From owner-biophysics@net.bio.net Tue Feb 09 22:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics,bionet.xtallography References: <36b81714.0@news.netdirect.net.uk> <36BE3682.977F323B@bioreason.com> <36beffa3.0@news.netdirect.net.uk> <36BF48D4.B38DC74E@bioreason.com> Subject: Re: Is ignorant rambling, was: DNA Structure: An Age of Refinement... Date: Wed, 10 Feb 1999 17:33:47 -0000 Lines: 70 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.227.212 Message-ID: <36c1be39.0@news.netdirect.net.uk> X-Trace: 10 Feb 1999 17:13:29 GMT, 195.7.227.212 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!amsterdam1-snf1!news.gtei.net!diablo.theplanet.net!newspeer.clara.net!news.clara.net!ayres.ftech.net!news.ftech.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.212 Xref: biosci bionet.biophysics:4774 bionet.xtallography:4592 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 .