What I have learned from the rejected submissions

New year, new start in thinking about how science works and in particular trying to understand the mind of the viral phylogeneticist. These are deductions based on the negative referee comments I have received recently.

1. The field is very compartmentalised.
2. Two editors who are significant in the field and one of which at least uses FastTree have NO IDEA whatsoever about how it works to give local bootstraps.
3. Condensed trees with bootstrap cut-offs are not widely understood in the community (they need to read more and use their brains).
4. Most of the community do not read very much especially theory and the level of maths is often poor.
5. If you want to publish you need to keep it simple with a single idea and single question as referees do not seem to be able to manage two ideas at the same time.
6. Make what you want to say clear - being discrete and tactful and not shouting the implications allows others to deliberately misinterpret your words to create a straw man that they can demolish.
7. Think like a martial arts master. Use your opponent's attack against them. Turn their comments into your strengths. There is nothing better than the referee who suggested that my experiment was badly designed because of sampling. If they had understood what I was saying in the paper they would know that was exactly my point. Anyone sampling based on influenza subtype is doing something stupid. It is a shame that most of that referee's papers will have done the same.
8. Be prepared for a long slow fight. They are entrenched. You know that they are wrong and that all they have done is flawed. You have to wait for time and the evidence to grow for their entire edifice to crash around their ears.