Trust and Retractions

30 Apr, 2012 by Morgan Freeberg

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Now here is a picture that’s worth a zillion words…

Look what’s going on there now. Green line is retraction incidents, measured in “notices” per 100,000 publications in scientific journals. Now, you could argue there may be problems with measuring it this way…but nevertheless, if the plotting is shaped like this, it’s gotta mean something. And the line more or less gels with public perception of the problems with science across time, if it doesn’t define an even greater issue with this thing we call “science” in actuality, compared to what is perceived.

Conservatives and moderates are losing faith in the institution, whereas liberals continue to pledge fealty.

The situation might very well be — it must be stated — much more complicated than this. Bu-u-u-u-t…I don’t think so. Liberals like feeling all scientifical & stuff, they mock conservatives for not sharing in the passion, it assuages their egos to wallow in the mental stew that they’re being all science-y and the conservatives aren’t cool or nuanced or sophisticated or hip enough to follow along…but what’s really going on is that conservatives, as is usually the case, do a better job of factoring in the history of the way things turned out, prior to figuring out what’s going on & what to do about it.

From Bad Data, Bad!, hat tip to Terri by way of Bird Dog at Maggie’s Farm.

I see Primer Caps and Heavy Pendulums is now up to 252 comments, which is sure to be a record for The Blog That Nobody Reads. I’m not quite so impressed by the number, as I am by the subject of this record-breaker…climate change. This genuinely surprises me, as I thought it would have something to do with legalizing pot, or Sarah Palin. What was I just saying about factoring in the history of the way things turned out…it would seem, now & then, that doesn’t work. Sarah Palin & pot have always been way out in front, as ways of stirrin’ the puddin’. What changed?

This thread got up there exactly the same way your car reaches a destination — by means of something going around very quickly in a circle. We have a gadfly, who is evidently not a single person, who is busy citing lots of scientific research and even demonstrating an understanding of some of the more involved parts of it, while showcasing a rather dazzling ignorance of the elementary aspects. His/her/its/their objection to my point looks like: Do you accept that the Earth is warming? and I say, no, I don’t…my objections have to do with the many problems involved in measuring things, and the total, or near-total, silence about the nature of these problems & what is done to overcome them. Whereupon, the mysterious entity chastises me for being skeptical to the wrong things, and commands me to go through the data, withholding any further commentary until such time as I find a problem. Uh, the data that were acquired through these means of measurement that I’m questioning. In varying levels of detail, depending on which cycle we’re on in the stupid-go-round, I define the nature of one of many points in the inference pipeline of “Um, you don’t really know that”…and my partner in discourse continues to chastise me without even showing an understanding of what I’m talking about. Like I said. Showcasing a dazzling ignorance of the elementary aspects. The climate-alarmist has data, he has a method for capturing the data…poopy head skeptic comes along and criticizes the way the data were captured, the alarmist’s way of shutting him up is to task him on a snipe hunt, endlessly combing through the data. This person knows what kind of footnotes to put up, and is familiar with the terminology, but cannot reliably locate where the point of dispute is in a disagreement. ++sniff++ ++snif++ Smells like…college kid.

From the New York Times column linked in a prior post at Bad Data

In the fall of 2010, Dr. Ferric C. Fang made an unsettling discovery. Dr. Fang, who is editor in chief of the journal Infection and Immunity, found that one of his authors had doctored several papers.

It was a new experience for him. “Prior to that time,” he said in an interview, “Infection and Immunity had only retracted nine articles over a 40-year period.”

The journal wound up retracting six of the papers from the author, Naoki Mori of the University of the Ryukyus in Japan. And it soon became clear that Infection and Immunity was hardly the only victim of Dr. Mori’s misconduct. Since then, other scientific journals have retracted two dozen of his papers, according to the watchdog blog Retraction Watch.

“Nobody had noticed the whole thing was rotten,” said Dr. Fang, who is a professor at the University of Washington School of Medicine.

Dr. Fang became curious how far the rot extended. To find out, he teamed up with a fellow editor at the journal, Dr. Arturo Casadevall of the Albert Einstein College of Medicine in New York. And before long they reached a troubling conclusion: not only that retractions were rising at an alarming rate, but that retractions were just a manifestation of a much more profound problem – “a symptom of a dysfunctional scientific climate,” as Dr. Fang put it.

Dr. Casadevall, now editor in chief of the journal mBio, said he feared that science had turned into a winner-take-all game with perverse incentives that lead scientists to cut corners and, in some cases, commit acts of misconduct.

“This is a tremendous threat,” he said.
:
Several factors are at play here, scientists say. One may be that because journals are now online, bad papers are simply reaching a wider audience, making it more likely that errors will be spotted. “You can sit at your laptop and pull a lot of different papers together,” Dr. Fang said.

But other forces are more pernicious. To survive professionally, scientists feel the need to publish as many papers as possible, and to get them into high-profile journals. And sometimes they cut corners or even commit misconduct to get there.

There is something of a vacuum-cleaner-sucking-itself-out-of-existence thing going on here, since we now have reason to distrust and doubt the things the scientists say, especially when they trot out these scary graphs, so to find out how bad the problem is, we’re going to listen to what the scientists have to say about it and look at some scary graphs.

But there is an important concept being illustrated here, which is well worthy of exploration because it has escaped the notice of many among us, particularly, those among us who have the most to say. The concept is one of simple uncertainty. Don’t Star Trek androids and Vulcans talk this way all the time? “Captain, there is a seventy-three percent probability that…” et cetera.

A funny thing happened in the big long monster-thread. The gadfly posted a chart from the NOAA that was very difficult to read. It turned out, neither the gadfly nor the geniuses at NOAA responsible for putting it together, had ever viewed it against anything but a white background. It was a .GIF file with a transparency layer that didn’t belong there, you see…so, I used an image processing tool to fix their own artifact for them, stripping out the transparency.

This is, coincidentally, a perfect metaphor for what is happening. SCIENCE SEZ…such-and-such a thing. The liberals and other laymen who like to feel all scientifical & junk before they really have a handle on the concepts involved, take note of the findings without also taking note, Vulcan-like, of what the potential is that this is a true & accurate reading of the thing being measured. Just like a different image file format that only supports the luminence and chroma of the pixel, but with no alpha/transparency channel present, presumes 1.0 for the transparency (meaning, all of the pixels are absolutely opaque). From the merry-go-round arguing with our resident gadfly, we’ve seen this is exactly what is happening. They understand “findings” and they want to debate it with people who say it might not necessarily be so, but they refuse to understand, let alone have a discourse about, the simple human-knowledge concept of uncertainty about things. They live in a 24-bit RGB world, you might say. There is reality, there are measurements…these are functionally synonymous. Question the measurements? How dare you!

Cross-posted at House of Eratosthenes and Washington Rebel.