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Don’t be a rube

An interesting article in The Guardian on the rise of the profit-oriented part of scientific publishing. One part of the article describes how companies like Elsevier and Pergamon make so much money: “It is as if the New Yorker or the Economist demanded that journalists write and edit each other’s work for free, and asked the government to foot the bill.” How much money? Try revenue of $24 billion. Elsevier’s profit margin: 36%.

Now some scientists have argued that journals are outdated and provide no added value; GG has argued this isn’t true. But with the existence of non-profit publishers, does it make sense to feed these very profitable monsters?

Well, no. Worse, many scientists don’t seem to understand that their science is no longer theirs once it is in one of those journals.

Some of us have sworn off of Elsevier journals, not reviewing for them or publishing in them (though we sometimes get dragged in by colleagues). That is walking away from a lot of poor journals and a few really good ones. In the days of paper journals, this was a clear choice. Even now, Elsevier’s tactics even for open-access have driven some away. But close examination of what societies are doing suggests that avoiding vendors many view as unscrupulous is getting harder and harder.

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When you have a hammer…

…all the world is a nail.  And the currently popular hammers are things like Twitter and Instagram and Tinder.  While some have long advocated the first two as important tools for scientists, the last has been used as a model for scanning through preprints.  Lots and lots of preprints. The Science story on this says “A web application inspired by the dating app Tinder lets you make snap judgments about preprints—papers published online before peer review—simply by swiping left, right, up, or down.”

Nothing says “science” like “snap judgment”.

While GG lambasted an effort to capture social media-ish solutions as a means of post-publication peer review, how about tools to let you find what cutting edge science is appearing? That Science report on social media linked above says that is what social media is good for.  Um, really?

GG studies the Sierra Nevada.  Try going to Twitter and searching on #SierraNevada.  Bet you didn’t think there were that many people so fascinated with taking pictures of beer bottles. Add, say, #science. Chaff winnowed some, but very little wheat. Add #tectonics. Crickets.

The idea of this new app (Papr) is that if only you were able to see lots and lots of stuff quickly, you’d find some gems to explore. Really?  Students complain bitterly about a firehose approach in the classroom, and the solution here is, um, a firehose? (To be fair, it appears the app developers are not necessarily expecting great things here).

Forget that.  What we want and need are tools to reduce chaff, not accelerate it.

What we need is something akin to Amazon’s suggestions tool.  Imagine visiting the preprint store to get a couple of papers you know you want.  One maybe is on a topic you care about–say, the Sierra Nevada.  Another maybe deals with a technique, say full waveform tomography.  A third uses some unusual statistical tests. You download these and the preprint store suggests a few other preprints based on the full text content of the papers you got. Why that instead of keywords? Keywords have a way of being too picky. You might call work “tectonics” and GG might call it “geodynamics” and thus the keywords searches might pass by each other. But if the text is still talking about changes in elevation, changes in lithospheric structure–those are less likely to get overlooked.  If this tool is smart enough to recognize quasi-synonyms and phrases, all the better.

Such a tool grows more powerful the more you work with it. While on that first try, you will also get recommendations on papers overlapping in non-interesting ways (say, applications of the techniques in paper 1, the geographic area under study in paper 2, and the measurement types in paper 3), the more you interact with this, the better it gets.

Here’s the sad thing: the tools to make something like this have been around for decades.  The best spam filters (like SpamSieve) use a form of Bayesian filtering based on message content in addition to black- and whitelists. Earth science got much of its literature into a single “preprint store” long ago in GeoScienceWorld. And yet here we are, swiping left again and again and again….

Citation citations

Neat article in Slate on how damaging bad citation practices are (using as key example the origins of the increase in opioid prescriptions that have now led to this abuse crisis) (thanks, RetractionWatch, for the pointer). Go read it.  GG’s already sounded off a few times on the mystery of lousy citation practices here and here, so we’ll just leave it at that.

The “scientific method”, a needless stumbling block. With a note on falsification

Paul Braterman points out the difficulty of the straitjacket of middle school “scientific method” and how that runs into challenges with historical science (something GG approached more timidly in an old post “Can you falsify an earth science hypothesis?“)

Primate's Progress

Science does not have a separate special method learning about world, the “scientific method” as taught in schools is a damaging illusion, and the falsifiability criterion has itself been falsified

Below, R: How not to; “The Scientific Method”, as inflicted on Science Fair participants. Click to enlarge

Consider this, from a justly esteemed chemistry text:

Scientists are always on the lookout for patterns.… Once they have detected patterns, scientists develop hypotheses… After formulating a hypotheses, scientists design further experiments [emphasis in original]

Or this, from a very recent post to a popular website:

The scientific method in a nutshell:
1. Ask a question
2. Do background research
3. Construct a hypothesis
4. Test your hypothesis by doing experiments
5. Analyze your data and draw conclusions
6. Communicate your results [emphasis in original]

Then, if you find yourself nodding in agreement, consider this:

Since a scientific theory, by…

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Entering year four…

Three years ago the Grumpy Geophysicist made his debut, enticing 447 visitors over the remainder of 2014 into this odd collection of rants. That was about 4 visitors per post (yes, things are better now).  As noted in the “About” page, though, this has never been about getting lots of likes, it is rather a combination of therapy and writing practice. Nevertheless, on occasion GG has accidentally stumbled into something others found interesting (well, a few, not like anything here has gone viral), and so was curious just what those interesting posts were. So without further ado, a few of the most viewed posts from the first three years of the Grumpy Geophysicist (giving many of you a chance to see what you missed…which, perhaps, will confirm why you weren’t looking here earlier). (Small posts don’t get counted so thoroughly).

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Precise Opposition

GG has previously been frustrated with the combination of imprecise speech of anti-fracking groups as well as the double speak of industry. The reason you might want to be precise might be well illustrated by a recent home explosion in Colorado.

The exploding house killed two men working on a hot water heater in the basement; usually when you hear these things, it turns out there is a gas leak or something like that in play. The startling news has been the move by Anadarko Petroleum Corp. to shut down 3000 wells they are operating while the wells are checked out (that is more than 5% of the active wells in the state). The exploded house was 170 feet from a 1993 well reactivated this past January. Although a new well can not be drilled there, houses can be built that close to existing wells (these houses are only a couple years old).

Oil companies are loathe to shut down operations (see opposition to claims of induced earthquakes, for instance). Shutting down this number of wells even as investigators are saying that they still don’t know what happened strongly suggests something may have gone wrong. Given that the oil company feels that shutting down wells is likely to reduce a risk, they are presumably not thinking that any gas leaked up around a bad casing job in the well but instead are concerned there might be leaks in the underground lines connecting wells to pipelines or storage facilities.

And here’s the thing.  This is not a modern, horizontally-drilled heavily fracked well. This is one of those older-style vertical wells. So when anti-fracking groups say they don’t want to stop oil and gas development but do want to stop fracking (as was the case in Longmont, Colorado a couple years back), this is the kind of well they think is OK. So once again a reminder: fracking is very rarely a cause of problems, but all the other stuff with oil and gas development is the real problem people are complaining about.

The irony might well be that if Anadarko’s infrastructure was the cause of the blast, there is likely to be enough of an outcry to allow far more stringent rules on any new oil and gas development–even though a blast caused by a leak of a subdivision gas supply line would probably not shut down the use of natural gas in houses. So “anti-fracking” groups might get their wish not because of fracking problems per se but because houses were built in the vicinity of active oil and gas operations.

(Equally ironic is the request from the Boulder County Board of Supervisors for companies to shut down all their vertical wells in the county–apparently unaware that it is the near-surface infrastructure that could be the problem, which can exist at both directional and vertical well pads).

It should be interesting to see what happens. Almost certainly it points to a need to check up on the older oil and gas infrastructure in the state. Whether it changes the politics of new oil and gas operations remains to be seen.

Interring the Good

The evil that men do lives after them; the good is oft interred with their bones.- Wm. Shakespeare, Julius Caesar

We are all human and recognize in others strengths and weaknesses.  Generally we choose to amplify those: those whose accomplishments seem notable are heroes, those whose failings seem pronounced become villains. What has become more common in the past few decades is to revise evaluations using present standards of conduct. So, for instance, you might think of Columbus, who was lauded for centuries for opening the New World to the Old, but in recent years that accomplishment has come to be viewed as a mixed blessing or an outright calamity, leading to fewer places recognizing this as a holiday.

But Columbus’s loss of stature is in large part a change in our view of the accomplishment and less a revision of how we view Columbus the man (though he has taken hits there, too). A more pertinent example might be Thomas Jefferson, whose accomplishments as a statesman and president retain their luster, but whose personal behavior (most notably being a slave owner) has caused many to deride him. Is Thomas Jefferson now more villain than hero?

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