Consider this response to a recently rejected manuscript:
"This manuscript seems inappropriate for [journal name removed]. Its purpose is to question the foundation of molecular phylogenetics, a well-established field. Moreover, the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated. I doubt that the readership of [journal name removed] would find the arguments presented particularly compelling. It is well known that DNA is the material of inheritance, and that morphological homoplasy is common. Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods. No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".The response is an exemplary in its language, attitude and ignorance of comparative biology, that is taxonomy, systematics and biogeography.
Let us start with the first point, namely, attitude:
"Its purpose is to question the foundation of molecular phylogenetics, a well-established field".Molecular Systematics, like any other field in science, is open to questioning. It is not immune like faith or religion as some, I suspect, believe. Moreover, it is not "well established", that is based on a sound foundation. There is little discussion about the foundations of molecular systematics, which the next comment reveals, namely:
"the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated".These "non-standard" definitions are presented below:
Homologies are the only evidence for relationship; A molecular tree based on the relationships of taxa at the terminal branches is not a genealogy, but a cladogram. A cladogram however can be tested and represents all possible relationships in a taxonOne might ask, "Where is homology in molecular systematics?" The question of homology has been raging in morphological systematics for almost 300 years. In molecular systematics it is simply ignored. I ask what are the foundations of molecular systematics? What makes it so well established? Why is it one of the few fields in science where its foundations are rarely discussed? These questions make sense in the light of molecular systematic culture.
Molecular systematics also uses a convincing language. Stating that "DNA is the material of inheritance" creates an air of reverence that defies questioning. In fact it is a diversion. We are the material of inheritance. DNA is just part of it. The above statement is reductive, that is to say, it says that only our smallest 'bits' are relevant. We may take that statement further and say that 'Morphology is simply an expression of DNA', or take it one step further and state 'DNA tells us everything about genealogy and phylogentics, morphology is irrelevant, after all morphological homoplasy is common'. Language can be used in a deceptive way as the above example demonstrates.
Ignorance is another part of the molecular systematic culture. Consider for instance this statement:
"Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods".This conflates a few important points. Firstly homoplasy, that is, the "correspondence between parts or organs acquired as the result of parallel evolution or convergence" (Merriam-Webster's Dictionary Online), is not exactly 'detectable' in cladistic analysis. It causes characters to conflict resulting in polytomies, that is the absence of pattern, and therefore, of information. Cladistic analysis is there to find patterns, not uncover homoplasy.
Ignorance of history is another vital part of the molecular systematic culture, for instance:
"No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".We have addressed this point in an earlier post. No matter how old an argument or discussion is, the points made may still be relevant today. In the case of the above comment, the discussions of yesteryear still have not concluded. The discussions were replaced by a thirst for technology. Molecular systematics is enslaved in a technological culture. The algorithms or black boxes determine which phylogeny is best. The question of whether it is really homologous is never discussed. The foundations of molecular systematics lies in its applications, literally the programs made to run molecular sequences. We ask, is this a science that is based on solid foundations - a "well established field"?