tag:blogger.com,1999:blog-36768584.post5361204628350272040..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Obviousness: Rarely ObviousKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-36768584.post-16563428943687684732017-03-23T16:59:08.652-04:002017-03-23T16:59:08.652-04:00> You mean the people who put it into practice ...> You mean the people who put it into practice and are also funded by tax payers money? Idiot...<br /><br />I would not call those running universities idiots. Crooks may be. <br /><br />First they take huge cut (80-90%) from taxpayers money as "overhead" to pay the administrative overlords. Then they hire cheap slaves from India and China as graduate students to do the actual work. Counting nights and weekends those slaves work for, they may get paid $5/hr or less, while their liberal professors preach the virtue of $15/hr minimum payment to the sucker public. At the end, if the Chinese/Indian guy discovers something, the professors gets 1/3rd of the patent and the patent troll university administrators get another 1/3. So, the slave is essentially cut off from his discovery by 2:1 vote, because the professors always side with the administrators.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-50497019628690392682017-03-23T11:48:37.904-04:002017-03-23T11:48:37.904-04:00"despite priority date, claims can be added p..."despite priority date, claims can be added post fling under some patent authorities, the US included. So narrower claims can be added provided the initial filing was broad enough to encompass them. The initial fling would establish the priority date. If the claims were added post ONTs AGBT12 talk, to a broad initial filing, that would not be unusual. Looking at the revision history would reveal if this was the case or not."<br /><br />Added claims cannot claim the same priority date as the original filing.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-82320822000416069942017-03-23T11:48:09.459-04:002017-03-23T11:48:09.459-04:00> Detkin said. “A patent troll is somebody who ...> Detkin said. “A patent troll is somebody who tries to make a lot of money from a patent that they are not practicing, have no intention of practicing and in most cases never practiced.”<br /><br />That describes universities to a tee.<br /><br />It is also funny that his next step was to start a patent troll company named Intellectual Ventures :)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-36528592762730987402017-03-23T10:01:07.956-04:002017-03-23T10:01:07.956-04:00"If someone could theoretically carry out the..."If someone could theoretically carry out the method outlined in the patent using only a pen and paper, it shouldn't be patentable."<br /><br />I think that's what used to be called a "mental act". However, it seems the USPTO has a much lower bar.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-48314632163021000712017-03-23T07:50:21.457-04:002017-03-23T07:50:21.457-04:00> Computer industry has been patenting cryptogr...> Computer industry has been patenting cryptography algorithms and compression algorithms for a long time.<br /><br />Perhaps, but the people who write patents do attempt to structure them in such a way that it appears that they are more than just algorithms:<br /><br />US5533051 -- a method of operating a digital processing device for compressing data represented in digital form... a method of extracting redundancy from a stream of electrically encoded binary data<br /><br />US5724428 -- A simple encryption and decryption <i>device</i> has been developed ... a method of communicating information<br /><br />To a casual observer these don't appear to be pure algorithm patents, and that's frequently all that matters to get it past the patent examiners. Until a patent is tested by the courts, it's not correct to use the awarding of the patent as a demonstration of validity. To quote the top answer on the stackexchange post you linked:<br /><br />"""<br />Then there's also the problem that the people in the patent office are generally simply not qualified to determine whether a particular software invention is patentable or not, leaving it up to the courts to decide whether a patent was valid when the owner tries to assert their rights to it. That means if you're a small company and you "infringe" on an invalid patent, you likely don't have the resources to fight the patent anyway (even if it's invalid).<br />"""<br /><br />And from the second-top answer:<br /><br />"""<br />in the US Supreme Court case In re Bilski, the Court rejected the "machine-or-transformation test" as the sole test of patentability. (One of the Justices dissented from the opinion, stating that the Court did not go far enough in rejecting these kinds of patents wholesale.) The result is that many business method patents are now invalid, and the USPTO has begun denying software algorithms and other method patents - not all of them, but a few.<br /><br />I'd suggest going to Groklaw's Bilski page and reading more about it.<br /><br />It's worth adding that the more recent Alice Corp. v. CLS Bank International case, the Supreme Court recently overturned the CAFC's decision to affirm software patents. The patents cover what amounts to escrow, when done over the Internet. The Supreme Court held that merely adding "over the Internet" or "on a computer" is not enough to make a patent covering an abstract idea valid. This substantially narrows the field for software patents, but does not make them invalid.<br />"""<br /><br />My own interpretation of all of this is that a patent can't depend entirely on a software algorithm; there needs to be a component of the patent claims that depends on a non-algorithmic process or inventive piece of hardware (and a general-purpose computer is not sufficient for that). If someone could theoretically carry out the method outlined in the patent using only a pen and paper, it shouldn't be patentable.David Eccleshttps://www.blogger.com/profile/11754558756169247029noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-23723704502731427662017-03-23T06:40:12.857-04:002017-03-23T06:40:12.857-04:00> "Apart from legal bills which are astron...> "Apart from legal bills which are astronomically high for both I imagine. District court actions take years so it always comes down to who has most cash in the bank to see it through. I bet when a decision comes one will be long gone (my bet is PacBio as this looks like a desperate act from someone sinking)"<br /><br />I find comments about Pacbio's seemingly desperate last acts surprising especially if you compare it to ONT in the context of paying customers. Pacbio sells atleast 90mm USD of stuff every year. So it has paying customers and some of them have said they run all their machines non-stop 24hrs a day (Histogenetics etc), so it doesn't appear like these customers will just go away like that. <br /><br />If one was to guess ONT's revenues based on the update from Clive Brown (he reported that there were now 4000 minions, there were about 3000 last year, so an addition of 1000 ~ 1mm USD, one can guess the revenues to be under 5mm, even assuming a very generous usage, about 10k flow cells at the highest price - please do correct if you have a better number). This is unlikely to be commercially viable and that's the reason why the GridIon was launched pricing effectively the same thing for 25x the price, with Promethion also in the works and the Minion also available, a number of offerings suggesting a confused business model or some ingenious plan that only insiders are aware of.<br /><br />I think the 'desperation' that people read into Pacb probably has to do with it being publicly listed. Imagine ONT being publicly listed with revenues at 750k last year and about 5-10mm this year with operating margins around 25%.... On irrational (or rational for ONT bears) days the market might value it closer to 100mm than to 1000mm.<br /><br />The patent action can be simply interpreted as trying to disadvantage a potential competitor. Especially one that they claim has copied a previous patent on the hairpin to its advantage.<br /><br />It's probably fair to say, these are two closely matched competitors, ONT offering longer read lengths and promising higher throughput, lower accuracy with less reproducibility while Pacbio offers something more reliable, with not as exciting read lengths at a higher price for now.<br /><br />It's certainly not netflix vs blockbuster, if anyone has an illuminating comparison for this competition for a poor second place (vs Illumina) with another industry that would be v useful.<br /><br /><br /><br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-75439202794162564872017-03-22T17:40:24.609-04:002017-03-22T17:40:24.609-04:00Here is a totally unrelated quote:
Peter Detkin c...Here is a totally unrelated quote:<br /><br />Peter Detkin coined the term ‘troll’ to avoid more lawsuits: “We were sued for libel for the use of the term ‘patent extortionist’ so I came up with the ‘patent trolls’,” Detkin said. “A patent troll is somebody who tries to make a lot of money from a patent that they are not practicing, have no intention of practicing and in most cases never practiced.”<br /><br />Just saying, obviously nothing to see here...Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-61521264232998939592017-03-22T17:31:58.636-04:002017-03-22T17:31:58.636-04:00"What nonsense. "Open source" is no..."What nonsense. "Open source" is not a license to violate patents. Once again, you need to check the history of RSA cryptography algorithms and compression algorithms."<br /><br />I think his point was that if the customer infringes then they are hardly going to sue them as it is likely they also use their product or may in the future. In Life Sciences I am not aware of any company being bold/stupid enough to sue a university.<br /><br />One may argue that regardless Nanopore are still enabling infringement though so it is irrelevant.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-46419094696526853422017-03-22T16:31:30.502-04:002017-03-22T16:31:30.502-04:00> An algorithm on its own is not patentable:
T...> An algorithm on its own is not patentable:<br /><br />This appears like an uninformed statement. Computer industry has been patenting cryptography algorithms and compression algorithms for a long time.<br /><br />https://www.google.com/patents/US5533051<br /><br />https://www.google.com/patents/US5724428<br /><br />http://softwareengineering.stackexchange.com/questions/32482/can-an-algorithm-be-patented<br /><br />> Any of the supposedly patented base calling methods could be made by 3rd party academics under open source, in which case we assume pacB will then be suing US universities.<br /><br />What nonsense. "Open source" is not a license to violate patents. Once again, you need to check the history of RSA cryptography algorithms and compression algorithms.<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-32261983534927015792017-03-22T14:53:22.125-04:002017-03-22T14:53:22.125-04:00If ONT loses, its options in developing algorithms... If ONT loses, its options in developing algorithms will get reduced.<br /><br />An algorithm on its own is not patentable:<br /><br />http://yaroslavvb.blogspot.co.nz/2011/02/how-to-patent-algorithm-in-us.html<br /><br />https://en.wikipedia.org/wiki/Software_patent<br /><br />It needs to be combined into an invention in order to be eligible for a patent (or protection). If ONT uses a new algorithm on an existing [patented, or publicly known] device, it shouldn't be possible for a patent infringement to occur for patents with the new algorithm and a priority date after the creation/use of the existing device. I'm using "shouldn't be" rather than "isn't", because I'm very much not a lawyer, and what matters is what the lawyers are able to argue, rather than what armchair bioinformaticians believe.<br /><br />On the CRISPR outcome, according to Wikipedia "the Broad patents with claims covering the application of CRISPR/cas9 in eukaryotic cells was distinct from the invention claimed by University of California":<br /><br />https://en.wikipedia.org/wiki/CRISPR#Patents_and_commercialization<br /><br />To me, this means that the patent claims were not identical. This does not mean that the claims did not explore the same concept. While there would have been some overlap, it's the entirety of each claim that matters for patent infringement (presumably also including an obvious extension of a claim). If each patent had a non-obvious and different dependent component for all claims, it would be difficult to justify infringement.David Eccleshttps://www.blogger.com/profile/11754558756169247029noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-34976691669872533692017-03-22T12:02:17.290-04:002017-03-22T12:02:17.290-04:00"if ONT loses, its options in developing algo..."if ONT loses, its options in developing algorithms will get reduced."<br /><br />IF pacB has enough cash to last out the suit, and IF the patent is valid and holds up. The patent in question is only US although they are suiting ONT on 2D elsewhere but that now looks irrelevant. Any of the supposedly patented base calling methods could be made by 3rd party academics under open source, in which case we assume pacB will then be suing US universities.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-49973869173178149382017-03-22T11:58:17.675-04:002017-03-22T11:58:17.675-04:00"What I find interesting is that the battle i..."What I find interesting is that the battle is taking place entirely in Nanopore's side of the business"<br /><br />Apart from legal bills which are astronomically high for both I imagine. District court actions take years so it always comes down to who has most cash in the bank to see it through. I bet when a decision comes one will be long gone (my bet is PacBio as this looks like a desperate act from someone sinking)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-55470022624777130082017-03-22T11:01:09.321-04:002017-03-22T11:01:09.321-04:00In Silicon valley, patent/trademark battle had alw...In Silicon valley, patent/trademark battle had always been a way to delay competitors. Oracle and Google had been fighting on whether others can create Java-like language (different name, same APIs), because Oracle owns Java trademark. <br /><br />What I find interesting is that the battle is taking place entirely in Nanopore's side of the business. Even if ONT wins the battle, Pacbio will not have any impact on its own side of the business and IP ownership. OTOH, if ONT loses, its options in developing algorithms will get reduced.<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-36933801393034376852017-03-22T04:46:02.416-04:002017-03-22T04:46:02.416-04:00"So it would not appear the patent cribbed fr..."So it would not appear the patent cribbed from Oxford's presentation."<br /><br />despite priority date, claims can be added post fling under some patent authorities, the US included. So narrower claims can be added provided the initial filing was broad enough to encompass them. The initial fling would establish the priority date. If the claims were added post ONTs AGBT12 talk, to a broad initial filing, that would not be unusual. Looking at the revision history would reveal if this was the case or not.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-12310990187803674902017-03-22T04:33:17.574-04:002017-03-22T04:33:17.574-04:00you also got the question of enablement. Pacbio ha...you also got the question of enablement. Pacbio have not implemented any of the claims.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-32248971885278511332017-03-22T02:43:56.393-04:002017-03-22T02:43:56.393-04:00"Just to head off one rumor, I will note that..."Just to head off one rumor, I will note that PacBio's filing US20100331194, which I think is what established the priority date, long predates Oxford's electrifying 2012 AGBT presentation, and this application mentions N-mer methods and the range of algorithms described above."<br /><br />No, but their filing does follow hot on the heels of Illumina first investing in Nanopore. That must have really spooked them as the priority document looks like a brainstorm of anything they had seen, heard, or thought of relating to nanopores. They file it then they sit back and wait to see what Nanopore actually do in their product, from Nanopore's presentations and patent filings. Once PacBio know they can then file a stream of continuations specifically targeted to a key aspects. It is a well known trick and the USPTO is considering limiting the number of continuations to fight back against the patent trolls.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-56251586233555470622017-03-22T00:18:15.146-04:002017-03-22T00:18:15.146-04:00I have (unfortunately) had to read quite a few pat...I have (unfortunately) had to read quite a few patents lately. There is so much of what I would consider obvious crap out there, but our lawyers tell me that this is beside the point, that it is quite difficult to invalidate a granted claim. Yes, RNN are likely not in the PacBio patent (which by the way has a single primary claim, everything else is secondary) but I am guessing PacB's lawyers would argue that RNNs do little more than matching patterns that are determined by n-mers. ONTs latest material from. Just a few days ago state that R9 generates data from 5-mers. Good luck trying to explain to a jury the difference between the two approaches. Anonymousnoreply@blogger.com