Getting back to the title of this thread....I don't think one should completely invalidate an area of study, (ie molecular taxonomy) just because a particular paper is very bad or has incorrect information. Just because something is published, even if in a reputable Journal, does not mean it has been well reasoned or correctly evaluated. The writers may not know what they are doing, or may not truly understand the methods they are using. Just because an under-educated person manages to get a paper published, which is subsequently shown to be wrong, does not invalidate the entire branch of study itself.
One well known case is of a paper that appeared over a decade ago in a major British Medical Journal that tried to show a link between Autism and Vaccines, based on a very limited number of test subjects ( I think it was less than 20 or 30 subjects, if I remember correctly.) The paper was soon shown to be full of errors in the design of the tests, in reasoning, and incorrect in the conclusions it drew. (Even so, it was not retracted until just recently I think, after it was finally shown the the investigator had falsified much of his data. Retractions can take ages sometimes.)
And yet, who hasn't at least heard of the concerns of the general public that vaccines may still be somehow related to Autism. And in the ensuing years, we have see a rise in the communicable diseases that the vaccines are supposed to protect against, sometimes resulting in serious illness or even death.
All this due to a bad paper that was published years ago, and whose claims have never been able to be replicated in another well designed study, whose methods were shown to be shoddy and the data of which was at least in part falsified.
There are many well designed subsequent studies, with published results, involving thousands of subjects, that show no relationship between vaccines and Autism. The methods or research can be used well or poorly, but it does not make the methodology itself the problem.
