Contents

List of Figures ix

List of Boxes xi

Acknowledgments xiii

Introduction xv

PART I. FUNDAMENTALS

1. Philosophical Background Matters 3

2. The Scientific Hypothesis Today 31

3.

4. Kinds of Science 86

5. Statistics and Statistical Hypotheses 114

6. Bayesian Basics and the Scientific Hypothesis 143

7. The Reproducibility Crisis 161

8. Advantages of the Hypothesis 196

9. What Scientists Think About Scientific Thinking 219

PART II. OPPOSITION AND COGNITIVE CONCERNS

10. Opponents of the Hypothesis: Stuart Firestein, David J. Glass,

and David Deutsch 237

11. Automatic Thinking: Hypotheses, Biases, and

Inductive Reasoning 278

12. Thinking Rationally About Heuristics and Biases 298

viii CONTENTS

PART III. PRESENT POLICIES AND THE FUTURE

13. The Hypothesis in Science Education 329

14. How to Improve Your Own Scientific Thinking 351

15. The Future of the Hypothesis: The Big Data Mindset

Versus the Robot Scientist 374

Epilogue: Centaur Science—The Future of the Hypothesis 397

Index 399

Figures

2.1. Schematic diagram of the recursive hypothesis testing cycle according to

the Scientific Method and Karl Popper's standard of falsification. 33

4.1. The “long-tail” of science. 97

4.2. Diagram of the relationships among Discovery Science, Hypothesis-based

science, Big and Small Science, and Big and Little Data. 98

6.1. Venn Diagram of a sample Bayesian problem. 146

9.1. Is there a Reproducibility Crisis? 220

9.2. How much formal instruction on the scientific method, including the

hypothesis did you receive? 221

9.3. How confident are you in your knowledge of the scientific method and

the hypothesis? 222

9.4. How important were different modes of science to you at different stages

of your career? 223

9.5.

9.6. How important are the scientific method and the hypothesis to

today's science? 225

9.7. How often do you explicitly state the hypothesis of your research papers? 226

9.8. On what scientific mode is the most important work in your field

mainly based? 227

9.9. Does hypothesis-based research have anything to do with the

Reproducibility Crisis? 228

9.10. Is the hypothesis weighted too heavily in scientific publications and grants? 228

9.11. What do scientific papers reveal about how (neuro)scientists think

about the hypothesis? 230

10.1. Schematic drawing of experimental set up. 250

14.1. Diagraming hypotheses in scientific papers. 354

15.1. A basic Bayesian network illustrating how causal interactions among

conditions influence outcomes. 382

15.2. Diagram illustrating how Adam, the Robot Scientists, solves problems

in yeast genetics. 391

Boxes

5.1. Two Statistical Standards for Quality Control 132

6.1. Bayes Factors and Odds Ratios 151

6.2. Falsification Using Bayesian Model Selection Methods 157

7.1. Irrepro ducibility Can Lead to Better Science 168

7.2. When Reproducibility Took a Backseat to Truth: The LTP Wars 184

10.1. Isaac Newton and Francis Bacon: Not Arch-Foes of the Hypothesis After All 244

12.1. Expected Utility Theory: A Brief Overview 305

14.1. The Passive Voice and the Hypothesis 360

15.1. Was GFT Testing an Implicit Hypothesis or a Prediction? 380