Stepping in the Same River Twice: Replication in Biological Research

by Ayelet Shavit (Editor), Aaron M. Ellison (Editor), W. John Kress (Foreword by)

Overview

An international team of biologists, philosophers, and historians of science explores the critically important process of replication in biological and biomedical research

Without replication, the trustworthiness of scientific research remains in doubt. Although replication is increasingly recognized as a central problem in many scientific disciplines, repeating the same scientific observations of experiments or reproducing the same set of analyses from existing data is remarkably difficult. In this important volume, an international team of biologists, philosophers, and historians of science addresses challenges and solutions for valid replication of research in medicine, ecology, natural history, agriculture, physiology, and computer science.
 
After the introduction to important concepts and historical background, the book offers paired chapters that provide theoretical overviews followed by detailed case studies. These studies range widely in topics, from infectious-diseases and environmental monitoring to museum collections, meta-analysis, bioinformatics, and more. The closing chapters explicate and quantify problems in the case studies, and the volume concludes with important recommendations for best practices.

Product Details

ISBN-13:	9780300209549
Publisher:	Yale University Press
Publication date:	04/25/2017
Pages:	344
Product dimensions:	6.20(w) x 9.40(h) x 1.20(d)

About the Author

Ayelet Shavit, a philosopher of science, is a senior lecturer and head of the philosophy program at Tel Hai College. She lives at Kibbutz K'far Giladi, Israel. Aaron M. Ellison is the senior research fellow in ecology, Harvard University, Harvard Forest. He lives in Royalston, MA.

Table of Contents

Foreword W. John Kress xi

Preface xvii

Acknowledgments xxi

Part 1 Introduction: Replication Across Disciplines

1 Toward a Taxonomy of Scientific Replication Ayelet Shavit Aaron M. Ellison 3

2 Borges on Replication and Concept Formation Yemima Ben-Menahem 23

3 The Historical Emergence of Replication: Reifying Geography through Repeated Surveys Haim Goren 37

Part 2 Replication in Biology: Overviews and Case Studies

The Value of Natural History Collections

4 Natural History Collections as Dynamic Research Archives Tamar Dayan Bella Galil 55

5 Looking to the Past to Plan for the Future: Using Natural History Collections as Historical Baselines Rebecca J. Rowe 64

Repeatable Monitoring and Observations

6 Monitoring: Repeated Sampling for Understanding Nature Avi Perevolotsky Naama Berg Orit Ginzburg Ron Drori 83

7 Monitoring the State of Nature in Israel Ron Drori Naama Berg Avi Perevolotsky 94

8 Creating Coherent Time Series through Repeated Measurements in a Marine Monitoring Program Yonathan Snaked Amatzia Genin 112

Replication and Experiments

9 Contingent Repeatability of Experiments in Time and Space Aaron M. Ellison 125

10 The Influence of Variation among Replicates on Repeatability Jacob Pitcovski Ehud Shahar Avigdor Cahaner 139

Meta-analysis and the Need for Repeatability

11 Replication and Repetition in Systematic Reviews and Metaanalyses in Medicine Leonard Leibovici Mical Paul 157

12 Clinical Heterogeneity in Multiple Trials of the Antimicrobial Treatment of Cholera Mical Paul Ya'ara Leibovici-Weissman Leonard Leibovici 163

The Role, of Metadata in Creating Reproducible Research

13 Reliable Metadata and the Creation of Trustworthy, Reproducible, and Re-usable Data Sets Kristin Vanderbilt David Blankman 179

14 Replication of Data Analyses: Provenance in R Emery R. Boose Barbara S. Lerner 195

Part 3 Integration and Synthesis

15 Turning Oranges into Apples: Using Detectability Correction and Bias Heuristics to Compare Imperfectly Repeated Observations Morgan W. Tingley 215

16 Dissecting and Reconstructing Time and Space for Replicable Biological Research Barbara Helm Ayelet Shavit 233

17 Best Practices for Creating Replicable Research Aaron M. Ellison 250

Epilogue: A Chorus's Dance with Replication Ayelet Shavit 265

Bibliography 271

List of Contributors 305

Index 311

Editorial Reviews

A compelling case for standardizing methods and creating a more open scientific community.”—Choice

“This book, a thematically coherent collection of 17 chapters, which includes some thought-provoking philosophizing, focuses on the issue of experimental replication, primarily in ecological research, with some consideration of other scientific/biological areas.”—Quarterly Review of Biology

“This book mulls and kneads the concept of replicability—moving us toward that point where such a concept is a smooth round pebble, comfortably fitting into our pocket. It is a model for treating the philosophically rich concepts used (and abused) in science."—Michael Paul Nelson, Ruth H. Spaniol Chair of Renewable Resources and Professor of Environmental Philosophy and Ethics, Oregon State University

“The central themes of this volume are replication, repeatability, and reproducibility, which individually and in concert form a cornerstone in all fields of science and all aspects of scientific enquiry. This volume has no antecedent.”—James L. Patton, University of California, Berkeley

"The book is a work of surprising breadth, incorporating philosophy and literature and a wide variety of scientific approaches. It provides insights about replication that would not emerge from any single discipline.”—John H. Porter, University of Virginia

From the Publisher