As teachers, we know that undergraduate science education is evolving. Simply conveying facts does not produce a scientifically literate student, a long-held perception now reinforced by numerous studies. Students of science need more: a better window on what science is and how it is done, a clear presentation of key concepts that rises above the recitation of details, an articulation of the philosophical underpinnings of the scientific discipline at hand, exercises that demand analysis of real data, and an appreciation for the contributions of science to the well-being of humans throughout the world. As undergraduate science educators rise to these challenges, we are faced with both higher numbers of students and declining resources. How can we all do more with less?

Textbooks are an important part of the equation. A good textbook must now be more than a guide to the information that defines a discipline. For instructors, a textbook must organize information, incorporate assessment tools, and provide resources to help bring a discipline to life. For students, a textbook must relate science to everyday experience, highlight the key concepts, and show each student the process that generated those key concepts.

This book had its genesis at a meeting of the authors in Napa Valley in January 2006. From the outset, we set ambitious goals designed to address the key challenges we face as teachers.

Molecular biology has a wealth of important stories to tell. We wanted to convey the excitement that drives modern molecular biology, the creativity at the bench, and the genuine wonder that takes hold as the workings of a new biological process are revealed. This theme is set in the first chapter, dedicated in large measure to an introduction to the scientific process. Every chapter then begins with a Moment of Discovery, highlighting a researcher’s own description of a memorable moment in his or her career. After Chapter 1, every chapter ends with a How We Know section, with stories relating the often circuitous path to a new insight. Additional anecdotes—scientists in action—are woven into the text and the accompanying Highlights. As students read the text, the laboratories and the people behind the discoveries will never be far away.

This second edition is an update, and much more. It has allowed us to refine the initial vision we had when we started this project and to augment that vision with unparalleled resources that will bring the subject to life for students and educators alike.

Scientific breakthroughs represent the exhilarating culmination of a lot of hard work. Each chapter opens with a description of a significant breakthrough in molecular biology, told by the scientist who made the discovery. The scientists featured in the Moments of Discovery are David Allis, Norm Arnheim, Bonnie Bassler, Steve Benner, James Berger, Carlos Bustamante, Rose Byrne, Jamie Cate, Joe DeRisi, Roxana Georgescu, Lin He, Tracy Johnson, Melissa Jurica, Judith Kimble, Robert Lehman, Steve Mayo, Harry Noller, Smita Patel, Lorraine Symington, Jack Szostak, Robert Tjian, and Wei Yang.

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Each chapter ends with a How We Know section that combines fascinating stories of research and researchers with experimental data for students to analyze.

The reality is far different. Data can take a researcher in unexpected directions. An experiment designed to test one hypothesis can end up revealing something quite different. The analysis of real data is a fundamental skill to be honed by every student of science. We have tried to address this need aggressively. Each chapter in this text features a challenging set of problems, including at least one requiring the analysis of data from the scientific literature. Many of these are linked to the discoveries described in the How We Know sections. Each chapter also ends with some Unanswered Questions, providing just a sampling of the endless challenges that remain for those with the motivation to tackle them.

A short section at the end of each chapter describes important areas still open to discovery, showing students that even well-covered subjects, such as nucleic acid structure and DNA replication, are far from fully explored.

Extensive problem sets at the end of each chapter give students the opportunity to think about and work with the chapter’s key ideas. New problems have been added in each chapter for this second edition. Each problem set concludes with a Data Analysis Problem, giving students the critical experience of interpreting real research data. Solutions to all problems can be found at the back of the book.

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Presenting the major concepts clearly, in the text as well as in the illustrations, is crucial to teaching students how science is done. We have worked to use straightforward language and a conversational writing style to draw students in to the material. We have collaborated closely with our illustrator, Adam Steinberg, to create clean, focused figures. Featured Key Conventions highlight the implicit but often unstated conventions used when sequences and structures are displayed and in naming biological molecules.

In brief paragraphs, the Key Conventions clearly lay out for students some fundamental principles often glossed over.

Good figures should speak for themselves. We have worked to keep our figures simple and the figure legends as brief as possible. The illustrations in the text are the product of close collaboration with our colleague Adam Steinberg. Together with the talented artists at Dragonfly Media Group, Adam has helped to hone and implement our vision.

Every time a molecular biologist studies a developmental pathway in nematodes, identifies key parts of an enzyme active site by determining what parts are conserved among species, or searches for the gene underlying a human genetic disease, he or she is relying on evolutionary theory. Evolution is a foundational concept, upon which every discipline in the biological sciences is built. In this text, evolution is a theme that pervades every chapter, beginning with a major section in Chapter 1 and continuing as the topic of many Highlights and chapter segments.

These discussions are designed to enhance students’ understanding and appreciation of the relevance of each chapter’s material. There are four categories of Highlights:

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As researchers, we know that it is critical to understand the benefits and limitations of experimental techniques. We strive to give students a sense of how an experiment is designed and what makes the use of a particular technique or model organism appropriate. The techniques covered in this book are:

Ames test 424

Chemical modification interference 700

Chemical protection footprinting 700

Chemical synthesis of nucleic acids 201

ChIP-Chip 345

ChIP-Seq 345

Chromatography

     Affinity chromatography 100

           Using terminal tags 237

           Using tandem affinity purification (TAP) tags 242

     Column chromatography 100

     Gel-exclusion chromatography 100

     Ion-exchange chromatography 100

     Thin-layer chromatography 584

CRISPR/Cas 246

Detecting A=T-rich segments of DNA by denaturation analysis 197

DNA cloning 212

DNA cloning with artificial chromosomes (BACs, YACs) 218

DNA footprinting 700

DNA genotyping (DNA fingerprinting, DNA profiling, STR analysis) 224

DNA library creation (cDNA, genomic) 220

DNA microarrays 244

DNA sequencing

     Automated Sanger sequencing 226

     Deep sequencing 232

     Genome sequencing techniques 260

     Ion torrent 232

     Next generation sequencing 229

     Pyrosequencing 229

     Reversible terminator sequencing 230

     Sanger sequencing 226

     Single molecule real time (SMRT) sequencing 230

Electrophoresis

     Agarose gel electrophoresis 199

     Isoelectric focusing 277

     Pulsed field gel electrophoresis (PFGE) 220

     Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) 100

     Two-dimensional gel electrophoresis 277

Electrophoretic mobility shift assay (EMSA) 700

Electroporation 217

Epitope tagging 240

Haplotype analysis 269

Immunoprecipitation 242

Linkage analysis 272

Localization of GFP fusion proteins 239

Mass spectrometry 278

Northern blotting 199

Nuclear magnetic resonance (NMR) 115

Optical trapping 344

Photolithography 244

Phylogenetic analysis 270

Phylogenetic profiling 279

Polymerase chain reaction (PCR) 222

     Quantitative PCR (qPCR) 222

     Reverse transcriptase PCR (RT-PCR) 222

Protein chips 280

Protein localization via indirect immunofluorescence 240

Recombinant protein expression 232

RNA interference (RNAi) 774

RNA-Seq 276

Selection and screening 217

Site-directed mutagenesis 235

Somatic cell nuclear transfer (SCNT) 538

Southern blotting 199

Transformation 217

Western blotting 241

X-ray crystallography 120

Yeast three-hybrid analysis 243

Yeast two-hybrid analysis 243