[Taxacom] DNA homologies

[John Grehan]

> with permission Sir, this is shear nonsense
> any heritable character change, at random or not at random, can label a
> clade in a cladistic analysis [NOT an opinion, just logics]

The trouble is if it is a random mutation it can change in any one of the bases and not necessarily stay unchanged in particular lineages and so track their phylogeny.

> this is not the crucial point, you can align by hand (see below)
> except that a basic "expertise", i.e. a simple introductory course in
> current phylogenetic methods, would of course be necessary

Alignment is just a way of guessing. Whether by hand or not, the procedure implements a recipe for making the choices given certain assumptions.

> >However, I do point out that there seems to be a contradiction between
> >cladistic
> >requirements for primitive states in outgroups and the assumption of
> >continuous molecular divergence in all lineages
> 
> this classic assumption is only implemented in phenetic analyses of
> molecular (or any other) data, not in cladistic/parsimony analyses of
> molecular (or any other) data

Right! But one has people who believe in the molecular clock also using cladistic analysis.

> again you are describing phenetic analysis, not all current molecular
> analyses (just ask any student passing by in the corridor, for control)

No argument that people put bases through cladistic algorithms, but they are still dealing with data that have been constructed through overall similarity (phenetics).
>
> your rhetoric strategy (or hardly conceivable mistake) is now clear enough
> for me
> you are persistently playing the game of ignoring that molecular analyses
> are in no way "obligatorily phenetic", neither in the data set nor in the
> phylogeny inference procedure, i.e. ignoring that classic
> cladistic/parsimony molecular analyses are current in the litterature
> (if not exactly your pet "compatibility analysis", at least standard
> cladistic analysis - just a mouse click away, i.e. just some character
> deletion away if you prefer hand work)

If you are right then your arguments have not led me to that view. This is either because I am ignorant, resistant, or because you are wrong or your argument is too poorly constructed to lead me to a different view. Such things always happen in science and it eventually comes out in the wash.

> not to mention the Journal "Cladistics" (of course you regularly find at
> least some three or four cladistic molecular analyses per issue in there),
> just take Systematic Biology, vol 55 n° 4 august 2006

As before, they can claim the studies are cladistic because they put the characters through a cladistic algorithm. We just happen to disagree on this.

> please listen, John: this is not only cladistic analysis of molecular
> data,
> this is combined cladistic analysis of molecular and morphological data,

At present it seems to me like mixing apples and oranges.

> I really fear you have to accept such facts, or accept the rejection of
> your counter-factual paper [NOT censorship at all: the effective
> publication of the above mentioned paper, as well as the 26 selected ones
> mentioned in there, is enough proof that they were not censored for
> disobedience to molecules-all-mighty!]

But saying that morphology may not have to accommodate DNA similarity at all (i.e. through combination)is a much more radical proposition. It raises the possibility that morphology is an equal science and there is no necessary need for systematists to have to include a molecular repertoire in order to get funded or their work recognized as valid. Censorship is a reality in science.

> Agreed, no problem, but the specific point at stake is beyond this trivial
> consideration: namely your extensive and persistent misrepresentation of
> phylogenetic analyses;
> the fact that some molecularists are occasionally propagandists is no
> argument for using the same counter-propaganda style in the place of
> serious work

I acknowledge your opinion.

> symptomatically, your general charge against "algorithms" for molecular
> alignment is surprisingly naive:
> algorithms are not evil spirits, they are human-made tools that can
> perfectly implement your very own logic a consistent way, and simply help
> you saving time and avoiding some goofs, as any elementarily trained
> biologist should know at the beginning of the 21st century

We appear to agree on algorithms. I never said they were evil in any such way. The point for molecular systematics is that one must use an algorithm in order to establish the starting data.

"empirically see" and
> "observe
> each character claim directly" [to quote your own terms], 

In deciding how many substitutions vs how many gaps one has not empirical foundation other than some sort of optimization theory so one has to subordinate individual choices to that theory.

> now the Q question is: will your own hand-made, hence strictly
> "algorithm-free" alignment of anthropoids DNA, 

Even by hand one institutes some kind of procedure in order to decide how many substitutions vs how many gaps so it's not algorithm-free.

It is evident that are not going to find agreement on some issues and this kind of disagreement is normal to science. One or both of us may be wrong. Either way it does not really matter so much as the comments and counter comments have been useful and interesting - to me if no one else. But if one finds the lack of concordance to be frustrating then please do not bother to comment.

John