I was thinking the other day about how difficult it is, once you’re experienced in some field, to put yourself back in the position of someone who isn’t. This is a factor in writing the entire blog, naturally, since many of its readers are hanging around to learn about some things that they didn’t know, and a fair percentage of them aren’t even medicinal chemists (or chemists of any type) at all. I try to write up complicated topics in a way that at least leaves a few handholds for people to climb up, with varying levels of success.
But what brought on these recent thoughts was the blog post I did on literature crap, bad papers that should be retracted and aren’t. We’ve seen during the pandemic how people have used/abused the scientific literature, and that’s come from every sort of participant. There have been uncountable poor-quality papers that got published just because they had a “Covid hook” – some of them were well-intentioned but written too quickly and in too sloppy a manner, while others were just cynical efforts to pad the CV and clean out some folders. Papers got published when they shouldn’t have been, and papers got published in better journals than they deserved.
And that’s just the legitimate publishing scene. Down in the depths, in the pay-for-play scam “journals” that promise you “peer review” and accept any manuscript within hours (pending receipt of payment), things were of course worse. Now one of the bad things about current scientific publishing is that a blurry zone has developed between these two worlds, as exemplified by Scientific Reports. There have been interesting and useful papers that have appeared in that venue, but they have been surrounded by junk and filler, and by worse. Here’s an example from a completely different field (mycology) of a two-year effort to get an obviously defective and substandard paper pulled from that journal, and it was not an easy task. Eventually SR seems to have made the paper disappear by citing some technical issues without addressing the scientific shortcomings.
Pandemically, there have been many papers published that have given fuel to conspiracy theorists. Some of this couldn’t be helped. There are (and always will be) plenty of legitimate avenues of inquiry that will set people off. An easy example is the origin-of-Covid issue. You have the “zoonotic spillover in the market” hypothesis, and the “inadvertant lab leak of a wild-type virus” one, and there’s also the “leak of a human-engineered virus” one, too. That last one attracts a crowd that is crazier on the average than the others, but the hypothesis is a legitimate one that can be (and has been) investigated. Right now, I think the evidence is strongest for the first of those and weakest for the third. But that last one is never going to go away, because there are True Believers who are never going to let it fade, and they can cite a lot of literature to back up their position. I don’t think that those papers are very good or very convincing, but to an outsider the whole dispute can look like it’s on a completely level playing field: this bunch of highly educated people with a stack of manuscripts and data versus that bunch of highly educated people with a stack of manuscripts and data.
And that brings me back around to the outsider’s-view problem. If you’re not aware of how scientific publishing works, then a paper from the International Journal Of Important Research or pick-your-scam-journal-name might seem perfectly fine and a great reference to support your position, whatever it might be: Covid, glyphosate, 5G cell phone towers, etc. If you’re not a scientist yourself, these things look as real as any other scientific paper. Real people (desperate and/or cynical real people) publish actual manuscripts in them as well, padding their publication lists in the easiest (or perhaps only) way that they can. Many times I’ve had the problem of explaining to someone that no, the World Journal of Reports on Research Results (just made that one up) is not a “journal” per se but a pay-to-play dumping ground that would publish extracts of Finnegan’s Wake or the 1952 Tucson phone book if the check cleared.
But you don’t have to go to that level. Start at the top, in our own field: if you scroll through the Journal Of Medicinal Chemistry, you will see (of course) one J Med Chem paper after another rolling past your gaze. But they are not all equal, and never have been, and that goes for any journal’s table of contents as well. For J Med Chem, you will see (for example) a big several-years-old look at a failed project from a big pharma company, finally written up because the project has at long last died and the only thing left to do is write the thing up while there are still people around who remember what happened. About a third of folks on it will have left by the time the paper appears, leaving complicated typographic symbols scattered around the co-authors list. Next to that will be a short review article about some drug class or target – these are generally decent and sometimes really valuable, but overall of varying levels of competence and thoroughness. There will be papers that are trying to stretch some particular aspect of the work described (might be modeling, might be disease relevance, might even be the novelty of the structures) further than it can quite go, in order to justify getting into J Med Chem at all. Some papers will be from academic groups and may well be light on the stuff that industry would have spent more time and effort on (animal studies of sufficient power, pharmacokinetics and metabolism, formulations). And some of those industry papers will be from projects that are too long gone to be of much interest other than as reference data for someone, somewhere, someday.
So right next to a detailed report on the development of a first-in-class therapeutic that’s recently hit the market will be an easily skippable paper on some class of compound that has never yielded a drug and probably never will, but keeps appearing in the literature because they’re easy to synthesize, along with some not-so-great docking hypotheses and little or no cell or animal data at all. If you don’t know anything about drug discovery or medicinal chemistry, these appear equal as well – after all, they’re both in J. Med. Chem., right? I assume that the same goes if I scroll through the contents of any journal in a field that I don’t know as well – why shouldn’t it?
This is why there are various levels of journals, naturally, but these days, with so many journals (even just the legit ones) and so many places to publish, it can be tough to pick out those levels. It’s very hard, from a publishing standpoint, to run a journal that publishes only Obviously Great Stuff, because there’s not always enough Great Stuff to fill out an issue (and beside, there are some other Great Stuff journals that your authors might decamp to if you give them too much trouble or take too long with their manuscript). But you can devalue that reputation if you don’t watch out, too. To me, this is what has happened over the last few years with Angewandte Chemie. I used to go through it regularly, but they have taken to publishing so many papers that I can’t keep up any more, and even when I try to it seems like I’m stopping to read fewer and fewer of them.
I have no obvious solutions to the various problems. Some of the problems are obvious – I mean, we really, really do have too many journals, for one. But the incentives to launch new ones are still there, so they keep on coming. The incentives for authors to publish substandard papers, just to have something published, are still there, too, and always have been. And at the junk end, the incentives to take people’s money are as strong as ever. Everyone’s doing just what you would figure that they would do, and look at the place.
