Hello Andrew !
Thankyou for your detailed and considered response. First of all, let me
apologise for the "obstructive" remark; I was actually thinking of someone
else though the context of my remarks did not make that clear ! Sorry.
You are no doubt right that if there is an unconscious bias in an algorithm,
or in the way it is used, it will not be evident from reading the
literature. Of course most work in molecular biology is, and perhaps
always was, carried out by teams, largely because teams can naturally
embrace
a wider range of skills in that way. Thus it is not practicable for me, on
my own at present, to become expert in every relevant field, such as
crystallography, refinement algorithms, etc., or indeed your own specialism
of molecular dynamics, for example. I can only develop a layman's
familiarity.
I think I can see clearly, however, that there is a substantial body of
experimental work, encapsulated in the Puzzles, for which the original
workers did not offer an explanation, and for which the DNA double helix
does not give us useful insights either. As far as I can see, the true
side-by-side structure for high polymer DNA found by Lee et al. will satisfy
all the Puzzles in a natural, unforced way, and, in the Puzzles (Version 2)
which I am thinking to post soon, I shall set out to make this as clear as I
can.
What I seek to do is
1 to engage the interest of fellow scientists who collectively would
have the range of skills and access to facilities which could at least test
the structure of Lee at al., for example, topologically, or by Fourier
analysis against fibre diffraction patterns, or by molecular force field
calculations (!), etc., and
2 to try to find a way to reconcile what we collectively think we
know about DNA fibre structures and oligonucleotide structures, which, on
the one hand seem to be all rather similar and plectonaemic, but, on the
other hand, plectonaemic winding would not seem to resolve the Puzzles.
You mention that the force field calculations give reasonable energies for
the double helix and that the conformation should be expected quite often,
but I find myself wondering what that means. The double helical
conformation should be expected quite often compared to what alternatives ?
Could it be the case that the true side-by-side structure of Lee et al.
might also be expected quite often ?
On a related, broader point to do with the manner in which scientists treat
with each other, we have experienced here in the UK a steady, long-run
decline in the numbers of high calibre youngsters enrolling on science &
engineering degree courses. (I would not know if there is a similar trend in
the 'States). Factors bearing on this seem to include the perceptions that
science is "all facts" and that there is no scope for people to have
opinions and develop values, and that science is a de-humanised activity,
compared, say, to politics, sociology, English, etc.
As you may know, the scientific establishment here, and perhaps in the US
also, is keen that scientists make greater efforts to explain in
comprehensible terms, to a lay public what they do and why people more
generally should engage in debates about the future direction and
application of science.
The current posting from Professor Sheldrick exemplifies best practice as it
sets out in an explanation, in terms comprehensible to a
non-crystallographer, just the help I need.
Clive Delmonte
