Assignments 2018
Class #1: Wednesday, January 31
Introduction to the course and to each other, and a discussion of a life in science.
Class agenda:
- Course mechanics, expectations, and schedule.
- An informal talk (by me) about my career (with Q and A).
- A roundtable presentation of your backgrounds and your interests in the subjects of this course.
Readings to inform the discussions:
H Varmus: The Art and Politics of Science (Norton, 2009)
Read the Introduction and a chapter or two that interests you
(https://www.ncbi.nlm.nih.gov/books/NBK190622/)
I.A. Richards, Practical Criticism (1930), Introduction, pp 3-18 The role of evidence in the arts and humanities
Available online at Internet Archive https://archive.org/stream/practicalcritici030142mbp#page/n27/mode/2
Some stories about how others became scientists:
http://library.cshl.edu/oralhistory/
Other relevant references:
Francois Jacob: The Statue Within (Cold Spring Harbor Press, 1995) (available online: http://ineedbooks.xyz/?book=0879694769)
Perhaps the best written of the many memoirs of famous scientists; this one features World War II, remarkable modesty, and compelling, graceful prose.
JD Watson, The Double Helix (1969)(perhaps the most famous and enjoyable book about one person’s view of the competition, frustration, social complexities, and exuberance of making a great discovery in the life sciences; for some interesting, contentious commentary, look at the contemporary reviews, especially this one: http://www4.ncsu.edu/~kimler/hi481/Chargaff_review.pdf) http://faculty.washington.edu/hqian/amath532/Watson_The_Double_Helix.pdf
Matthew Cobb: Life’s Greatest Secret: The Race to Crack the Genetic Code (2015) (purchase from Amazon etc). An excellent, recent book describing one of the most exciting moments in the molecular revolution.
Class #2: Wednesday, February 7th
What inspires people to become scientists?
Assigned viewing:
Arrowsmith (1931), movie directed by John Ford, starring Ronald Coleman and Helen Hayes. (Link below)
https://drive.google.com/file/d/0B2xkDGAZil76RlE3SkZnUXNlR2c/view?usp=drivesdk
Additional reading: passages or chapters from one or more of the following books:
Paul de Kruif, The Microbe Hunters (a collection of essays published in 1926 about heroic scientists in the age of discovery of the infectious causes of disease; many scientists of my vintage claim this book as an inspiration for their choice of career)
https://laurieximenez.files.wordpress.com/2011/02/1a_microbehunters_pauldekruif.pdf
S.Lewis, Martin Arrowsmith (the award-winning novel from 1925 that is the basis for the movie; de Kruif introduced Lewis to scientists at the Rockefeller Institute in NYC to get him interested!) https://archive.org/details/martinarrowsmith030614mb
C.P. Snow, The Search (a short novel written in 1934 by an eminent 20th-century British novelist/politician/physicist about the early stages of the career of a British physicist; cheap paper versions available from Amazon).
E.Schrodinger, What is Life? (1944)(an essay by a famous physicist about the physical properties of living things that raised intriguing questions about how life could operate according to the laws of physics) https://archive.org/details/WhatIsLife-EdwardSchrodinger
H.F. Judson, The Eighth Day of Creation (a magisterial yet intimate and informal history of the rise of molecular biology as a discipline, teaching how the central precepts of modern biology were elucidated) http://fr.ebooke.info/?book=0879694785
Andrea Barrett, Archangel (a 2004 collection of short stories about the growing influence of biological science on young people in the late 19th and early 20th century by a contemporary writer) No free ride here: https://www.amazon.com/Archangel- Fiction-Andrea-Barrett/dp/0393348776
Questions to consider:
In general: What are the motivations for a career in science?
For Arrowsmith (movie or book):
What special pressures or attractions exist in the conduct of research on human subjects?
What justifies the randomized clinical trial?
What patient protections would you want to impose?
What pressures were operating on Martin Arrowsmith when he made his decisions about distribution of his “vaccine”?
What would have been the right decision for you? Why?
Follow up to Arrowsmith:
Article in Dec 2016 STAT about treatment of infection with bacterial virus:
https://www.statnews.com/2016/12/07/virus-bacteria-phage-therapy/
DG McNeil, “New Ebola Vaccine Gives 100 Percent Protection,” NY Times Dec 22, 2016. https://www.nytimes.com/2016/12/22/health/ebola-vaccine.html
Class #3: Wednesday, February 14th
What are the purpose and importance of science?
Assigned readings:
Vannevar Bush, The Endless Frontier (1945). Essential summary pp.5-9. But also valuable to browse through the volume. https://archive.org/stream/scienceendlessfr00unit#page/42/mode/2up
Francis Bacon: see the paragraphs at the bottom
Consider science from several perspectives:
Public purpose: A way for communities and nations to prosper by developing technical skills that promote progress (V. Bush, F. Bacon, and D. Sobel), based on the findings of fundamental science
Personal satisfactions: A way to get a grip on the meaning of life, a kind of philosophy, based on the way things are (S. Greenblatt), a way “to explain the world” (S. Weinberg), and a way to enjoy life through stimulating, thought-provoking careers (F. Crick, G. Stent)
Background readings:
S. Greenblatt, The Swerve (2014) You can listen for free at https://archive.org/details/00000000_20141012 (listen to the Preface, pp 1-13)
Lucretius, On the Nature of Things (or his predecessors: Democritus, Leucippus) http://oll.libertyfund.org/titles/carus-on-the-nature-of-things,
http://classics.mit.edu/Carus/nature_things.html and other presentations online.
F. Crick, What Mad Pursuit: A Personal View of Scientific Discovery (1990) Especially Chapter 2 (The Gossip Test)
https://www.amazon.com/What-Mad-Pursuit-Scientific-Discovery/dp/0465091385(or PA Lawrence, “Francis Crick: A Singular Approach to Scientific Discovery,” Cell 167: 1436, 2016). http://www.cell.com/cell/pdf/S0092-8674(16)31529-X.pdf
G. Stent, The coming of the Golden Age: a view of the end of progress (1969) Too expensive to acquire! https://www.amazon.com/Coming-Golden-Age-View-Progress/dp/0385019378
S. Weinberg, To Explain the World (2015) A dense, long, clear history of science by a great contemporary physicist https://www.amazon.com/Explain-World-Discovery-Modern-Science/dp/0062346660
(instructively reviewed by Jim Holt in NYROB, Sept 24, 2015, p 53-54; http://www.nybooks.com/articles/2015/09/24/steven-weinberg-core-science/
D. Sobel, Longitude, The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. A highly enjoyable essay that shows the utility of science and an unusual way to fund it: prizes! https://www.pdf-archive.com/2014/07/31/longitude/
Francis Bacon (a mini-synopsis)
From Wikipedia: “Bacon considered that it is of greatest importance to science not to keep doing intellectual discussions or seeking merely contemplative aims, but that it should work for the bettering of mankind’s life by bringing forth new inventions, having even stated that “inventions are also, as it were, new creations and imitations of divine works”.[2] He cites examples from the ancient world, saying that in Ancient Egypt the inventors were reputed among the gods, and in a higher position than the heroes of the political sphere, such as legislators, liberators and the like. He explores the far-reaching and world-changing character of inventions, such as in the stretch:
“Printing, gunpowder and the compass: These three have changed the whole face and state of things throughout the world; the first in literature, the second in warfare, the third in navigation; whence have followed innumerable changes, in so much that no empire, no sect, no star seems to have exerted greater power and influence in human affairs than these mechanical discoveries.” Novum Organum, see Section CXXIX (p 37 of 139) on iPad version)
Questions to consider:
What was the historical context in which Vannevar Bush wrote Science: The Endless Frontier? And how did that affect his formulation?
What are the implications of his vision of the relationship of government to science with respect to pursuit of basic science? Universities? Ownership of intellectual property?
How is that vision threatened by the current Administration? For one version, read the recent article by Ron Daniels, President of Johns Hopkins University in the current issue of Issues in Science and Technology: http://issues.org/34-2/perspective-knee-capping-excellence/ or see the recent article by Eric Lander that addresses the issues more broadly on the MHC360 website :
What needs to be done about this?
How do you weigh national (public) interests in the support of science against the personal value of a life of inquiry and discovery?
Does society benefit from the commitment of individuals to seeing life in a certain way?
Class #4, Wednesday, February 21st
Credibility of science
What are the failures and uncertainties of science and their consequences?
Our objectives in this session are to discuss the weaknesses of the scientific method
—-its inherent uncertainty and its fallibility, as well as the undermining of science by misconduct and poor practices (such as those that produce work that is not reproducible).
Another way to think about these problems is to ask: Why do scientists get things wrong and what should we do about it? The answers include misconduct (willful cheating); sloppiness; and the fundamental difficulties of deciphering how the world works (that is, science is hard and never-ending, and mistakes are inevitable).
We will consider what can be done to minimize error and fraud and what the consequences of these properties of science might be for public policy, including policies based on flawed science, public distrust of science, and the willful misuse or abuse of the nature of science to advance special interests.
INSTRUCTIONS TO STUDENTS:
1)Misconduct.
Everyone should watch this short talk on YouTube by Howard Schachman, who made a compelling case for a strict definition of what constitutes misconduct: https://www.youtube.com/watch?v=k554m3CghYI
2)Reproducibility
Science has always been defended as sound because important conclusions proposed by individual laboratories are accepted by a scientific community that has repeated or built on the evidence that supports the conclusions. But this claim has recently been challenged.
Everyone should read this brief account of the difficulty that pharmaceutical companies claim to have had in reproducing work that could affect what drug companies work on:
http://www.nature.com/nature/journal/v483/n7391/full/483531a.html
Several people have argued that we should have mechanisms for reproducing important or widely cited work. Think about the benefits and difficulties of doing this. At least three people should look at January 2017 papers from the open access journal, eLIFE (https://elifesciences.org/archive/2017/01)
to see what is being done and what some people think about the efforts to demonstrate reproducibility.
At a minimum, those three should look at the very short essay by Nosek and Errington: https://elifesciences.org/content/6/e23383
Some of you interested in cancer biology should look at an article about one of the five replication efforts (perhaps one about certain mutations in melanomas: https://elifesciences.org/content/6/e22662)
Another possible contributor to the replication problem is “publication bias”, a tendency to favor publication of so-called “positive results.” Some of you from the social sciences might find this interesting:
https://www.ncbi.nlm.nih.gov/pubmed/?term=nissen+gb%2C+magidson+t%2C+gross+k
- Failures of scientific methods can have important practical consequences.
One striking example, recently in the news, concerns the use of science in the judicial system. At least one person, preferably more, should read the executive summary of a recent report from the President’s Council of Advisors on Science and Technology (PCAST) on the imperfect accuracy of such methods:
Forensic Science in Criminal Courts: Ensuring Scientific Validity of Feature-Comparison Methods (PCAST, Executive Office of the President, September 2016)
Philosophers of science have long worried about what is necessary for scientific observations to become the basis of accepted conclusions about how the world works. One of the best-known theses is this one:
Karl Popper, The Logic of Scientific Discovery,1935. At least three people should browse sufficiently in this book to summarize Popper’s widely cited point of view.
Excerpt: http://personal.lse.ac.uk/ROBERT49/teaching/ph103/2013-2014/pdf/Popper_LSD_Ch1.pdf
Squashed version: http://sqapo.com/popper.htm
Brief optional amusements:
- Sara Whitlock, “A new PhD student learns her first lesson: Certainty doesn’t exist in science,” STAT 12/30/16
https://www.statnews.com/2016/12/30/science-grad-student-lesson/
- PLOS ONE essay on the role of the media and institutions in promoting questionable conclusions:
https://www.statnews.com/2017/03/02/science-media-news/
4) The inevitability and virtues of scientific errors
These titles refer to the virtues of making mistakes in honorable efforts to solve big problems. None of this is required reading, but I’d be pleased if one or more of you wanted to follow up on Watson’s The Double Helix by reading the two chapters in Livio’s excellent book that describe how Linus Pauling (arguably the greatest chemist of the 20th century) got misled about the structure of DNA and lost out to Watson, Crick, and others.
- Livio, Brilliant Blunders From Darwin to Einstein: Colossal Mistakes by Great Scientists That Changed Our Understanding of Life and the Universe, Simon and Schuster, 2013. (Chapters 6 and 7)
- Schultz, Being Wrong: Adventures in the Margin of Error, HarperCollins, 2010.
Hannah Bloch, “Failure is an option,” National Geographic, September 2013.
5) Consequences of the inherent inaccuracy of science and its propensity to error for the formulation of public policy.
We will think about this in relation to current debates about some highly sensitive topics: climate change, vaccination, evolution, and compensation for sports injuries, and we will also discuss these issues as they affected the control of tobacco use.
Climate change
Everyone should read Robert Proctor’s brief summary of the issue and its contemporary relevance:
The debates about climate change can affect legislation, regulation, and budgets; everyone should look at this very recent development and consider the consequences:
For those who have not followed the science about climate change, here is a brief, useful consensus view:
http://www.nytimes.com/interactive/2015/11/28/science/what-is-climate-change.html
Sports injuries
There are complex medical issues here and a lot is at stake for team owners. You may notice a pattern in the way the issues are framed.
http://www.nytimes.com/2017/02/08/sports/hockey/nhl-chronic-traumatic-encephalopathy-cte-juliet-macur.html?smprod=nytcore-ipad&smid=nytcore-ipad-share The league’s onerous demand in a class-action suit on head injuries seems to show little regard for medical privacy and accepted scientific facts.
Other contentious issues (with different degrees of consensus)
Does immunization increase the risk of autism?
Is evolution of species still a theory or an established fact?
Does tobacco use increase the risk of cancers and other diseases?
I am making no specific reading assignments for these topics but our discussion will be informed by anything that anyone chooses to read from a vast literature.
Additional readings
To enlarge the discussion beyond science to politics and to think about how the political approaches are framed, here are a few relevant, recent books on the political uses of uncertainty:
N. Oreskes and E.M. Conway: Merchants of Doubt: How a Handful of Scientists Obscured the Truth on Issues from Tobacco Smoke to Global Warming (Bloomsbury Press, 2010). I will summarize the argument for our discussion.
J. Nesbit: Poison Tea: How Big Oil and Big Tobacco Invented the Tea Party and Captured the GOP (St. Martin’s Press, 2016)
Shawn Otto, The War on Science (Milkweed, 2016)
THE PURPOSE, PRACTICE, AND POLITICS OF SCIENCE
SESSION #5:
Science in the Public Square:
Education, Advocacy, Policy, and Explanation
The interface between science and society is crucial to democratic societies, and the ability of scientists to engage directly with the public (a field known as science communication) has gained urgent attention over the past decade. We’ll briefly consider the history of scientists talking to the general public (Aristotle, Humphry Davy, and Charles Darwin, among the earlier practitioners), and then explore this increasingly important (and fractious) boundary through the lens of science explanation, political advocacy, communication of policy, and popularizations of science for broad public consumption.
The in-class discussion will focus on three aspects of science communication. The first will discuss public engagement for the purposes of either prediction or probabilistic risk warnings; a paradigmatic breakdown in communication surrounding the 2011 L’Aquila earthquake in Italy will be a central part of this segment.
Next, we’ll discuss the virtues and perils of popularization (Carl Sagan, Daniel Gilbert); recent skirmishes between scientist communicators (Steven Pinker) and outside communicators (Malcolm Gladwell); and how technology (Internet, blogs, TED talks) have transformed the landscape of science communication. With this in mind, we’ll also discuss the current clash of science advocacy and anti-science forces in an era where facts are up for grabs.
Finally, we will reserve a little time toward the end of the session to discuss—with the help of J.B.S. Haldane’s “How to Write a Popular Scientific Article”—principles of clear communication as you begin to think about your student presentations.
REQUIRED CLASS READINGS:
—Stephen S. Hall, “At Fault,” Nature (pdf)
—Daniel Gilbert, “Talking to Humans: Is It a Good Idea?”:
http://www.danielgilbert.com/SPSP2016.pdf
—Michael Mann, “If You See Something, Say Something,” New York Times:
https://www.nytimes.com/2014/01/19/opinion/sunday/if-you-see-something-say-something.html
—Joel Clement, “I’m a Scientist. I’m Blowing the Whistle on the Trump Administration,” Washington Post:
—New York Times and ProPublica, “E.P.A. Officials, Disheartened by Agency’s Direction, Are Leaving in Droves”:
https://www.nytimes.com/2017/12/22/climate/epa-buyouts-pruitt.html
—J. B. S. Haldane, “How to Write a Popular Scientific Article” (pdf)
OPTIONAL CLASS READINGS:
—Charles Darwin, Chapter 1, “The Voyage of the Beagle”
—Steven Pinker on Malcolm Gladwell, New York Times Book Review:
http://www.nytimes.com/2009/11/15/books/review/Pinker-t.html?_r=2&emc=booksupdateema1&nl=books&
—George Orwell, “What Is Science?”
http://orwell.ru/library/articles/science/english/e_scien
—Peter Medawar, “Science and Literature” (in Pluto’s Republic, 1986) (pdf)
—Boris Kachka, “Proust Wasn’t a Neuroscientist. Neither Was Jonah Lehrer” (New York, 2012)
http://nymag.com/news/features/jonah-lehrer-2012-11/
—“President Trump’s War on Science,” New York Times Editorial Board:
https://www.nytimes.com/2017/09/09/opinion/sunday/trump-epa-pruitt-science.html
Questions to Consider:
- What are the responsibilities, and risks, of communicating scientific information to the public?
- Does public advocacy undermine the evidence-based, non-biased mission of scientific research?
- Who makes for the more “reliable narrator” in disseminating scientific information to the public—scientists themselves or mediators like journalists? Are there situations where you would rather hear from a scientist than a journalist, and vice versa?
- How does a writer or speaker figure out how to “pitch” a scientific explanation at the right level for a general audience?
Session #6 March 7th. Equity issues in science and its applications
Scientists would like to think that their work is done for the benefit of all, but it is evident that the benefits are not shared equally, even in the countries in which the work is done. This is so because of numerous factors—most obviously, economic disparities that influence whether people can afford the services and products that science enables, but also because of location, educational levels, gender, and ethnicity. Furthermore, we would like to believe that opportunities to participate in scientific work are available equally to all who have the necessary talents, but it is evident that social networks, gender, and race strongly influence access to those opportunities.
In this session, we will talk about some notable examples of the lack of equity and discuss ways in which the more subtle factors—especially issues of gender and ethnicity—can be studied, understood, and perhaps ameliorated.
In doing the readings below, think about the following questions:
- What are the possible origins of the disparities in health outcomes among groups of US citizens?
- How can we distinguish between prejudice and other factors to account for the under-representation of female and minority personnel in the sciences?
- Some of the assigned papers make use of social sciences to enhance understanding of gender and racial disparities. What kinds of changes in the medical and scientific enterprise would you recommend upon reading these papers?
- How does the current debate about US immigration policies affect science?
Assigned readings:
- Social scientists have been studying the factors that influence the participation of population groups in the scientific enterprise. Here are two recent, much discussed examples of such studies that might help address the problems of inclusion and fair treatment of minority populations in the US scientific enterprise:
C.A. Moss-Racusin et al, Science faculty subtle gender biases favor male students. PNAS 109: 16474, 2012. http://www.pnas.org/content/109/41/16474.full.pdf
Donna K. Ginther1,*, Walter T. Schaffer2, Joshua Schnell3, Beth Masimore3, Faye Liu3, Laurel L. Haak3, Raynard Kington2,†
Race, Ethnicity, and NIH Research Awards
Science 19 Aug 2011:Vol. 333, Issue 6045, pp. 1015-1019 DOI: 10.1126/science.1196783http://science.sciencemag.org/content/333/6045/1015/tab-pdf
https://www.ncbi.nlm.nih.gov/pubmed/21852498
- One of the benefits of science that we might expect to be available to all in an enlightened society is advanced health care. The following two papers are classic studies that attempt to identify factors accounting for disparate outcomes:
Peter B. Bach, MD; Deborah Schrag, MD, MPH; Otis W. Brawley, MD; Aaron Galaznik; Sofia Yakren; Colin B. Begg, PhD
Survival of Blacks and Whites After a Cancer Diagnosis
JAMA. 2002;287(16):2106-2113. doi:10.1001/jama.287.16.2106
http://jamanetwork.com/journals/jama/fullarticle/194853
KEVIN A. SCHULMAN, M.D., JESSE A. BERLIN, SC.D., WILLIAM HARLESS, PH.D., JON F. KERNER, PH.D., SHYRL SISTRUNK, M.D., BERNARD J. GERSH, M.B., CH.B., D.PHIL., ROSS DUBÉ, CHRISTOPHER K. TALEGHANI, M.D., JENNIFER E. BURKE, M.A., M.S., SANKEY WILLIAMS, M.D., JOHN M. EISENBERG, M.D.,
AND JOSÉ J. ESCARCE, M.D., PH.D.
THE EFFECT OF RACE AND SEX ON PHYSICIANS’ RECOMMENDATIONS FOR CARDIAC CATHETERIZATION New England Journal of Medicine 340:618, 1999.http://www.nejm.org/doi/pdf/10.1056/NEJM199902253400806
- Another aspect of the story may depend on the way in which clinical trials are done; here is an illustration of the problem from a recent news article:
(“As immunotherapy research takes off, the patients getting the treatment have been overwhelmingly white. Researchers know this and say they are trying to correct it.”)
Additional readings (not required but interesting):
- Several interesting women scientists have been written about. One of them, the astrophysicist Vera Rubin, died recently: here is an obituary by Dennis Overbye:
(“Dr. Rubin, who was awarded the National Medal of Science in 1993, ushered in the cosmic realization that most of the universe is invisible.”)
- Another, perhaps the most famous, woman scientist is the crystallographer, Rosalind Franklin, about whom numerous biographies (including Rosalind Franklin and DNA by Anne Sayre [Norton, 1975]) and a play (Photograph 51) have been written.
- A recently published account by a woman who studies plant biology has received a lot of praise last year:
Hope Jahren, Lab Girl, Knopf, 2016. (Reviewed in Nature in 2016)
- An exceptional Stanford neuroscientist, Ben Barres, also a transgendered person, died in December and the obituaries in Nature (553282, 2018) and the New York Times (December 29, 2017) were very informative about the role gender plays in science.
- A notable black embryologist, E.E. Just, is the subject of another terrific biography:Manning, K. R., Black Apollo of Science. The Life of Ernest Everett Just. Oxford University Press, New York/Oxford, 1983.
A briefer version of Just’s career can be viewed here: http://www.genetics.org/content/179/4/1735
- One recent entry on the occasion of the 200th anniversary of the birth of Frederick Douglass from the NY Times online, February 22nd about how scientists construed race in the 19th century:
- Not so long ago, Jewish scientists were also subject to life-threatening discrimination. Some of it is summarized by Jeremy Bernstein’s essay in The New York Review of Books, December 8, 2016 (“Great Scientists Against Terrible Odds”)
Session #7, March 28th Portrayal of science in the arts
Assignment #1: Watch the film called GATTACA (1997).
The movie portrays a future, one perhaps not far away, in which genetic information obtained at birth governs lives and dictates what people might be allowed to do.
Here is the link to Gattaca.
We will talk about the following questions:
–How close is the premise to current scientific reality? Closer than it was twenty years ago when the film was made?
–How likely is it that genetic information can be as predictive as the film implies?
–What are the political benefits of making a film of this sort?
–What do you expect the film to achieve as entertainment, instruction, or a call to action?
Kevin will obtain the movie and provide links to it.
Assignment #2: Read the original short novel Frankenstein written by Mary Shelley two hundred years ago (1818) when she was younger than most of you. The book can be acquired inexpensively for a Kindle reader or in libraries and used book stores. Kevin will also try to find a link to a free version; I didn’t succeed.
There are movie versions—the most famous was made in 1931—and several derivatives (such as The Bride of Frankenstein, etc) but none of the cinematic versions adhere closely to the original text.
Consider these questions as you read:
–What inspired the writing of this strange novel?
–Why do you think it has had such a powerful and sustained hold on the public’s imagination and on the public’s conception of science?
–The novel deals with the origin of life and makes many allusions to other writings about the creation of human beings. What does that mean about the relationship of science and religion?
Because of the novel’s bicentennial, special attention is being given to Frankenstein this year, including new editions of the text and critical appraisals. One especially brilliant essay about the writing of the book just appeared in the New Yorker Magazine (and can be heard on a podcast):
Life and Letters: It’s Still Alive, by Jill Lepore. Two hundred years of “Frankenstein.” http://nyer.cm/1bH4KoU
Additional, optional material: There are many other interesting examples of ways in which science and scientists are depicted in the arts. I have listed some of these below; none is required for class but you might look at them in the future and I am likely to refer to them during our session.
Fiction:
CP Snow, The Search (1934) An early novel by the physicist turned novelist and politician, CP Snow, about the trials of starting out in competitive academic science in England.
Allegra Goodman, Intuition (2006) A deft novel about young scientists working in a biomedical research laboratory in a place modeled on the Whitehead Institute at MIT.
Andrea Barrett, The Voyage of the Narwhal (1998) A prize-winning novel about the rigors of geographical discovery in the late 19th century by a writer who teaches the literature of science at Williams College.
Carl Djerrasi, Cantor’s Dilemma (1989) An insightful novel by a famous chemist about how doubt pervades the relationship between an cancer researcher and his trainees when important but uncertain results are obtained.
Theatre:
QED A portrayal of the famously irreverent physicist, Richard Feynmann.
Wit A moving account of a John Donne scholar dying of ovarian cancer.
Photograph 51 A dramatization of Rosalind Franklin’s relationship with Watson, Crick, Wilkins, and others during the discovery of DNA structure.
Copenhagen The German physicist Werner Heisenberg goes to visit his mentor, Niels Bohr in you-know-where.
Proof A young women reveals her mathematical skills.
Film:
The Man Who Knew Infinity A recent well-reviewed biopic about the Indian math genius, Ramanujan, and his mentor at Cambridge University.
Arrowsmith This you have seen for Session #2.
Dr. Ehrlich’s Magic Bullet An oldie about discovering a treatment for syphilis.
Contagion A realistic account of the birth of an epidemic.
Paintings:
by William Blake, Gerrit Dou, Rembrandt van Rijn, Hans Holbein, and many others
(you can find most of these on line)
Session #8, April 11, 2018
How scientific findings are disseminated
In this class, we will discuss how the results of scientific work are communicated to other scientists and to the wider public. We will focus mainly on publication of primary scientific articles; consider the economics, fairness, and influence of the system used for publication; and gauge how well the scientific community has exploited the new opportunities provided by computer sciences and the internet. We will emphasize biomedical research because that is where changes have been occurring at the greatest rate over the past couple of decades and with the most contentious arguments. (And it is also where your instructor has had a role.)
Required reading:
Chapter 15 (“Science Publishing and Science Libraries in the Internet Age”) from my book, The Art and Politics of Science (https://www.ncbi.nlm.nih.gov/books/NBK190606/), which describes the development of public digital libraries and open access publishing for the life sciences.
The chapter also alludes to the virtues of preprint servers in physics and some other sciences. Preprint servers in biology have been promoted more recently for the life sciences in:
http://science.sciencemag.org/content/sci/352/6288/899.full.pdf
(For an interesting perspective on one aspect of the problem, see: RD Vale and AA Hyman, “Priority of discovery in the life sciences” eLIFE 2016;5:e16931.)
Science magazine has also provided a useful summary of the various attitudes that biologists have towards the use of preprints:
http://www.sciencemag.org/news/2017/09/are-preprints-future-biology-survival-guide-scientists
In your reading of these materials, consider the following questions:
–What factors enable and restrict access to new scientific findings?
–What are the ideal methods for getting such information to other scientists? To the general public?
–What are the costs of publishing and who should pay them? (The public? Funders of science? Scientists themselves?)
–What is the role of scientific reports as opposed to news accounts, history of science, and textbooks?
–Why is publishing so important and also so contentious? What is the relationship of publication to career development? How should peers evaluate a scientist’s record?
Session #9. April 11, 2018 Ownership in science.
Topics: Industrial science: interfaces with government and academia, including ownership and patenting of intellectual property
In the second part of this extended class, we will first discuss how science contributes to the economy, considering some of the conflicts that occur in the transformation of scientific discoveries into practical items of commercial value. We will talk about some articles, legal rulings, and books that illustrate problems about ownership (patents and licensing) and financial returns (to basic scientists and product developers), and we will think about what is in the best interests of the public versus the owners of intellectual property.
To whet your appetite for these topics: assigned reading about current events:
(1) http://www.nytimes.com/2016/12/19/health/harnessing-the-us-taxpayer-to-fight-cancer-and-make-profits.html?smprod=nytcore-ipad&smid=nytcore-ipad-share
Public funding is backing a new immunotherapy treatment, but the bulk of any profits will go to a private company. So are taxpayers getting a good deal?
An academic provides an inside view of the relationships being forged with corporations, and the accompanying expectations.
(3) https://www.nytimes.com/2017/03/10/opinion/bernie-sanders-trump-should-avoid-a-bad-zika-deal.html
Bernie Sanders and a former head of the NIH square off over the development of a vaccine against Zika virus
In considering these three recent conflicts, we will depend on several aspects of patent law.
Article I, section 8, reads, “Congress shall have power… to promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries.”
Here are some relevant readings:
(1) Charles R. McManis & Sucheol Noh, “The Impact of the Bayh-Dole Act on Genetic Research and Development: Evaluating the Arguments and Empirical Evidence to Date” (An accessible legal essay that reviews some important aspects of the Bayh-Dole Act of 1980, legislation that strongly influenced how academic institutions pursue ownership of biological findings and products.) A PDF is on the class website.
(2)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225052/pdf/40142_2014_Article_55.pdf
An essay by Robert Cook-Deegan, a leading scholar on genetics and the law, about the Supreme Court’s decision on DNA patenting in a case that invalidated the patent held by Myriad Genetics on the BRCA1 gene. Reference #23 has the Court’s decision, an important document (US Supreme Court, American Association of Pathologists v.Myriad )
(3) The latest and most intense patenting fight in recent times has been over the gene-editing method often referred to as CRISPR/Cas9. An account of the ruling can be found in the NY Times by Andrew Pollack: https://www.nytimes.com/2017/02/15/science/broad-institute-harvard-mit-gene-editing-patent.html
Here is one of many articles about the effects of the fight on science: “Pursuit of profit poisons collaboration,” by Jacob S. Sherkow, Nature, April 14, 2016 https://www.ncbi.nlm.nih.gov/pubmed/27075081
(4) Debate about the invention and royalties from the HIV test kit was among my most difficult problems in my first year as NIH Director. One account of the settlement is here: http://articles.latimes.com/1994-07-12/news/mn-14822_1_hiv-test-kit
(Another account can be found in my memoir, The Art and Politics of Science.)
Some interesting, longer, optional readings on these topics
These are not required for class but keep them in mind if you want to read more about ownership of intellectual property, fights over priority in science, and other items related to turning discoveries into fame and profits. All can be found at Amazon.com
Jardine, The Man who Measured London (a lively biography about Robert Hooke, a remarkable scientist and difficult person who played critical roles in English science, the Royal Society, and the plan for London in the late 17th Century)
Skloot, The Immortal Life of Henrietta Lacks (a very popular social history of the origins and politics of the most famous cell line in medical research: HeLa cells)
Hall, Invisible Frontiers (an excellent account of the early days of the recombinant DNA industry by a journalist who met with you in February)
Kornberg, The Golden Helix (a personal story of the founding of the company DNAX by a Nobel Prize-winning biochemist )
Werth, The Billion Dollar Molecule (a highly readable story about the development of a biotech company by superb chemists)
Shreeve, The Genome Wars (one of several good accounts of the race to finish and possibly commercialize the human genome)
Hoffman and C. Djerassi, Oxygen (a play by two distinguished chemists aboutestablishing priority for the discovery of oxygen; another example of representation of science in the arts)
Session 10# April 18th, 2018 Guest lecturer: Jonathan Weiner
“How is writing about science like doing science?”
In some ways, writing nonfiction stories about science can be like doing science itself. With each story, science writers have to ask themselves hard questions about evidence, significance, objectivity. This evening we will explore some parallels between science writing and science, using a few science stories as case studies.
Please read:
“The Really Big One,” by Kathryn Schulz. New Yorker, 2015.
And please read any one of these three:
Chapter One, The Beak of the Finch, by Jonathan Weiner
Excerpt, The Next One Hundred Years, by Jonathan Weiner
“The Tangle,” by Jonathan Weiner. New Yorker, 2005.
April 25 Session #11
Scientific communities: Changes in the demography of science
In this session, we will consider the several factors that determine the vitality of scientific communities. We will view those factors and their consequences from the perspectives of social planners and leaders of science who are thinking about the likelihood of success in scientific careers. Some of the factors include the kinds and numbers of jobs available for the conduct of scientific work; the educational and training mechanisms required to develop the scientific work force; the mechanisms used to support scientific studies (including, especially, grants in the public sector and also allocations for research in the private sector); and government policies and political support for them.
The timing of this session is coincidentally propitious: on April 12th, the National Research Council issued a long-awaited and Congressionally mandated report entitled The Next Generation of Biomedical and Behavioral Sciences Researchers:
Breaking Through. The report was inspired by widespread concerns, during the past decade or more, that newly trained investigators in the biomedical sciences are increasingly at risk of being unable to fulfill their potential because of a paucity of suitable positions and financial support for their scientific work. Such limitations have been viewed as threats to the future of the U.S. scientific enterprise and as perverse conditions fostering an unhealthy, “hyper-competitive” atmosphere in the current world of medical science.
During our class on April 25, we will discuss the causes and consequences of the current state of affairs and some possible remedies. The following questions are among those you should think about:
–What do you see as the major events that have created the current crisis of confidence in our traditionally successful research enterprise?
–Given current conditions and systems for training, research, and funding, what feasible short-term changes would you recommend?
–If you could dictate the availability of talent (the labor force), research positions in academic, government, and commercial sectors, and funds for the support of research, how would you organize the system?
To help you think about these issues, please look at the following materials:
- The new report from the NRC, which is freely available for downloading from the National Academies website (https://www.nap.edu/download/25008)
I would recommend reading the Summary and any additional chapters or appendices that you find especially interesting.
- A short paper that I co-authored with three senior colleagues in 2014 and attracted widespread attention. It seemed to capture current anxieties about how imbalances of the labor force and resources (especially jobs and grants) were affecting the performance of science. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000813/
- A preprint (!) from a similar group of authors, representing the advocacy group called Rescuing Biomedical Research (RBR), that makes some specific recommendations for improving prospects for NIH grant support for young investigators. https://peerj.com/preprints/26465/ (This article will likely appear in Science magazine soon; it illustrates the utility of posting preprints, a topic we discussed on April 10th.)
Of course, there is a great deal written on these topics, and you can find references to most of that work in the NRC report or in our paper in PNAS. But if you read the PNAS paper and the recommendations in the NRC report summary, we will have the basis for a lively discussion.
For some of you, this topic has important practical consequences; for others, I hope the significance of the issues for the future of medical science will be apparent.
May 2 Session #12 Controversial Science
As you have learned during this course, science is a complex activity with complicated relationships to government, business, the arts, the law, and virtually all other elements in our society.
In this final session before your project presentations, we are going to talk about the ways in which scientific work is treated when it is thought to pose risks to society. When the dangers are obvious and extreme—for example, the design and testing of atomic weapons or the production of biological weapons—we use a variety of legal tools and rigorously monitored precautions, such as bans, international treaties, or the labeling of research as “classified” so that only properly credentialed individuals have access to it. And of course the vast majority of scientific work is thought to pose minimal or no risk of harm.
But in some instances, scientific work may be viewed as having “dual” potential: the likelihood of producing new knowledge that has beneficial applications but some chance of being used—unwittingly or with malevolent intent—to cause harm. Such research is often called “dual use research of concern” (abbreviated as DURC). Many features of DURC are summarized in a recent report (which I co-chaired) from the National Research Council. The report is attached as a PDF or can be read online from this link: https://www.nap.edu/read/24761/chapter/1
It will be useful to skim the background information and the recommendations.
Some questions about controversial research:
Should scientists be able to follow their curiosity wherever it leads? Of course not. But what are the limits?
What influences those limits? Danger to health, property, security, environment? Ethics? Beliefs? Costs?
Who should set the limits? The executive branch? Law-makers? The scientific community?
What are the dangers of setting limits?
How should scientists proceed when matters are unresolved by authorities? When should dangers be considered: before starting an experiment or when it is time to publish?
What has been done in the past? And what has been learned from those experiences?
What shall we do about current uncertainties?
Readings to inform our discussion
- DURC and bioterrorism. Several of the controversies in the world of DURC have involved the study of viruses that could be used as weapons or could initiate epidemics as a result of careless handling of genetically modified agents. Some examples include:
—Work on the horsepox viruses that was too late to be included in the DURC report, here reported on NPR:
—studies of influenza viruses engineered to be able to be transmitted by the airborne route:
http://www.sciencemag.org/news/2011/11/scientists-brace-media-storm-around-controversial-flu-studies
- Gene editing with CRISPR/Cas9 and other tools. There is now enormous interest in the use of gene editing to treat diseases, make improved agricultural products, and even change the human germ line. Foreign Affairs magazine has devoted most of a recent issue to this topic; see for example the article by Bill Gates:
or a plea from an ethicist to consider forms of regulation:
The National Academies have also weighed in with a report on germ line editing, summarized in this news release:
http://www8.nationalacademies.org/onpinews/newsitem.aspx?RecordID=24623
- Historical examples. Two famous episodes of controversial science give some perspective on the current debates.
The most notable was the controversy in the mid-1970’s about the use of recombinant DNA technologies. There are many places to read about this, but here are a couple:
One reflection by the main organizer, Paul Berg of Stanford:
https://www.nature.com/articles/455290a’
Another by the man who was the head of NIH at the time, Don Fredrickson:
https://www.ncbi.nlm.nih.gov/books/NBK234217/
The other worth mentioning is the long-standing controversy about studies of human embryos and the so-called “pluripotent” stem cells derived from them. Some of this is discussed in Chapter 13 from my memoir:
https://www.ncbi.nlm.nih.gov/books/NBK190607/
A short recent synopsis outlines the prospects for use of such cells in experimental work and medical treatment:
https://www.nature.com/articles/d41586-018-03268-4
DURC Report