Thinking about Science E-Book

Ferric C Fang

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: ASM
• Sprache: Englisch

Seitenzahl: 1091

Veröffentlichungsjahr: 2023

Beschreibung

Thinking about Science: Good Science, Bad Science, and How to Make It Better A riveting exploration of the world of science, diving headfirst into its triumphs and tribulations. Penned by seasoned microbiologists Ferric C. Fang and Arturo Casadevall, this book offers a comprehensive analysis of the scientific enterprise through various lenses, including historical, philosophical, and personal. From their unique vantage points as researchers, clinicians, and educators, Fang and Casadevall dissect the intricate mechanisms of science, shedding light on its strengths and weaknesses. Through engaging historical anecdotes, personal narratives, and insightful academic studies, they present a candid evaluation of science's performance, including a thought-provoking examination of its role during the COVID-19 pandemic. A must-read for anyone curious about the present predicaments and future potential of science, Thinking about Science: Good Science, Bad Science, and How to Make It Better is more than just a book; it's a roadmap to understanding and improving the scientific endeavor for the benefit of society at large. "The authors have given us a thoughtful description of science and the joy of discovery, an unflinching diagnosis of where improvements are needed, and recommendations for remedies well worth considering. Scientists, science and society would benefit if this book were read by both future and established scientists, as well as the administrators, policymakers, and regulators who are in a position to help us do better." Michael Kalichman, UC San Diego "With a deep understanding of the profound impact of science on society, the authors provide thought-provoking perspectives on changes in the scientific enterprise that will support sustainable, equitable practices, and engender public trust. An engaging read for everyone with an interest in science or science policy." Stanley Maloy, San Diego State University

Leseprobe

Thinking about Science

Good Science, Bad Science, and How to Make It Better

FERRIC C. FANG

University of Washington School of Medicine

Seattle, Washington

ARTURO CASADEVALL

The Johns Hopkins University Bloomberg School of Public Health and School of Medicine

Baltimore, Maryland

Copyright © 2024 American Society for Microbiology. All rights reserved.

Copublication by the American Society for Microbiology and John Wiley & Sons, Inc.

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The right of Ferric C. Fang and Arturo Casadevall to be identified as the author(s) of this work/the editorial material in this work has been asserted in accordance with law.

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Boxes, Figures, and Tables

Boxes

Box 1.1

Science and technology

Box 1.2

Mathematics and science

Box 1.3

Was science inevitable?

Box 1.4

Science and uncertainty

Box 1.5

Where do formulas in science come from?

Box 2.1

Careful description leads to cosmic understanding

Box 2.2

“Descriptive” is a fraught word in the scientific lexicon

Box 2.3

Careful description can lead to revolutionary new insights

Box 3.1

The illusion of scientific processes as clockwork

Box 3.2

Mechanism leads to rational drug design

Box 5.1

Elegance in the crust

Box 5.2

Elegance in medicine

Box 6.1

Rigor, deception, and intellectual honesty

Box 6.2

Rigor and reproducibility

Box 7.1

Efforts to improve the reproducibility of biomedical sciences

Box 8.1

Importance in real time

Box 8.2

Important science in the 1890s: Anna Williams and diphtheria antitoxin

Box 9.1

Forgetting history cost lives in the COVID‐19 pandemic

Box 10.1

Do scientific generalists pay a penalty today?

Box 11.1

Revolutionary science as an antidote for depression

Box 12.1

How basic research allowed scientists to meet the HIV challenge

Box 12.2

Reverse translation: drug toxicity triggers bedside‐to‐bench research

Box 13.1

Science and the moonshot

Box 14.1

The cultivation of

Mycobacterium ulcerans

Box 15.1

Using science teaching to highlight inequality and recognize diversity in science

Box 17.1

A study of problematic images in published papers

Box 17.2

The

Molecular and Cellular Biology

study

Box 17.3

Post‐publication review

Box 18.1

A problematic paper triggers a congressional hearing

Box 19.1

The Higgs boson as a case study in the capriciousness of credit allocation in science

Box 20.1

Polio vaccine wars: Albert Sabin versus Jonas Salk

Box 20.2

Conflict resolution in science

Box 21.1

The Nobel Prize distorts the history of DNA

Box 21.2

More fun than a Nobel Prize

Box 21.3

An alternative Nobel Prize scheme

Box 22.1

Preprints and rejected science

Box 22.2

The fate of rejected papers

Box 22.3

The importance of failure in science

Box 23.1

Transformative research that almost wasn’t

Box 23.2

Randomization as a mechanism for bias reduction

Box 24.1

Fake peer review

Box 25.1

Types of error

Box 25.2

The worst error in science?

Box 26.1

How to choose a journal? Then and now

Box 26.2

The cult of numerology in science

Box 26.3

Other numbers used for the measurement (and mismeasurement) of science

Box 27.1

Biosafety versus biosecurity

Box 27.2

Daniel Carrión, medical martyr

Box 29.1

Should a chapter on deplorable science include a quote from Wernher von Braun?

Box 29.2

Is it ethical to use findings from unethical research?

Box 30.1

Ten lessons from COVID‐19 for science

Box 31.1

Training scientists as generalists

Figures

Fig. 1.1

Inductive versus deductive reasoning

Box 1.4 Fig.

Ancient Roman mosaic from 3rd century

CE

depicting Anaximander holding a sundial

Box 2.1 Fig.

Henrietta Swan Leavitt (1868–1921)

Box 2.3 Fig.

Alfred Wegener (1880–1930)

Fig. 2.1

John Snow’s cholera map

Box 3.1 Fig.

A pendulum clock designed by Galileo, as drawn by Vincenzo Viviani in 1659

Box 3.2 Fig.

Gertrude Elion (1918–1999)

Fig. 4.1

Modern extension of the central dogma of molecular biology

Box 5.2 Fig.

Rates of cervical cancer in Swedish women stratified by vaccination status

Fig. 5.1

Journal articles in PubMed containing the keyword “elegant” as a function of publication year

Fig. 5.2

The concept of elegance in science

Fig. 6.1

A Pentateuch for improving rigor in the biomedical sciences

Box 7.1 Fig.

Factors that might improve reproducibility

Fig. 8.1

Scientific importance is all about the SPIN

Box 8.2 Fig.

Anna Wessels Williams (1863–1954)

Fig. 9.1

Elie Metchnikoff (1845–1916)

Box 10.1 Fig.

Carl Sagan (1934–1996)

Fig. 11.1

Thomas Kuhn (1922–1996)

Fig. 12.1

U.S. research and development spending as a percentage of the gross domestic product, 1953 to 2016

Fig. 12.2

Trends in U.S. investment in research and development

Fig. 13.1

Illustration from Jules Verne’s

From the Earth to the Moon, and Round It

Fig. 14.1

Three Princes of Serendip

Box 15.1 Fig.

June Dalziel Almeida (1930–2007)

Fig. 15.1

Important contributors to the germ theory of disease

Fig. 17.1

Dr. Elisabeth Bik

Fig. 17.2

Examples of simple duplication

Fig. 17.3

Examples of duplication with repositioning

Fig. 17.4

Examples of duplication with alteration

Fig. 17.5

Percentage of papers containing inappropriate image duplications by year of publication

Fig. 18.1

Example of data fabrication

Fig. 19.1

The economics of science

Box 19.1 Fig.

Peter Higgs, 2013 Nobel laureate in Physics

Box 20.1 Fig.

Albert Sabin and Jonas Salk

Box 21.2 Fig.

Jocelyn Bell Burnell in 1967 and 2009

Box 22.3 Fig.

Oswald Avery in 1937, thriving on disappointment

Box 23.1 Fig.

Katalin Karikó

Fig. 23.1

Proposed scheme for a modified funding lottery

Fig. 24.1

Correlation between impact factor and retraction index

Fig. 24.2

Citation network of a retracted paper

Fig. 24.3

Trends in retractions as a function of time

Fig. 25.1

Major causes of error

Box 25.1 Fig.

Type I versus type II error

Fig. 25.2

Errata and error‐related retractions over time

Fig. 26.1

Distribution of the number of citations for neuroscience articles in six major journals, 2000–2007

Box 27.2 Fig.

Daniel Alcides Carrión García (1857–1885)

Fig. 28.1

Max Planck (1858–1947), c. 1930

Box 29.1 Fig.

Saturn V rocket

Fig. 30.1

First COVID‐19 vaccine recipient in the United States

Fig. 30.2

Reduction of airborne virus transmission by face mask use

Fig. 31.1

Overall R01 grant success rates at the National Institutes of Health, 1965 to 2021

Box 31.1 Fig.

The three R’s

Fig. 31.2

The chain of research integrity

Tables

Table 3.1

A scientist considers the illumination of a dark room

Table 3.2

A scientist considers the cause of a skin lesion

Table 6.1

Some elements of scientific redundancy

Table 6.2

ASA principles for the use of

P

values

Table 7.1

Some causes of irreproducibility and error in biomedical sciences

Table 11.1

Characteristics and impact of scientific revolutions

Table 11.2

Some practical societal benefits from scientific revolutions

Table 16.1

Warning signs of pseudoscience

Table 19.1

Competition for money versus credit

Table 21.1

Some controversial Nobel Prizes in the sciences

Table 23.1

Potential sources of bias in grant application peer review

Table 24.1

Retraction problems and suggested solutions

Table 25.1

Categories of errors before and after 2000

Table 25.2

Examples of unretracted articles containing significant errors

Table 25.3

Examples of common errors and suggested remedies

Table 27.1

A few of the scientists believed to have been injured or killed from research‐related exposures

Table 28.1

Some Nobel laureates who have strayed from their areas of expertise

Table 30.1

A comparison of pandemic responses

Table 31.1

Sample checklist for an observation in which a stimulus elicits an effect

Preface

We live in an age of science and technology. Science has allowed us to understand our place in the universe and our relationship to all life on Earth. Technology has provided a sophisticated computer on which to compose this book and allowed us to reshape our world to make life safer, more productive, and more comfortable. This has never been clearer than during this time of plague, as the COVID‐19 pandemic enters its fourth year and finally shows signs of receding. The advanced technology of COVID‐19 vaccines has greatly reduced the mortality of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection and provided a vivid demonstration of the tangible benefits of science for society. As harrowing as the last few years have been, just think of what they would have been like if we didn’t have science.

And yet, there are signs that not all is well with the scientific enterprise. The pace of transformative biomedical innovation appears to be slowing (1, 2). Fraud, sloppiness, and error have required the retraction of publications from the literature. Record numbers of research trainees are opting out of academic career pathways. Surveys report declining public confidence in scientists. With looming challenges from future pandemics, climate change, and shortages of food, water, and energy, it is vital for the world’s scientific enterprise to be firing on all cylinders, to use an automotive metaphor (which will happily become anachronistic as electric vehicles displace those with internal combustion engines). This volume is a collection of essays exploring the nature of science and the way that it is performed today. In thinking about science, both good and bad, we will cast a light on contemporary scientific culture and practice, provide guideposts for young scientists, and propose a blueprint for reforming the way that science is done.

This book is written for scientists and science students, but also for technologists, engineers, mathematicians, teachers, journalists, administrators, policymakers, and anyone with an interest in science and how scientists think. The project began 15 years ago when we were editors at the journal Infection and Immunity. Our initial collaborative essay, called “Descriptive Science,” was prompted by the tendency of many reviewers to dismiss work with the adjective “descriptive,” despite the fact that description is the foundation of much of science (3). Encouraged by the positive responses from our colleagues, we subsequently collaborated on more than 40 articles, editorials, or commentaries. Many of the essays in this collection had their genesis in conversations or email exchanges, which eventually developed into editorials or commentaries. Each has been recently updated and supplemented with additional material for publication in this book. Nine of the chapters are completely new and have not been published elsewhere.

Our goal has been to create a volume that can be read either sequentially or as individual chapters, each constituting a freestanding essay that can be read and understood independently, although we have connected the themes through cross‐referencing. Anyone reading the book from cover to cover will note some repetition, as certain issues arise again and again in various contexts. This is intentional and was necessary for the chapters to be able to stand on their own. We hope that this will help to reinforce these points.

Over the years, we have often commented to each other how writing these essays has improved our understanding of science and made us better scientists. We hope the same will be true for our readers. You will find that much of the material is slanted toward issues in the biomedical sciences, with a particular preference for the subdisciplines of microbiology and immunology. This reflects the fact that we are both active scientists with research programs focused on microbial pathogenesis. We make no apologies for writing about what we know best and note that other science essayists, such as Thomas Kuhn (4) and Eugene Wigner (5) writing about scientific revolutions and the unreasonable effectiveness of mathematics, have focused largely on examples from the physical sciences. In fact, we think that our biomedical emphasis makes sense since the 21st century is heralded to be the biological century. We subscribe to the view that science is a continuous discipline and observations made in one domain can apply to other domains as well. Nevertheless, we have attempted whenever possible to bring the physical sciences into the context of our essays, and readers will find numerous references to Newtonian physics, plate tectonics, and particle physics. We purposefully refer to some of the same scientific discoveries in multiple chapters in order to illustrate the continuity of themes across different aspects of science using familiar examples. Hence, some scientists, such as Alfred Wegener, Oswald Avery, and Rosalind Franklin, appear in more than one chapter, and we hope you will enjoy becoming more acquainted with them.

In many ways, Thinking about Science is a commentary on the current state of science in the early 21st century, with a particular emphasis on biomedical research. Although both of us are unabashed admirers of science and the scientific process, the reader may note a critical tone in many of these chapters. This, too, is intentional and reflects the fact that many chapters are written to highlight a problem in science in the hope of correcting it. The “Historical Science” chapter laments how often science ignores and neglects its history. In fact, we hope that the book provides an accurate snapshot, from the perspective of scientists working in the present day, for future historians of science. Similarly, we hope that chapters such as “Descriptive Science,” “Mechanistic Science,” “Reductionistic and Holistic Science,” and “Important Science” have captured the tension of our time regarding preferred scientific approaches. “Impacted Science” describes a contemporary sociological malady that we hope will become obsolete in future years as science reforms its value system. “Dismal Science” delves into the economics of science, and we hope that more economists will take an interest in this important topic that remains largely unexplored. “Plague Science” feels unfinished, as every week brings a new development in the COVID‐19 pandemic, and yet we hope that the words therein capture a sense of this moment in early 2023 by documenting successes and failures in confronting a novel viral scourge. In updating the early chapters of our collaboration, we have been both pleasantly surprised at the progress in certain areas, such as prepublication review, efforts to improve reproducibility, and efforts to improve equality and diversity in science, and dismayed by how little has been done in others, such as persistent problems with peer review and funding.

For us, this book has provided an opportunity to reflect and to gather and update our thoughts after 15 years of friendship and collaboration. This is, of course, a work in progress, and we will continue our work as practitioners, observers, and commentators of contemporary science who want to improve the scientific enterprise. We encourage readers to write to us with their comments, criticisms, and suggestions so that we can continue to think about science together.

January 2023

1. Park M, Leahey E, Funk RJ

. 2023. Papers and patents are becoming less disruptive over time.

Nature

613

:138–144.

http://dx.doi.org/10.1038/s41586‐022‐05543‐x

.

2. Casadevall A

. 2018. Is the pace of biomedical innovation slowing?

Perspect Biol Med

61

:584–593.

http://dx.doi.org/10.1353/pbm.2018.0067

.

3. Casadevall A, Fang FC

. 2008. Descriptive science.

Infect Immun

76

:3835–3836.

http://dx.doi.org/10.1128/IAI.00743‐08

.

4. Kuhn TS

. 1970.

The Structure of Scientific Revolutions

, 2nd ed. The University of Chicago Press, Chicago, IL.

5. Wigner EP

. 1960. The unreasonable effectiveness of mathematics in the natural sciences.

Commun Pure Appl Math

13

:1–14.

http://dx.doi.org/10.1002/cpa.3160130102

.

Acknowledgments

The opinions expressed in this book are our own, and we take full responsibility for any errors (see chapter 25). We gratefully acknowledge the contributions of coauthors who have collaborated with us on previous publications, including Joan Bennett, Elisabeth Bik, Anthony Bowen, Erika Davies, Roger Davis, Daniele Fanelli, Michael Imperiale, Amy Kullas, Margaret McFall‐Ngai, R. Grant Steen, and Andrew Stern. We also thank our many colleagues who have provided important insights and feedback on the topics covered in this book, including Gundula Bosch, Nichole Broderick, Lee Ellis, Sunil Kumar, Adam Marcus, Ivan Oransky, Liise‐anne Pirofski, and Jessica Scoffield. We are grateful to the American Society for Microbiology for their longstanding support and for giving us a venue to publish our papers and ideas, in particular Stefano Bertuzzi, Christine Charlip, Shannon Vassell, Shaundra Branova, and our editor, Megan Angelini. We thank our mentors and students, who have taught us so much and renewed our passion for science. Finally, but certainly not least, we thank our families for their love, encouragement, and indulgence during the many late nights and weekends that we have spent thinking about science instead of other things. This book is dedicated to them.

About the Authors

Ferric C. Fang and Arturo Casadevall are physician‐scientists and journal editors who have studied infectious diseases for more than three decades and have a longstanding interest in the culture and sociology of science. Dr. Fang is presently a Professor in the Departments of Laboratory Medicine and Pathology, Microbiology, Medicine, and Global Health at the University of Washington School of Medicine, and Dr. Casadevall is presently a Bloomberg Distinguished Professor in the Johns Hopkins Schools of Public Health and Medicine.

Ferric C. Fang

Arturo Casadevall

IDEFINITIONS OF SCIENCE