To summarise the Cladistics editorial:
- Authors should always show parsimony trees. Alternative phylogenies can be shown in addition if they are different and there is "a pertinent reason" to do so. This is not really new, as when I published a paper in Cladistics a few years ago I was already asked to do the same. In other journals I have seen the reviewers or editors demand likelihood analyses. I am a methods pragmatist and can live with either. If the data are strong, the results will be the same anyway.
- The editors consider parsimony analysis to be preferable to other methods for "philosophical" reasons. As far as I can tell, most biologists would be more impressed by biological and pragmatic reasons; I know I am. They also stress repeatability, intelligibility and clarity, implying somewhat that model based methods don't have those. This I find odd except perhaps in the case of certain Bayesian analyses suffering from an over-abundance of unknowable priors.
- The editors point out that all methods have their weaknesses, and that we have to live with not knowing the truth for certain. Seems obvious.
- The editors think that they are doing something right because the journal has a high impact factor. Well... let's just say that I have very mixed feelings about impact factors.
- 8x Equating the Cladistics editors to religious fundamentalists or calling them otherwise dogmatic.
- 3x Mocking Cladistics as too traditional and/or stuck in the 1980ies.
- 1x Some analogy to physics that I don't quite understand.
- 3x Ridicule without argument.
- 1x Call for boycott.
- 1x A different journal advertises itself as accepting all phylogenetic approaches.
- 5x Meta, as in expressing amusement at somebody else's comment.
As for parsimony being outdated, that belief is just the flip-side of what the editors are being criticised for. Dogmatic rejection of any and all parsimony analysis is not actually any more rational than dogmatic rejection of everything but parsimony. The belief that parsimony shouldn't be used any more is also generally based on a very selective perception of the literature, e.g. the mistaken assumption that likelihood analyses do not suffer from long branch attraction. These are all tools, they all have their advantages and disadvantages, and they all have their use cases. Often it is quite simply a good idea to use two different ones to see if the results agree, or the one that you would otherwise consider to be the best is computationally too demanding for your dataset.
So now to the second criticism. If several methods all have their use cases, isn't it then dogmatic to reject papers that don't use parsimony, merely on that basis? Well, in principle I really see no problem with a journal deciding to serve any given niche, including a methodological one. We do, after all, also have journals like Molecular Phylogenetics and Evolution, and I do not see any of the people tweeting at #parsimonygate calling its editors anti-science because they would presumably reject all morphology-only manuscripts. They just decided that they were going to serve the molecular niche. It's in the title!
Similarly, I have a hunch that few, if any, of the outraged tweeters would see a problem if somebody founded a new journal called Bayesian Phylogenetics that accepted only studies using the eponymous methodology. They would probably say that there are still plenty of other phylogenetics journals, and this is just serving a niche. And again, they'd be correct!
Maybe I am mistaken - maybe such a Bayesian-only journal would draw the same denunciations from these tweeters - but given the fact that we have lots of other focused journals that nobody complains about and given the proud use of additional hash tags such as "Bayesian4Life" I suspect that a lot of the criticism really feeds at least partly on the feeling that parsimony analyses shouldn't be allowed at all at this stage.
In other words, at least some of the criticism seems hypocritical (dogmatic opponents of parsimony calling its proponents dogmatic) or hyperbolic. The charges of dogmatism, ignoring evidence, and quasi-religiosity in particular seem to confuse a preference for a method with a preference for wrong results.
But yes, that editorial could have easily been written to be less of a target. It doesn't just say that while there are several alternative, equally valid tools all with their own advantages and disadvantages the journal is going to break a lance for parsimony, although it does say that too; but it also at least implies that all other methods are inferior. It is unsurprising that this would raise the hackles of those who are convinced of the exact opposite. Where it could have referred to the active development of new parsimony methods even in the last few years (e.g. Most Parsimonious Reconciliations, Doyon et al. 2010) to showcase their continued relevance, its youngest reference is from 1983. It was obvious that this would be mocked as backwards.
But even if somebody is really convinced that Bayes is the only way to go, calling for a boycott seems ... a bit ... of an overreaction. Should we all boycott the Botanical Journal of the Linnean Society since they decided to stop accepting purely alpha-taxonomic papers? Or American Journal of Botany after it stopped accepting primer notes? Or that journal where I saw a reviewer demand likelihood inference of ancestral character states although one glance at the tree made clear that the results would be the same anyway? Can of worms.