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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Friday Sprog Blogging: screen-time or scream-time.

Earlier this week, the younger Free-Ride offspring “made a bad decision” about time utilization at the after school program, electing to play outside and do a project before doing homework, meaning the homework was still unfinished when I arrived to fetch the sprogs.
The standard consequence for this is, apparently, one of the greatest horrors that can be visited upon a third grader: the loss of screen-time (which in the Free-Ride household covers television, computers, and hand-held game systems).

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Common ground and deeply held differences: a reply to Bruins for Animals.

In a post last month, I noted that not all (maybe even not many) supporters of animal rights are violent extremists, and that Bruins for Animals is a group committed to the animal rights position that was happy to take a public stand against the use of violence and intimidation to further the cause of animal liberation.
On Wednesday, Kristy Anderson (the co-founder of Bruins for Animals), Ashley Smith (the president), and Jill Ryther (the group’s advisor) posted a critical response to my post. In the spirit of continuing dialogue, I’d like to respond to that response.
They write:

AR activists can rightly accept praise and credit for encouraging the two sides to come together in what was an unprecedented public and civil dialogue. However, one glaring and rather twisted irony too often overlooked is the fact that those very same participants who speak against aggressive campaigns against the animal experimentation industry and who are quick to praise AR advocates’ stance on nonviolence are themselves engaged in (or are supporters of) violence and intimidation towards sentient beings on a daily basis.

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Friday Sprog Blogging: science fair questions.

Earlier this week, I got to judge projects at a Science Fair, which, as usual, was loads of fun.
This year, however, owing to budget cuts and staffing cuts and things like that, there will be no science fair at the sprogs’ elementary school. We are wistful about this, especially after the fun we had at their science fair last year. But just because there’s not a science fair this year doesn’t mean the sprogs are without questions they’d like to explore with science fair projects. As they were flitting about with their other activities, I got each of them to give me a list of three such questions.
From the elder Free-Ride offspring:

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What’s the point of peer review?

Once again, I’m going to “get meta” on that recent paper on blogs as a channel of scientific communication I mentioned in my last post. Here, the larger question I’d like to consider is how peer review — the back and forth between authors and reviewers, mediated (and perhaps even refereed by) journal editors — does, could, and perhaps should play out.
Prefacing his post about the paper, Bora writes:

First, let me get the Conflict Of Interest out of the way. I am on the Editorial Board of the Journal of Science Communication. I helped the journal find reviewers for this particular manuscript. And I have reviewed it myself. Wanting to see this journal be the best it can be, I was somewhat dismayed that the paper was published despite not being revised in any way that reflects a response to any of my criticisms I voiced in my review.

Bora’s post, in other words, drew heavily on comments he wrote for the author of the paper to consider (and, presumably, to take into account in her revision of the manuscript) before it was published.
Since, as it turns out, the author didn’t make revisions addressing Bora’s criticisms that ended up in the published version of the paper, Bora went ahead and made those criticisms part of the (now public) discussion of the published paper. He still endorses those criticisms, so he chooses to share them with the larger audience the paper has now that it has been published.

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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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Pi Day bake-off 2010: Chocolate Almond Cherry (Tofu) Pie.

Longtime readers of this blog may remember last year’s orgy of pies on the run-up to Pi Day (March 14th, or 3-14). This March at Casa Free-Ride, there’s been less pie making, in large part due to the fact that I’m no longer on sabbatical (either from my job or from coaching soccer).
But the bake-off is on again, so I figured that I needed to feed you all one really good pie (or pie recipe, anyway).
This pie melds three flavors that play very well together: rich chocolate, tart cherries, and almonds. As a bonus, it puts those flavors together in a pie that is rich but not heavy, one that doesn’t lean on eggs, or cream cheese, or butter, or milk.
I make this pie with a food processor, but if you don’t have one, you can manage with a blender, a heavy rolling pin, and a knife and cutting board.

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Friday Sprog Blogging: Animal research and people who don’t like it.

Because there are some conversations you have to have with your kids even if you wish you didn’t have to have them:
Dr. Free-Ride: I wanted to talk to you about a situation that has come up for a friend of mine and is a little worrisome. So, you know I went down to UCLA the other week, right?
Younger offspring: Yeah.
Dr. Free-Ride: Do you know what I was there for?
Elder offspring: A conference?

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Archetypal classroom moments.

Why is it that it’s not until you’re right in the middle of a class discussion, one where lots of people are actively engaged, asking good questions and raising important issues, and where you know that you are working against the clock to get all the contributions in, that you discover …

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