Sometimes Scientists Spread Misinformation

24 Aug

To err is human. Good scientists are aware of that, painfully so. The model scientist obsessively checks everything twice over and still keeps eyes peeled for loose ends. So it is a shock to learn that some of us are culpable for spreading misinformation.

Ken and I find that articles with serious errors, even articles based on fraudulent data, continue to be approvingly cited—cited without any mention of any concern—long after the problems have been publicized. Using a novel database of over 3,000 retracted articles and over 74,000 citations to these articles, we find that at least 31% of the citations to retracted articles happen a year after the publication of the retraction notice. And that over 90% of these citations are approving.

What gives our findings particular teeth is the role citations play in science. Many, if not most, claims in a scientific article rely on work done by others. And scientists use citations to back such claims. The readers rely on scientists to note any concerns that impinge on the underlying evidence for the claim. And when scientists cite problematic articles without noting any concerns they very plausibly misinform their readers.

Though 74,000 is a large enough number to be deeply concerning, retractions are relatively infrequent. And that may lead some people to discount these results. Retractions may be infrequent but citations to retracted articles post-retraction are extremely revealing. Retractions are a low-low bar. Retractions are often a result of convincing evidence of serious malpractice, generally fraud or serious error. Anything else, for example, a serious error in data analysis, is usually allowed to self-correct. And if scientists are approvingly citing retracted articles after they have been retracted, it means that they have failed to hurdle the low-low bar. Such failure suggests a broader malaise.

To investigate the broader malaise, Ken and I exploited data from an article published in Nature that notes a statistical error in a series of articles published in prominent journals. Once again, we find that approving citations to erroneous articles persist after the error has been publicized. After the error has been publicized, the rate of citation to erroneous articles is, if anything, higher, and 98% of the citations are approving.

In all, it seems, we are failing.

The New Unit of Scientific Production

11 Aug

One fundamental principle of science is that there is no privileged observer. You get to question what people did. But to question, you first must know what people did. So part of good scientific practice is to make it easy for people to understand how the sausage was made—how the data were collected, transformed, and analyzed—and ideally, why you chose to make the sausage that particular way. Papers are ok places for describing all this, but we now have better tools: version controlled repositories with notebooks and readme files.

The barrier to understanding is not just lack of information, but also poorly organized information. There are three different arcs of information: cross-sectional (where everything is and how it relates to each other), temporal (how the pieces evolve over time), and inter-personal (who is making the changes). To be organized cross-sectionally, you need to be macro organized (where is the data, where are the scripts, what do each of the scripts do, how do I know what the data mean, etc.), and micro organized (have logic and organization to each script; this also means following good coding style). Temporal organization in version control simply requires you to have meaningful commit messages. And inter-personal organization requires no effort at all, beyond the logic of pull requests.

The obvious benefits of this new way are known. But what is less discussed is that this new way allows you to critique specific pull requests and decisions made in certain commits. This provides an entirely new way to make progress in science. The new unit of science also means that we just don’t dole out credits in crude currency like journal articles but we can also provide lower denominations. We can credit each edit, each suggestion. And why not. The third big benefit is that we can build epistemological trees where the logic of disagreement is clear.

The dead tree edition is dead. It is also time to retire the e-version of the dead tree edition.

Sigh-tations

1 May

In 2010, Google estimated that approximately 130M books had been published.

As a species, we still know very little about the world. But what we know already far exceeds what any of us can learn in a lifetime.

Scientists are acutely aware of the point. They must specialize, as chances of learning all the key facts about anything but the narrowest of the domains are slim. They must also resort to shorthand to communicate what is known and what is new. The shorthand that they use is—citations. However, this vital building block of science is often rife with problems. The three key problems with how scientists cite are:

1. Cite in an imprecise manner. This broad claim is supported by X. Or, our results are consistent with XYZ. (Our results are consistent with is consistent with directional thinking than thinking in terms of effect size. That means all sorts of effects are consistent, even those 10x as large.) For an example of how I think work should be cited, see Table 1 of this paper.

2. Do not carefully read what they cite. This includes misstating key claims and citing retracted articles approvingly (see here). The corollary is that scientists do not closely scrutinize papers they cite, with the extent of scrutiny explained by how much they agree with the results (see the next point). For a provocative example, see here.)

3. Cite in a motivated manner. Scientists ‘up’ the thesis of articles they agree with, for instance, misstating correlation as causation. And they blow up minor methodological points with articles whose results their paper’s result is ‘inconsistent’ with. (A brief note on motivated citations: here).

How Do We Know?

17 Aug

How can fallible creatures like us know something? The scientific method is about answering that question well. To answer the question well, we have made at least three big innovations:

1. Empiricism. But no privileged observer. What you observe should be reproducible by all others.

2. Open to criticism: If you are not convinced about the method of observation, the claims being made, criticize. Offer reason or proof.

3. Mathematical Foundations: Reliance on math or formal logic to deduce what claims can be made if certain conditions are met.

These innovations along with two more innovations have allowed us to ‘scale.’ Foremost among the innovations that allow us to scale is our ability to work together. And our ability to preserve information on stone, paper, electrons, allows us to collaborate with and build on the work done by people who are now dead. The same principle that allows us to build as gargantuan a structure as the Hoover Dam and entire cities allows us to learn about complex phenomenon. And that takes us to the final principle of science.

Peer to Peer

20 Mar

Peers are equals, except as reviewers, when they are more like capricious dictators. (Or when they are members of a peerage.)

We review our peers’ work because we know that we are all fallible. And because we know that the single best way we can overcome our own limitations is by relying on well-motivated, informed, others. We review to catch what our peers may have missed, to flag important methodological issues, to provide suggestions for clarifying and improving the presentation of results, among other such things. But given a disappointingly long history of capricious reviews, authors need assurance. So consider including in the next review a version of the following note:

Reviewers are fallible too. So this review doesn’t come with the implied contract to follow all ill-advised things or suffer. If you disagree with something, I would appreciate a small note. But rejecting a bad proposal is as important as accepting a good one.

Fear no capriciousness. And I wish you well.

Motivated Citations

13 Jan

The best kind of insight is the ‘duh’ insight—catching something that is exceedingly common, almost routine, but something that no one talks about. I believe this is one such insight.

The standards for citing congenial research (that supports the hypothesis of choice) are considerably lower than the standards for citing uncongenial research. It is an important kind of academic corruption. And it means that the prospects of teleological progress toward truth in science, as currently practiced, are bleak. An alternate ecosystem that provides objective ratings for each piece of research is likely to be more successful. (As opposed to the ‘echo-system’—here are the people who find stuff that ‘agrees’ with what I find—in place today.)

An empirical implication of the point is that the average ranking of journals in which congenial research that is cited is published is likely to be lower than in which uncongenial research is published. Though, for many of the ‘conflicts’ in science, all sides of the conflict will have top-tier publications—-which is to say that the measure is somewhat crude.

The deeper point is that readers generally do not judge the quality of the work cited for support of specific arguments, taking many of the arguments at face value. This, in turn, means that the role of journal rankings is somewhat limited. Or more provocatively, to improve science, we need to make sure that even research published in low ranked journals is of sufficient quality.

The Case for Ending Closed Academic Publishing

21 Mar

A few commercial publishers publish a large chunk of top flight of academic research. And earn a pretty penny doing so. The standard operating model of the publishers is as follows: pay the editorial board no more than $70-$100k, pay for typesetting and publishing, and in turn get copyrights to academic papers. And then go on and charge already locked in institutional customers—university and government libraries—and ordinary scholars extortionary rates. The model is gratuitously dysfunctional.

Assuming there are no long term contracts with the publishers, the system ought to be rapidly dismantled. But if dismantling is easy, creating something better may not be. It just happens to be. A majority of the cost of publishing is in printing on paper. Twenty first century has made printing large organized bundles on paper largely obsolete; those who need it can print on paper at home. Beyond that, open source software for administering a journal already exists. And the model of a single editor with veto powers seems anachronistic. Editing duties can be spread around much like peer review. As unpaid peer review can survive as it always has, though better mechanisms can be thought about. If some money is still needed for administration, it could be gotten easily by charging a nominal submission tax, waived where the author self identifies as being unable to pay.

Bad Science: A Partial Diagnosis And Some Remedies

3 Sep

Lack of reproducibility is a symptom of science in crisis. An eye-catching symptom to be sure, but hardly the only one vying for attention. Recent analyses suggest that nearly two-thirds of the (relevant set of) articles published in prominent political science journals condition on post-treatment variables (see here.) Another set of analysis suggests that half of the relevant set of articles published in prominent neuroscience journals treat difference in significant and non-significant result as the basis for the claim that difference between the two is significant (see here). What is behind this? My guess: poor understanding of statistics, poor editorial processes, and poor strategic incentives.

  1. Poor understanding of statistics: It is likely the primary reason. For it would be good harsh to impute bad faith on part of those who use post-treatment variables as control or treating difference between significant and non-significant result as significant. There is likely a fair bit of ignorance — be it on the part of authors or reviewers. If it is ignorance, then the challenge doesn’t seem as daunting. Let us devise good course materials, online lectures, and teach. And for more advanced scholars, some outreach. (And it may involve teaching scientists how to write-up their results.)

  2. Poor editorial processes: Whatever the failings of authors, they aren’t being caught during the review process. (It would be good to know how often reviewers are actually the source of bad recommendations.) More helpfully, it may be a good idea to create small questionnaires before submission that alert authors about common statistical issues.

  3. Poor strategic incentives: If authors think that journals are implicitly biased towards significant findings, we need to communicate effectively that it isn’t so.

Stemming the Propagation of Error

2 Sep

About half of the (relevant set of) articles published in neuroscience mistake difference between a significant result and an insignificant result as evidence for the two being significantly different (see here). It would be good to see if the articles that make this mistake, for instance, received fewer citations post publication of the article revealing the problem. If not, we probably have more work to do. We probably need to improve ways by which scholars are alerted about the problems in articles they are reading (and interested in citing). And that may include building different interfaces for the various ‘portals’ (Google Scholar, JSTOR etc., and journal publishers) that scholars heavily use. For instance, creating UIs that thread reproduction attempts, retractions, articles finding serious errors within the original article, etc.

Reviewing the Peer Review

24 Jul

Update: Current version is posted here.

Science is a process. And for a good deal of time, peer review has been an essential part of the process. Looked independently by people with no experience with it, it makes a fair bit of sense. For there is only one well-known way of increasing the quality of an academic paper — additional independent thinking. And who better than engaged, trained colleagues.

But this seemingly sound part of the process is creaking. Today, you can’t bring two academics together without them venting their frustration about the broken review system. The plaint is that the current system is a lose-lose-lose. All the parties — the authors, the editors, and the reviewers — lose lots and lots of time. And the change in quality as a result of suggested changes is variable, generally small, and sometimes negative. Given how critical the peer review is in the scientific production, it deserves closer attention, preferably with good data.

But data on peer review aren’t available to be analyzed. Thus, some anecdotal data. Of the 80 or so reviews that I have filed and for which editors have been kind enough to share comments by other reviewers, two things have jumped at me: a) hefty variation in quality of reviews, b) and equally hefty variation in recommendations for the final disposition. It would be good to quantify the two. The latter is easy enough to quantify.

Reliability of the review process has implications for how many recommenders we need to reliably accept or reject the same article. Counter-intuitively, increasing the number of reviewers per manuscript may not increase the overall burden of reviewing. Partly because everyone knows that the review process is so noisy, there is an incentive to submit articles that people know aren’t good enough. Some submitters likely reason that there is a reasonable chance of a `low quality’ article being accepted at top places. Thus, low reliability peer review systems may actually increase the number of submissions. Greater number of submissions, in turn, increases editors’ and reviewer’s load and hence reduces the quality of reviews, and lowers the reliability of recommendations still further. It is a vicious cycle. And the answer may be as simple as making the peer review process more reliable. At any rate, these data ought to be publicly released. Side-by-side, editors should consider experimenting with number of reviewers to collect more data on the point.

Quantifying the quality of reviews is a much harder problem. What do we mean by a good review? A review that points to important problems in the manuscript and, where possible, suggests solutions? Likely so. But this is much trickier to code. But perhaps there isn’t as much a point to quantifying this. What is needed perhaps is guidance. Much like child-rearing, there is no manual for reviewing. There really should be. What should reviewers attend to? What are they missing? And most critically, how do we incentivize this process?

When thinking about incentives, there are three parties whose incentives we need to restructure — the author, the editor, and the reviewer. Authors’ incentives can be restructured by making the process less noisy, as we discuss above. And by making submissions costly. All editors know this: electronic submissions have greatly increased the number of submissions. (It would be useful to study what the consequence of move to electronic submission has been on quality of articles.) As for the editors — if the editors are not blinded to the author (and the author knows this), they are likely to factor in the author’s status in choosing the reviewers, in whether or not to defer to the reviewers’ recommendations, and in making the final call. Thus we need triple blinded pipelines.

Whether or not the reviewer’s identity is known to the editor when s/he is reading the reviewer’s comments also likely affects reviewer’s contributions — in both good and bad ways. For instance, there is every chance that junior scholars in trying to impress editors file more negative reviews than they would if they would if they knew that the editor had no way of tying the identity of the reviewer with the review. Beyond altering anonymity, one way to incentivize reviewers would be to publish the reviews publicly, perhaps as part of the paper. Just like online appendices, we can have a set of reviews published online with each article.

With that, some concrete suggestions beyond the ones already discussed. Expectedly — given they come from a quantitative social scientist — they fall into two broad brackets: releasing and learning from the data already available, and collecting more data.

Existing Data

A fair bit of data can be potentially released without violating anonymity. For instance,

  • Whether manuscript was desk rejected or not
  • How many reviewers were invited
  • Time taken by each reviewer to accept (NA for those from whom you never heard)
  • Total time in review for each article (till R and R or reject) (And separate set of column for each revision)
  • Time taken by each reviewer
  • Recommendation by each reviewer
  • Length of each review
  • How many reviewers did the author(s) suggest?
  • How often were suggested reviewers followed-up on?

In fact, much of the data submitted in multiple-choice question format can probably be released easily. If editors are hesitant, a group of scholars can come together and we can crowdsource collection of review data. People can deposit their reviews and the associated manuscript in a specific format to a server. And to maintain confidentiality, we can sandbox these data allowing scholars to run a variety of pre-screened scripts on it. Or else journals can institute similar mechanisms.

Collecting More Data

  • In economics, people have tried to institute shorter deadlines for reviewers to effect of reducing review times. We can try that out.
  • In terms of incentives, it may be a good idea to try out cash but also perhaps experimenting with a system where reviewers are told that their comments will be public. I, for one, think it would lead to more responsible reviewing. It would be also good to experiment with triple-blind reviewing.

If you have additional thoughts on the issue, please propose them at: https://gist.github.com/soodoku/b20e6d31d21e83ed5e39

Here’s to making advances in the production of science and our pursuit for truth.