Ok, great! Thrill me with your acumen!
You started out OK, then went pure Duane Gish. Phylogenetics is "Largely opinion" you say?
I suggest maybe reading Felsenstein's
"Inferring Phylogenies" or Nei and Kumar's
"Molecular Evolution and Phylogenetics".
Speaking of rhetoric...
You do realize - given your claims of decades of reading and work in the relevant sciences - that molecular phylogenetics methods are TESTED? Their outputs are not 'opinions'. Due to the nature of molecular data there are certainly confounding phenomena that can, depending on the type and amount of data being used, produce inconsistent outputs and the like. But that no more invalidates molecular phylogenies than does the fact that there are Old Earth Creationists and Young earth Creationists and this invalidates the veracity of Scripture (there are other things than can do that).
Such projection is rarely seen in the public at large, but it is part of the anti-evolutionist's tool kit.
This is the crux of my 'challenge' that you eventually addressed
here, but as is your usual fashion, you wrote much more than was needed to simply avoid actually addressing the issue.
The issue I brought up is that you seem to focus on the length of the sequences. I pointed out that it is very common to have differing lengths of sequence for the 'same gene' due to areas of interest, reference sequences, sequencing difficulties, etc., and wondered if you had or would look into that possibility rather than attributing it all to some nefarious conspiracy.
Your response was largely irrelevant, but the bottom line, in my estimation, was that yes - you focused solely on the length of the sequences, which, due to my knowledge of the techniques involved and the impetus for generating sequence data in the first place, was superficial at best. As seen here:
Seems that your decades of reading would have informed you that genes often acquire different functions (e.g., genes important during development often play rather mundane roles later on) and that genes can be copied/modified and end up performing other functions.
But I suppose all that amassed knowledge is all just 'speculation' and opinion, too, right?
Half-true, at best.
I do enjoy the substantial amount of projection that ensues:
You just described creationism to a T.
Actually, if I had only the shallow, cherry-picked information you provided, I might be skeptical.
Alas, when I chose to work in phylogenetics lab in grad school, I was exposed to REAMS of data, not just a couple of cherry-picked 'what-do-you-think-of-THIS!!!' poorly described examples.
When one looks at the totality of available evidence (or even a chunk of it), looks at the actual large-scale patterns as opposed to a couple of anomalies, it becomes not just intuitively correct, but empirically supported conclusion.
