Tag: Ioannidis

24
Jan

Why I disagree with Andrew Gelman's critique of my paper about the rate of false discoveries in the medical literature

With a colleague, I wrote a paper titled, "Empirical estimates suggest most published medical research is true"  which we quietly posted to ArXiv a few days ago. I posted to the ArXiv in the interest of open science and because we didn't want to delay the dissemination of our approach during the long review process. I didn't email anyone about the paper or talk to anyone about it, except my friends here locally.

I underestimated the internet. Yesterday, the paper was covered in this piece on the MIT Tech review. That exposure was enough for the paper to appear in a few different outlets. I'm totally comfortable with the paper, but was not anticipating all of the attention so quickly.

In particular, I was a little surprised to see it appear on Andrew Gelman's blog with the disheartening title, "I don’t believe the paper, “Empirical estimates suggest most published medical research is true.” That is, most published medical research may well be true, but I’m not at all convinced by the analysis being used to support this claim." I responded briefly this morning to his post, but then had to run off to teach class. After thinking about it a little more, I realized I have some objections to his critique.

His main criticisms of our paper are: (1) with type I/type II errors instead of type S versus type M errors (paragraph 2), (2) that we didn't look at replication, we performed inference (paragraph 4), (3) that there is p-value hacking going on (paragraph 4), and (4) he thinks that our model does not apply because p-value hacking my change the assumptions underlying this model in genomics.

I will handle each of these individually:

(1) This is primarily semantics. Andrew is concerned with interesting/uninteresting with his Type S and Type M Errors. We are concerned with true/false positives as defined by type I and type II errors (and a null hypothesis). You might believe that the null is never true - but then by the standards of the original paper all published research is true. Or you might say that a non-null result might have an effect size too small to be interesting - but the framework being used here is hypothesis testing and we have stated how we defined a true positive in that framework explicitly.  We define the error rate by the rate of classifying thing as null when they should be classified as alternative and vice versa. We then estimate the false discovery rate, under the framework used to calculate those p-values. So this is not a criticism of our work with evidence, rather it is a stated difference of opinion about the philosophy of statistics not supported by conclusive data.

(2) Gelman says he originally thought we would follow up specific p-values to see if the results replicated and makes that a critique of our paper. That would definitely be another approach to the problem. Instead, we chose to perform statistical inference using justified and widely used statistical techniques. Others have taken the replication route, but of course that approach too would be fraught with difficulty - are the exact conditions replicable (e.g. for a clinical trial), can we sample from the same population (if it has changed or is hard to sample), and what do we mean by replicates (would two p-values less than 0.05 be convincing?). This again is not a criticism of our approach, but a statement of another, different analysis Gelman was wishing to see.

(3)-(4) Gelman states, "You don’t have to be Uri Simonsohn to know that there’s a lot of p-hacking going on." Indeed Uri Samuelson wrote a paper where he talks about the potential for p-value hacking. He does not collect data from real experiments/analyses, but uses simulations, theoretical arguments, and prospective experiments designed to show specific problems. While these arguments are useful and informative, it gives no indication of the extent of p-value hacking in the medical literature. So this argument is made on the basis of a supposition by Gelman that this happens broadly, rather than on data.

My objection to his criticism is that his critiques are based primarily on philosophy (1), a wish that we had done the study a different way (2), and assumptions about the way science works with only anecdotal evidence (3-4).

One thing you could very reasonably argue is how sensitive our approach is to violations of our assumptions (which Gelman implied with criticisms 3-4). To address this,  my co-author and I have now performed a simulation analysis. In the first simulation, we considered a case where every p-value less than 0.05 was reported and the p-values were uniformly distributed, just as our assumptions would state. We then plot our estimates of the swfdr versus the truth. Here our estimator works pretty well.

 

all-significant

We also simulate a pretty serious p-value hacking scenario where people report only the minimum p-value they observe out of 20 p-values. Here our assumption of uniformity is strongly violated. But we still get pretty accurate estimates of the swfdr for the range of values (14%) we report in our paper.

only-min

Since I recognize this is only a couple of simulations, I have also put the code up on Github with the rest of our code for the paper so other people can test it out.

Whether you are convinced by Gelman, or convinced by my response, I agree with him that it is pretty unlikely that "most published research is false" so I'm glad our paper is at least bringing that important point up. I also hope that by introducing a new estimator of the science-wise fdr we inspire more methodological development and that philosophical criticisms won't prevent people from looking at the data in new ways.

 

 

 

04
Jan

Does NIH fund innovative work? Does Nature care about publishing accurate articles?

Editor's Note: In a recent post we disagreed with a Nature article claiming that NIH doesn't support innovation. Our colleague Steven Salzberg actually looked at the data and wrote the guest post below. 

Nature published an article last month with the provocative title "Research grants: Conform and be funded."  The authors looked at papers with over 1000 citations to find out whether scientists "who do the most influential scientific work get funded by the NIH."  Their dramatic conclusion, widely reported, was that only 40% of such influential scientists get funding.

Dramatic, but wrong.  I re-analyzed the authors' data and wrote a letter to Nature, which was published today along with the authors response, which more or less ignored my points.  Unfortunately, Nature cut my already-short letter in half, so what readers see in the journal omits half my argument.  My entire letter is published here, thanks to my colleagues at Simply Statistics.  I titled it "NIH funds the overwhelming majority of highly influential original science results," because that's what the original study should have concluded from their very own data.  Here goes:

To the Editors:

In their recent commentary, "Conform and be funded," Joshua Nicholson and John Ioannidis claim that "too many US authors of the most innovative and influential papers in the life sciences do not receive NIH funding."  They support their thesis with an analysis of 200 papers sampled from 700 life science papers with over 1,000 citations.  Their main finding was that only 40% of "primary authors" on these papers are PIs on NIH grants, from which they argue that the peer review system "encourage[s] conformity if not mediocrity."

While this makes for an appealing headline, the authors' own data does not support their conclusion.  I downloaded the full text for a random sample of 125 of the 700 highly cited papers [data available upon request].  A majority of these papers were either reviews (63), which do not report original findings, or not in the life sciences (17) despite being included in the authors' database.  For the remaining 45 papers, I looked at each paper to see if the work was supported by NIH.  In a few cases where the paper did not include this information, I used the NIH grants database to determine if the corresponding author has current NIH support.  34 out of 45 (75%) of these highly-cited papers were supported by NIH.  The 11 papers not supported included papers published by other branches of the U.S. government, including the CDC and the U.S. Army, for which NIH support would not be appropriate.  Thus, using the authors' own data, one would have to conclude that NIH has supported a large majority of highly influential life sciences discoveries in the past twelve years.

The authors – and the editors at Nature, who contributed to the article – suffer from the same biases that Ioannidis himself has often criticized.  Their inclusion of inappropriate articles and especially the choice to require that both the first and last author be PIs on an NIH grant, even when the first author was a student, produced an artificially low number that misrepresents the degree to which NIH supports innovative original research.

It seems pretty clear that Nature wanted a headline about how NIH doesn't support innovation, and Ioannidis was happy to give it to them.  Now, I'd love it if NIH had the funds to support more scientists, and I'd also be in favor of funding at least some work retrospectively - based on recent major achievements, for example, rather than proposed future work.  But the evidence doesn't support the "Conform and be funded" headline, however much Nature might want it to be true.