Mishandled criticism of PLOS ONE

The scientific community was rightfully brought to arms when it was discovered a PLOS ONE article referred to a “Creator” multiple times (seemingly implying the human hand was the result of intelligent design), and it didn’t take long for this makeshift army to turn its attention to the journal as a whole. Using their tweets as arrows, self-proclaimed editors of the journal threatened to resign if the article wasn’t retracted, while others claimed this showed the journal was a “joke”.

It is unclear if the mention of the “Creator” is simply due to a language barrier, and it hasn’t been shown that any of the science in the paper is unsound or fraudulent, and it is possible this is just an honest mistake. And it isn’t unusual for large errors to make it through peer-review and the editorial process, or worse, fabricated data or flawed experimental designs. In fact, journals such as Nature and Science have happily published some of the most ridiculed papers in history, some of which haven’t even been retracted, and yet no one is calling for editors at these journals to step down or claiming that these mistakes show a general pattern of negligence.

The reason for this is the scientists using this opportunity to attack PLOS ONE have been sharpening their weapons for some time now. PLOS was meant to be a beacon of hope for the open access movement, freeing papers from paywalls and impact factors while managing to keep article costs down and reducing the time to publication. This is an image taken from Michael Eisen’s blog (he is co-founder of PLOS):

However, PLOS ONE quickly became a mega-journal due to its policy of not using impact to judge scientific publications, essentially accepting any paper that walks through its doors (allowing them to become profitable in the process). Perhaps there are some scientists that have submitted their papers to PLOS ONE because they believe in what PLOS ONE supposedly stands for, but the majority of researchers who submit to PLOS ONE do so only after having their paper rejected everywhere else. PLOS ONE has essentially become the standard last resort place to publish.

PLOS ONE is just respectable enough to be able to claim it’s related to high impact journals, albeit a distant cousin or an ugly sister, so researchers manage to talk themselves into publishing there. And hey, you could always claim you published there because you believe in open access. You just have to make sure you don’t mind the smell, because your paper is going to be amongst straight up garbage. Many of the papers in PLOS ONE would be much better suited as short blog posts instead of official publications diluting the scientific literature.

One such paper, which was soundly derided on twitter, had the audacity to introduce an R function for heatmaps, despite the fact several functions already exist for generating heatmaps (and they are awesome). But their function had fewer options than the current functions, and this somehow made their function better. To top it off, they referred to their plots as quilt plots instead of heatmaps in a likely attempt to pull a fast one on the editors, and well, I guess it worked.

The papers in PLOS ONE are in general so bad that I am genuinely afraid to see the papers that the journal turns down. And yet, as a strong believer in open science I would be able to look past this and publish in PLOS ONE myself if the journal was truly the ideal it is meant to be. Claiming to have a quick turnaround time to publication, there is strong evidence to the contrary. Meant to be a model for how an open access journal should operate, it doesn’t have open peer-review, which new journals such as PeerJ and F1000Research offer. As an online only journal it is supposed to be affordable for authors to publish there, but its APCs are in the thousands while it is essentially free to publish in PeerJ.

The fact that the editors of PLOS ONE let the word “Creator” slip into the published literature doesn’t make the entire journal a joke or say anything about the other papers published in PLOS ONE, but it also doesn’t mean PLOS ONE is not already a joke and many of the papers in PLOS ONE should never have been published. If PLOS ONE is going to open the floodgates for papers to get published in the name of open access, then it needs to truly be open access. That means the paper is preprinted as soon as it is submitted, and the peer-reviewers are identified by name and the peer-review process is made public.

If PLOS ONE continues along its charted course, then it really isn’t that different from the journals it supposedly despises. Every journal is essentially as open access as PLOS ONE because you can easily email articles to your friends or use Sci-Hub to download the article yourself. As a result, right now PLOS ONE is just the place where failed projects find a home or researchers looking to game the system pad their resume. Hopefully if there is a “Creator” they created this opportunity for PLOS ONE to fix its course.