Evidence for a limit to effective peer review

I missed it first time around but apparently, back in October, Nature published a somewhat-controversial article: Evidence for a limit to human lifespan. It came to my attention in a recent tweet:

The source: a fact-check article from Dutch news organisation NRC titled “Nature article is wrong about 115 year limit on human lifespan“. NRC seem rather interested in this research article. They have published another more recent critique of the work, titled “Statistical problems, but not enough to warrant a rejection” and a discussion of that critique, Peer review post-mortem: how a flawed aging study was published in Nature.

Unfortunately, the first NRC article does itself no favours by using non-comparable x-axis scales for its charts and not really explaining very well how the different datasets (IDL and GRG) were used. Data nerds everywhere then, are wondering whether to repeat the analysis themselves and perhaps fire off a letter to Nature.

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An Analysis of Contributions to PubMed Commons

I recently saw a tweet floating by which included a link to some recent statistics from PubMed Commons, the NCBI service for commenting on scientific articles in PubMed. Perhaps it was this post at their blog. So I thought now would be a good time to write some code to analyse PubMed Commons data.

The tl;dr version: here’s the Github repository and the RPubs report.

For further details and some charts, read on.

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Data corruption using Excel: 12+ years and counting

Why, it seems like only 12 years since we read Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics.

And can it really be 4 years since we reviewed the topic of gene name corruption in Gene name errors and Excel: lessons not learned?

Well, here we are again in 2016 with Gene name errors are widespread in the scientific literature. This study examined 35 175 supplementary Excel data files from 3 597 published articles. Simple yet clever, isn’t it. I bet you wish you’d thought of doing that. I do. The conclusion: about 20% of the articles have associated data files in which gene names have been corrupted by Excel.

What if there is no tomorrow? There wasn’t one today.

We tell you not to use Excel. You counter with a host of reasons why you have to use Excel. None of them are good reasons. I don’t know what else to say. Except to reiterate that probably 80% or more of the data analyst’s time is spent on data cleaning and a good proportion of the dirt arises from avoidable errors.

Novelty: an update

A recent tweet:


PubMed articles containing “novel” in title or abstract 1845 – 2014

made me think (1) has it really been 5 years, (2) gee, my ggplot skills were dreadful back then and (3) did I really not know how to correct for the increase in total publications?

So here is the update, at Github and a document at RPubs.

“Novel” findings, as judged by the usage of that word in titles and abstracts really have undergone a startling increase since about 1975. Indeed, almost 7.2% of findings were “novel” in 2014, compared with 3.2% for the period 1845 – 2014. That said, if we plot using a log scale as suggested by Tal on the original post, the rate of usage appears to be slowing down. See image, right (click for larger version).

As before, none of this is novel.

Note to journals: “methodologically sound” applies to figures too

PeerJ, like PLoS ONE, aims to publish work on the basis of “soundness” (scientific and methodological) as opposed to subjective notions of impact, interest or significance. I’d argue that effective, appropriate data visualisation is a good measure of methodology. I’d also argue that on that basis, Evolution of a research field – a micro (RNA) example fails the soundness test.
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Measuring quality is hard

Four articles. Click on the images for larger versions.

Exhibit A:¬†the infamous “(insert statistical method here)”. Exhibit B: “just make up an elemental analysis“. Exhibit C: a methods paper in which a significant proportion of the text was copied verbatim from a previous article. Finally, exhibit D, which shall be forever known as the “crappy Gabor” paper.

Exhibit A

Exhibit A

Exhibit B

Exhibit B

Exhibit C

Exhibit C

Exhibit D

Exhibit D

Notice anything?
I think that altmetrics are a great initiative. So long as we’re clear that what’s being measured is attention, not quality.

A new low in “databases”: the PDF

I’ve had a half-formed, but not very interesting blog post in my head for some months now. It’s about a conversation I had with a PhD student, around 10 years ago, after she went to a bioinformatics talk titled “Excel is not a database” and how she laughed as I’d been telling her that “for years already”. That’s basically the post so as I say, not that interesting, except as an illustration that we’ve been talking about this stuff for a long time (and little has changed).

HEp-2 or not HEp2?

HEp-2 or not HEp2?

Anyway, we have something better. I was exploring PubMed Commons, which is becoming a very good resource. The top-featured comment looks very interesting (see image, right).

Intrigued, I went to investigate the Database of Cross-contaminated or Misidentified Cell Lines, hovered over the download link and saw that it’s – wait for it – a PDF. I’ll say that again. The “database” is a PDF.

The sad thing is that this looks like very useful, interesting information which I’m sure would be used widely if presented in an appropriate (open) format and better-publicised. Please, biological science, stop embarrassing yourself. If you don’t know how to do data properly, talk to someone who does.

New publication: A panel of genes methylated with high frequency in colorectal cancer

I’m pleased to announce an open-access publication with my name on it:

Mitchell, S.M., Ross, J.P., Drew, H.R., Ho, T., Brown, G.S., Saunders, N.F.W., Duesing, K.R., Buckley, M.J., Dunne, R., Beetson, I., Rand, K.N., McEvoy, A., Thomas, M.L., Baker, R.T., Wattchow, D.A., Young, G.P., Lockett, T.J., Pedersen, S.K., LaPointe L.C. and Molloy, P.L. (2014). A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 14:54.

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