And now for something completely different (gap costs)

Dan Davison Davison at UH.EDU
Fri Jun 26 15:26:07 EST 1992


Steve Benner said:
> We are sorry to have upset Dan so badly.

Judging from e-mail, there are more than a few people confused by the
paper. 

> Perhaps Dan will become more relaxed if he realizes: (a) that
> Science publishes papers that reports results of general interest to a
> wide range of scientists, not papers for specialists; 

That's not an excuse for a paper where the methods cannot be judged
*nor* for a paper that doesn't explicitly reference other papers
(preprints, in press, tech reports, whatever) the information that
would let one evaluate the science.

> (b) that the details of the methods needed to reproduce our results are
> available to Dan should he contact us, or should he read our full papers;

Which ones? There's nothing in the Science paper except for a
technical report on DARWIN that appears to be remotely applicable. I
can't read papers you don't reference.

> (c) that the caption to Figure 2 already addresses for the careful reader
> Dan's most trenchant objections.

I will take this off-line, but in no way does that caption explain my
objections to the work *as presented*.

>  Regardless of what the prior literature says, the data show that a
> linear gap penalty is not appropriate. 

I said something wrong, then. I did not mean to imply that the affine
gap costs are the be-all and end-all; that would be absurd. And the
literature does not state that affines are best. All I meant was that
affine gap costs *are* supported by an understandable paper.

> We recommend the non-linear gap penalty model; the model in the
> appendix is provided only for those who do not wish to follow this
> recommendation. 



I will repeat: the science may be good, but you can't tell from the
paper.

dan davison
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison at uh.edu/DAVISON at UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.





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