Dear MorphMetters,
Yesterday David Polly reminded us of the existence of a 3.5-page draft
fragment emailed by Andrea Cardini on September 5, 2018 and headed as by
"Cardini, O'Higgins, Polly, Rohlf, Bookstein." So, yes, David Polly was
indeed present at the creation. It begins with paragraphs of an
introduction acknowledged to be "largely borrowed" from me and continues
with a summary of some of Cardini's simulation results, which are
consistent with mine but reported using mostly different simulations and
quantifications, together with a sketch of a discussion quite different
from mine. This fragment, particularly its style of simulating and
reporting, may have served later as the basis of the second of the two
papers as I referred to it both in my Monday morphmet posting and in my
biorxiv preprint. (I say "may have" because I have not seen any more recent
state of that second manuscript.) So my Monday note to morphmet pointing to
my biorxiv preprint should have mentioned the September document as part of
the history of our project before it split into two. I apologize to David
for not realizing the role he played in this early history, and apologize
to Andrea for overlooking this early draft of the less algebraic half of
our joint project. I hope the authors of this second paper will post it to
biorxiv as urgently as mine was posted once theirs, too, is in final draft.
FB
On Tuesday, May 14, 2019 at 1:32:24 PM UTC-4, MORPHMET wrote:
>
> Dear MorphMetters,
>
> Some of you may have been in the auditorium in the Department of Botany,
> University of Vienna, back in March when Philipp Mitteroecker and I were
> the two scheduled discussants for the conference "GMAustria19" on
> applications of geometric morphometrics. Several of the papers delivered
> there used between-group principal components analysis (bgPCA), and after
> each of those papers I mentioned in the course of my commentary that bgPCA
> was fatally flawed in applications to most GMM data sets and should NEVER
> be used here. In my keynote address, which closed the meeting, I had one
> cryptic slide about this assertion, with an example that flashed on the
> screen but was immediately replaced by the next slide.
>
> The typical response to both my own talk and my criticism of the talks of
> others, as far as bgPCA was concerned, was along the lines of "Hunh?" or
> sometimes "What are you blathering about this time? Isn't bgPCA in the
> standard toolkit?" I answered that the Bookstein paper they should read was
> just then being written, as one of a pair jointly arising from
> conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following
> an original hunch of Cardini's, and that my argument would be pretty
> convincing once it was actually written down. The claim isn't that people
> are using bgPCA incorrectly. They're using it according to the published
> formulas, yes, but the method itself yields biological nonsense much too
> often.
>
> That was March. In April, two different articles in Nature (one by
> Detroit et al., one by Chen et al.) buttressed claims about sister species
> of Homo sapiens using the bgPCA method, and so suddenly it became clear
> that we authors had to do something quickly lest this become an epidemic of
> bad biometrics. So we accelerated our writing. My paper was the first to be
> finished, probably because it is a single-authored item by an emeritus with
> no other obligations, and it seemed like a good idea to upload the final
> draft to https://www.biorxiv.org even before submitting the paper, so
> that any letter to the editors of Nature could include a link to the
> argument as to exactly WHY bgPCA is nearly always unsound and its
> inferences invalid for applications in contemporary GMM.
>
> That is the draft that has just appeared as
>
> https://www.biorxiv.org/content/10.1101/627448v1
>
> For those of you who were at the March meeting, this is the argument
> (complete with formulas) defending my stern condemnation there. I won't try
> to summarize it in this morphmet note -- if you're interested, just read
> the abstract on page 1 of the link. For those of you who have already
> published bgPCA analyses, you know who you are -- my paper argues strongly
> that you need to go back and revisit the inferences of those papers in a
> mood of much more intense multivariate skepticism. For the rest of you,
> please consider this draft manuscript to be a wake-up call. A technique
> that has appeared in dozens of papers and that was, alas, specifically
> praised by Mitteroecker and Bookstein personally (back in 2011) could
> nevertheless, when examined closely (for the first time!), turn out to be
> algebraic garbage when applied to data sets where there are far more shape
> coordinates than specimens. But isn't that the usual situation in GMM these
> days?
>
> As always, I welcome all responses, both positive and
