TDI-discuss

Download

tdi-discuss@salilab.org

July 2006

1 participants
1 discussions

FOSS, Science, and Public activism
by proclus＠gnu-darwin.org 01 Jul '06

01 Jul '06

-----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=60… 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=… 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-----

1 0