Re: [tlug] Open Access Journals

["Stephen J. Turnbull" <stephen@example.com>]

Raymond Wan writes:
 > On Mon, Mar 31, 2014 at 12:16 AM, Stephen J. Turnbull
 > <stephen@example.com> wrote:

 > > At the other end of the quality scale, how my colleagues do the
 > > shit-stick test doesn't involve laboratory measurement.  [...]
 > 
 > ...your research area, too?  I thought it was just what I'm seeing in
 > bioinformatics...  Nice to have company...  ;-)

Well, I will say one thing in favor of bioinformatics vs. economics.
In economics, the received theory is basically "linear" in the sense
that the important relationships "add up" and "scale up", and can be
analyzed to get a precise "solution".  The theory is very plausible on
its own terms, but "those with discipline" know that it's essentially
an approximation and can never be anything else, due to genuine
randomness and "sensitive dependency on initial conditions" (chaos!) 
where measurement of "conditions" is inaccurate.[1]  "Shit-stick"
economics is basically about denying those facts, and "taking the
model too seriously" (as one of my professors used to say).  All too
often, in the process seriously abusing the statistics.  It *can't*
provide interesting reproducible anomolies![2]

AIUI, much of bioinformatics is about *historical* DNA, which is
"complex" rather than "chaotic".  Unfortunately I don't really know
enough to define those terms, basically though we're trying to
understand past evolution at the DNA level rather than predict the
future evolution, and then DNA is basically a digital computer --
matching DNA to phenotype may be "sloppy", but the DNA itself can be
described "precisely", although it is very complex.  So useful
patterns not justifiable by existing theory, and reproducible
anomolies contradicting existing theory, can occur in bioinformatics.

As Attila and I were discussing, complexity is still missing a lot of
theory, and even lacks a central "core" of discipline about how to do
research.[3]  While a very few of the researchers (Arrow, Holland) in
"Complexity" display an ability to understand and even contribute
across the board, most of these folks were monomaniacs (Arthur, who
couldn't let go of the term "increasing returns" which basically was a
one-way "off switch" for listening economists' minds; Gell-Mann, who
turned "sustainability [in the face of disequilibrium]" into "save the
rainforests", the "artifical life" guy, etc.)  Gell-Mann and Feynman
at least are certified geniuses, but (at least from the book) seem to
have missed a fundamental point.

So I personally (but not intimately familiar with your field) would
tend to be more tolerant of research "lacking discipline" in
bioinformatics than in economics, simply because only a multimodal
genius like Arrow or Einstein can start to see how to gather the
threads of discussion into a coherent discipline of complexity.


Footnotes: 
[1]  And economics can't be an experimental science, because the
informative experiments involve betting the subject's lifestyle (where
the subject might be a whole nation!) and that's ethically and
politically unacceptable.

[2]  It occurs to me that one way to think of one of my long-range
projects is that it's an attempt to make that statement precise.

[3]  As an outsider to the field, I suspect that it will fragment into
many fields, in much the same way that the "GNU/Linux" platform has
fragmented into many projects, some of which are clearly outside of
the "free software movement", and a few of which are hardly open
source at best (Chrome, Android) or obviously not (Flash).