Thursday, April 1, 2010

SourceForge.net: GNU-Darwin Distribution: News

Project News for GNU-Darwin Distribution

  • Re: Bootstrapping your body towards maximum life span

    Here is a little more obvious prior art in the resveratrol story.

    I was reading the latest from Biochemistry about bioflavinoids as
    possible cancer treatment agents. Here is the link, although some of
    the material is unfortunately not public access ;-}.

    http://dx.doi.org/10.1021/bi7000664

    I cribbed below some references that indicate the action of the
    bioflavinoid molecules against tyrosine kinase activity. It is obvious
    and clear prior art that resveratrol will also act against tyrosine
    kinase activity, because it is similar in structure to the bioflavinoids
    as well as to the substrate, tyrosine. Ultimately, this interferes with
    the protein kinase C cascade, which leads to many of the anti-cancer,
    health inducing, and life extending benefits. To my knowledge, this
    activity of resveratrol remains unpublished until _now_.

    As always, please feel free to pass along my messages as you like. In
    particular, this message should be considered as a prior art declaration
    against any CR-memetic related patent. Resveratrol is freely available
    from grapes, roots, nuts, and berries; and it is widely available as a
    supplement in the dosage required to produce beneficial effects. At
    this time, choose the highest dosage supplement that you can find, but
    this situation may change in the future ;-}>.

    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/


    18. Akiyama, T., Ishida, K., Nakagawa, S., Ogaara, H., Watanabe, S., Itoh, N. M., Shibuya, M., and Fukami, Y. (1987) Genistein, a specific inhibitor of tyrosine-specific protein kinases, J. Biol. Chem. 262, 5592-5595. [ChemPort] [Medline]
    19. Hagiwara, M., Inoue, S., Tanaka, T., Nunoki, K., Ito, M., and Hidaka, H. (1988) Differential effects of flavonoids as inhibitors of tyrosine protein kinases and serine/threonine protein kinases, Biochem. Pharmacol. 37, 2987-2992. [ChemPort] [Medline] [CrossRef]
    20. Geahlen, R. L., Koonchanok, N. M., McLaughlin, J. L., and Pratt, D. E. (1989) Inhibition of protein-tyrosine kinase activity by flavonoids and related compounds, J. Nat. Prod. 52, 982-986. [ChemPort] [Medline]
    21. Cushman, M., Nagarathnam, D., Burg, D. L., and Geahlen, R. L. (1991) Synthesis and protein-tyrosine kinase inhibitory activities of flavonoid analogues, J. Med. Chem. 34, 798-806. [ChemPort] [Medline]
    22. Yang, E. B., Guo, Y. J., Zhang, K., Chen, Y. Z., and Mack, P. (2001) Inhibition of epidermal growth factor receptor tyrosine kinase by chalcone derivatives, Biochim. Biophys. Acta 1550, 144-152. [ChemPort] [Medline]
    23. Hollosy, F., and Keri, G. (2004) Plant-derived protein tyrosine kinase inhibitors as anticancer agents, Curr. Med. Chem.: Anti-Cancer Agents 4, 173-197. [ChemPort]

    On 9 Feb, To: proclus@gnu-darwin.org wrote:
    >
    > I thought that you might like a little essay I wrote about caloric
    > restriction as a war protest. It is a sort of HOWTO for the general
    > public. Feel free to pass the link along, or write back as you like.
    >
    > http://proclus.gnu-darwin.org/~proclus/bootstrap.html
    >
    > Regards,
    > proclus
    > http://www.gnu-darwin.org/
    >

    --
    Visit proclus realm! http://proclus.tripod.com/
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    2007-05-15 18:48:42 GMT by proclus

  • Johns Hopkins University FOSS software for crystallography

    Most of you will know that protein crystallography software is the
    primary reason why I started GNU-Darwin, because I wanted at the time to
    do my work on an Apple computer. I would like to call your attention to
    the FOSS software page of my lab at Johns Hopkins. It is possible to do
    all of the crystallographic work using publicly available software,
    which includes open access to the source code. Nearly all of this
    software builds on our OS, thanks in part to the efforts of the Distro.
    Here is the link.

    http://biophysics.med.jhu.edu/cgi-bin/software/software_list?category=foss

    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 our science verifiable to the
    public.

    If you would like to review the underpinning of these ideas, check the
    FOSS, Science, and Public activism essay.

    http://proclus.gnu-darwin.org/aCommunique2.html

    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/

    --
    Visit proclus realm! http://proclus.tripod.com/
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    2007-01-16 18:53:51 GMT by proclus

  • Action item: Intel Accused of Being an "Open Source Fraud"

    This is a crucially important matter, akin to the AppleACPIPlatform
    driver problem in Apple's current Darwin revision. Let's rid these blobs from our FOSS operating systems, and let the hardware companies know that
    they are not compatible with such.

    Intel Accused of Being an "Open Source Fraud"
    from the you-bought-it-now-you-can't-use-it dept.
    posted by ScuttleMonkey on Tuesday October 03, @05:19 (Intel)
    http://bsd.slashdot.org/article.pl?sid=06/10/03/032259

    Regards,
    proclus
    http://www.gnu-darwin.org/


    --
    Visit proclus realm! http://proclus.tripod.com/
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    2006-10-05 20:28:21 GMT by proclus

  • The kernel building fiasco

    On 8 Aug, plumber Idraulico wrote:
    > Open Answer

    This reminds me of my intuition to post it to the lists, so that people
    can see that we are getting stonewalled by Apple. From a certain
    standpoint, it is a joke to release the kernel source code without
    releasing the AppleACPIPlatform driver. As a result, people are getting
    disinformed now. It seems apparent where Apple has hidden the DRM.

    See below.

    Regards,
    proclus
    http://www.gnu-darwin.org/


    > ------ Forwarded message ------
    > From: Kevin Van Vechten <kvv@apple.com>
    > Subject: Re: kernel building
    > Date: Tue, 8 Aug 2006 11:16:21 -0700
    > To: proclus@gnu-darwin.org
    > Cc: opensource@apple.com
    >
    >
    > On Aug 8, 2006, at 9:40 AM, proclus@gnu-darwin.org wrote:
    >
    >
    >> Sorry about the CC, as I was unsure of the address. I am excited to
    >> see the situation with the kernel resolved, as expected. Some of us
    >> never lost our faith in this ;-}.
    >>
    >>
    >>> http://kernel.macosforge.org/?p=4
    >>>
    >>
    >> I am anxious to see the development of the community around this new
    >> forum.
    >>
    >
    > Thank you, we hope this forum will benefit developers interested in
    > working with the xnu kernel.
    >
    >
    >>> http://kernel.macosforge.org/intel-build-instructions.html
    >>>
    >>
    >> This is a good start, but I would like to see more information with
    >> regard to building the kernel extensions, instead of installing
    >> binaries. I think that I can help with this, and there is another
    >> GNU-Darwin developer who could help as well. It is important that
    >> they
    >> build in Darwin-only environments. If you all think this is a good
    >> idea, let me know, and I'll sign up.
    >>
    >> Of course, we still need to see the source code for the
    >> AppleACPIPlatform driver, which is necessary in order to boot the
    >> current Darwin OS, or we need a replacement driver, in order for this
    >> to happen in earnest. We are anxious for cooperation, and await your
    >> response.
    >>
    >
    > Unfortunately the sources to these kernel extensions cannot be made
    > available (with the exception of IOUSBFamily, which hopefully will be
    > available in the near future).
    >
    > Thank you for your understanding,
    >
    > - Kevin
    >
    > --
    > Kevin Van Vechten <kvv@apple.com>
    > Apple Computer, Inc.


    --
    Visit proclus realm! http://proclus.tripod.com/
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    2006-08-08 19:04:15 GMT by proclus

  • FOSS, Science, and Public activism

    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 http://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/


    2006-06-30 01:09:38 GMT by proclus

Here are some GNU-Darwin News releases going back to the very beginning. More to come.

Regards,
proclus
http://www.gnu-darwin.org/

Posted via web from proclus-gnu-darwin's posterous

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