[Cosmo-torun] Re: AA/2004/2055

[Boud Roukema]

Witam,
  IMHO the A&A editors are rather confused - here's their letter in
response to our algebra paper http://de.arxiv.org/abs/astro-ph/0409533.

Why did they write such a confused letter? IMHO that sort of speculation
is probably better not discussed publicly. The fact is that they sent me
a confused letter, and IMHO there should be a reply.

Note that our paper does not contain any reference to software at all.

> From aanda.paris at obspm.fr Fri Oct  1 17:28:03 2004
> Date: Wed, 29 Sep 2004 13:50:39 +0200
> From: aanda.paris at obspm.fr
> To: boud at astro.uni.torun.pl
> Subject: AA/2004/2055
>
> 29/09/2004
>
> Dr Boudewijn F. Roukema
> boud at astro.uni.torun.pl
>
> Our Ref. : AA/2004/2055
>
>
> Dear Boud,

>  We are sorry that we cannot consider your paper for publication in
> A&A, since it is based on the HealPix software, that has been
> developped by Gorski et al, and is still actively developped and
> improved, and is widely distributed on the web (now on the ESO web
> site), and is widely used. It is distributed freely, with all the
> code sources (in fortran 90 or in C, etc..), and therefore your
> publication could be considered as a plagiat. The authors themselves
> could have done this paper, and if they have not judged it worth
> while, you have just to convince them to do so, or at least
> collaborate with them to do so.

> A paper like this, with them as co-authors, would not have this
> problem.

> But apparently they judge that the publication on the web as it is
> now is sufficient,

>
> with best wishes,
>
> The Editors


For the moment this is only a *proposal* of a reply to A&A. However,
it is a public discussion with the aim of finding consensus using the
formal consensus method. Having a secret discussion is pointless when
we are doing public science and education.

Anyway, here's the proposal. Comments, suggestions, welcome.

Deadline: Fri 8 October 2004

(of course, if anyone needs a longer deadline, please say so).

pozdr
boud


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%   PROPOSED REPLY TO A&A   %%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%  DEADLINE fri 8 oct 2004  %%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


Dear Editors,

On Wed, 29 Sep 2004 aanda.paris at obspm.fr wrote:

> 29/09/2004
>
> Dr Boudewijn F. Roukema
> boud at astro.uni.torun.pl
>
> Our Ref. : AA/2004/2055
>
>
> Dear Boud,
>

>  We are sorry that we cannot consider your paper for publication in
> A&A, since it is based on the HealPix software, that has been

The second half of the above statement is false. Our paper contains
algebra regarding a pixelisation system which is independent of any
software implementation.  It is not based on the HealPix software.

> developped by Gorski et al, and is still actively developped and
> improved, and is widely distributed on the web (now on the ESO web
> site), and is widely used. It is distributed freely, with all the

This status of the Gorski et al software package is irrelevant
regarding the scientific value of the algebra - "ideas, principles,
algorithms" - behind the pixelisation system.  This is independent of
any software implementation.

Nevertheless, since you refer to that software, you might like to note
that the Gorski et al software is *not* distributed under a free
software licence (see http://www.gnu.org).  It is formally correct
that it is distributed at zero cost, but it is *not* "free software".

The Gorski et al software licence may not be redistributed without the
permission of the authors. This violates software freedoms 2 and 3:

http://www.gnu.org/philosophy/free-sw.html

You are certainly aware that Astronomy & Astrophysics is a European
journal, and many European governments are now committed to using free
software. One of the most powerful elements of free software is the
GNU General Public Licence, issued by the Free Software Foundation. I
think it is relevant in this case to quote the GNU Manifesto, which
you may not have read:

http://www.gnu.org/gnu/manifesto.html

;  "Don't programmers deserve a reward for their creativity?"
;
; If anything deserves a reward, it is social contribution. Creativity
; can be a social contribution, but only in so far as society is free to
; use the results. If programmers deserve to be rewarded for creating
; innovative programs, by the same token they deserve to be punished if
; they restrict the use of these programs.

(in French: http://www.gnu.org/philosophy/free-sw.fr.html )

Gorski et al restrict the use of their programs.

Again, however, this is unrelated to our paper, which has nothing to
do with software: it only regards algebra.

> code sources (in fortran 90 or in C, etc..), and therefore your
> publication could be considered as a plagiat. The authors themselves

Our paper contains no reference to software, so it is difficult to understand
your reference to "plagiat".

Please consider the COUNCIL DIRECTIVE of 14 May 1991 on the legal protection
of computer programs (91/250/EEC) of THE COUNCIL OF THE EUROPEAN COMMUNITIES,

http://www.scaramanga.co.uk/archives/directive-91-250-EEC.html

: Whereas, for the avoidance of doubt, it has to be made clear that only
: the expression of a computer program is protected and that ideas and
: principles which underlie any element of a program, including those
: which underlie its interfaces, are not protected by copyright under
: this Directive;
:
: Whereas, in accordance with this principle of copyright, to the extent
: that logic, algorithms and programming languages comprise ideas and
: principles, those ideas and principles are not protected under this
: Directive;
:
:
: 2. Protection in accordance with this Directive shall apply to the
: expression in any form of a computer program. Ideas and principles
: which underlie any element of a computer program, including those
: which underlie its interfaces, are not protected by copyright under
: this Directive.

There is no computer program *expressed* in the submitted paper, though
there are clearly ideas in the paper which *can* be expressed in a
computer program. If our paper is correct, and this can only be independently
decided by an independent referee, then the ideas in our paper must
correspond to the non-free software package distributed at ESO.

However, this is the task of the referee to decide, not the Editors.

You might also like to note the point of view of Numerical Recipes:

http://www.library.cornell.edu/nr/bookfpdf/f0-1.pdf

; Copyright does not protect ideas, but only the expression of those
; ideas in a particular form. In the case of a computer program, the ideas
; consist of the program's methodology and algorithm, including the
; necessary sequence of steps adopted by the programmer. The expression of
; those ideas is the program source code (particularly any arbitrary or
; stylistic choices embodied in it), its derived object code, and any
; other derivative works.
;
; If you analyze the ideas contained in a program, and then express those
; ideas in your own completely different implementation, then that new
; program implementation belongs to you. That is what we have done for those
; programs in this book that are not entirely of our own devising.

Note that here, Numerical Recipes state that they have used the ideas
and algorithms of computer programs devised by others - "not entirely
of our own devising" - but have implemented them in their own style.

Yet let us return to our article: it does not concern software - it only
concerns the solution to a system of coordinates, which the authors chose
to publish in 1999 without including the full algebra of the system.
Calculating the algebra requires a bit of work - that is what is presented
in the paper so that other cosmologists can profit from this without having
to rederive it from scratch.

> could have done this paper, and if they have not judged it worth
> while, you have just to convince them to do so, or at least
> collaborate with them to do so.  A paper like this, with them as
> co-authors, would not have this problem.  But apparently they judge
> that the publication on the web as it is now is sufficient,

We did propose co-authorship to the authors of the software on 8 Sep 2004:

http://cosmo.torun.pl/pipermail/cosmo-torun/2004-September/000522.html

and we pointed out that if we did not hear any response by 22 Sep, we would
presume that they were uninterested.

On 21 Sep, some of those authors chose to publish a paper similar to the
one we had already sent them:

http://de.arxiv.org/abs/astro-ph/0409513

In this paper, BTW, in formulae (13) and (14), there is a clear
inspiration from our own notation in Sections 2.2.1 and 2.2.2 of our
paper, but without citation.

However, back to the subject.

Our paper is based on solving the unsolved definitions in Gorski et al
1999a, 1999b.

It is completely independent of any software. Moreover, the effect is
to make it possible for cosmologists to implement software solutions
for a pixel-coordinate system which monopolises cosmological
observational data and presently is not implemented in free software.

The algebraic solution to this pixel-coordinate system has not been published
in any astronomical journal.

It is difficult to understand how Astronomy & Astrophysics can refuse to
publish original work which is useful and practical for cosmologists wishing
to avoid the use of non-free software.

The opinions of the authors of non-free software are irrelevant for
Astronomy & Astrophysics.

Any article published in Astronomy & Astrophysics must contain a bibliography.

What is the meaning of this bibliography?

In many cases when an article is cited, it means that the authors of
the article have used some of the ideas and algorithms in the cited
articles, and it is considered normal scientific practice to give
credit to those authors of the cited articles, while nevertheless
showing how those ideas can be improved and/or corrected, and possibly
arguing that the ideas in the cited article are fundamentally wrong.

What does A&A normally do when an article is accompanied by a bibliography
(i.e. nearly every article, IMHO), especially in the case where the authors
of the submitted article and those of the cited article may have different
points of view on the correctness or usefulness of those ideas or how
to implement them in scientific research?

IMHO, it sends the article to an independent referee.

It does not tell the authors of the submitted article that use of
ideas which are, in principle, implicitly present in another article
could be considered "plagiat" and that consent of the authors of the
cited article is necessary for publication of the submitted article.

At least, that is my understanding of how A&A works.

Software has no extra copyright protection to text.

But again, it should be made clear: if you read our submitted paper, you will
see that it is independent of any software. Please read it.

Best regards
Boud


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%  END OF PROPOSED REPLY TO A&A   %%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%  DEADLINE fri 8 oct 2004  %%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%