A friend, who had decided not to pursue a PhD and an academic career after finishing his Masters degree, asked me how it's possible that so many of the papers that are published in peer-reviewed journals are - well - bullshit. As a response, I told him about a recent experience of mine.
A while ago, I was asked to review a paper by a journal with a pretty high impact factor. I agreed: the paper was right in my area of expertise and sounded very interesting. When I read the manuscript, however, I was less enthusiastic. Let's say: I've seen better papers desk-rejected by lower impact factor journals. This was a sloppily designed study with overstated conclusions. I wrote the review by my standard template: First, summarise the paper in a few sentences, then write something nice about it, then list major and minor points, with suggestions that would address them whenever possible. I hold on to the belief that any study that the authors thought was worth conducting is also worth publishing, at least in some form. In the paper, I detected a potential major confound, and I had the impression that the authors wanted to hide some of the information relating to it, so I asked for clarifications.
I submitted my review, and as always, a while later, received the decision letter. The other reviews were also lukewarm at best, so I was very surprised that the action editor invited a revision! When the authors resubmitted the paper, I agreed to review it again. However, most of my comments remained unaddressed, and my overall impression was that of the authors trying to hide some of the design flaws to blow up the importance of the conclusions. I wrote a slightly less reserved review, stating more clearly that I didn't think the paper should be published unless the authors addressed my comments. When I was invited to participate in the third round of reviews, I declined: I just didn't want to deal with it.
Several months later, I saw the paper published in the very same high impact factor journal. As the academic world is small, I now knew for sure what I had suspected despite the anonymity of the peer review process: the senior author of that paper was a friend of the action editor's.
This is, of course, an anecdote, coloured by my own perceptions and preconceptions. There is nothing to suggest, other than my own impression, that the paper was published only because of the friendship between the author and editor. Maybe (probably) I'm way too skeptical in my reading of articles. That was also one of the reasons why I had declined to do a third round of review: I wanted to leave it up to the editor and the other reviewers to decide whether my concerns were justified. But let's be honest: Is anyone truly surprised that there are some cases where editors are more lenient when they personally know the author(s)? And, if we are truly honest, isn't this just a very natural thing that we do ourselves whenever we judge our colleagues' papers, be it as reviewers or editors or simply as readers: letting people we know and like get away with things that we would judge strangers harshly for?
Maybe this anecdote, along with your own personal experiences, is convincing enough to show that at least sometimes, personal interest interferes with objective judgements and allows articles to pass peer review when they wouldn't hold up to scrutiny under other circumstances. This raises two questions, to which I don't have an answer: How often does this happen, and is this really a problem? And, more importantly, what is a better system?
For years, I've been an advocate for as much transparency as possible in all aspects of the research process, and in line with this principle, I started signing my reviews shortly after I finished my PhD (though I stopped signing them later). Now, I am coming to the conclusion that anonymity has substantial advantages, not only if the reviewers don't know the identity of the authors, but also if the editors don't know the identity of the authors. Would this help? Well, maybe not. Years ago, I've been told by a senior researcher that it doesn't matter whether peer review is anonymous or not, because it's normally obvious who exactly - or at least which lab - produced the paper. In my experience (I've reviewed ca. 60 papers since then), I'd say this is often true, and when I review an anonymous paper I cannot stop myself from taking a guess at who the authors are.
So, to conclude, I don't have the answers to the two questions I asked above. But I do know that experiencing such anecdotes leaves me discouraged and frustrated about a system where one's chances of being employed are determined based on whether one publishes in high impact factor journals or not.