[Biobiz] FOSS, Science, and Public activism

[proclus at gnu-darwin.org]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

(Sorry if you get more than one copy of this message, but I felt
that it was urgent to get this important info out.)

The values of freedom and openness are crucial to understanding 
itself, so that civilization and public welfare now depend on 
them, as I argue below.  These values may find their best 
expression in the free and open source software (FOSS) movement, 
and the foresightful example of FOSS developers should now be
beneficially applied to many other disciplines in the context of a
global and public Internet.

It is crucial that we occasionally take time to discuss the
reasons _why_ we release our source code, and this is one of 
those occasions.  There are good reasons for the freedom and
openness which are characteristics of FOSS development, reasons
which should receive wider attention now that they can be readily
communicated to other arenas.  The consequences of doing otherwise
are often catastrophic.

For example, it incomprehensible that Genentech could consider
withdrawing a cheap cure for blindness (ARMD) from the market.

http://lists.essential.org/pipermail/random-bits/2006-june/001374.html

The mechanism of this drug is public knowledge.

http://sourceforge.net/mailarchive/forum.php?thread_id=14183567&forum_id=6042

This abhorrent situation is a great example of the kind of thing
that will happen if people don't get behind the values of freedom
and openness that we are espousing.  Please let Genentech know
that you find what they are doing offensive.  Publicize the mechanism
so that new compounds can be obtained as replacements.  For the 
future, continued vociferous public activism is required to prevent
such outrages from occurring in the future.

It becomes clear that the compounds which come from common roots,
fruits, and vegetables are a shared human heritage and the free and
open source of the future.  Tannins are another interesting case in
point, because as molecules, and as anti-oxidents, they are similar to
resveratrol (resV), and that molecular mechanism has been anchored to
the public domain via a prior art declaration.  It is a so-called
CR-memetic, which may increase healthy human longevity by many
decades.  Here are some links about it.

Resveratrol mechanism posts from GNU-Darwin list
http://proclus.gnu-darwin.org/gdposts.html

CR protocol for human bodies
http://proclus.gnu-darwin.org/bootstrap.html

Here is some important recent news about it.

http://www.imminst.org/forum/index.php?s=&act=print&client=printer&f=237&t=10749

It is exciting to suppose that people can get off the pharmaceuticals
that they are taking with calorie restriction or CR-memetics.  I
personally am trying to get off the cholesterol drug Pravachol, a
statin compound, starting a few of weeks ago.  Write me, and I'll let
you know how it turns out.  From the article...

"Fontana says ...  evidence of "younger" hearts in people on calorie
restriction, suggest that humans on CR have the same adaptive
responses as did animals whose rates of aging were slowed by CR."

I think that it is time to look at the tannins in tobacco leaves.  
There may be other treasures lurking there too.  As you may be
aware there is ample public research into any possible beneficial
compounds that may be obtained from tobacco leaves.  The mechanisms
are there waiting to be discovered.  If you want to post them, just
reply to me and I'd be delighted to host them.

The public establishment of prior art is a time-honed method of
entering inventions into the public domain.  We now have other
methods at our disposal as well.   If you are planning to establish
prior art against future CR-memetic related patents, you might want
to have a look at www.creativecommons.org.  Perhaps it goes without
saying at this point that you should please choose a license that
provides for free and broad public access to your memetic.

In that way you will assure that the public health is served by 
anchoring them to the public common, where they cannot be exploited
by those who would withhold them for their own profit.  The DRM 
situation is precisely analogous to this.  Can you imagine doing
science in a world where your ability to read and write your data is
filtered through secret protocols that are hidden from you? I
recommend the Defective By Design campaign to fight the outrage of
DRM, which is incompatible with the scientific pursuit.

http://www.defectivebydesign.org/

It is clear that scientific tools must be demonstrably and
penetratingly understood, or else our claims will likely be skewed
and called into question.  Free and open source software is
a great example of how to make your science verifiable to the
public.  Establishing prior art against future patents is 
another good one, which is precisely analogous in method, 
making the result explicit to the public, free and open to all.
Thank goodness for the free and open software movement, which
gave us such a great example of how to serve the public in this
manner.

I am willing to grant that there are particular exceptions to
these rules of freedom and openness, and such exceptions may be
relatively harmless; however, let us posit the opposite, that
freedom and openness are _not_ crucial to understanding.  Think of
the implications.  When people are compelled to learn, they do not
receive the intended message.  It is not understood correctly
or completely.   When crucial facts are withheld from the people
you are trying to teach they become paranoid, possibly unteachable. 
Freedom and openness are obviously the best approach to understanding.

This is not a metaphor for the pursuit of science, but a fact. 
We are learning from nature, and it is ultimately required that
our tools be demonstrably and penetratingly understood, or else
we will receive incorrect lessons from nature.  Clearly this
requires public access to the source code and more.  This 
is why many of us are pressing for public access to scientific
publications.

Moreover FOSS tools are becoming ever more important to the
pursuit of the scientific endeavor itself.  In our biophysics
department we are obsolescing proprietary hardware and software
in favor of open standards and free software, which is a
widespread phenomenon in the science sector, and sure to continue.
We build most of the workstations ourselves with commodity hardware,
but we also have some clusters running Debian and FedoraCore.

Some of you will know that I am the lead developer for the
GNU-Darwin distribution.  GNU-Darwin has a FOSS operating system,
which is getting alot of press these days.  Here is an example

How Apple and Microsoft are advancing desktop Linux
http://www.desktopLinux.com/news/ns7294331817.html

I see the article as counter-productive against building a FOSS
coalition that includes democracy, freedom, and public access 
activists, Apple, GNU-Darwin, GNU, and GNU/Linux all linked
together in spectrum.

It is important to alert the whole FOSS community that Darwin
cannot be classified as a free or open source operation system
as of the Darwin-8 revision, because AppleACPIplatform-39 which
is required to boot the system is proprietary.  It is notable that
only the current version of Darwin from Apple is a non-free OS.
GNU-Darwin has a free version, an earlier revision that includes
the source code.  It is FOSS, and we call upon Apple to maintain
Darwin as such, as it has been in the past.  We hope that the
current situation with the kernel and ACPI driver will soon be
remedied so that Darwin will continue as a FOSS OS.

We are asking for free software developers to please write to the
*nix core of Darwin, which is the core OS for both Mac OS X and
GNU-Darwin OS.  Darwin OS, which underlies both systems, comprises
parts from GNU, the BSD's, mach, plus Apple's substantial
contributions to the free software community.  Be consistent with your
philosophy and avoid linkage to proprietary binaries, such as OpenGL
and CoreAudio, except when it is imperatively required in order to
lead users to the values of software freedom.  Under that principle,
another reason to maintain compatibility with the *nix core, is so
that your code will be readily portable to new platforms and usable
by free-software-only aficionados too.  

GNU-Darwin OS is not an obsolete implementation of Darwin OS, or to be
superseded by Mac OS X.  We are trying to lead users to freedom, not
away from it.  By maintaining Darwin core compatibility your code will
remain valuable as the marketplace and industry continues to evolve
(trust me here), particularly as DRM-related problems continue to come
forward. Of course, that means releasing your source code under a FOSS
license, such as APSL.  Darwin OS is a free and open source operating
system that is not going away, so try to focus your coding towards
supporting that standard instead of proprietary software.

Here is the essence of the current problem with Darwin OS.  Apple
replaced working boot code with the following proprietary drivers, 
which are required for the system to boot.

Darwin-7:
AppleAPIC.kext/
Applei386genericplatform.kext/

Darwin-8:
AppleACPIplatform

In addition the kernel (xnu) has been taken proprietary in the
recent revisions.  We are not asking for Apple to give away such
things, but rather to continue maintaining Darwin OS as FOSS, which
it already was. 

After repeated attempts by many FOSS developers to get this
situation remedied, nothing has happened.  It is now time for us to
better use the measures at our disposal in order to assure that
Darwin OS remains free and open.  If you are unhappy that xnu and 
the boot drivers have not been released, I would encourage you to
spread your dissatisfaction to other forums, so that Apple will take
notice and commit to a workable free and open Darwin OS from now on.  

Moving on to coalition strategy now, some of you may not know that
GNU/Linux system administration is one of my day jobs.  I manage a
wide range of systems.  Here is a screen-shot of my work desktop, so
that you can see I use the same tools at work that I use at home at
night on GNU-Darwin.  (weekends too, so please read I am your friend)

http://proclus.gnu-darwin.org/debian.html

The only time that I ever use proprietary software is when I am trying
to help other users learn free and open source free software.  I'm a 
long time Apple and GNU/Linux user, and here is the old proof doc ;-}.

http://proclus.tripod.com/indulge.html

Now, it is embarrassing but, I want you to have a look at my cv.

http://biophysics.med.jhmi.edu/love/thesis/cv6.html

In all my years I have never used Microsoft Windows.  There are only
two exceptions to this statement, where I was helping Windows users to
access our servers at Hopkins.  Clearly, you can get a few things done
without it ;-}.

One of the primary reasons for founding GNU-Darwin was to help people
to put Microsoft behind them,  and it is definitely possible to do it
now.  You have many resources at your disposal to help you leave
Microsoft behind.  Look at the link below to see what you can do
with free software.  Apple, GNU-Darwin, GNU.org, and GNU/Linux will
all help, and we are largely all helping together, because we have a
shared foundation of free software.

http://www.gnu-darwin.org/gdc/

Microsoft is only one example.  That is why we are so insistent that
Apple keep true to free and open source software principles.  We
should ultimately try to leave all proprietary software behind us, so
that we can participate fully in the freedom and openness of the
internet culture and public domain.  What more do we need, when we
have such a rich store of information and so many capable people at
our sides?

Finally, as a scientist, it is obvious to me that this situation is
relevant current and ongoing discussion in the scientific community,
and as such, it is also clear that many members of the various lists
would be interested in the current state of Darwin with respect to
FOSS and with respect to science.  

Here is the crucial point.

The principles of FOSS and scientific inquiry converge.  In
practical terms, how else can you know is what happening in your
experiments?  Free and open source software, open standards, best
promote the scientific endeavor by mirroring its method, but also
they assure that the work is accessible to the public.

Freedom and openness are crucial to understanding, and foundational
to the scientific endeavor, and they should not be compromised. 
There are a few examples of exceptions, but clearly, this matter
will find further debate in the appropriate forums.  We should not
quell debate because a few people are offended or complaining.  
- From a scientific perspective that would be incorrect.

On that last point, I would suggest that Apple get on the right side
of the debate, and they will make tremendous headway.  Now is the
time.

Some people will find this message annoying and divisive, and the
delete button is ready at hand for them, but other people will find 
it interesting and engaging.  All as you like.  Let us not quell
discussion because a few people are annoyed.

Some will call this a troll, but I hope that folks will see through
such name-calling.  Trolls are mythological creatures, so don't
believe in them.  Everyone has a right to have their opinion
heard, even if those opinions are divisive or unpopular.  It is
clear that the idea of trolls is being used to attack freedom of
expression.  In fact, freedom of expression demands that we
listen to the so-called-trolls sometimes, and if you are civil, it
helps, so don't resort to name-calling. 

On cross-posting; when there are matters of urgent importance that
affect a broad range of subscriber lists, courtesy must sometimes
take a back seat, and cross-posting is an example of that. 
Cross-posting is to be encouraged when the subject of the post is on
topic.  Each of the various lists will respond in the way that seems
appropriate to the people in that forum, and the threads on the
various lists will diverge accordingly.  As the threads diverge, the
cross-posting addresses should be removed as needed.  Relevance to
all people is an unattainable goal, but messages of the broadest
applicability should have the broadest reach, and discussion should
not be stymied because some find it irrelevant.  I have given this
method due consideration; it is not trolling, not spam, not off-topic,
and cross-posting is an example of something that is sometimes
required according to the felt importance and relevance of a given
subject matter.  

In summary, Freedom and openness are now the bedrock of our
civilization and public welfare depends on these values, so that we 
should actively engage ourselves in preserving and making them happen.
In keeping with these principles it is crucial to note that there are
exceptions to etiquette, otherwise free expression will be overly
channeled, damped, and ultimately suppressed in our forums.  This
notion of courtesy will certainly receive additional consideration,
but meanwhile, let us together get to work on the activism now.  

Duly, I am amenable to valid criticism and able to respond, but please
reply with kindness.  Obviously, feel free to write back, copy, or
send these comments along to anyone else as you see fit.

Regards,
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

Interoffice Mail: 608B WBSB, SoM

office: 410-614-2267
lab:    410-614-3179
fax:    410-502-6910
cell:   443-824-3451
http://www.gnu-darwin.org/
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.1 (Darwin)

iD8DBQFEpIl6u0oI3iz5oZcRAtpQAJ9X7D6kq1vmWKXkG/3LBvx3gGrK1QCZAbgI
8Ww6QABLiZtmFmS9Ekea5nI=
=a0Oy
-----END PGP SIGNATURE-----