How hard is it to clean up the scientific literature?

ResearchBlogging.org
Science is supposed to be a project centered on building a body of reliable knowledge about the universe and how various pieces of it work. This means that the researchers contributing to this body of knowledge — for example, by submitting manuscripts to peer reviewed scientific journals — are supposed to be honest and accurate in what they report. They are not supposed to make up their data, or adjust it to fit the conclusion they were hoping the data would support. Without this commitment, science turns into creative writing with more graphs and less character development.
Because the goal is supposed to be a body of reliable knowledge upon which the whole scientific community can draw to build more knowledge, it’s especially problematic when particular pieces of the scientific literature turn out to be dishonest or misleading. Fabrication, falsification, and plagiarism are varieties of dishonesty that members of the scientific community look upon as high crimes. Indeed, they are activities that are defined as scientific misconduct and (at least in theory) prosecuted vigorously.
You would hope that one consequence of identifying scientists who have made dishonest contributions to the scientific literature would be that those dishonest contributions would be removed from that literature. But whether that hope is realized is an empirical question — one taken up by Anne Victoria Neale, Justin Northrup, Rhonda Dailey, Ellen Marks, and Judith Abrams in an article titled “Correction and use of biomedical literature affected by scientific misconduct” published in 2007 in the journal Science and Engineering Ethics. Here’s how Neale et al. frame their research:

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Do you want people to discuss your published work?

There’s a recent paper on blogs as a channel of scientific communication that has been making the rounds. Other bloggers have discussed the paper and its methodology in some detail (including but not limited to Bora and DrugMonkey and Dr. Isis), so I’m not going to do that. Rather, I want to pull back and “get meta” with the blogospheric discussion of the paper, and especially the suggestion that it might be out of bounds for science bloggers (some of whom write the blogs that provided the data for the paper in question) to mount such a vigorous critique of a paper that was, as it turns out, authored by a graduate student.
So, let’s consider the situation more generally:

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Objectivity, conflicts of interest, and book reviews.

Let’s say you’re a book review editor for a large circulation science periodical. You receive books from publishers and you look for scientists with the relevant expertise to write reviews that really engage the content of the books they are reviewing.
The thing with having the relevant expertise, though, is that it may put you right in the middle of a controversy that the book you’ve been asked to review is probing or advancing.
In other words, it may be tricky to find a reviewer who is conversant in the scientific issues the book raises and simultaneously reasonably objective about those issues. If you know enough to grok the horse race, you may actually have a horse in that race.
The question, however, is whether large circulation science periodicals are offering book reviews with the tacit promise that they are objective (or as objective as an individual’s own assessment of a book can be).
To get a quick sense of your expectations on this, here’s a poll:

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Ask Dr. Free-Ride: True love waits (until the end of the semester).

By email, a reader asks for advice on a situation in which the personal and the professional seem like they might be on a collision course:

I am a junior at a small (< 2000 students) liberal arts college. I got recruited to be a TA for an upper division science class, and it’s going swimmingly. I’m basically a troubleshooter during labs, which the professor supervises. The problem is that I’ve fallen for one of the students, also a junior. Is it possible for me to ethically date her? The university’s handbooks are little help–sexual harassment is very strictly prohibited, but even faculty are technically allowed to date their students–and my instincts keep flip-flopping. On the one hand, teacher-student relationships are automatically suspect, but on the other I’m not sure that it’s significantly different from TAing the close friends that are in the class.
I obviously have no intention of changing grades or doing anything resembling sexual harassment, and I’m pretty good (sometimes too good) at being objective and keeping work and my social life separate. The grading is also pretty objective, and the professor goes over it to be sure my grades are reasonable. If it is possible, what do I need to look out for? Do I need to inform the professor (she knows I’m friends with the subject of my infatuation)? And in the event that we do go out, do I have to tell her that I grade her tests and labs (it’s unusual for a TA to grade in upper division courses in our department)? It seems like it might be easier if she didn’t know, but it would be at least lying by omission.
I know this probably sounds like it ought to be addressed to Dan Savage, but I’d really appreciate your advice and any advice your readers might have.
Thanks so much,
“Forbidden Chemistry”

I’ll allow as how Dan Savage knows a lot, but when was the last time he thought about the ethical challenges of power gradients in educational and training environments?

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ClimateGate, the Michael Mann inquiry, and accepted scientific practices.

In my earlier post about the findings of the Penn State inquiry committee looking into allegations of research misconduct against Michael Mann, I mentioned that the one allegation that was found to merit further investigation may have broad implications for how the public understands what good scientific work looks like, and for how scientists themselves understand what good scientific work looks like.
Some of the commenters on that post seemed interested in discussing those implications. Others, not so much. As commenter Evan Harper notes:

It is clear that there are two discussions in parallel here; one is serious, thoughtful, and focused on the very real and very difficult questions at hand. The other is utterly inane, comprising vague ideological broadsides against nebulous AGW conspirators, many of which evince elementary misunderstandings about the underlying science.
If I wanted to read the second kind of conversation, there are a million blogs out there with which I could torture myself. But I want to read – and perhaps participate in – the first kind of conversation. Here and now, I cannot do that, because the second conversation is drowning out the first.
Were that comment moderators could crack down on these poisonous nonsense-peddlers. Their right to swing their (ham)fists ends where our noses begin

Ask and you shall receive.

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In the wake of ClimateGate: findings of the misconduct inquiry against Michael Mann.

Remember “ClimateGate”, that well-publicized storm of controversy that erupted when numerous email messages from the Climate Research Unit (CRU) webserver at the University of East Anglia were stolen by hackers and widely distributed? One of the events set in motion by ClimateGate was a formal inquiry concerning allegations of research conduct against Dr. Michael E. Mann, a professor in the Department of Meteorology at The Pennsylvania State University.
The report (PDF) from that inquiry has been released, so we’re going to have a look at it here.
This report contains a lot of discussion of how the committee pursuing the inquiry was constituted, and of which university policies govern how the committee is constituted, and of how membership of the committee was updated when members left the university for other positions, etc. I’m going to gloss over those details, but they’re all there in the ten page report if you’re interested in that kind of thing.
My focus here will be on what set the inquiry in motion to begin with, on the specific allegations they considered against Dr. Mann, on how the committee gathered information relevant to the allegations, and on the findings and decisions at which they arrived. Let me state up front that committee decided that one allegation merited further consideration in an “investigation” (which is the stage of the process that follows upon an “inquiry”), and that to my eye, that investigation may end up having broader implications for the practice of science in academia.
But let’s start at the beginning. From the inquiry report:

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#scio10 aftermath: some thoughts on “Talking Trash: Online Outreach from the Great Pacific Garbage Patch”.

Here are some of the thoughts and questions that stayed with me from this session. (Here are my tweets from the session and the session’s wiki page.)
Among other things, this panel took up the article panelist Lindsey Hoshaw wrote about the garbage patch for the New York Times and some of the reaction to it (including from panelist Miriam Goldstein).
Lindsey’s article was interesting because of the process. To get a spot on the ship going out to the North Pacific gyre, where the garbage patch is, she had to come up with funding. (We learned during the session that ship time on some of these expeditions can run to $18,000 a day.) Rather than pitching the story idea to the New York Times and hitting them with the bill, or covering the cost of the ship time herself, she “crowd-sourced” her participation — that is, she turned to readers of Spot.Us, a nonprofit web project that supports freelance journalists, for donations. The pitch she gave when asking for this money described deliverables:

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#scio10 aftermath: some thoughts on “Rebooting Science Journalism in the Age of the Web”.

Here are some of the thoughts and questions that stayed with me from this session. (Here are my tweets from the session and the session’s wiki page.)
The panelists made a point of stepping away from the scientists vs. bloggers frame (as well as the question of whether bloggers are or are not properly considered journalists). They said some interesting things about what defines a journalist — perhaps a set of distinctive values (like a commitment to truth and accuracy, possibly also to the importance of telling an engaging story). This, rather than having a particular paying gig as a journalist, marked the people who were “doing journalism”, whatever the medium.

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#scio10 aftermath: my tweets from “Getting the Science Right: The importance of fact checking mainstream science publications — an underappreciated and essential art — and the role scientists can and should (but often don’t) play in it.”

Session description: Much of the science that goes out to the general public through books, newspapers, blogs and many other sources is not professionally fact checked. As a result, much of the public’s understanding of science is based on factual errors. This discussion will focus on what scientists and journalists can do to fix that problem, and the importance of playing a pro-active role in the process.
The session was led by Rebecca Skloot (@RebeccaSkloot), Sheril Kirshenbaum (@Sheril_), and David Dobbs (@David_Dobbs).
Here’s the session’s wiki page.

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