Monthly Archives: December 2014

I’m so glad we’ve had this time together.

Posted on by

Today the editors of the Scientific American Blog Network are announcing a new vision for the network, one with increased editorial oversight and more editorial curation of the subjects covered by network bloggers. Part of that shift involves a pruning of blogs from the existing network, including this one.

Three and a half years ago, in July 2011, “Doing Good Science” was a brand new blog. I had been writing my other blog, “Adventures in Ethics and Science”, since February 2005, and owing to a relatively high proportion of working scientists and science students in my readership and commentariat, some of my discussions of responsible conduct of research there seemed to me to have drifted into “inside baseball” territory.

From the start, my project here has been aimed at connecting a broader audience with ethical issues in science.

Some of these are ethical issues connected to how scientific knowledge is built, while others involve ethical implications of how scientific knowledge is applied to needs and wants from beyond the scientific community. A common thread in our discussions has been the inescapably human dimension of science — the fact that scientific knowledge is built by standard-issue human beings, working in coordination to get a more reliable handle on the features of our world than any individual human could get on their own.

Scientists are humans, just like the rest of us, but engaged in a powerful set of activities without which our universe would be much less intelligible.

Sharing that universe with each other is the point of ethics. How scientists and non-scientists share a world — how they share information and find common ground despite the diversity of their goals and values — has been another central concern of our discussions here. C.P. Snow famously described a chasm between “the two cultures,” scientists and intellectuals of a more literary and humanistic bent. To the extent that there is a gap between people building different kinds of knowledge in our world, it is surely worth bridging. Even more urgent, I’d argue, is the problem of bridging the gap between intellectuals of all stripes and their fellow humans who do not identify themselves primarily as knowledge-builders.

Scientific concerns are human concerns. Human needs and aspirations may be served by scientific research and intervention. And, at the end of the day, we have just one world that we must share with each other. Sharing a world may be easier if non-scientists better understand the knowledge-building project in which scientists are engaged (including its human dimensions). I expect it would also be easier if scientists had a better understanding of the central concerns, hopes, and fears of the non-scientists in their world.

Building this understanding is an ongoing project, one I am committed to pursuing.

Though this is the last “Doing Good Science” post at Scientific American, the blog will continue at a new home (coordinates to be posted here once it’s set up). And, you may see me from time to time on the Guest Blog.

In the meantime, if you’re a tweeter, you can find me on Twitter.

Thanks very much for the conversations. It’s been a privilege to share this corner of the world with you.

Pennywise and pound-foolish: misidentified cells and competitive pressures in scientific knowledge-building.

Posted on by

The overarching project of science is building reliable knowledge about the world, but the way this knowledge-building happens in our world is in the context of competition. For example, scientists compete with each other to be the first to make a new discovery, and they compete with each other for finite pools of grant money with which to conduct more research and make further discoveries.

I’ve heard the competitive pressures on scientists described as a useful way to motivate scientists to be clever and efficient (and not to knock off early lest some more dedicated lab get to your discovery first). But there are situations where it’s less obvious that fierce competition for scarce resources leads to choices that really align with the goal of building reliable knowledge about the world.

This week, on NPR’s Morning Edition, Richard Harris reported a pair of stories on how researchers who work with cells in culture grapple with the problem of their intended cell line being contaminated and overtaken by a different cell line. Harris tells us:

One of the worst cases involves a breast cancer cell line called MDA-435 (or MDA-MB-435). After the cell line was identified in 1976, breast cancer scientists eagerly adopted it.

When injected in animals, the cells spread the way breast cancer metastasizes in women, “and that’s not a very common feature of most breast cancer cell lines,” says Stephen Ethier, a cancer geneticist at the Medical University of South Carolina. “So as a result of that, people began asking for those cells, and so there are many laboratories all over the world, who have published hundreds of papers using the MDA-435 cell line as a model for breast cancer metastasis.”

In fact, scientists published more than a thousand papers with this cell line over the years. About 15 years ago, scientists using newly developed DNA tests took a close look at these cells. And they were shocked to discover that they weren’t from a breast cancer cell at all. The breast cancer cell line had been crowded out by skin cancer cells.

“We now know with certainty that the MDA-435 cell line is identical to a melanoma cell line,” Ethier says.

And it turns out that contamination traces back for decades. Several scientists published papers about this to alert the field, “but nevertheless, there are people out there who haven’t gotten the memo, apparently,” he says.

Decades worth of work and more than a thousand published research papers were supposed to add up to a lot of knowledge about a particular kind of breast cancer cell, except it wasn’t knowledge about breast cancer cells at all because the cells in the cell line had been misidentified. Probably scientists know something from that work, but it isn’t the knowledge they thought they had before the contamination was detected.

On the basis of the discovery that this much knowledge-building had been compromised by being based on misidentified cells, you might imagine researchers would prioritize precise identification of the cells they use. But, as Harris found, this obvious bit of quality control meets resistance. For one thing, researchers seem unwilling to pay the extra financial costs it would take:

This may all come down to money. Scientists can avoid most of these problems by purchasing cells from a company that routinely tests them. But most scientists would rather walk down the hall and borrow cells from another lab.

“Academics share their cell lines like candy because they don’t want to go back and spend another $300,” said Richard Neve from Genentech. “It is economics. And they don’t want to spend another $100 to [verify] that’s still the same cell line.”

Note here that scientists could still economize by sharing cell lines with their colleagues instead of purchasing them but paying for the tests to nail down the identity of the shared cells. However, many do not.

(Consider, though, how awkward it might be to test cells you’ve gotten from a colleague only to discover that they are not the kind of cells your colleague thought they were. How do you break the news to your colleague that their work — including published papers in scientific journals — is likely to be mistaken and misleading? How likely would this make other colleagues to share their cell lines with you, knowing that you might bring them similarly bad news as a result of their generosity?)

Journals like Nature have tried to encourage scientists to test their cell lines by adding it to an authors’ checklist for researchers submitting papers. Most authors do not check the box indicating they have tested their cells.

One result here is that the knowledge that comes from these studies and gets reported in scientific journals may not be as solid as it seems:

When scientists at [Genentech] find an intriguing result from an academic lab, the first thing they do is try to replicate the result.

Neve said often they can’t, and misidentified cells are a common reason.

This is a problem that is not just of concern to scientists. The rest of us depend on scientists to build reliable knowledge about the world in part because it might matter for what kinds of treatments are developed for diseases that affect us. Moreover, much of this research is paid for with public money — which means the public has an interest in whether the funding is doing what it is supposed to be doing.

However, Harris notes that funding agencies seem unwilling to act decisively to address the issue of research based on misidentified cell lines:

“We are fully convinced that this is a significant enough problem that we have to take steps to address it,” Jon Lorsch, director of the NIH’s National Institute of General Medical Sciences, said during the panel discussion.

One obvious step would be to require scientists who get federal funding to test their cells. Howard Soule, chief science officer at the Prostate Cancer Foundation, said that’s what his charity requires of the scientists it funds.

There’s a commercial lab that will run this test for about $140, so “this is not going to break the bank,” Soule said.

But Lorsch at the NIH argued that it’s not so simple on the scale at which his institute hands out funding. “We really can’t go and police 10,000 grants,” Lorsch said.

“Sure you can,” Soule shot back. “How can you not?”

Lorsch said if they do police this issue, “there are dozens and dozens of other issues” that the NIH should logically police as well. “It becomes a Hydra,” Lorsch said. “You know, you chop off one head and others grow.”

Biomedical research gets more expensive all the time, and the NIH is reluctant to pile on a whole bunch of new rules. It’s a balancing act.

“If we become too draconian we’re going to end up squashing creativity and slowing down research, which is not good for the taxpayers because they aren’t going to get as much for their money,” Lorsch said.

To my eye, Lorsch’s argument against requiring researchers to test their cells focuses on the competitive aspect of scientific research to the exclusion of the knowledge-building aspect.

What does it matter if the taxpayers get more research generated and published if a significant amount of that research output is irreproducible because of misidentified cells? In the absence of tests to properly identify the cells being used, there’s no clear way to tell just by looking at the journal articles which ones are reliable and which ones are not. Post-publication quality control requires researchers to repeat experiments and compare their results to those published, something that will cost significantly more than if the initial researchers tested their cells in the first place.

However, research funding is generally awarded to build new knowledge, not to test existing knowledge claims. Scientists get credit for making new discoveries, not for determining that other scientists’ discoveries can be reproduced.

NIH could make it a condition of funding that researchers working with cell lines get those cell lines tested, and arguably this would be the most cost-efficient way to ensure results that are reliable rather than based on misidentification. I find Lorsch’s claim that there are dozens of other kinds of quality control of this sort NIH could demand, so they cannot demand this, unpersuasive. Even if there are many things to fix, it doesn’t mean you must fix them all at once. Incremental improvements in quality control are surely better than none at all.

His further suggestion that engaging in NIH-mandated quality control will quash scientific creativity strikes me as silly. Scientists are at their most creative when they are working within constraints to solve problems. Indeed, were NIH to require that researchers test their cells, there is no reason to think this additional constraint could not be easily incorporated into researchers’ current competition for NIH funding.

The big question, really, is whether NIH is prioritizing funding a higher volume of research, or higher quality research. Presumably, the public is better served by a smaller number of published studies that make reliable claims about the actual cells researchers are working with than by a large number of published studies making hard-to-verify claims about misidentified cells.

If scientific competition is inescapable, at least let’s make sure that the incentives encourage the careful steps required to build reliable knowledge. If those careful steps are widely seen as an impediment in succeeding in the competition, we derail the goal that the competitive pressures were supposed to enhance.

Twenty-five years later.

Posted on by

Twenty-five years ago today, on December 6, 1989, in Montreal, fourteen women were murdered for being women in what their murderer perceived to be a space that rightly belonged to men:

Geneviève Bergeron (born 1968), civil engineering student

Hélène Colgan (born 1966), mechanical engineering student

Nathalie Croteau (born 1966), mechanical engineering student

Barbara Daigneault (born 1967), mechanical engineering student

Anne-Marie Edward (born 1968), chemical engineering student

Maud Haviernick (born 1960), materials engineering student

Maryse Laganière (born 1964), budget clerk in the École Polytechnique’s finance department

Maryse Leclair (born 1966), materials engineering student

Anne-Marie Lemay (born 1967), mechanical engineering student

Sonia Pelletier (born 1961), mechanical engineering student

Michèle Richard (born 1968), materials engineering student

Annie St-Arneault (born 1966), mechanical engineering student

Annie Turcotte (born 1969), materials engineering student

Barbara Klucznik-Widajewicz (born 1958), nursing student

They were murdered because their killer was disgruntled that he been denied admission to the École Polytechnique, the site of the massacre, and because he blamed women occupying positions that were traditionally occupied by men for this disappointment, among others. When their killer entered the engineering classroom where the killing began, he first told the men to leave the room, because his goal was to kill the women. In their killer’s pocket, discovered after his death, was a list of more women he had planned to kill, if only he had the time.

Shelley Page was a 24-year-old reporter who was sent to cover the Montreal massacre for The Toronto Star. On this, the 25th anniversary of the event, she writes:

I fear I sanitized the event of its feminist anger and then infantilized and diminished the victims, turning them from elite engineering students who’d fought for a place among men into teddy-bear loving daughters, sisters and girlfriends.

Twenty-five years later, as I re-evaluate my stories and with the benefit of analysis of the coverage that massacre spawned, I see how journalists— male and female producers, news directors, reporters, anchors — subtly changed the meaning of the tragedy to one that the public would get behind, silencing so-called “angry feminists.”

Twenty-five years ago, I was a 21-year-old finishing my first term in a chemistry Ph.D. program. I was studying for final exams and the qualifying exams that would be held in January, so I was not following the news about much of anything outside my bubble of graduate school. When I did hear about the Montreal massacre, it was a punch in the gut.

It was enough already to fight against the subtle and not-so-subtle doubt (from the faculty in our programs, from our classmates, even from our students) that women were cut out for science or engineering. Now it was clear that there existed people committed enough to science and engineering being male domains that they might kill us to enforce that.

The murders were political. They did not target particular individual women in the forbidden domain of engineering on the basis of particular personal grievances. Being a member of the hated group in the social space the murderer thought should be for men only was enough.

But the murders also ended the lives of fourteen particular individual women, women who were daughters and sisters and friends and girlfriends.

The tragedies were deeply personal for the survivors of the fourteen women who were murdered. They were also personal for those of us who understood (even if we couldn’t articulate it) that we occupied the same kinds of social positions, and struggled with the same barriers to access and inclusion, as these fourteen murdered women had. They made us sad, and scared, and angry.

The personal is political. The challenge is in seeing how we are connected, the structures underlying what frequently feel to us like intensely individual experiences.

I’m inclined to think it’s a mistake to look for the meaning of the Montreal massacre. There are many interconnected meanings to find here.

That individual teddy bear-loving girls and women can still be formidable scientists and engineers.

That breaking down barriers to inclusion can come at a cost to oneself as an individual (which can make it harder for others who have gotten into those male preserves to feel like it’s OK for them to leave before the barriers are completely dismantled).

That some are still dedicated to maintaining those barriers to inclusion, and where that dedication will end — with words, or threats, or violent acts — is impossible to tell just by looking at the gatekeeper.

Because they were murdered 25 years ago today, we will never know what contributions these fourteen women might have made — what projects they might have guided, what problems they might have solved, the impact they might have made as mentors or role models, as teachers, as colleagues, as friends, as lovers, as parents, as engaged citizens.

In their memory, we ought to make sure other women are free to find out what they can contribute without having to waste their energy taking down barriers and without having to fear for their lives.

James Watson’s sense of entitlement, and misunderstandings of science that need to be countered.

Posted on by

James Watson, who shared a Nobel Prize in 1962 for discovering the double helix structure of DNA, is in the news, offering his Nobel Prize medal at auction. As reported by the Telegraph:

Mr Watson, who shared the 1962 Nobel Prize for uncovering the double helix structure of DNA, sparked an outcry in 2007 when he suggested that people of African descent were inherently less intelligent than white people.

If the medal is sold Mr Watson said he would use some of the proceeds to make donations to the “institutions that have looked after me”, such as University of Chicago, where he was awarded his undergraduate degree, and Clare College, Cambridge.

Mr Watson said his income had plummeted following his controversial remarks in 2007, which forced him to retire from the Cold Spring Harbor Laboratory on Long Island, New York. He still holds the position of chancellor emeritus there.

“Because I was an ‘unperson’ I was fired from the boards of companies, so I have no income, apart from my academic income,” he said.

He would also use some of the proceeds to buy an artwork, he said. “I really would love to own a [painting by David] Hockney”. …

Mr Watson said he hoped the publicity surrounding the sale of the medal would provide an opportunity for him to “re-enter public life”. Since the furore in 2007 he has not delivered any public lectures.

There’s a lot I could say here about James Watson, the assumptions under which he is laboring, and the potential impacts on science and the public’s engagement with it. In fact, I have said much of it before, although not always in reference to James Watson in particular. However, given the likelihood that we’ll keep hearing the same unhelpful responses to James Watson and his ilk if we don’t grapple with some of the fundamental misunderstandings of science at work here, it’s worth covering this ground again.

First, I’ll start with some of the claims I see Watson making around his decision to auction his Nobel Prize medal:

  • He needs money, given that he has “no income beyond [his] academic income”. One might take this as an indication that academic salaries in general ought to be raised (although I’m willing to bet a few buck that Watson’s inadequate academic income is at least as much as that of the average academic actively engaged in research and/or teaching in the U.S. today). However, Watson gives no sign of calling for such an across-the-board increase, since…
  • He connects his lack of income to being fired from boards of companies and to his inability to book public speaking engagements after his 2007 remarks on race.
  • He equates this removal from boards and lack of invitations to speak with being an “unperson”.

What comes across to me here is that James Watson sees himself as special, as entitled to seats on boards and speaker invitations. On what basis, we might ask, is he entitled to these perks, especially in the face of a scientific community just brimming with talented members currently working at the cutting edge(s) of scientific knowledge-building? It is worth noting that some who attended recent talks by Watson judged them to be nothing special:

Possibly, then, speaking engagements may have dried up at least partly because James Watson was not such an engaging speaker — with an asking price of $50,000 for a paid speaking engagement, whether you give good talk is a relevant criterion — rather than being driven entirely by his remarks on race in 2007, or before 2007. However, Watson seems sure that these remarks are the proximate cause of his lack of invitations to give public talks since 2007. And, he finds this result not to be in accord with what a scientist like himself deserves.

Positioning James Watson as a very special scientist who deserves special treatment above and beyond the recognition of the Nobel committee feeds the problematic narrative of scientific knowledge as an achievement of great men (and yes, in this narrative, it is usually great men who are recognized). This narrative ignores the fundamentally social nature of scientific knowledge-building and the fact that objectivity is the result of teamwork.

Of course, it’s even more galling to have James Watson portrayed (including by himself) as an exceptional hero of science rather than as part of a knowledge-building community given the role of Rosalind Franklin’s work in determining the structure of DNA — and given Watson’s apparent contempt for Franklin, rather than regard for her as a member of the knowledge-building team, in The Double Helix.

Indeed, part of the danger of the hero narrative is that scientists themselves may start to believe it. They can come to see themselves as individuals possessing more powers of objectivity than other humans (thus fundamentally misunderstanding where objectivity comes from), with privileged access to truth, with insights that don’t need to be rigorously tested or supported with empirical evidence. (Watson’s 2007 claims about race fit in this territory .)

Scientists making authoritative claims beyond what science can support is a bigger problem. To the extent that the public also buys into the hero narrative of science, that public is likely to take what Nobel Prize winners say as authoritative, even in the absence of good empirical evidence. Here Watson keeps company with William Shockley and his claims on race, Kary Mullis and his claims on HIV, and Linus Pauling and his advocacy of mega-doses of vitamin C. Some may argue that non-scientists need to be more careful consumers of scientific claims, but it would surely help if scientists themselves would recognize the limits of their own expertise and refrain from overselling either their claims or their individual knowledge-building power.

Where Watson’s claims about race are concerned, the harm of positioning him as an exceptional scientist goes further than reinforcing a common misunderstanding of where scientific knowledge comes from. These views, asserted authoritatively by a Nobel Prize winner, give cover to people who want to believe that their racist views are justified by scientific knowledge.

As well, as I have argued before (in regard to Richard Feynman and sexism), the hero narrative can be harmful to the goal of scientific outreach given the fact that human scientists usually have some problematic features and that these problematic features are often ignored, minimized, or even justified (e.g., as “a product of the time”) in order to foreground the hero’s great achievement and sell the science. There seems to be no shortage of folks willing to label Watson’s racist views as unfortunate but also as something that should not overshadow his discovery of the structure of DNA. In order that the unfortunate views not overshadow the big scientific contribution, some of these folks would rather we stop talking about Watson’s having made the claims he has made about racial difference (although Watson shows no apparent regret for holding these views, only for having voiced them to reporters).

However, especially for people in the groups that James Watson has claimed are genetically inferior, asserting that Watson’s massive scientific achievement trumps his problematic claims about race can be alienating. His scientific achievement doesn’t magically remove the malign effects of the statements he has made from a very large soapbox, using his authority as a Nobel Prize winning scientist. Ignoring those malign effects, or urging people to ignore them because of the scientific achievement which gave him that big soapbox, sounds an awful lot like saying that including the whole James Watson package in science is more important than including black people as scientific practitioners or science fans.

The hero narrative gives James Watson’s claims more power than they deserve. The hero narrative also makes urgent the need to deem James Watson’s “foibles” forgivable so we can appreciate his contribution to knowledge. None of this is helpful to the practice of science. None of it helps non-scientists engage more responsibly with scientific claims or scientific practitioners.

Holding James Watson to account for his claims, holding him responsible for scientific standards of evidence, doesn’t render him an unperson. Indeed, it amounts to treating him as a person engaged in the scientific knowledge-building project, as well as a person sharing a world with the rest of us.

* * * * *
Michael Hendricks offers a more concise argument against the hero narrative in science.

And, if you’re not up on the role of Rosalind Franklin in the discovery of the structure of DNA, these seventh graders can get you started: