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PubPat Wins a Reexamination of Cotransformation Patent
Monday, May 10 2004 @ 01:26 PM EDT

PubPat is beginning to show results for its work. Their request for a reexamination of a patent Columbia University obtained on a key patent on cotransformation, a process for inserting foreign DNA into a host cell to produce certain proteins, has been granted. The press release says the USPTO isued an Order granting the request because they found that PubPat's request raised "a substantial new question of patentability" regarding every claim of the patent.

This patent has to do with pharmaceuticals, not computers, but the Public Patent Foundation has also more recently filed a formal request with the USPTO, as you may remember, asking them to revoke Microsoft's patent on the FAT file system because, they say, it's causing significant public harm. "Microsoft is using its control over the interchange of digital media to aid its ongoing effort to deter competition," the request stated. With the request, they filed some prior art to demonstate that the patent was obvious and shouldn't have been granted in the first place.

That is the process, and it's good if we all become knowledgeable about the way this process works, since everyone seems to think this will be the next battlefront. Happily, the USPTO has been so profligate in issuing patents, there is some relief possible, and this is how you get it.

Migeul de Icaza adds to the chorus today, warning about patents being the next cancer we will have to deal with. He also contributes some links to pictures in a comment responding to an objection someone had that people in third world countries can't afford computers even at a $300 price:

"In regions where this is not possible, governments have started the adoption of community sites where people can use computers for free, the equivalent of going to the post office to send mail. Brazil has the telecentros in Sao Paolo and Rio Grande do Sul.

"Spain has Andalucia and Extremadura, and the trend is catching up.


"Or go and browse them all:


He says something intriguing about Longhorn and prior art:

"Ximian met with Microsoft executives a few months ago -- as part of a symposiuym -- and it's not a secret that Microsoft is aware of the Mono developments. Miguel explains: 'If there is indeed a new technology that Microsoft holds a patent to and they do not explicitly allow us to use, we will remove that code, or rework the code in a way that does not infringe the patent. We do not like the current patent environment in the US, but we have to play by the rules.' Miguel also gave us a number of technical examples around Corba having technologies for years that Microsoft only now starts to be using in their products. 'Longhorn's Indigo or Avalon, all was done before by us and others', said Miguel. 'Most of the new technologies in Longhorn have existed in the past in one way or another, but they failed to get shipped with a vehicle as Microsoft Windows to users, so they live only on CVS repositories, old research papers, and old systems.' He has so many such examples it that makes him sleep tight at night and not worry about such things."

Prior art is legally valuable, and published papers count. Here is PubPat's press release in full.


Order Finds "Substantial New Question" of Patentability for Entire Patent

NEW YORK -- The United States Patent and Trademark Office has issued an Order granting the Public Patent Foundation's Request for Reexamination of a key patent on cotransformation, a process for inserting foreign DNA into a host cell to produce certain proteins that is the basis for a wide range of pharmaceutical products, including EpogenR for anemia, ActivaseR for heart attacks and stroke, AvonexR for multiple sclerosis, and RecombinateR for hemophilia. In its Order, the Patent Office found that PUBPAT's request raised "a substantial new question of patentability" regarding every claim of the patent.

The patent holder, Columbia University, now has the opportunity to make an opening statement to the Patent Office, to which PUBPAT has the right to make a response. After opening statements, the Patent Office will proceed to determine whether the patent is indeed invalid in light of the new questions raised by PUBPAT's request. Third party requests for reexamination, like the one filed by PUBPAT, are successful in having the subject patent either narrowed or completely revoked roughly 70% of the time.

"We are obviously very pleased with the Patent Office's decision to grant our request to reexamine the Axel cotransformation patent," said Dan Ravicher, PUBPAT's Executive Director and Founder. "This is the first step towards ending the harm being caused to the public by this patent that never should have been issued."

More information about the Request for Reexamination, including a copy of the Patent Office's Order Granting the request, can be found at


Daniel Ravicher, Executive Director, Public Patent Foundation: 212-545-5337;;

About PUBPAT: The Public Patent Foundation ("PUBPAT") is a not-for-profit legal services organization working to protect the public from the harms caused by the patent system. PUBPAT provides the general public, particularly those persons or businesses otherwise deprived of access to the system governing patents, with representation, advocacy, and education. To be kept informed of PUBPAT News, subscribe to the PUBPAT News List by sending an email with "subscribe" in the subject line to To be removed from the PUBPAT News List, send an email with "unsubscribe" in the subject line to:



PubPat Wins a Reexamination of Cotransformation Patent | 119 comments | Create New Account
Comments belong to whoever posts them. Please notify us of inappropriate comments.
Corrections Here Please
Authored by: PJ on Monday, May 10 2004 @ 01:27 PM EDT
Please put all my mistakes here, so I can correct easily. Thank you for

[ Reply to This | # ]

PubPat Wins a Reexamination of Cotransformation Patent
Authored by: pb on Monday, May 10 2004 @ 01:33 PM EDT
AFAIK, MS's patents relate specifically to VFAT (LFN
extensions) and not FAT itself... I remember PubPat's
press release did not make this fact clear at all, so I
hope their formal request and evidence is a bit more solid
than that.

[ Reply to This | # ]

Urls and updates here!
Authored by: Anonymous on Monday, May 10 2004 @ 01:34 PM EDT

[ Reply to This | # ]

Derivative work
Authored by: risacher on Monday, May 10 2004 @ 01:49 PM EDT
I'd just like that guy (Daniel Ravicher) to quit infringing on my name. It's
patently obvious that it's a derivative work.


-Daniel Risacher

[ Reply to This | # ]

A related question
Authored by: Anonymous on Monday, May 10 2004 @ 01:53 PM EDT
I realize this is a hair off subject but I think this is important. I was
wondering if PJ or some of the other knowledgeable people here could tell me if
I do in fact own the software I buy. I was having an interesting conversation
concerning this on zdnet and wanted to get a better answer. According to these
guys I do in fact own the software
regardless of what the EULA says.

I look at Software in the same way I do a music CD. Someone wrote and produced
the songs put them on a CD and sold it to me. I can then go home listen to the
CD for as long as I like, yet still turn around and sell it as a used item.
Software is the same thing in my book. Someone wrote the software, put it on a
cd and sold it to me. I can then go home and use the software, yet should be
able to sell it once I am done with it. This is also assuming that I remove it
from my system, just like assuming I didn't copy the CD before I sold it.

[ Reply to This | # ]

FAT File System
Authored by: Anonymous on Monday, May 10 2004 @ 02:05 PM EDT

Back in 1978 the Radio Shack TRSDOS Operating System used a disk space
allocation scheme very similar (identical) to the FAT system that MS has
patented. RS called the allocation units "granules." MS uses the
term "Clusters."

I am not a lawyer or patent expert, but this does appear to be prior art.


[ Reply to This | # ]

OT: New Enderle Article
Authored by: dmscvc123 on Monday, May 10 2004 @ 02:50 PM EDT
Here's a new article by Rob Enderle on the coming battle between Linux and

I actually found it a rather good article, not that I agreed with everything he

[ Reply to This | # ]

Open Source is crucial to defense against software patents
Authored by: Anonymous on Monday, May 10 2004 @ 03:00 PM EDT
It would not shock me if one of the most important contributions of open source is defense against software patents. It is undoubtably true that the majority of software patents being granted today were not first invented by the organization getting the patent, but the fact that the original invention was almost certainly done in a closed-source enviroment make has four devastating problems:
  • It is difficult to prove that the prior invention did indeed occur first
  • For prior art to be used to invalidate a patent, that prior art would have to be public. Now, I believe that it is possible for closed-source software to be valid prior art, but you would have to prove that your public product software used the invention privately. It would be difficult.
  • It is impossible for the community-at-large to search for prior art in closed source programs.
  • The company that invented the technique oringally might not be interested in fighting the patent.

  • Each of these problems will be obviated by a strong open source community, especially as open source moves beyond operating systems into more applications areas.

    Note well that this is strictly an open-source, as opposed to free-software issue.

    Thad Beier

    [ Reply to This | # ]

    OT SCOX down over 10% today
    Authored by: cricketjeff on Monday, May 10 2004 @ 03:23 PM EDT
    And still falling it seems Yahoo 1 day chart here couldn't happen to a nicer bunch

    [ Reply to This | # ]

    PubPat Wins a Reexamination of Cotransformation Patent
    Authored by: ExcludedMiddle on Monday, May 10 2004 @ 03:24 PM EDT
    This is going to seem picky, but I can't seem to help myself. This sentence bugs

    "Happily, the USPTO has been so profligate in issuing patents, there is
    some relief possible, and this is how you get it."

    I keep thinking that you're happy that they have been profligate in issuing
    patents! (By the way, you do score points for using profligate. It's one of my

    I would suggest:

    Although the USPTO has been so profligate in issuing patents, happily, there is
    some relief possible, and this is how you get it.

    If you disagree, please ignore me like everyone else does!

    [ Reply to This | # ]

    Groklaw Patent project?
    Authored by: lightsail on Monday, May 10 2004 @ 03:28 PM EDT
    In the escalting patent war, we need a weapon:

    A resource of prior art, built from established standards and the vast FOSS
    software, that would shedd light on what is and is not patentable.

    A open resource would provide the Open source community a means to refute
    current and future patents.

    A mechanism could be created to generate the needed prior art for the patenting
    of open source methods as a defense in the current intellectual property war.
    Open source patents could be assigned to a pool for the use as a defense. The
    needed prior art could be part for the licensing of "GPL" patents.

    I think that we must face the need to be able to fight fire with fire.

    [ Reply to This | # ]

    OT: SCO Stock Sales
    Authored by: dmscvc123 on Monday, May 10 2004 @ 04:25 PM EDT
    I was just going through SCO's insider activity:
    I looked up Thomas Ramondi since he's been real busy. I'm not so much surprised
    that he's selling but rather under the terms that he's selling under.

    He's getting option prices at around $1.00 (understandable), but what isn't
    understandable is how when the stock is in the crapper that this guy can sell
    his shares at around 10X what he's paying for them and way more than the market

    What gives that this guy is able to both buy the shares for significantly below
    market and sell them significantly above market?

    Oh, here's the Forbes profile:
    I especially liked this part in Forbes "SCO Group ("SCO")
    (formerly Caldera Systems Inc.), a Linux-based software company."

    [ Reply to This | # ]

    OT - Get your dose of the Darl comedy special
    Authored by: utahbob55 on Monday, May 10 2004 @ 05:21 PM EDT

    Finally, the press is actually beginning to question McB's credibility. The headline says it all:
    SCO experiences brief moment of clarity; therapists encouraged

    From Enjoy, I sure did.

    [ Reply to This | # ]

    PubPat Wins; Europeans Fighting Patents Need Help
    Authored by: Anonymous on Monday, May 10 2004 @ 08:21 PM EDT
    Anybody with time, resources, European connections, please check out
    <> in English

    French, German & Spanish versions available.

    [ Reply to This | # ]

    Lovable chumps
    Authored by: Anonymous on Tuesday, May 11 2004 @ 06:03 AM EDT
    I love what they're doing, but they have *got* to knock off the Big Business
    Bashing. If they are going to challenge on the grounds of prior art or
    obviousness, fine and good. Muddying that with meta commentary on the harm that
    the patent is causing is spin, and I don't see it impressing the USPTO one whit.

    [ Reply to This | # ]

    USPTO overworked and underfunded
    Authored by: Anonymous on Tuesday, May 11 2004 @ 12:21 PM EDT
    I have heard mention that the USPTO is under funded and relies on fees for
    funding. Some 90% of the patents applications are being granted because they
    need the funding.

    Simple solution is to make it worth more to them to NOT grant a patent than to
    grant one. Lay down your non-refundable application fee and a refundable upon
    granting deposit (say about 50%). It would encourage them to do a little more
    prior art search as well as duh obvious check. Also if they failed a few more
    they would not be quite so overworked now would they?

    Also what needs to go is granting of patents that are so vague as to not be able
    to reproduce what it being patented (lose the deposit on that one too). Not to
    mention the interpretation of patents that already stand are a little over
    broad, e.g. one click shopping means what exactly?


    [ Reply to This | # ]

    Words and the Law
    Authored by: Anonymous on Tuesday, May 11 2004 @ 05:20 PM EDT
    It bothers and puzzles me the way the scope certain words and phrases is
    narrowed to the point it's like they aren't even there. "Non-obvious"
    for starters, or "limited time" (as in "To secure for a limited
    time to authors...."), as I understand it, "moral turpitude"
    clauses in executive contracts have become all but unenforceable.

    The words were clearly put there for a purpose other than filling space, writing
    laws isn't like a third grade book report where you have to fill one page,
    single spaced.

    If "one click ordering" is non-obvious, what isn't? I don't even know
    how long copyrights last anymore, it keeps changing, but a fair minded observer
    would have to agree they extend beyond "a limited time" in any
    meaningful sense of the word(s). In a finite universe, all time is limited, but
    treating the phrase as a mere cosmological fact is no different than removing it
    from the constitution with white-out.

    For patents I just find it galling that due to patent office understaffing,
    underfunding, expedience, or buck passing that the "non-obvious"
    requirement is blatantly ignored. It's unfortunate that the patent office can't
    be sued for the economic damage their promiscuous granting of undeserving
    patents causes; they'd be forced to choose dilligence over taking the path of
    least resistance.

    [ Reply to This | # ]

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