-216

...the faithful replication of genetic information to the making of a body. Most of these problems have more than one solution, and many of them have an astronomical...

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14. Evolvability and Neutral Mutations

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pp. 217-227

...sense. Consider an enzyme-coding gene that is subject to different mutations in different individuals of a population. These mutations cause the enzyme’s activity to fluctuate among different individuals. If such heritable genetic variation...

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15. Redundancy of Parts or Distributed Robustness?

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pp. 228-246

...This chapter asks which of two possible mechanistic causes of robustness is more important in genetic systems. These two causes are redundancy of a system’s parts and distributed robustness, which emerges from the distributed nature...

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16. Robustness as an Evolved Adaptation to Mutations

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pp. 247-269

...solutions to problems that organisms face. Second, in a system that embodies any one such solution, robustness can further vary and increase in evolution, as examples scattered...

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17. Robustness as an Evolved Adaptation to Environmental Change and Noise

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pp. 270-280

...The previous chapter discussed the role mutations play in the evolution of robustness. This chapter focuses on an alternative explanation for the evolution of mutational robustness...

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18. Robustness and Fragility: Advantages to Variation and Trade-offs

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pp. 281-294

...exist, trade-offs that can prevent the increase of robustness in evolution. For example, maximally robust enzymes would not be able to catalyze chemical reactions, because the molecular...

PART IV: ROBUSTNESS BEYOND THE ORGANISM

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19. Robustness in Natural Systems and Self-Organization

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pp. 297-309

...In this chapter, I point out parallels and, more importantly, differences between robustness in living systems—organisms and their parts—and other, nonliving systems...

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20. Robustness in Man-made Systems

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pp. 310-320

...fundamentally similar? Do they achieve robustness in similar or different ways? The answers to these questions could fill another book. In this chapter—really more...

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Epilogue: Seven Open Questions for Systems Biology

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pp. 321-322

...The following are key open questions and problems that emerged from the preceding chapters. We will understand mutational robustness to the extent that we answer these questions for a wide variety of biological systems. Currently, however, none...

Bibliography

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pp. 323-358

Index

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pp. 359-367