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Thread: Patented algorithm

  1. #1

    Angry Patented algorithm

    Oh, you patented your algorithm. How nice for you. Guess that means I'll be withdrawing all my machines.

    I really expected better from people supposedly working on pure scientific research.

    By patenting your algorithm you prevent people from using your algorithm in the advancement of science, or from possibly improving on your algorithm to the benefit of all mankind.

    I'm disgusted.


  2. #2

    Re: Patented algorithm

    Originally posted by Chinstrap
    Oh, you patented your algorithm. How nice for you. Guess that means I'll be withdrawing all my machines.

    I really expected better from people supposedly working on pure scientific research.

    By patenting your algorithm you prevent people from using your algorithm in the advancement of science, or from possibly improving on your algorithm to the benefit of all mankind.

    I'm disgusted.

    Actually, patenting our algorithm simply protects it as our own Intellectual Property. It prevents other people from using our algorithm, or something very similar, to make profit, without giving us proper credit. It does NOT in any way prevent others from using it for non-profit purposes, such as the 'advancement of science'. So I'm afraid your concerns are misplaced.

    If you check the patent, you will see that it was filed long before DFP even existed. It is common pratice to patent new ideas and algorithms in many areas of research.
    Howard Feldman

  3. #3
    No, that is what a copyright does for you. Copyright your works? Absolutely. Go for it. You have every right. Patent it? Now I can't do anything that works similarly to your system for fear of lawsuits.

    Let's say that I was a geneticist. I'm looking at your algorithm and go "Oh wow, if I were to just change this thing right here a little bit it could be sped up 1000 fold!". Now we could effectively have a 1000x speed-up of this type of research. But, you patented your algorithm, so I can't use it as a basis for my own improved version.

    This is science people. For the help of the human race. Not a money making system. Not capitalism (not that I have anything against capitalism, in its place). We are supposed to be advancing human knowledge here in any way possible. Unfortunately, hospitals and scientific institutions think of themselves more as businesses now, and consider themselves to be in competition with each other rather than trying to cooperate in improving life for everyone.

  4. #4
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    Smile

    Intellectural property issues have become so complex at research institutions such as hospitals, universities, and labs. Most of us have to deal with so many standing policies that it gets in the way of publishing and sharing our research. Sometimes the policies are for a good reason, many times they are not.

    I for one am glad to see the algorithm patented. It makes it possible for the originators (and their host institution), keep control of it. I am glad to be working on a project where my contribution, though small, is unique, unduplicated, and contributes to validation of NEW knowledge.

    Congratulations.

  5. #5
    Originally posted by Chinstrap
    No, that is what a copyright does for you. Copyright your works? Absolutely. Go for it. You have every right. Patent it? Now I can't do anything that works similarly to your system for fear of lawsuits.
    Why on earth are you surprised about this? This issue was declared quite clearly on the official project website. Any money made from the patent does go into further medical research since Mount Sinai Hospital is a non-profit institution. If this was not done, then Howard could easily run into problems if another organization or company patents similar technology and then went after The Distributed Folding Project for patent infringement.

    You also seem to fail to understand how the copyright and patent system works in the US. You CAN'T copyright an invention or software algorithem, only patent it. Howard has already pointed out that non-profit organizations can use the algorithem, it is merely for profit companies that would have to pay. Try to at least get your terms straight before posting tirades on this board.
    A member of TSF http://teamstirfry.net/

  6. #6
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    Originally posted by Chinstrap
    Let's say that I was a geneticist. I'm looking at your algorithm and go "Oh wow, if I were to just change this thing right here a little bit it could be sped up 1000 fold!". Now we could effectively have a 1000x speed-up of this type of research. But, you patented your algorithm, so I can't use it as a basis for my own improved version.
    So you tell Howard about your idea, and he thinks it's good, so it gets used. What's the big deal again?

  7. #7
    25/25Mbit is nearly enough :p pointwood's Avatar
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    Thumbs down

    This is a software patent, right?

    Software patents are evil and nothing but evil. Anyone telling you otherwise is lying, plain and simple. There are several reasons why, but it's very late here and I'm not the best one at explaining it, certainly not in english.

    As far as I understand, patents on medicin is a different issue, because the industry works in a different way. I'm not convinced they are a good idea there either though.

    I'm really sorry because I really, really like this project, but I will not support a project that "uses" software patents.

    Unless I'm proved wrong and this is not a software patent or the patent is released into public domain (which I doubt will happen), I will stop crunching for this project.
    Pointwood
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  8. #8
    Ancient Programmer Paratima's Avatar
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    Pointwood, read Aegion's post again, please.

    Blanket statements like "All software patents are evil" are not well thought out. You could make a statement like "Guns are evil" and get quite a lot of people to agree. But guns protect people, too. I agree that the concept of software patents is undesirable in the kind of world we hope we're building. But it's a fact of scientific life here and now that you have to defend your ideas or someone will come along and beat you to death with them.

    Howard and the MSHRI people would be seriously remiss if they didn't take steps to protect their work from people who are driven only by profits.

  9. #9
    both of you are pulling your support from this project, because of what COULD be done with the patent.

    who's howard sueing? NOBODY
    who's howard prosecuting? NOBODY

    Chinstrap: You opened a forum account to announce this. your voice has no weight in my mind. please keep your opinions to yourself in the future. We dont need politics here.

    Pointwood: Paratima's post is correct. anyone who uses blanket statements like that is making a hollow argument. you also make the comment that English is not your first language. i derive from this that you are not american or canadian. i must also derive (from your lack of input) That your understanding of patent law OR intelectual property law, is not of those countries either.

    all that's being done here is protecting the project.

    ""If this was not done, then Howard could easily run into problems if another organization or company patents similar technology and then went after The Distributed Folding Project for patent infringement""
    --Aegion

    aegion has the right idea, i'm sorry you two others dont.

    Kileran

  10. #10
    25/25Mbit is nearly enough :p pointwood's Avatar
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    Patents and software just doesn't go well together, you can read more here: http://swpat.ffii.org/index.en.html

    Another site I would refer to is http://softwarepatenter.dk/ but you'll not understand anything on that page unless you understand Danish

    I don't agree with Aegion here. Howard should have no problems documenting the things he has created and when, so if someone claims a patent infringement, Howard shouldn't have a problem - unless of course the patent is older than his work, but that's the way the patent system works.

    And what's the problem with copyright?

    Kileran: What could be done is enough for me.

    No, I'm not American (I'm from Denmark, as you have probably already realised), but I spent quite some time studying the problems associated with software patents and that doesn't really change whether it's America or not. I also know people that have spent *years* on this.

    You wouldn't need a gun to protect yourself, if guns didn't exist, would you? There are far more negative "side" than positive in regards to guns. The same is true with software patents. The difference is that we actually have a resonable chance of getting rid of software patents, I honestly/sadly don't think the same is true with guns.

    The fact that Chinstrap opened an account just to say that says a lot IMHO. He obviously think software patents are a really bad thing and he took the time to tell Howard that. He could have just silently stopped crunching and Howard would have no idea why. As you can see, he's not alone and I believe that Howard would like to know why people stop crunching - we are, after all, a pretty important part of his project.

    Now, why do I react the way I do? Pretty simple actually. I work with software everyday and every day I could loose my job and the company I work for could go bankrupt because someone patented some stupidly simple thing and have decided to sue us. I work at a little company - we wouldn't be able to afford that. I don't like the fact that my future and the future of the company I work for could be changed so drastically, just because of a broken patent system. You can ask: What's the chance of that happening?" I would say it is pretty small, but even though patents on software "as such" is not possible in Europe currently, we already have thousands of software patents and they have long ago made problems here for several companies.
    Pointwood
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  11. #11
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    A patent does nothing to protect your IP rights by itself. It only gives you the ability to protect your IP rights if you choose to. You can also choose to license your invention for whatever price you choose (almost) to whomevery you choose. It could easily be licensed for free if they choose to. So it's not the patent itself that causes any harm to knowledge distribution but rather over-zealous enforcement which is entirely voluntary on the part of the patentee. In fact, all patents are laid-open (made publiclly available) so patenting your work GUARANTEES it's dissemination far and wide. (And yes companies do watch the issued patents within their area of interest). Protecting your invention even in a pursuit such as this can be useful. For instance, say someone comes up with a way to leverage the approach used here to do en-masse cloning or bio-engineering of humans. Far fetched, I know. The patent would allow Howard et al to prevent the use of their invention for that purpose by refusing to grant a license for the purpose and suing anyone who did use it for that purpose. But it all comes down to the choices the patentee makes with respect to protecting its IP rights once it has them. withdrawing support from the project on the basis of establishing IP rights seems foolish to me. Withdrawing support on the basis of abusing the IP rights they have is not foolish. But as I believe Kileran pointed out, Howard et al aren't suing anyone. so this entire issue is overblown and premature.

    ms

  12. #12
    25/25Mbit is nearly enough :p pointwood's Avatar
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    Originally posted by Brian the Roman
    In fact, all patents are laid-open (made publiclly available) so patenting your work GUARANTEES it's dissemination far and wide. (And yes companies do watch the issued patents within their area of interest).
    Where do you have that information from. It is an expensive, time consuming process to "watch out for patents" and most small companies simply can't afford that. Studies show that only the biggest companies do that. Here is one: http://www.software-patenter.dk/rapport_patprot.html

    Furthermore - do you think patents are easy to understand? Software patents are written by laywers, for laywers - not developers (do you know of any developer that studies software patents and understands them?). Bye, bye, "knowledge sharing".

    Furthermore, small companies generally can't afford a lawsuit or afford suing a different company for a possible infringement. And if the company they want to sue is a big company, who do you think have the best chance of winning? What's the chance that the bigger company have one or more patents that the smaller company infringes?
    Pointwood
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  13. #13
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    So basically, pointwood, small companies can't enforce their own patents if they have them, and they get screwed if they infringe on someone else's.

    Well for one, if they infringe on someone else's IP, they deserve to get screwed. That's the reason patents exist; to make sure no one uses your ideas without getting permission (in other words, a "license") from you.

    As for large companies using your patent without a license, in theory the fact that litigation is possible is a deterrent to that. Now theory is not practice, obviously, especially if the large company knows you don't have the resources to sue it. But getting a patent can't hurt the small company, right?

    In general, I'd agree that software patents are evil (even stuff like the MP3 patent is evil; that's why I use Ogg/Vorbis personally), but in a case like this, where the technology isn't in wide use or a candidate for wide use, who cares? The public isn't going to get screwed by it (especially considering the fact that Howard's policy on it is "free for noncommercial use"; he only wants to be compensated if you're making a profit off it).

  14. #14
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    I'm an IT consultant currently working for the patent branch of the Canadian Intellectual Property Office. From our requirements gathering process, some of the senior users have told us that companies do monitor patents issued and applications laid-open within their area of interest. I assume that this is probably larger companies because of resource constraints.

  15. #15
    25/25Mbit is nearly enough :p pointwood's Avatar
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    Originally posted by bwkaz
    [B]Well for one, if they infringe on someone else's IP, they deserve to get screwed. That's the reason patents exist; to make sure no one uses your ideas without getting permission (in other words, a "license") from you.
    And what if they don't, but get sued anyway?

    But getting a patent can't hurt the small company, right?
    Well, except they spend a lot of money on getting the patent, money that otherwise could be used to make their product better instead.

    Since they now have the software patent, I think their policy is resonable, but it doesn't chance my opinion.

    Brian the Roman: I'm not familiar with how the Canadian Office works, but if it is similar as to how it is in Denmark, that is not surprising. If they said that no one used it, then they in-directly say that the work they do is irrelevant and that would be kinda stupid to say...
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  16. #16
    Hi all,

    First, to remind those of you, I'm Christopher Hogue, Scientist, Samuel Lunenfeld Research Institute and Assistant Professor, Dept. of Biochemistry, University of Toronto.

    I am Howard's graduate supervisor and the scientist responsible for this project.


    I see that the issue of software patenting concers many of you.

    I'm here to say that it also concerns me.

    This note is intended to make it clear where I stand on the issue of software patents, and why we have patented the TRADES algorithm, which makes protein structures within the DistributedFolding project


    I am a developer and I do study software patents. As an example I would like you to consider this recent patent granted to Millennium Pharmaceuticals on the topic of distribued computing:

    US Patent 6,470,346 Remote computation framwork.
    Inventors: Morwood; Mark Roy (Cambridge, MA)
    Assignee: Millennium Pharmaceuticals, Inc. (Cambridge, MA)
    Appl. No.: 167821
    Filed: October 7, 1998

    Covers a computer system of remote servers to provide additional memory and processing time for bioinformatics applications. The patent describes a remote computation system to enable a requesting client to invoke any arbitrary command line on a remote server. The remote computation process and dispatches computation requests received from clients to approrirate computation servers, manages the computation requests, and allows vending or gathering of results that are sent back to the requesting client.

    Here is the patent if you care to read it.
    http://patft.uspto.gov/netacgi/nph-P...&RS=PN/6470346

    This patent troubles me because it covers the same area of software that our MoBiDiCK system (the predecessor to DistributedFolding) was built on and other cluster and distribued software systems like PVM, and PBS. I started designing MoBiDiCK in 1997, and have source code dating from 1997 on the project. This Millenium patent could make the DistributedFolding, Folding@Home and other similar projects subject to Millenium's legal action.

    But I don't lose sleep over them suing me. :sleepy: Millenium would probably assess whether it was worth it to sue us over the patent and discover that we have no $$ for them to recover to pay their legal bills. Likewise, please recall that I don't have enough grant funds to buy servers for all the ports we want to do. Also keep in mind that my grant funds do not cover legal action to defend the patent, so don't think for a minute that I'm about to go suing anyone!

    We aren't using distributed computing in a commercial sense, but others are, like United Devices, Parabon and others. It will be interesting to see if Millenium takes action against them.

    So you can see I am affected by software patents every day even as an academic. There are many others that Incyte and Millenium have that are troublesome to me in that they aren't really novel or inventive, but describe systems I have already built, published or deployed.

    Such general software patents that one can argue are "obvious" have prior art precedents that exist in open source projects some of which date back to 1995. The problem is that the patent office doesn't look in old source code. Please let us be clear. GENERAL software patents are troublesome and I agree with all people who hold this viewpoint on this thread.

    Now then the patent we have on the distributed folding alogorithm is NOT a GENERAL SOFTWARE patent like the Millenium patent I have described. It is an invention of a method to make protein structures that is novel, and our having a patent means that we have made proteins in a new way. It does not mean we have solved the protein folding problem.

    Please recall our very average CASP5 results. A solution to the protein folding problem is not in our grasp with this algorithm alone! As such the patent itself has little or no commercial value.

    The TRADES software package is avaliable to academics from our web site in executable form, and has been for several years now. We have never done anything to hinder anyone's pursuit of the protein folding problem. If you wish to use our algorithm in research, it is there, go and use it!

    To be even more clear where I stand on intellectual property, I would point out that our BIND.ca (Biomolecular Interaction Database) system has been put into a patent application in 1998, but we already released it under a GNU license (see Sourceforge.net the SLRI Toolkit) with the blessing of Mount Sinai Hospital (a nonprofit hospital).

    I had to argue why it should be made open source to a Hospital committee to get their approval. A public good database had to be open source! Still, a patent may be granted for the BIND schema, (not a GENERAL SOFTWARE patent) but we have already decided to release it as an open source project.

    So can anyone on this thread tell me of any other group in the world that has released their patented (or about to be patented) software into the public domain under the terms of the GNU license??? Someone on this thread speculated about it, but, ladies and gentlemen we have already done it.

    So then, If you believe that intellectual property protection can work for the benefit of research, that's what I believe. I patent software with a defensive strategy, not an offensive one. And, whenever I can convince the Mount Sinai Hospital committee on commercial development to drop their requirements for patenting and to release source code, I do, and have done so.

    We are not interested in slowing down research in protein folding. We have found with last year's CASP5 and other crunching that the problem is not in the algorithm to make protein structures (where the patent covers) but rather in having a protein fold scoring function that can choose the low-RMSD structure blindly from a 10 billion sized sample.

    Our patent does not cover anything about protein scoring functions. If you want to make one, you can, and you may use our algorithm to do so, freely, just download the TRADES package and go to it. If you are bright enough to invent a scoring function that works, then you'll discover we have a lot to offer in help. If anyone wants information on scientific papers to read to understand how to make scoring functions, post it here or write us and we will help get you started.

    I hope this makes my standpoint clear on the issue of software patents. We patented the TRADES algorithm because I would lose my job if I didn't follow Mount Sinai Hospital's intellectual property policy. BUT, our system is progressive and I have gotten permission to release other patentable project software (BIND.ca) under GNU. So that's my track record on the issue.

    Few other scientists have won such concessions from their host institutions. I do not pursue general software patents. Furthermore I am ready, eager and willing to assist anyone working in the public domain who needs prior art establishment to break offensive, and obvious general software patents as the one I described above. I know where a lot of prior art information exists.

    For those of you that have contribued in the past and those deciding to stick with us, thanks to all of you for your crunching support.

    Christopher Hogue
    Scientist, Samuel Lunenfeld Research Institue, Mount Sinai Hosptial and
    Assistant Professor, Dept. of Biochemistry, University of Toronto
    Samuel Lunenfeld Research Instittue and Assistant Professor, University of Toronto

  17. #17
    Thank you for stating your case.

    For some it might not be enough but for those of us who have dealt with both you and Howard since early in the life of the Distributed Folding project and have many reasons to trust you and few or none to distrust you, this should suffice.

  18. #18
    25/25Mbit is nearly enough :p pointwood's Avatar
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    A lot of other stuff is going on in my life and I'm pretty wasted, so this will just be a short notice...for now

    First, thanks for your great post, I'm glad to learn that software patents concerns you!

    Next, I would like to say that I do not distrust you or Howard. I respect you both a lot - I think you have done a lot to makes us, the contributers, welcome. It's one of the absolute main reasons I really like this project!

    And now it's way past my bedtime

    I'll try to post something tomorrow.
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  19. #19
    TeAm AnandTech Insidious's Avatar
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    A lot of other stuff is going on in my life and I'm pretty wasted
    Wasted? Ok, there's credibility

    Last edited by Insidious; 02-18-2003 at 09:09 PM.
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  20. #20
    Ancient Programmer Paratima's Avatar
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    Nah, that's too harsh. It's all just words. pointy's OK.

    Stress clouds the judgement and he's been stressed lately.

    Give him a chance to work his way back around.

  21. #21
    TeAm AnandTech Insidious's Avatar
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    Originally posted by Paratima
    Nah, that's too harsh. It's all just words. pointy's OK.

    Stress clouds the judgement and he's been stressed lately.

    Give him a chance to work his way back around.
    Fair enough.....

    however, I'm gonna leave up my original thought because it is pertinant.

    and if it matters, I think that it would be unfair to expect Howard (or any other scientific author) to eat peanut butter while the rest of the world lives well on the back of his hard work)

    $.02
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  22. #22
    25/25Mbit is nearly enough :p pointwood's Avatar
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    Insidious: I don't quite understand the problem with my previous comment

    First, I think you forget that not everyone live in the same timezone

    Second, you have no idea what is going on in my personal life right now or the reasons why I was "wasted" last night. I can, however, assure you that I wouldn't exactly describe my life as fun currently

    Paratima: Thx!

    and if it matters, I think that it would be unfair to expect Howard (or any other scientific author) to eat peanut butter while the rest of the world lives well on the back of his hard work)
    Absolutely not - I've not said that I expected that either. You have completely misunderstood my posts if that's your impression.

    ----

    Now, to continue the patent discussion. I actually didn't expect Howard or Christopher Hogue were the persons that made the decision about whether to apply for a software patent or not. It's a demand from the University/Hospital (I'm actually a bit confused what it is Howard and Christopher Hogue works for?).

    Most people think patents are a good thing and I think those that controls the University/Hospital aren't aware of the fact that that simply isn't true. The patent system doesn't work for software.

    Now, it is clear that Christopher Hogue isn't happy about the fact that they have to apply for software patents (unless I've completely misunderstood his post ). How do I as a participant of this project, make his claims that software patents doesn't help his research? The obvious thing to do is of course to tell them that (which I think I've done ) and to stop supporting the project based on this reason.

    Currently, I've stopped contributing to this project for exactly this reason. No, it most likely will not change anything, but doing nothing certainly doesn't change a thing either. To make a change, a lot of people would have to do the same as I.

    Christopher Hogue did bring forward a lot of good points in regards to their policy and that they simply can't afford to use this patent for anything but defensive.

    He also mentions a patent that he concerns him, but that they most likely wouldn't be sued because they don't have any money and therefore it would be pointless to sue them. Well, sometimes it is not entirely pointless - if your patent is dubious, then your best bet may be to sue someone that can't afford to pay for good legal assistance since that will make your chance of winning much better and give the patent a lot more credibility.
    Pointwood
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  23. #23
    First, let me just say that eveyone is entitled to their opinions and free to do what they want, support this project or not.

    That said, allow me to just reiterate that, even should we eventually completely solve the protein folding problem with an amazing new algorithm, all information pertaining to the method is or will be disseminated in scientific journals for other scientists to see and make use of as they please. A patent in no way prevents scientists from using or modifying/improving on our algorithm with their own ideas. What it does prevent is from someone making a minor change to our algorithm, building it into a commercial product and then selling it for profit (which only makes sense to me). Thus the existence of the patent on our algorithm (and note it is the algorithm that is patented, not the software - no mention of distributed computing is even mentioned in the patent) in no way impedes the progress of science or the sharing of information.
    Howard Feldman

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