Court: Essentially All Gene Patents Are Invalid

Association for Molecular Pathology and ACLU v. USPTO and Myriad (S.D.N.Y. 2010) (Judge Sweet)

In a powerful move away from standard thoughts on patentability standards, the district court for the Southern District of New York has held that Myriad's patents claiming "isolated DNA" do not qualify as patentable subject matter under 35 USC 101.

The claims-in-suit directed to "isolated DNA" containing human BRCA1/2 gene sequences reflect the USPTO's practice of granting patents on DNA sequences so long as those sequences are claimed in the form of "isolated DNA." THis practice is premised on the view that DNA should be treated no differently from any other chemical compound, and that its purification from the body, using well-known techniques, renders it patentable by transforming it into something distinctly different in character. Many, however, including scientists in the field of molecular biology and genomics, have considered this practice a "lawyer's trick" that circumvents the prohibitions on the direct patenting of DNA in our bodies but which, in practice, reaches the same result. The resolution of these motions is based upon long recognized principles of molecular biology and genetics: DNA represents the physical embodiment of biological information, distinct in its essential characteristics from any other chemical found in nature. It is concluded that DNA's existence in an "isolated" form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issue directed to "isolated DNA" containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 USC 101.

Similarly, because the claimed comparisons of DNA sequences are abstract mental processes, they also constitute unpatentable subjct matter under Section 101.

This decision is the result of an action brought by a coalition of scientists and public interest groups in 2009. The group challenged Myriad's breast cancer gene patents as violating both the patent laws and the US Constitution.

The Federal Circuit is likely to reverse this decision — opening the door to an important Supreme Court showdown.

Download Myriad Opinion

About Dennis Crouch

Law Professor at the University of Missouri School of Law. Co-director of the Center for Intellectual Property and Entrepreneurship.

233 thoughts on “Court: Essentially All Gene Patents Are Invalid

  1. Why is a polynucleotide different from all other molecules?

    Judge Sweet happened to issue this decision on March 29th, just a few hours before this year’s Passover Seder, when Jews traditionally ask “Why is this night different from all other nights?”

    His answer to the question posed above is “because it contains biological information.”

    Okay, that’s nice, but is that a scientific distinction that should support the statutory unpatentability of a novel and nonobvious polynucleotide, while allowing patentability of other natural products such as adrenaline, Taxol and tetracycline?

    I guess it would be if you accept as science that there’s a Higher Power that wrote the “information” into the genome. [Compare Richard Dawkins on The God Delusion with Robert J. Sawyer’s novel Calculating God.]

    But didn’t a federal judge hold in 2005 after a lengthy trial that “Intelligent Design is not science”? And, oh yes, wasn’t that conclusion vigorously spearheaded by …. the ACLU? link to en.wikipedia.org

    Hmmm.

    For some more on this, see my posting at link to elman.com

  2. This one almost slipped by, but IANAE is absolutely right again.

    Of course, this is obvious to us who are as good as Michael Jordan, but the rest of you can join RWA at teh snobbery festival and drink tea together wishing you were as good as you like to think that you are.

  3. I think Sweet hit upon the right characterization of the appropriate test.

    There’s a big difference between “this invention is patent-eligible because it is markedly different from anything found in nature” and “the minimal standard for patent-eligible subject matter is that it be markedly different from anything found in nature”.

    It’s like the difference between “Michael Jordan is a good basketball player” and “you have to be as good as Michael Jordan to be considered a good basketball player”.

  4. Ned said:

    “WER, did Diamond v. Chakrabarty hold that an “engineered” composition of matter that was identical with, and indistinguishable from, that found in nature to be patentable?”

    No. The Court in that case would have no reason to make such a holding, as the bacterium in question was engineered to do something it did not normally do.

    Here’s a description of the Chakrabarty invention from the opinion:

    “This human-made, genetically engineered bacterium is capable of breaking down multiple components of crude oil. Because of this property, which is possessed by no naturally occurring bacteria, Chakrabarty’s invention is believed to have significant value for the treatment of oil spills.”

    The issue was whether a living organism (i.e., a microorganism) was patentable subject matter under 101, and that was the holding. The rationale:

    “Judged in this light, respondent’s micro-organism plainly qualifies as patentable subject matter. His claim is not to a hitherto unknown natural phenomenon, but to a nonnaturally occurring manufacture or composition of matter — a product of human ingenuity “having a distinctive name, character [and] use.””

    The Court was careful to distinguish Funk, and that’s where the “markedly different characteristics” phrase was used:

    “Here, by contrast, the patentee has produced a new bacterium with markedly different characteristics from any found in nature, and one having the potential for significant utility. His discovery is not nature’s handiwork, but his own; accordingly it is patentable subject matter under § 101.”

    I think Sweet hit upon the right characterization of the appropriate test. The decision is most vulnerable to attack, I think, based upon the factual determination of whether the claimed DNA meets this text. I have been reading MM’s technical discussion on this point with great interest….

  5. TINLA IANYL

    The “experimental use” exception is not that broad, as you’ve discovered. See Duke Univ. v. Madey. It’s always been narrow, but universities have somehow always thought themselves to occupy some moral high ground that made them exempt. They don’t, but the PR hit and the samll dollars involved, plus the difficulty of detecting infringement usually makes them a poor target for an infringement suit.

  6. Wait, I may have spoken too soon. It looks like there was some case law that came alomg and changed things a bit, so the exception does nto reach back to cover activity trying to develop new drugs or tests, but only to seek FDA approval for a generic version of an existing drug prior to expiration of the patent. The same case law also says Universties aren’t protected under the experimental use exception becaeu the research is perfromed in furtherence of theior legitimate business, which is teaching students. So I may have to mea culpa. I’ll get back to you.

  7. For what is worse then disincentivizing further research into alternative tests? It is disincentivizing the kind of research that resulted in the original test.

    Worse still is disincentivizing the treatment or cure because someone has a patent on the test.

    I’m no biotech expert, but I question whether we’re giving a prize for reaching the finish line, or merely letting someone put up a barrier as he passes the first checkpoint along the way.

  8. That’s why I said it makes researchers immune. 271(e) is an experimental use exception. But running test procedures as part of research sounds like experimental use to me.

    If they had the data they needed, then they should have stopped testing. If not, then they should not have backed down in the face of a baseless threat.

    In either event, what they should not have done, and what I resent them doing, is whipping the scientific community into a furor in a misleading manner that counts on people misunderstanding the law to try and change the law in a way that will, in turn, disincentivize groundbreaking research by removing the promise of a dominant patent in the field.

    For what is worse then disincentivizing further research into alternative tests? It is disincentivizing the kind of research that resulted in the original test. Preventing patents on isolated genes disincentivizes that kind of research, when others can capitalize on that hard work to more cheaply develop a competing test by capitalizing on the hard work and resource expenditure of the original researchers.

  9. TINLA IANYL

    271(e)(1) doesn’t make universities immune. They have to be doing research to generate data for FDA approval. Here the universities were essentially running test procedures as part academic research not directed to FDA approval. Indeed, in some cases the testing was almost for profit in nature.

  10. Lurking less: 287(c) probably does not let doctors off the hook. Read the definition of “medical activity” in the statute:

    2) For the purposes of this subsection:
    (A) the term “medical activity” means the performance of a medical or surgical procedure on a body, but shall not include
    (i) the use of a patented machine, manufacture, or composition of matter in violation of such patent,
    (ii) the practice of a patented use of a composition of matter in violation of such patent, or
    (iii) the practice of a process in violation of a biotechnology patent.

  11. @ Moonpie for: “Here’s an experiment: find some tissue ‘in nature’ containing some dead smallpox and inject it into your body. Wait a couple weeks and let us know what happens. Then expose yourself to some ‘live’ smallpox vaccine.”

    I’m not feeling so good.

  12. Thomas,

    Congress passed a law, 35 U.S.C. 271(e)(1), that makes researchers in this area immune to patent infringement. The argument that Universities can’t perform research does not hold water. There is no ethical issue in that regard. What you are saying cannot be entirely correct.

    On the other hand, the problem for Universities is that the Universities will find it more difficult to license their patents on successful results of that research. Their licensees most likely will also have to obtain a license from Myriad, so long as the patent claim to the isolated DNA is in force. So, with diminished prospects of obtaining licensees, the profit motive is diminished for Universities, and the motivation to expend resources on the research is reduced.

    So, make no mistake. The motives of the Universities are not so pure. It’s greed, plain and simple. We used to live in a world in which the Universities performed research and published results and dedicated the knowledge to the public domain. They still have the capability to do that. They just don’t want to do that anymore.

  13. The result in this case should not be surprising in view of the facts. Research universities studying breast cancer issues were threatened by Myriad and, in fact, stopped their breast cancer research. There is an ethical issue here that screams for social responsibility and justice for the cause of unfettered medical inquiry into a devastating illness. While the District Court’s opinion may seem overly broad, I do not think that the overall result will be reversed. That overall result is one that most Americans would support.

  14. I am impressed with one Malcolm Mooney. Kudos.

    Wait, is NAL trying to make IANAE jealous?

    (Or is that Cranky? Or is this some type of incestuous thing, since IANAE is Malcolm, and Malcom is Cranky?)

    I need a scorecard – NAL, can you get me a scorecard?

  15. Re the novel properties of isolated DNA: try to do a BRCA assay with unisolated DNA. Go ahead – you won’t infringe! Not working for you? Could it have something to do with the “isolated” part?

    Judge Sweet relies heavily on old cases (noted by Ted in post #3), and he doesn’t care to read them too closely. Take the 1948 Funk Bros. case, holding a combination of bacterial strains to be unpatentable subject matter. Sweet relies on the what, but ignores the why: “Their use in combination does not improve in any way their natural functioning. They serve the ends nature originally provided and act quite independently of any effort of the patentee.” Does that really describe an isolated DNA sequence, used as a probe or primer?

    Sweet repeately cites American Fruit (1931), which held unpatentable an article of nature (oranges) to which another article of nature (borax) had been added: “Addition of borax … does not produce from the raw material an article for use which possesses a new or distinctive form, quality, or property. The added substance only protects the natural article … There is no change in the name, appearance, or general character of the fruit. It remains a fresh orange, fit only for the same beneficial uses as theretofore.” Again, hardly descriptive of an isolated DNA molecule.

    The CAFC will make short work of this decision.

  16. I ask myself, how in the world did we ever agree to let doctors off the hook?

    Posted by: Ned Heller | Apr 02, 2010 at 02:13 PM

    In the U.S., doctors are off the hook based on 35 USC 287(c). That section was added due to Pallin v. Singer, 1995 U.S. Dist. LEXIS 20824, 36 U.S.P.Q.2d 1050 (D.Vt. 1995), if you want to take a look.

  17. Nobody Asked

    Read the opinion. The ACLU is not a plaintiff. They are the public interest law firm representing the plaintiffs. The plaintiffs have standing. Their law firm does not need standing.

  18. Jim: As for the proposition that a physical embodiment of information is unpatentable, let’s hope Judge Sweet never gets hold of a Beauregard claim

    Truly, because in contrast to DNA, there is zero relationship between the structure of the computer-readable medium and the utility-imparting “information” recited in the Beauregard claim.

    The solution is in a clever design-around, competing technology, or legislation that curbs the scope of such claims (preferably without killing off the motivation to develop diagnostic DNA assays).

    Or the government could exercise its so-called “march-in rights,” created by those evil socialists Bob Dole and Evan Bayh, but as yet never exercised.

  19. From the point of view of a chemist, the DNA is not “isolated” or “purified” from nature — it’s chemically altered, cut out of the cell’s much longer DNA. Chemical bonds have been broken, the molecular weight reduced by orders of magnitude. It’s no longer associated with the regulatory regions that control expression in vivo. GF’s observation is on target: the isolated DNA in question is altered from its natural state to a greater degree than, say, isolated penicillin. Calling it “isolated” is hardly a “lawyer’s trick.”

    (As for the proposition that a physical embodiment of information is unpatentable, let’s hope Judge Sweet never gets hold of a Beauregard claim.)

    No question in my mind that the CAFC will shred this decision. If Myriad’s hegemony (and $5,000 price tag) over detecting BRCA genes in patients is a bad thing for society, the solution isn’t likely to be found in a courtroom. The solution is in a clever design-around, competing technology, or legislation that curbs the scope of such claims (preferably without killing off the motivation to develop diagnostic DNA assays).

  20. Malcolm: Brian has stated that the ‘utility’ is for diagnosing disease. Is that the utility you are going to use? I don’t see this ‘utility’ mentioned in Myriad’s composition claims, at least not the ones I’ve looked at recently.

    Well, detecting mutations that associated w/ increased risk of disease, yes, but still, interesting point. I think I am probably inferring too much about the Myriad claims from Judge Sweet. Myriad seems to have separated many of their isolated DNA claims from their method claims in separate patents, although one of the BRCA1 gene patents in question (282) also claims “A kit for detecting mutations in the BRCA1 gene”. Not sure if that qualifies for what Malcolm is saying. My understanding of all this may have improved, but it’s still quite poor…

  21. Hans, you and I seem to agree that the novelty is in the use of the information in some form of treatment. That should be claimed. But, as you said, since doctors are immune, treatment claims are valueless.

    I ask myself, how in the world did we ever agree to let doctors off the hook? At the time, I had some influence in various organizations considering the advisability of the proposed exclusion. I said nothing.

  22. Good point, Malcolm. The utility is not actually claimed (it is in the “infer” claim). So, I amend my point to the “disclosed” utility.

    Now, if the novel utility was somehow claimed, that should end the discussion.

  23. Ned:

    the Feds will have to hold that isolated DNA that encodes the same proteins as natural DNA is materially different in order to overturn Sweet. I think this test should focus on the claimed utility, and not on irrelevant structures that have do not affect the utility one way or the other.

    What is the “claimed utility” Ned? Please identify. And then explain how I can use the DNA in its natural state — in a cell, in a human body, bundled up in chromatin with billions of other nucleic acids, proteins, and other chemicals — for this purpose. If there is no ‘material difference’ between the DNA in its natural state and the claimed DNA, then it should be easy to explain.

    Brian has stated that the ‘utility’ is for diagnosing disease. Is that the utility you are going to use? I don’t see this ‘utility’ mentioned in Myriad’s composition claims, at least not the ones I’ve looked at recently.

  24. Ned: The question becomes whether the engineered composition is materially different. That is the question addressed by Sweet.

    If this test is correct, and I think it is, then the Feds will have to hold that isolated DNA that encodes the same proteins as natural DNA is materially different in order to overturn Sweet. I think this test should focus on the claimed utility, and not on irrelevant structures that have do not affect the utility one way or the other.

    Ned, this is essentially what I’ve been trying to figure out, whether or not the test needs to focus on the claimed utility, so thanks! Although I would say that it’s not necessarily the protein encoding per se, but the sequence information, whether it’s encoding a protein, a splice site, stop codon, or something like that.

    So I think I understand Sweet’s argument ok, but it will be interesting to see if he gets “slapped down” by the feds, as Malcolm thinks. Whether this is being properly handled under current law is still a bit beyond me, but I think I’ll be able to understand the Feds decision, when it comes.

    Thanks to Malcolm and everyone else for educating me. And glad I helped, Ned – I figured I was just freeloading…

  25. I’m trying to view this from the perspective of law, but it occurs to me that as a scientist, I would never think of DNA this way – isolated or not. Structure and function are inexorably linked. Judge Sweet seems to have proclaimed that with respect to DNA, they can be treated differently under the law, although seems to be arguing this only applies to DNA.

  26. Ned, re your 11:05 am post: go back to my original comment and you’ll see that I corrected my erroneous statement immediately afterwards. Good catch, though.

  27. Ned, in the U.S. you can patent a new use for an old compound in the form of a method. In the case of a therapeutic, such a patent, called a method of treatment patent, isn’t particularly valuable, because instead of suing the manufacturer of the drug for direct infringement, you have to sue for indirect infringement (can’t sue the doctor, because he/she has immunity). Other countries do not permit this. Practitioners in these countries tried to get around this prohibition with what became known as a “Swiss-type” claim. Instead of claiming a method of treatment, you would claim “use of drug x in the manufacture of a medicament for the treatment of y.” But the EPO’s Enlarged Board of Apppeal just killed this claiming strategy last month.

  28. I was struck by someone early in this thread that said the reason one patents the pre-existing composition of matter per se when one discovers a use for it, is that a later discoverer of a different use could be selling the composition, perhaps for a different use, and it would be difficult to show contributory infringement if the patent had to be limited to the discovered use.

    I find this rational bizzare. In Mayo, a researcher was accused of infringement for ordering the very same tests, but for a different purpose unrelated to the novel therapy. This illustrates, dramatically, the vice in the claims.

    I submit that one cannot patent an old composition (think gold) simply because one finds a new use for it. Ditto if I am the first discoverer.

    So, when I then say that instead of patenting the composition, I patent the engineered composition, should that end the conversation.

    Not really, at least according to Sweet and I think according to the Supremes in Chakrabarty. The question becomes whether the engineered composition is materially different. That is the question addressed by Sweet.

    If this test is correct, and I think it is, then the Feds will have to hold that isolated DNA that encodes the same proteins as natural DNA is materially different in order to overturn Sweet. I think this test should focus on the claimed utility, and not on irrelevant structures that have do not affect the utility one way or the other.

    Brian, thanks for your help on this.

  29. Nature is an awfully big place.

    Bucky balls are found in nature.

    All the transuranics are found in nature–at some diminishing small concentration somewhere.

    If you define your vessel small enough (say, the size of a single molecule), every organic molecule is found at high concentrations in nature.

    If you accept the judge’s reasoning, all compositions of matter are not patentable subject matter.

  30. WER said,

    “What is interesting is that the “markedly different characteristics from any found in nature” language is from Diamond v. Chakrabarty. Sweet’s decision is not contrary to that decision.

    What we have is a continuum between “as found in nature” (i.e., nonpatentable) and the genetically-engineered (i.e., patentable). Where along that continuum do you draw the line? Removal from the natural state? Isolation? Purification? Modification?”

    WER, did Diamond v. Chakrabarty hold that an “engineered” composition of matter that was identical with, and indistinguishable from, that found in nature to be patentable?

    I think Sweet’s point was that isolated DNA is the same as natural DNA — and if it is, one cannot patent it per se. One has to patent it’s use, which is the discovery.

  31. Malcolm said:

    ““Isolating” a sequence is just putting the information in a different place, encoded by a physically different set of atoms from the set you created it from.

    If you are the first to discover that a chemical contains new, non-obvious and useful “information”, then you can patent that chemical and prevent others from creating that chemcial using a “physically different set of atoms.”

    This cannot possibly be right. I find a new use for gold and I can patent gold?

  32. Max, I think you got it. While I side with Kevin and Malcolm on the “isolated DNA” issue, there is a reason that the biotechnology industry is pushing for a data exclusivity period of at least 12 years for new biologics, even though the data exclusivity period for new pharmaceuticals is only 5 years. This judge is absolutely no dummy.

  33. Readers, please excuse what follows. I am not a biotech-er and haven’t followed the thread properly. But I have just got through the decision, nearly to the end, and am so excited by Footnote 51 on page 123 that I want to share with you the following thought.

    Judge Sweet finds a sui generis way for DNA. For him, it is not a member of the class “chemical compound” so none of the jurisprudence on chemical compounds, compositions, combinations, collocations and mere mixtures applies to it.

    That leaves him free to dismiss the isolated DNA claims as claims directed to a carrier of information, rather than to a chemical compound. In handling the claims in this way, he puts no impediment in the way of future claims to any isolated compound except pieces of a genome.

    It puts the jurisprudence in line with TRIPS, and with those who view with distaste claims to software and business methods.

    Roll on Bilski, another Decision to be made on grounds of public policy.

    PS. Can anybody tell me why Stratton is not entitled to be named as one of the inventors?

  34. Brian wrote:

    “The “isolated” DNA carries the same protein coding information as the native DNA, and it is the protein coding information that tells us whether or not a deleterious mutation is present. ”

    No, that’s not true. It’s the reason why what used to be called “junk DNA” is no longer so-called. Protein-encoding is what genes do, but genes are not the sum total of DNA, and protein-encoding is not the sole province of genes (no matter how much this was thought 40 years ago).

    To carry Malcolm’s analogy further, for IMO it’s a good one, you get the protein if the letters “bow” appear in the gene. But only to a first approximation – it’s a naive view, that is no longer valid.

    There can be a bunch of exceptions that say “but not if situation X happens” and the rules for X are spelt out in DNA that is not covered by the relevant gene.

    Thus the information content of the isolated DNA – make protein BOW – may be quite different from in its native setting (in which case it could be ‘make BOW unless X, Y or Z is true’).

    (Not that it is a “may be”. Malcolm isn’t saying the information content is always different, I believe, since we don’t know enough about things to make that assertion yet.)

    Cheers, Luke

  35. I never thought I would be saying this, but I am impressed with one Malcolm Mooney.

    Kudos.

    Now if only the rest of the patent world were like this particular niche…

  36. Mean Gene Except that the bat doesn’t have as it’s sole utility being useful for telling us what type of tree it came from.

    Myriad’s claimed compositions also have more utility than “telling us where they came from.” If their only utility was to “tell us where they came from”, nobody would care about them.

    And by the way, most of Myriad’s claimed compositions “come from” a DNA synthesizer, if I’m not mistaken.

    I understand how the first person to isolate a gene may have had something patentable, but why would the next guy picking a different gene and isolating it be non-obvious?

    “I understand how the first person to isolate a cancer-preventing compound from a hundred trillion other compounds may have had something patentable, but why would the next guy picking a different compound and isolating it be non-obvious?”

  37. Brian The way it looks to me is that Myriad is claiming NOT to be claiming the BRCA1 gene as it exists in the cell, but because the protein coding information – the information being used to detect the presence of a mutation – has not changed, Judge Sweet is saying, yes you are.

    Judge Sweet may be saying that and that’s why Judge Sweet is going to get slapped down because this “logic”, if followed in other contexts, will prevent a lot of useful compositions from being patented.

  38. “but that’s like arguing that the “information content” of a baseball bat is “latent” in a tree trunk.”

    Except that the bat doesn’t have as it’s sole utility being useful for telling us what type of tree it came from. I understand how the first person to isolate a gene may have had something patentable, but why would the next guy picking a different gene and isolating it be non-obvious? I admit I’m not a bio guy. Does the method for isolating one gene not work for any other genes?

  39. It’s relevant because Myriad is NOT claiming the BRCA1 gene as it exists inside the cell.

    The way it looks to me is that Myriad is claiming NOT to be claiming the BRCA1 gene as it exists in the cell, but because the protein coding information – the information being used to detect the presence of a mutation – has not changed, Judge Sweet is saying, yes you are.

    But recognize that we are really talking about, at least in the composition claims, is structure, which can certainly be used to store “information”, but which is *properly* claimed and *properly* examined based on its structure.

    Is this another way of saying that this argument is properly handled under the purview of non-obviousness? ‘Cause I can totally dig that…

  40. I think I explained that: it’s the “information content” that determines how, when, and where any protein encoded by the series of nucleotides is to be expressed. You can argue that the “information content” of the “naturally occuring gene” is “latent” in relation to the information content of the “isolated gene” but that’s like arguing that the “information content” of a baseball bat is “latent” in a tree trunk. On some philosophical level, the argument might be correct, but it opens up a nasty can of worms in the patent context.

    This is really not what I’m arguing – or, to be more accurate, the point I am trying to discuss. You’ve explained what you mean by “information content” above, but I’m not buying that it’s relevant to the argument that DNA carries certain biological information, and that this information is not in any way altered by the “isolation” that Myriad has done. This is the argument that I understand Judge Sweet to be making. (and to be fair, that I was making, and am now trying to avoid making)

    More precisely, it is not the “how, when, and where any protein encoded by the series of nucleotides is to be expressed” that the claim of non-novelty seems to rest on, but the what – the protein itself. The “isolated” DNA carries the same protein coding information as the native DNA, and it is the protein coding information that tells us whether or not a deleterious mutation is present. The argument that is being made is that since this information is not changed by isolation and is not novel, then the isolate is not patentable. Now, this may not be a valid legal argument, but it does argue against deploying the “information content” of the “naturally occurring gene” as an argument in defense of the patent.

  41. Brian See, this is where I think people like me are losing you. Precisely what information content are you referring to?

    I think I explained that: it’s the “information content” that determines how, when, and where any protein encoded by the series of nucleotides is to be expressed. You can argue that the “information content” of the “naturally occuring gene” is “latent” in relation to the information content of the “isolated gene” but that’s like arguing that the “information content” of a baseball bat is “latent” in a tree trunk. On some philosophical level, the argument might be correct, but it opens up a nasty can of worms in the patent context.

    Sure, the in vivo relationships of DNA can define how that DNA is expressed in the cell, but I still don’t understand why this is relevant to the Myriad case.

    It’s relevant because Myriad is NOT claiming the BRCA1 gene as it exists inside the cell. It is claiming an isolated gene which is different because the “information content” of an isolated gene is different from the “information content” of the same gene in its natural setting, as you just admitted. But recognize that we are really talking about, at least in the composition claims, is structure, which can certainly be used to store “information”, but which is *properly* claimed and *properly* examined based on its structure.

    Myriad is testing for mutations.

    That’s right. But Myriad’s patent rights don’t cover the genomes of the people who have those mutations (or those who don’t have them). They do own rights to certain reagents and certain methods that can be used to detect those mutations. I suspect some of those rights were carelessly granted but the mere fact that they relate to the detection of mutations that occur naturally doesn’t mean that the patents are invalid, per se.

    For what it’s worth (and not to change the subject) but I do believe that if a naturally occuring gene has been identified in the prior art (e.g., by the whole sequencing of a genome accompanied by a computerized analysis of the codon/promoters etc) then its subsequent patentability in isolated form (including expression vectors) should be precluded. Non-obvious methods of using that isolated gene or its protein product, if any — another matter entirely.

  42. 6: What if the novel printing press was not “markedly different” from the old one? Does the analysis change if the old one also occured in nature? What if the new printing press is the old printing press with a few (non-function critical?) bolts taken out?

    You tell me, 6. You’re the Examiner. Seems to me these are factual questions of the sort that would preclude a one-size-fits-all conclusion of the sort proferred by Judge Sweet.

  43. I think the “diagnostics community” needs to get its act together and deal with the situation then.

    True enough. It won’t, though. There’s always somebody at the top who thinks they might soon be the beneficiary of one of these patents.

  44. The “information content” of a defined series of nucleic acids is inextricably linked to its structure and that includes the structure of any nucleic acids and other molecules that are adjacent to the nucleic acids.

    See, this is where I think people like me are losing you. Precisely what information content are you referring to? Sure, the in vivo relationships of DNA can define how that DNA is expressed in the cell, but I still don’t understand why this is relevant to the Myriad case. Myriad is testing for mutations. Mutations are changes in the base pair sequence, regardless of the presence of repressors or response elements or anything else that isn’t there in the tube containing the “isolated” DNA.

    To (dangerously) extend your analogy, Myriad isn’t trying to tell people whether you should be using a violin bow or bowing to your master, it’s telling people that they’ve written “bog” instead of “bow” (or pub ogner).

  45. Brian: however, it seems that a better way to think about it would be that they’ve received a patent so overly broad as to effectively rule out anyone else working with the sequence. Judge Sweet seems to have closed the loop for us here, handing down a finding that rules on what Myriad’s patents effectively are doing rather than what they specifically say. Thus, as you say, they are making new law.

    Am I getting closer?

    I think so. The problem here was not created by the law which allows one to patent novel and non-obivous isolated nucleic acids encoding genes, but by a patent office which was notoriously lax in its enforcement of the laws which prevent applicants from obtaining patents on overly broad composition claims or (in the case of some of Myriad’s method claims) claims which cover the mere act of thinking about information disclosed in a patent specification.

    My understanding is that they have used the threat of litigation to prevent the development of tests – commercial and clinical tests, that is, not academic research – that would catch mutations that their test is known to miss, based upon their sequence claims. I can’t really document this for you, but it is generally held to be the case in the diagnostics community (they are one of a few companies who are considered better at defending their patents than they are at testing).

    I think the “diagnostics community” needs to get its act together and deal with the situation then. There are a number of ways to invalidate annoying patents and even more ways to quiet an obnoxious barking dog.

  46. “But this isn’t true. The “information content” of a defined series of nucleic acids is inextricably linked to its structure and that includes the structure of any nucleic acids and other molecules that are adjacent to the nucleic acids.”

    Mhmmmmmmm. I think it is at this point where most people don’t understand how this could be true. If the introns (I think that was the term for the “nucleic acids and other molecules” or was amongst them) count towards the informational content then how is the cDNA truly representative of the BRCA 1/2? Seems to be logical that the only information you’re interested in is the part that is in the non-intron part, which is the same part as comprises the cDNA.

    “The relationship of a defined DNA sequence to another sequence in a cell can determine whether the defined sequence can be expressed as a functional protein, or whether it is not expressed at all, or whether it is expressed as a different protein based on which particular nucleic acid in the defined sequence is used as the starting site for “translation” of the DNA.”

    So the question is then, does the naturally occuring sequence with all the junk still in it behave in the same way as cDNA of the same sequence does in all (substantially all?) instances? The answer to this question determines whether or not the judge decided correctly. If yes, then he was right. If no, then there is a good chance he was wrong.

    “But so what? Nobody would argue that a novel printing press is not patentable just because it prints pamphlets that are identical to previously known pamphlets, especially if the novel printing press can be used to print 10 or 100 or 1000 more such pamphlets in half the time.”

    What if the novel printing press was not “markedly different” from the old one? Does the analysis change if the old one also occured in nature? What if the new printing press is the old printing press with a few (non-function critical?) bolts taken out?

  47. I’m going to assume you didn’t purposely ask a question that you knew contained a false premise. That’s a real waste of time.

    Sorry, you were the victim of a poorly edited paragraph, I meant to refer to my claim that only the sequence has utility, which I think I edited out there…

    But I greatly appreciate your contribution here. I am coming away much better informed, and I hope I am not wasting your time.

  48. Brian, the smart people at the PTO and the Federal Circuit are well aware of the ‘distinct characteristics’ of DNA. Search “MPEP” and “nucleic acid” and you’ll see what I mean. There is really nothing new here, except a bunch of people confused about the law (that would be you, sorry) rushing in to complain about it.

    Fair enough, although to be fair, I’m not rushing in to complain so much as rushing in to ask if there was anything new here, and finding the discussion a bit confusing. So, asked and answered…

    Absolutely.

    Is Myriad’s “litigation strategy” to sue anyone who synthesizes BRCA1 or who studies the prevalence of particular mutations in BRCA1 in people with breast cancer? That was not my impression. If I’m wrong, let me know.

    My understanding is that they have used the threat of litigation to prevent the development of tests – commercial and clinical tests, that is, not academic research – that would catch mutations that their test is known to miss, based upon their sequence claims. I can’t really document this for you, but it is generally held to be the case in the diagnostics community (they are one of a few companies who are considered better at defending their patents than they are at testing). It is certainly possible that these claims are overblown, but so far no one else has been able to offer tests for the mutations that Myriad’s test doesn’t cover.

    In looking into this – and with your clarifications – I’m beginning re-evaluate my thinking about this. I think it seems to me, Judge Sweet, and plenty others (usually scientists) that Myriad’s patent claims essentially claim a patent on the gene sequence, which is neither novel nor non-obvious. In looking a little further into the actual patents, however, it seems that a better way to think about it would be that they’ve received a patent so overly broad as to effectively rule out anyone else working with the sequence. Judge Sweet seems to have closed the loop for us here, handing down a finding that rules on what Myriad’s patents effectively are doing rather than what they specifically say. Thus, as you say, they are making new law.

    Am I getting closer?

  49. By analogy (and I recognize the danger), you are essentially asserting that the “information content” of the letters “bow” is the same whether it is used in the sentence “Where is my violin bow” or in the sentence “Bow down to your master” or in the sentence “bow wow” (suggested by Fido).

    I forgot to add: “The pub owner is drunk.”

  50. Ned: Malcolm, et al. on the Sweet will be overturned side of the fence, it strikes me that Sweet is fundamentally correct if one makes the assumption that DNA is not patentable regardless of the discovery of a utility for the DNA information.

    Confusing, Ned. Is that an assumption, or is it the conclusion of some argument that someone may or may not have already presented?

    The isolated DNA does not change the information content of the DNA at all.

    But this isn’t true. The “information content” of a defined series of nucleic acids is inextricably linked to its structure and that includes the structure of any nucleic acids and other molecules that are adjacent to the nucleic acids.

    There is an entire subfield of biology devoted to the study of gene silencing, where the “information content” of nucleic acids is hidden due to the position of the DNA in the chromosome, or the timing of its synthesis.

    The relationship of a defined DNA sequence to another sequence in a cell can determine whether the defined sequence can be expressed as a functional protein, or whether it is not expressed at all, or whether it is expressed as a different protein based on which particular nucleic acid in the defined sequence is used as the starting site for “translation” of the DNA.

    By analogy (and I recognize the danger), you are essentially asserting that the “information content” of the letters “bow” is the same whether it is used in the sentence “Where is my violin bow” or in the sentence “Bow down to your master” or in the sentence “bow wow” (suggested by Fido).

    Now it is true that in Myriad’s case their claims cover an isolated gene that could be used to produce a BRCA1 gene product that has the same sequence as the BRCA1 gene product produced in the cell. But so what? Nobody would argue that a novel printing press is not patentable just because it prints pamphlets that are identical to previously known pamphlets, especially if the novel printing press can be used to print 10 or 100 or 1000 more such pamphlets in half the time.

  51. How do you tell a male chromosome from a female chromosome? – Pull down their Jeans… bad, I know.

    I’m interested in seeing how this plays out with Venture Capital backed biotechs who’s IP is completely wrapped around a family or cluster of genes and related pathways…

  52. Malcolm, et al. on the Sweet will be overturned side of the fence, it strikes me that Sweet is fundamentally correct if one makes the assumption that DNA is not patentable regardless of the discovery of a utility for the DNA information. The isolated DNA does not change the information content of the DNA at all.

    We have discussed whether there is an patent exception to patenting DNA per se as opposed to its use in a new process or method. I think the there is. DNA, like a law of nature, exists and is not made by man. In this sense, it is not and cannot ever be “new.” This is why the law requires one to patent its use, not the preexisting DNA itself.

    This case has all the earmarks of a case that will soon find itself before the Supreme Court regardless of what the Federal Circuit does. I say this because of the importance of the subject matter to the nation.

  53. With regard to the gene claims, there are two steps to consider.

    First, what standard or test do you use for the natural product exception? Looking to several SCOTUS decisions, including Diamond v. Chakrabarty, Judge Sweet determined (as paraphrased by me) that the appropriate test was whether the invention had “markedly different characteristics” from the natural product (i.e. had a new or distinctive form, quality, or property). Mere purification of a natural material would not make the purified product patentable unless it resulted in properties and characteristics that were different in kind from those of the known product rather than in degree.

    This is arguably supported by the cases, although as EG posts above, reasonable legal minds can disagree. This case is going to require digging into some obscure SCOTUS opinions.

    What is interesting is that the “markedly different characteristics from any found in nature” language is from Diamond v. Chakrabarty. Sweet’s decision is not contrary to that decision.

    What we have is a continuum between “as found in nature” (i.e., nonpatentable) and the genetically-engineered (i.e., patentable). Where along that continuum do you draw the line? Removal from the natural state? Isolation? Purification? Modification?

    The second step then is to apply whatever test you come up with to the claims in question. This requires a factual analysis of what is meant by “isolated” DNA, etc.

    With regard to the method claims, Judge Sweet correctly applied applicable law (Bilski). We all know that Bilski is on appeal to SCOTUS, of course, but based upon the justices comments during oral argument, does anyone really think that they’re going to make it easier to get a method claim? While the machine-or-transformation test may soon be moot, I don’t think the method claims in question will survive whatever the justices come up with in Bilski.

  54. ****
    So what happens now to Gene Patents? do they just sit while this is overturned or not?
    ****

    Depends on whether or not they are litigated in Judge Sweet’s Courtroom.

  55. I think a lot of the criticism of these types of claims is fueled by poor understanding of the relevant laws.

    There is really nothing new here, except a bunch of people confused about the law (that would be you, sorry) rushing in to complain about it.

    From the department of redundancy department.

  56. Brian I realize I worded that strongly, but I did it purposely.

    I’m going to assume you didn’t purposely ask a question that you knew contained a false premise. That’s a real waste of time.

  57. Brian: It occurs to me to ask, however, if the fact that Judge Sweet seems to have thrown down a gauntlet here with respect to how DNA is treated in the law is a big deal in patent law? The Judge asserts that DNA is “distinct in its essential characteristics from any other chemical found in nature.” Setting aside for the moment the glaring omission of RNA, is there any chance that DNA will be understood as having distinct characteristics which necessitate different treatment under the law from epinephrine or digitalis etc.?

    Brian, the smart people at the PTO and the Federal Circuit are well aware of the ‘distinct characteristics’ of DNA. Search “MPEP” and “nucleic acid” and you’ll see what I mean. There is really nothing new here, except a bunch of people confused about the law (that would be you, sorry) rushing in to complain about it.

    Wow! Is Myriad claiming they’ve changed the hydrogen-bonding properties of DNA?

    No.

    Do they have previously unknown base pairings?

    Depends on what you mean by “previously unknown base pairings.” My understanding is that Myriad believes that it was the first to synthesize and describe certain chemical compositions that could be used to diagnose and study breast cancer in humans. The law doesn’t require that a composition needs to change our understanding of fundamental chemical principles in order to be patentable. It just requires that the compositions are new, useful and non-obvious.

    If Myriad were relying on the hydrogen-bonding properties of their molecule, then wouldn’t others be able to come along and offer other tests using the hydrogen-bonding properties of other molecules that match BRCA mutations that increase the risk of breast cancer but weren’t discovered by Myriad and are currently not offered by Mryiad?

    Absolutely.

    Myriad’s business model and their litigation strategy (i.e. they won’t let other BRCA tests be developed)

    If that is an accurate statement of Myriad’s “litigation strategy” then Myriad will likely see more of its claims invalidated as it tries to stretch the scope of those claims beyond what is supported.

    Is Myriad’s “litigation strategy” to sue anyone who synthesizes BRCA1 or who studies the prevalence of particular mutations in BRCA1 in people with breast cancer? That was not my impression. If I’m wrong, let me know.

  58. The question whether “isolated DNA” is different from DNA in nature simply turns on what “isolated” means in this context. According to the Glossary of Judicial Claim Construction from Pub Pat, caselaw indicates that it means separated from the other DNA and present in higher concentration, but does not require purifying. I don’t know for sure, but I think that means more than just restricted at cites to either side of the DNA sequence, so as to separate it from other parts of the sequence, or produced from the protein, as might occur in nature. My understanding of that part is a bit shaky, since I am not a biotech practitioner. It does seem to mean that the amount of that DNA sequence is in much higher concentration in the sample than occurs in nature. So, I think we must be talking about a PCR product here. I don’t think I see another interpretation. The Pub Pat Glossaries are available here:

    link to pubpat.org

    If it is the case that the isolated sequence is really a claim to the PCR product, and if they only disclosed PCR, and if someone came up with another way of achieving the isolated product, then there might be a written descrioption issue that would invalidate the claim.

    I don’t think it is correct that the patentee can phohibit development of other types of tests. Didn’t Congress pass a law specifically immunizing researches from infringement of these tyopes of claims. I think a lot of the criticism of these types of claims is fueled by poor understanding of the relevant laws.

  59. Ned: Isolation is apparently necessary for identification of what the DNA is and, if I understand this correctly, isolated DNA is different from naturally occurring DNA in a number of physical ways. Right?

    Well, this is where I have a hard time. Basically, my answer is no, not really, but I understand why in the context of IP you might want the answer to be yes. So I can accept that isolated DNA can be considered as being “different” from native. What I hear and read, however, are a lot of explanations that use these various differences to elide the fact that Myriad seems to have patented a sequence of DNA base pairs which is not at all novel.

    MM: Really? They aren’t relying on the hydrogen-bonding properties of their claimed molecules?

    Wow! Is Myriad claiming they’ve changed the hydrogen-bonding properties of DNA? Do they have previously unknown base pairings? I realize I worded that strongly, but I did it purposely. It boils down to this: No sequence, no test. If Myriad had found a way to alter the hydrogen-bonding properties (or any other property) that allowed them to detect BRCA mutations, then we wouldn’t be having this discussion.

    Let me try and clarify by asking a question. If Myriad were relying on the hydrogen-bonding properties of their molecule, then wouldn’t others be able to come along and offer other tests using the hydrogen-bonding properties of other molecules that match BRCA mutations that increase the risk of breast cancer but weren’t discovered by Myriad and are currently not offered by Mryiad?

    Both Myriad’s business model and their litigation strategy (i.e. they won’t let other BRCA tests be developed) suggest that their IP claim is, as Judge Sweet said, about DNA as “the physical embodiment of biological information”, rather than any other physical characteristic that “isolated” DNA has been argued to have.

    That being said, your clarification has been very helpful here, so thank you! Even coming at this from a scientific perspective, which I have, I can now see how, even if you accept what I’m saying, this can (should?) be dealt with as a matter of obviousness and not composition – win!

    It occurs to me to ask, however, if the fact that Judge Sweet seems to have thrown down a gauntlet here with respect to how DNA is treated in the law is a big deal in patent law? The Judge asserts that DNA is “distinct in its essential characteristics from any other chemical found in nature.” Setting aside for the moment the glaring omission of RNA, is there any chance that DNA will be understood as having distinct characteristics which necessitate different treatment under the law from epinephrine or digitalis etc.?

  60. Brian

    What I don’t understand is why the fact that none of those properties has anything to do with the utility for which Myriad uses their patent(s) is critical to the validity of those patent(s).

    I tried to parse this but I failed, Brian. Sorry.

    I will tell you that the law allows a composition claim to be invalidated as obvious even if the prior art suggests a different use for the claimed composition than that taught by the patentee. But for whatever reason, Judge Sweet chose to not to deal with obviousness and instead created his own law. Not a wise move.

    Myriad is in the business of telling women whether or not the BRCA genes in their bodies carry some of the known mutations that increase their risk of breast cancer. In this capacity, it is the sequence information, and no other aspect of the molecule, that allows them to do this.

    Really? They aren’t relying on the hydrogen-bonding properties of their claimed molecules?

  61. All that other excremental baloney… makes a focused discussion of any particular legal issue… that much more difficult.

    I guess there is a reason they say bad facts make bad law.

  62. 6: Actually MM, the patentdocs just posted a page about how at least some of the claims at issue are actually anticipated by some database we had in 1994. At least I think that’s what the article is saying.

    6, I’ve read it. I’ve said before (many times) that a lot of Myriad’s claims are junkk. They don’t even try to claim a novel gene-encoding nucleic acid composition, but rather seem to be drawn to groups of billions or trillions of oligos that encode for peptide fragments of the protein encoded by those genes. Those claims are crxp and should never have been issued by the PTO in the first place.

    All that other excremental baloney in Myriad’s patents makes a focused discussion of any particular legal issue (e.g., “can you patent an isolated newly discovered gene”) that much more difficult.

  63. “What is being claimed is an isolated chemical composition that has properties which differ from those found in any known “natural” composition.”

    Actually MM, the patentdocs just posted a page about how at least some of the claims at issue are actually anticipated by some database we had in 1994. At least I think that’s what the article is saying.

  64. “Well then maybe a law could be enacted to make the generic maker pay a fee or a tax. Like a license to the company that made it in the beginning? So then they could get there money back that way?”

    Ummm… they can license the patent.

  65. Myriad didn’t invent a new process for isolating genes or wasn’t the first to synthesize cDNA, were they? If not, why would isolating a specific gene be non-obvious? They discovered a correlation that existed in nature. Laudable, but not patentable. Why should they then be allowed to own the corresponding cDNA copy of the gene? As many others have said, the only utility of the proxy is for its direct link to the actual naturally occurring gene.

    Pick a gene, any gene, patent it, and camp it. If you’re lucky, some correlation between that gene and something of note exists, and when somebody discovers it, you could become rich! DNA campers – the updated version of WWW domain name campers.

  66. The comment about good luck cancer patients couldn’t be further form the truth.

    Research is completly stifled by gene patents as the monopoly granted is way too broad and strangles any form of competition at birth.

    Drug companies are there to make as much money as possible, the fact that they’ve managed to massage the system into getting these patents in the 1st place just shows easy it is given enough money and influence to get patents through no matter what thier validity.

  67. What I don’t understand is why the fact that none of those properties has anything to do with the utility for which Myriad uses their patent(s) is critical to the validity of those patent(s)

    per chance one needs to read teh claim as a whole?

  68. Ok, Dr. Patent,

    Please explain to me how the ACLU has standing? Are they anticipating a suit as an infringer which would warrant a DJ action, which is what Medimmune is about.

    Or, can standing be granted to them because of public policy grounds, like in the present case?

    Please enlighten me on the concept of how a party who will never be subjected to an infringement suit has standing?

  69. Well then maybe a law could be enacted to make the generic maker pay a fee or a tax. Like a license to the company that made it in the beginning? So then they could get there money back that way?

  70. People who think that there is a standing issue here either (1) haven’t read the opinion, (2) don’t understand what standing is, or (3) don’t understand what the Supreme Court’s Medimmune decision did to the law regarding DJ jurisdiction.

    Most likely all of the above.

  71. Sarah,

    Without patents, drug company R&D stops because it and the clinical testing that are needed to get FDA approval are so expensive. Without the patent, as soon as a new drug is sold, a generic company figures out what it is and starts competing. The original company never makes enough money to recover their investment. Since everyone knows this before the r&d starts, it never gets started.

  72. Brian, you make a good point about the “differences” being related to the utility. I believe at least in Parke-Davis, the differences were directly related to the utility. Unpurified adrenaline did not have the same utility as purified adrenaline.

    Isolation is apparently necessary for identification of what the DNA is and, if I understand this correctly, isolated DNA is different from naturally occurring DNA in a number of physical ways. Right?

  73. Brian, in quoting MM:

    “If you are the first to discover a chemical containing new, non-obvious and useful “information”, then you can patent that chemical…”

    you alight upon the point of most sensitivity.

    Why does the inventor get to monopolise the compound, per se, for 20 years or more? Why not give out monopolies limited to the specific utility? Wouldn’t then the scope of protection be more commensurate with the magnitude of the inventor’s contribution to the art?

    This is a public policy matter. Europe still gives protection for the compound, per se. But with the EPO’s “Problem and Solution Approach” to obviousness, it would be easy to cut the scope back to the particular utility, using the obviousness tool (ie, the compound, per se, is obvious).

  74. Hey, MM, thanks for responding.

    I understand that what is being claimed is an isolated chemical composition that has properties which differ from those found in any known “natural” composition. What I don’t understand is why the fact that none of those properties has anything to do with the utility for which Myriad uses their patent(s) is critical to the validity of those patent(s). It is the sequence, and only the sequence that has utility here. Several commenters have pointed out differences (it’s a salt, it’s not associated w/ any proteins, it can be put into a vector, etc.), but Myriad is not in the business of using DNA as salts or in plasmids or anything else that the “isolation” of the BRCA1&2 genes conceivably imparts. Myriad is in the business of telling women whether or not the BRCA genes in their bodies carry some of the known mutations that increase their risk of breast cancer. In this capacity, it is the sequence information, and no other aspect of the molecule, that allows them to do this. As you say, “If you are the first to discover a chemical containing new, non-obvious and useful “information”, then you can patent that chemical…” Fine, but so far no one here (or anywhere else I’ve read) has produced a compelling argument that the “information” contained in the BRCA1 gene “isolate” is new. It’s not. It’s the same information that is in the women who are worried about their risk of breast cancer – it has to be, or the test would not be able to tell us what it is designed to tell us. This is pretty much what judge Sweet says, and while I am pretty firm on the reason why the good judge is right, I am interested in why he/she may not be right as a matter of law.

    So no, I don’t understand why kids are grounded when they take the car for a drive without permission, as I am not fully aware of the rules these kids are bound by in regards to driving the car. I’m not really interested if they get grounded or not, I’m more interested to know how well (or not) the rules are consistent with sensible parenting.

  75. The issue that is scary here is that Judge Sweet has allowed parties to challenge a patent without being a party to a suit. So, I guess the ACLU or other party can challenge any patent without using the procedures that already exist (3rd party reexamination). Just sue the USPTO and the owner of the patent in a Federal Court.

    I would love to read a decision from the Fed Cir on the standing issue, or even the Supreme Court.

  76. A correction …

    I wrote : If you are the first to discover that a chemical contains new, non-obvious and useful “information”, then you can patent that chemical and prevent others from creating that chemcial using a “physically different set of atoms.”

    Should be: If you are the first to discover a chemical containing new, non-obvious and useful “information,” then you can patent that chemical and prevent others from creating that chemical using a “physically different set of atoms.”

  77. Brian: If the BRCA1 and 2 gene sequences didn’t exist in nature, they would have zero utility.

    The sequence information is not what is being claimed. What is being claimed is an isolated chemical composition that has properties which differ from those found in any known “natural” composition. Are some properties similar? Yes, but so what?

    “Isolating” a sequence is just putting the information in a different place, encoded by a physically different set of atoms from the set you created it from.

    If you are the first to discover that a chemical contains new, non-obvious and useful “information”, then you can patent that chemical and prevent others from creating that chemcial using a “physically different set of atoms.”

    If doing that makes it fundamentally different, then I’m going to argue that all my old Napster mp3s are “isolated”.

    Okay. I’m going to refer to my phone as a chicken. Now what?

    I think that if the law were to hold that “Myriad’s “isolated” BRCA1 and BRCA2 gene sequences are also “novel” as they don’t exist in nature”, then the law would be fundamentally in error.

    The word “novel” accurately describes something that did not previously exist. Useful compositions that did not previously exist and which are properly claimed (by describing their structure in terms that are understood by those skilled in the art) are patentable. I don’t think this is a “fundamental error” in the law, as the law has proven useful for encouraging the development of new and useful compositions of matter. Perhaps there are policy reasons that you disagree with the way that the law enables patents to be obtained on nucleic acid sequences. That’s a great issue for Congress to tackle (although I’d rather see other reforms take place first).

    if Sweet’s opinion is likely to be reversed, I’m trying to figure out why…

    Unfortunately, Sweet’s opinion is likely to be reversed for reasons that have little to do with whether the claimed compositions and methods are “novel” or not. Do you understand why kids are grounded when they take the car for a drive without permission? If so, then you should be able to understand why Sweet is likely to be reversed.

  78. Ned, I’m not sure what you are asking with the “pure” and “concentrated” question. As for the other question, “cDNA” is just a term of art to describe a single-stranded DNA molecule synthesized from a messenger RNA template by reverse transcription. Any given cDNA is “isolated” in that it is single-stranded, and free of untranslated sequence.

  79. I don’t see the cafc getting past the standing issue, which will thus put off this academic excercise for another day. This case will open the flood doors for hundreds of new suits if the cafc does not punt this on standing.

  80. Won’t drug companies continue to make medicine anyway? That seems a ridiculous to think they will stop making medicines and finding cures just because they can’t patent it. They still make loads of money. And as for research why won’t they continue to fund the colleges and research companies that find the cures? Why would that stop?

  81. EG: …Myriad’s “isolated” BRCA1 and BRCA2 gene sequences are also “novel” as they don’t exist in nature.

    I’ve read that paragraph a few times, and I can’t see how this is not just totally in error. I thought the whole point of this was not whether or not the BRCA1 and 2 gene sequences exist in nature, but whether you can or can’t patent something that exists in nature. If the BRCA1 and 2 gene sequences didn’t exist in nature, they would have zero utility. “Isolating” a sequence is just putting the information in a different place, encoded by a physically different set of atoms from the set you created it from. If doing that makes it fundamentally different, then I’m going to argue that all my old Napster mp3s are “isolated”.

    Now, I’m just an average scientist, not a lawyer, so my whole reason for reading here is to better understand the law, but I think that if the law were to hold that “Myriad’s “isolated” BRCA1 and BRCA2 gene sequences are also “novel” as they don’t exist in nature”, then the law would be fundamentally in error.

    If the courts end up ruling that you can patent a sequence, well then you can patent a sequence, but if Sweet’s opinion is likely to be reversed, I’m trying to figure out why…

  82. I’d like an explanation of why claim 1 of the ‘473 patent (directed to an isolated DNA comprising an altered BRCA1 DNA having a least one alteration) is invalid while claims 2 and 3 (directed to an isolated DNA comprising an altered BRCA1 DNA having one alteration)are not.

    Presumably claim 1 with its additional alterations is further removed from the “natural” sequence and so it escapes the imaginary hammer that Judge Sweet used to invalidate the other claims …?

  83. EM, the ACLU sued on only 15 claims. The Judge has no subject matter jurisdiction to rule on any other claim.

  84. Has everyone forgotten 35 USC 282 — that every claim of a patent is presumed valid independently of the validity of other claims? This decision expressly covers only 15 out of 179 claims in the Myriad patents. I’d like an explanation of why claim 1 of the ‘473 patent (directed to an isolated DNA comprising an altered BRCA1 DNA having a least one alteration) is invalid while claims 2 and 3 (directed to an isolated DNA comprising an altered BRCA1 DNA having one alteration)are not. How is anyone supposed to know what is covered by a patent and what isn’t?

    This decision is seriously flawed and must be reversed.

  85. Hans, does “pure” mean “concentrated.” I thought it meant “devoid of impurities.” What was Hand actually deciding in Parke-Davis?

    Hans, if “isolated” DNA = cDNA, and nothing else, why didn’t the court say that in his claim construction?

  86. Ned, the judge quite clearly understands that a cDNA (“isolated DNA”) corresponding to a “gene” does not exist naturally. His point is that there is no practical difference between a cDNA corresponding to a gene and the gene in its natural state, since they both make the same protein. The thing that drives Kevin and others crazy is this: if you want adrenaline, you can eat the dried and powdered adrenal glands of sheep and oxen, but you’re going to have to eat A LOT of the stuff in order to get any benefit; alternatively, you can “eat” a tiny amount of a chemical that has been purified from these adrenal glands and get the same benefit.

  87. Isolated DNA” is therefore construed to refer to a segment of DNA nucleotides existing separate from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome, and includes both DNA originating from a cell as well as DNA synthesized through chemical or heterologous biological means.”

    Then I refer Judge Sweet to my 12:47 pm comment. Not sure why he didn’t listen to Myriad’s attorneys, who surely presented similar facts.

  88. Chris, I was struck by how both Hand and Rich (Parke-Davis and Bergstrom) viewed the issue before them as one of novelty. Clearly Rich saw the Section 101 “newness” issue as falling under either Section 101 or Section 102.

    Sweet also analyzes the issue in terms of novelty — whether the claimed isolated DNA is different than that occurring in nature, i.e., whether it is new.

    Now Kevin above states that isolated DNA is, in fact, chemically different than native DNA. If true, this should settle the controversy. However, I do not recall this difference being argued in Sweet’s discussion of Myriads points. After reading the opinion, I had the firm understanding that there was no chemical difference between the two.

    “Isolated DNA” was a disputed claim term. It was defined in the specification. Here is the construction from page 92 of the opinion.

    “The term “isolated DNA” is defined by Plaintiffs
    as “a fragment of DNA substantially separated from other cellular components and other DNA.” PI. Br. at 10. Myriad disputes Plaintiffs’ definition insofar as it implies that fragments of DNA exist free-floating in the cell, separate from other cellular components, such as proteins and the
    other DNA in the chromosome. Myriad Br. at 16. The patent specifications expressly define “isolated DNA” as a DNA molecule “which is substantially separated from other cellular components which naturally accompany a native human sequence [such as] human genome sequences and proteins” and “includes recombinant or cloned DNA isolates
    and chemically synthesized analogs or analogs biologically synthesized by heterologous systems.” ‘473 patent, col. 19:6-15; ‘282 patent, col. 19:8-18; ‘492 patent, col. 17:62-18:5.

    “Isolated DNA” is therefore construed to refer to
    a segment of DNA nucleotides existing separate from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome, and includes both DNA originating from a cell as well as DNA synthesized through chemical or
    heterologous biological means.”

  89. The entire case is argued on the basis that the standard under 35 USC 101 is whether a particular composition or method relying on the composition is “markedly different from a product of nature”. The utility standard under 101 was set forth by the CAFC in In Re Dane Fischer (2005) Ct App Fed Cir 76 USPQ 2d 1225, addressing the issue of utility of EST’s, in which it was established that the standard should be whether the subject matter isolated from the native state can be shown to have a specific and substantial utility; and if such is shown, then the subject matter sought to be patented exhibits utility under 35 USC 101.

  90. Hey MM,

    Very impressed with your knowledge of biotech and ability to succinctly state it. Keep of the good work, I (a chemist) can learn something here.

  91. I do not think an individual or business should have patent protection for any DNA sequence existing in nature. The sequence is a product of nature and the method(s) for determining it obvious. To the extent the Myriad decision stands for this principle, it was decided correctly. Patentability should start when knowledge of a DNA sequence leads to diagnostic tests, disease coping strategies and, of course, disease cures. What I think is really happening is that these defacto sequence protection patents are desired as “place holders” to prevent competitors from developing and patenting those follow on advances first. However, it seems to me that this approach does not “Promote the Progress of Science and the Useful arts” as intended by the drafters of our constitution. Society benefits from progress in science and that progress is accelerated where there is competition. Moreover, I do not believe that “owning” a DNA sequence promotes investigation into the human genome and I agree it probably has the reverse effect. There is tremendous interest in understanding the human genome purely for the sake of scientific investigation and advancement. And this work is being conducted aggressively by researchers at public and private institutions worldwide. There is a tendency in these discussions to forget that US patent law only has force and effect in our country and its territories and possessions. We need to be mindful of this external competition and how we can best put our scientists, universities and businesses in the strongest competitive position. Is that achieved by stifling research in the US but not elsewhere? In any event, the potential for the follow-on patentable technologies becoming hugely profitable should provide adequate motivation for inventors and their assignees.

  92. +1 Kevin.

    “Following the ACLU’s lead, he appears to modify the doctrine such that physical embodiments of abstract ideas and natural processes that have been modified with human ingenuity are no longer patent eligible, without citing any authority or explaining the logic.”

    This is why the decision will be so easy to overturn. Sweet just hand-waved away the prior case law as being applicable to novelty and 102 while exclusive of 101, which is incorrect by his very own reasoning. Although 102 determinations are of course different than 101 determinations, in this case, the same question must be inevitably asked while determining whether the matter meets the requirements over each of 101 and 102: is the “isolated” DNA different from the naturally occurring DNA?

    Sweet instead uses the term “markedly different” and determines that isolated DNA is not “markedly different” from native DNA. I’m not a judge of any kind, but that sounds an awful lot like 103, and only a tiny bit like 101, to me. IMO, Sweet would have had a much better chance if he’d ruled that the patents were invalid under 103 because they were not “markedly different” from the native form, while saying that Hand’s 102 analysis did not apply to 103 determinations.

  93. Posted by: broje TINLA IANYL | Mar 31, 2010 at 01:21 PM: far be it from me to pull an AI and quote the Constituion, but “To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries.”

    Glad to know my work here has not been in vain.

  94. I expect that this is what the opinion will be amended to when the Supreme Court gets to it… I expect the majority of the court ruling will stand, because this infelicity in wording is really pretty minor.

    Except Nathanael, no court can rewrite the claim to fit your logic. The claim does not say “‘isolated DNA’ RESTRICTED TO sequences OF CODONS found in nature“…

    Rewriting claim language is actually notreally pretty minor“.

    I know the adage is that curiousity killed the cat, but wouldn’t it be better if infelicity killed the feline?

  95. Ned,

    I don’t think Sweet is saying that the claim would cover unpurified DNA, at least at it exists in nature. He seems to be saying that purification is not something that would sufficiently change the form to render it patent eligible.

    I think he is wrong on this count because the isolated gene is in a different chemical and physical form after purification. It is at least chemically disconnected from the rest of the DNA, which changes the chemical structure of the DNA phosphate backbone. It would also likely then be put into a salt form at the terminal phosphate of the chain, which was sufficient for Hand to render the free base form of adrenaline different than the salt. It could also be linked to other chains of DNA, such as in a vector which would alter its chemical and structural form. Also, it could be attached to label to allow identification of the natural gene in molecular diagnostics, which again would entail a change of chemical and physical form.

  96. As Professor Andrew Chin showed, there’s a way of defeating all oligonucleotide claims regardless of the outcome of the Myriad litigation — just put the sequences on a CD-ROM and deposit it in a library. link to unclaw.com

  97. The purification cases suggest the final patented product being a relatively homogeneous collection of substance that previously doesn’t exist in such homogeneity, and that such collection is useful. I’m thinking about the vitamin B12 and the adrenaline cases.

    The claim 1 here points to an “isolated” gene, i.e. a single strand of double helix with a certain sequence, as oppose to a collection of such single strands.

    So forgetting genes for a moment. Can one maintain that a useful lump of “purified X” is 101 patentable but a useful single molecular speck of “isolated X” is not because that naturally occurring molecule itself is not transformed pre- and post- transformation? Is it inane?

  98. Ned The bottom line, there has to be something different from the claimed product and the naturally occurring composition. I can understand a “purified” product being different. However, the claim here seems to cover both purified and unpurified DNA. That too was noted by Sweet.

    And if that’s the proper construction, then the claim is anticipated and there’s no controversy. Was there a Marking hearing where this was addressed, or did Myriad admit to this construction? I know from my earlier review of Myriad’s claims that many of them are laughably broad. Obviously some of them were not, though, and even made it past Judge Sweet.

  99. It seems to me that Judge Sweet is making up this “product of nature” doctrine. As far as I can tell, none of the cases he cites for the rule use that phrase.

    The cases he cites draw a distinction between abstract ideas, laws of nature, and natural and physical processes that have not been modified by man on the one hand, and physical embodiments of ideas that involve human manipulation of a physical form on the other.

    Following the ACLU’s lead, he appears to modify the doctrine such that physical embodiments of abstract ideas and natural processes that have been modified with human ingenuity are no longer patent eligible, without citing any authority or explaining the logic. Under this new doctrine, are electronic devices no longer patent eligible because they are composed of chemical elements found in nature? What would be patentable, then?

    Sweet’s discussion of the Parke-Davis case is similarly unsettling. Although he says that Hand only held isolated adrenaline to be patentable under 102, Hand must have assumed that the isolated compound was patent eligible by Sweet’s own logic. Specifically, at p. 99 of the opinion, Sweet explains that “the obligation to determine what type of discovery is taught to be patented must precede the determination of whether that discovery is, in fact, new or obvious.” Thus, Hand and all others who analyzed the case and found it patentable under 102 must have initially found it patent-eligible as well.

    In an ironic way, Hand’s 102 analysis also suggests that isolated gene sequences would be patentable under Sweet’s “product of nature” test. Specifically, Sweet has improperly overlaid a 102 analysis on the question of patent eligibility by requiring that a claimed isolated chemical compound not be found in nature. As Sweet tells us, Hand held that “the patented purified extract…was a different chemical substance from that found in the prior art,” specifically, because it had been isolated and and changed from a salt to a free base. Claimed DNA sequences have similarly been isolated and deionized or minimally altered, and thus they are different than what is found in nature, and pass the “product of nature” test.

    Also, what role does the fact that The Patent Act of 1952 was passed years after the Supreme Court cases Sweet cites play in the case? Specifically, even if he is right that the 1880’s cases establish the isolated DNA would be patent ineligible, wouldn’t the Act supersede those cases?

  100. “”Therefore, the patents at issue directed to “isolated DNA” containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 USC 101.”

    Not good.

    Had the learned judge said “. . .directed to ‘isolated DNA’ RESTRICTED TO sequences OF CODONS found in nature. . .” I think the opinion might have a snowball’s hope of surviving review. ”

    I expect that this is what the opinion will be amended to when the Supreme Court gets to it. You have zeroed in on the only problem with the entire court ruling. I expect the majority of the court ruling will stand, because this infelicity in wording is really pretty minor.

    The fact is that sequences *not* found in nature are generally *useless medically*. I certainly think a brand-new sequence not found in nature should be patentable if useful. Sequences found in nature are blatantly unpatentable and I’m glad the judge noticed.

    (As someone else said, the method of isolating genes is patentable, but the results of isolating them aren’t, any more than I can patent every individual sort of tea which I make by “boiling the leaves of plant X for X minutes” — whereas the process of boiling leaves to make a tea *would* be patentable if it weren’t prior art.)

    The gene patents also anticipate, as they foreclose novel uses of the genes. (And of course individual *uses* of the genes may still be patentable, just not the raw chemical sequences.)

    On the whole an excellent ruling, although we should wish the judge had written it in a more bulletproof fashion.

  101. Our universe is already living on borrowed time

    It’s not the universe that is on borrowed time…

    monkeys here don’t have infinite time

    Dammit, there goers all my anti-software Turing machine logic. Who knew?

  102. Hans’ take:

    1. Judge is no dummy.

    2. DNA has no substantial utility other than to encode protein, and the encoded protein is the same whether it is produced naturally or recombinantly. Oligonucleotides are useful for diagnostics and as research tools, but there is a reason that the PTO will not grant composition patents on oligos unless the full-length gene and its function are known (I know this was done to deal with the gazillions of EST applications, but I’ve always thought that anything short of the full-length should not be patent-eligible).

    2. Decision will be overturned by CAFC. Supremes will stay away.

    3. Anyone who thinks biologics are the same as pharmaceuticals hasn’t been paying attention to the “biosimilars” debate.

    4. You have to eat a lot of tree bark to be cured of cancer.

    5. Myriad’s testing franchise around BRCA1/2 will be unaffected no matter what happens in this case, and no matter what happens with Bilski and Prometheus v. Mayo. The know-how, brand recognition, and reimbursement infrastructure are more important than patents at this point.

  103. “So if a composition can theoretically be made by any natural process, then a claim to the composition is invalid, even if the composition has never been found in nature, isolated or not?

    That’s bold, 6. Wacky bold.”

    Hmmm, I wouldn’t say merely theoretically, the theory would have to be reasonably plausible.

    “I guess the same could be said of refrigerators, if the monkeys have acccess to all the natural resources. But then, some monkeys did make refrigerators, they just happened to evolve a little bit in the process.”

    One might think that, but guess what? Our universe is already living on borrowed time, monkeys here don’t have infinite time.

    FYI guys I think Kev just admitted that some of the Myriad claims are invalid under 102. Some new paper just came out showing how they proved it. Go check his latest post.

    Don’t hold me to that, but that’s what it looks like he’s trying to say to me. I just perused it.

    link to patentdocs.org

  104. EG, I did not conclude that isolated DNA was not different than natural DNA. I suggested, as did Myriad, that whether the DNA sequences of the two were identical or not is irrelevant if isolated DNA is different from the naturally occurring DNA in some “transformational way,” which is what occurs when something in nature is transformed into something materially different. This is the very definition of an article of manufacture. (Note, Chakrabarty held the claimed microorganism could be patented as either an article of manufacture or as a composition.)

    But, if as 6 suggests, that the claim really is to a composition of matter, then it becomes in my mind quite important whether the is any difference between the claimed composition and naturally occurring composition. Here, transformation should not be an issue. It is merely a question of whether there is any structural difference.

    There is debate here among the scientists on these issues. Sweet addressed all the purported differences advanced by Myriad between the isolated DNA and the naturally occurring DNA. He found no differences as both had to have the exact same chemical sequences. This reinforces the notion that was was claimed is the composition of matter.

    Sweet even hypothesized about a future mechanism to identify a particular DNA sequence without any isolation. Could one then patent the identified naturally occurring DNA sequence? Obviously not. I think this was his point.

    The bottom line, there has to be something different from the claimed product and the naturally occurring composition. I can understand a “purified” product being different. However, the claim here seems to cover both purified and unpurified DNA. That too was noted by Sweet.

    For those of you who really understand the technical issue, can you discuss why Sweet was right and why he was wrong on these issues?

  105. How come I said isn’t small pox a mutation of a germ outside the body? And it looks like I can’t write a full sentence, after it is posted? That seems to happen a lot.

  106. Lionel,

    I suggest taking a look at 35 USC 101 to address your assertion that isolated DNA should not be patentable because it does not involve creation.

    Specifically, according to the statute, “Whoever…discovers any new…composition of matter…may obtain a patent therefor”.

    Section 101, coupled with the hand-of-man requirement that the product not be identical to that found in nature, clearly indicates that isolated DNA sequences are patentable.

    DNA is a composition of matter. Isolating it changes its chemical and physical state, and puts it into a commercially useful form. Thus, when a new DNA sequence is discovered, and the sequence is isolated, it is patentable.

  107. So if a composition can theoretically be made by any natural process, then a claim to the composition is invalid, even if the composition has never been found in nature, isolated or not?

    That’s right. It may not exist in nature, but it would have been obvious to nature.

  108. 6 If it can be made in nature then we have no business allowing it under 101.

    So if a composition can theoretically be made by any natural process, then a claim to the composition is invalid, even if the composition has never been found in nature, isolated or not?

    That’s bold, 6. Wacky bold.

  109. *******
    If it can be made in nature then we have no business allowing it under 101.
    ********

    It’s also been said that a room full of monkeys with typewriters and infinite time on their habds would eventually produce the entirety works of Shakespeare. I guess the same could be said of refrigerators, if the monkeys have acccess to all the natural resources. But then, some monkeys did make refrigerators, they just happened to evolve a little bit in the process.

  110. So how are the dead smallpox viruses in the smallpox vaccine different then those found in nature once they, you know, die and stuff?

    Here’s an experiment: find some tissue “in nature” containing some dead smallpox and inject it into your body. Wait a couple weeks and let us know what happens. Then expose yourself to some “live” smallpox vaccine.

  111. Whether the decision is right or wrong, 6 almost all would still be here without Myriad patent or Myriad. Sounds ridiculous.

  112. “If you could show that the cDNA for a particular gene was known to exist in cells, that could be evidence for obviousness of the cDNA, I suppose.”

    It would also be evidence that, going one step further, all cDNA could be made in nature. If it can be made in nature then we have no business allowing it under 101. And I’m not too sure that you’d need evidence of only that one specific gene. Would this finding not hold true for all genes? I can’t speak to the answer for that, but if it does then ol’ Kev’s got problems in his argument.

  113. So how are the dead smallpox viruses in the smallpox vaccine different then those found in nature once they, you know, die and stuff?

    Good question. My point was only that once you change something you get around the problem this judge had with isolated genes. I couldn’t say what constitutes enough change, but I’m pretty confident ASA is patentable over SA in nature no matter what reasonable standard you might apply.

    This judge probably thought isolating a gene was like peeling an apple and claiming the flesh inside. If you made an apple pie without any guidance from the prior art, he’d still say that was pretty clever.

    And far be it from me to pull an AI and quote the Constituion,

    Meh, it’s not AI till you quote one of the people who wrote the constitution in an attempt to contradict the document itself.

    Besides, you still have to be an “inventor” to get a patent for your “discovery”. I’m sure the founding fathers had lots of writings that clear up that little inconsistency to the satisfaction of the person quoting them.

  114. “But just how, exactly, did the BRCA1/2 sequences make it into the human genome sequence maintained by NIH? Could it be, peradventure, that Myriad put it there? And even if it was there before, who, exactly, identified the sequence as having any relationship to breast cancer, so that you know to even compare your sequences this this particular region of the genome? Could it be that Myriad did this? Yes, you do need Myriad to make your comparison. You’re just ignoring Myriad’s original contribution.”

    If you read the decision there was another group working on the same thing and they published one day after myriad filed for a patent. One whole day. Big whoop.

    “I highly doubt that banning patents on methods of diagnosing diseases would have much impact on the development of diagnostic tests,”

    Exactly.

    “In fact, if we take your logic to the extreme there isn’t anything in this world that isn’t, at some point, derivable from nature.”

    Orly? Derive me a fridge from nature. Or maybe a computer. Some things require you to work up, rather than work down.

  115. So how are the dead smallpox viruses in the smallpox vaccine different then those found in nature once they, you know, die and stuff?

    And far be it from me to pull an AI and quote the Constituion, but “To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries.”

  116. There goes motivation to discover any new drugs.

    Fixed that for you.

    Also, the first A in “ASA” is where the aspirin was modified from what you find in willow bark.

  117. /sigh

    If isolated DNA should not be patentable, then I guess drugs isolated from nature, like valium from valerian root, like aspirin from willow bark, like the small pox vaccine, like blood pressure medicine from human parasites, should be unpatentable. There goes motivation to invent any new drugs.

  118. GF If people really do *not* want companies to come up with any new tests for diagnosing diseases, then they might as well just pass a law to outlaw it.

    I highly doubt that banning patents on methods of diagnosing diseases would have much impact on the development of diagnostic tests, particularly genetic tests. The incentives for companies to invest in and/or develop genetics tests which show that you need to buy their drugs will remain as strong as ever.

    Look at all the money pharma companies dump into advertising. Those ads aren’t patented. They are designed to create customers for their products. “Depressed? Ask your doctor if you need this.”

  119. In fact, if we take your logic to the extreme there isn’t anything in this world that isn’t, at some point, derivable from nature.

    Except for business methods not tied to a particular machine. But it turns out that people don’t like those either.

  120. “Are you in cahoots with NAL?”

    Ping,

    No, I’m not. Sorry if my posts are boring to you, but I try to back up what I say.

    Ned,

    You’re missing the point, just like Sweet did. The “isolated” DNA covered by Myriad’s patents does not exist in nature, separate and apart from its native environment. Using your logic, purified bacterial cultures or even purified drugs (like Taxol) obtained from plants would be unpatentble because the bacteria or drug in them already exists. That’s contrary to what Bergy held, and that case has not been overruled by the Federal Circuit or even SCOTUS. In fact, if we take your logic to the extreme there isn’t anything in this world that isn’t, at some point, derivable from nature. So where are you going to draw the line?

    NWPA,

    Thanks for pointing out another nonsensical analogy by Sweet about DNA simply being equivalent to biological code. So what are those arranged nucleotides called? Chemical structures. I’m sure the Federal Circuit will get a giggle out of Sweet calling them anything other than chemical structures.

  121. jon From my understanding of the above discussion, an isolated DNA is not different in any way from naturally occurring DNA.

    It would depend on how you define “isolated” and “naturally occuring,” of course. But taking the ordinary meaning of those terms, the isolated DNA (or structural gene, as the phosita would typically understand it in this context) is certainly different from the naturally occurring gene. For starters, most naturally occuring genes are not floating around in cell free from other DNA molecules. They are attached in a long string, coiled up, and their expression is profoundly influened by their surroundings. In the case of humans, the gene may contain intervening sequences that need to be excised by proteins in the cell before expression is possible. The expression of the naturally occuring is highly regulated and, if you want to study the protein product of the gene (assuming there is one),the naturally occuring gene is almost always worthless for this purpose because it is expressed at such a low level.

    The isolated gene, in contrast, can be manipulated at will. It can be placed into a new genomic context and over-expressed in a distantly related organism so that its product can be effectively studied.

    This is just one enormous practical difference between an isolated gene and a naturally occurring gene.

    6: there is a part in the decision that states that cDNA can occur naturally

    It’s true that cDNA can be naturally created from mRNA by a process known as “reverse transcription.”

    If you could show that the cDNA for a particular gene was known to exist in cells, that could be evidence for obviousness of the cDNA, I suppose. But I don’t believe there is much reverse transcription of human genes in human cells, unless you’re infected with a retrovirus, and even then it’s typically the viral nucleic acid that is reverse transcribed, not your own.

  122. I notice the heavy reliance on pre-1952 case law. And some dissenting opinions in the later cases.

    The footnote on page 123 is curious. I wonder if that footnote is intended to limit the holding to DNA sequences. Sort of a “every case turns on its facts” designation.

    -t

  123. Jon,

    “The naturally occurring reference sequence of BRCA1/2 is available in many places including the ‘human genome sequence’ maintained by the National Institutes of Health. The sequence is public. I don’t need myriad to compare my sequence to the known reference sequence, much as I don’t need permission to look in a dictionary for how to spell a misspelled word.”

    But just how, exactly, did the BRCA1/2 sequences make it into the human genome sequence maintained by NIH? Could it be, peradventure, that Myriad put it there? And even if it was there before, who, exactly, identified the sequence as having any relationship to breast cancer, so that you know to even compare your sequences this this particular region of the genome? Could it be that Myriad did this? Yes, you do need Myriad to make your comparison. You’re just ignoring Myriad’s original contribution.

    What pervades the thinking that genes should be unpatentable is the attitude that society is somehow “entitled” to the fruits of others’ labors, without compensation, because the fruits were somehow derived from something already out there in nature, albeit inaccessible in a different form. Sure, some societies have ignorantly and selfishly adopted such philosophies, but those societies have failed or languished, economically, politically, and morally. The premise of the the patent system is that we are willing to reward those who actually advance the cause of science and knowledge. We willing give up our “entitlement” to the valuable fruits of others’ labors, in exchange for something better. The patent system, despite its warts, has worked. Those who argue for unrestricted access to and commercialization of genetic materials, are the lazy riff-raff of our society who are simply looking for a free ride on the backs of those who innovate and risk their labor and money for the promise of a better future for us all. I’m sick and tired of this “entitlement” attitude. It doesn’t work. It is a scourge and a poison in our society, and is now infecting the patent world, as well.

  124. Myriad’s claim as drawn on the BRCA genes is not tied to a specific machine. As the resident microbiologist has pointed out, the BRCA gene is not altered in any way by this process thus there is no transformation of matter. Under CURRENT patent law [Bilski] it is not patent eligible under 101. It seems disingenuous to dismiss philosophical arguments of how the law should work as ignorant of precedent, while ignoring what the law currently is.

  125. The decision by Sweet is ill-informed (i.e., not-so-Sweet) and runs against ~50 years of case law.

    Sweet appears to be simply legislating from the bench. As any average biologist would know, “isolated” DNA (e.g, in a vector, amplified from mRNA, etc.) is arguably even more altered “by the hand of man” than a pharmaceutical purified from the bark of a tree (i.e., patentable under 101).

    If people really do *not* want companies to come up with any new tests for diagnosing diseases, then they might as well just pass a law to outlaw it.

    Good luck, Cancer Patients.

  126. “Wonder how many would still be here if Myriad hadn’t been granted the patent?”

    All of them?

    And Ned, that stuff about composition of matter v product is stupd. Stop saying it. Srsly.

    I will agree with you though that on its face ol’ Sweet’s analysis o tha case appears persuasive. I give it 50/50 at the Fed Circ. and 90/10 (ACLU) at the Supremes.

    Frankly, what I’d like to see is why, very specifically, Kev disagrees with the court on the law etc.

    I note also Kev that there is a part in the decision that states that cDNA can occur naturally. It was part of expert testimony. That wasn’t what you told me, and if true, will shoot a pretty big hole in your case.

  127. Good point Ned. Isolated gene already old at the date of the claim? Whatever next. I thought I knew what “isolated” meant, But isolated from what, I’m now wondering.

  128. In reference to the two claims, above, can someone who writes gene-related claims tell me whether it is common practice in that field to base the claims on references to tables in the specification? I know it’s sometimes allowed, I just never see it done.

    What a complete disaster that second claim is. How can you tell what “comprises” refers to? Somebody was actually willing to defend that mess in a court of law? Whew, now that’s testicular hypertropy!

    In the first claim shown, why would anyone include the “isolated” limitation? Is it meant to get around PA disclosing synthetic DNA of the same description?

    These gene-claimers are a breed unto themselves.

  129. Jon, EG, et al., I think the confusion (in my mind and perhaps in Sweet’s) is caused by treating the claim as a composition of matter claim. The DNA is the same isolated, as in nature. There is no “newness,” no novelty.

    In contrast, if one treats the claim as an article of manufacture, it is IRRELEVANT where the DNA is identical or not. Any such argument would be an red herring.

    Now, I can see how a purified pre-existing compound is new — which is the actual holding in Parke-Davis and In re Bergstrom — but if new, it is patentable as an article of manufacture, not as a composition of matter.

    From my understanding of the above discussion, an isolated DNA is not different in any way from naturally occurring DNA. I am not sure of this, as we might be confusing whether the DNA is new rather than whether isolated DNA is new. There is a difference.

    As I said in an earlier post, the plaintiffs apparently argued that even in nature, the DNA is isolated. But it might be momentarily, but isolated in the lab makes it useful for its identification.

    Imagine if I invented a machine that could read the DNA of an animal by simply scanning the animal. Nothing is transformed in any way. Could I patent the naturally occurring DNA under any legal theory? I think not.

    My machine analogy is this: I cannot repatent the machine if I discover a new use for it. I can patent the “oiled” machine, as it might then be useful; but the oiled machine is not the machine. The oiled machine is an article of manufacture.

    Now, if I invent a pattern recognition device and use it to determine what kind of machine is in a building, can I repatent the identified machine either as a new machine or as an article of manufacture? I think not.

  130. Patent explosion on the land grab scale does nothing for industry academics or the public.
    Gene patents are like patenting the disease instead of the drug that cures it. This strangles all competion at source which is why the fundementals of nature and obviousness are excluded.
    The simple fact is these should never have been given patents in the 1st place

  131. Jon,

    Whether you think it deserves a patent is immaterial – what is material is whether the evidence shows that the invention qualifies for a patent. Your argument conflates two different patent statutes (101 and 103) and is drawn to whether or not the sequences of the BRCA genes where known at the time of the filing of the application for patent. Were they? The fact that you can find them now is immaterial. If they were known at the time of filing and the procedure by which to isolate them was also known, then under the 103 statute, patentability would have to be considered. But that is NOT what Judge Sweet said. Apparently, according the Judge, because the sequences originated in nature, any subsequent manipulation (including isolation) fails to render them patentable (which actually conflicts with your agreement that if the inventors had modified them to make them work better). Many things originated in nature. The logical conclusion of this decision is that digitalis would never have been patentable because it was originally present in foxglove. And my knowledge of biology is just fine, thanks for asking!

  132. Another? How many are there out there would you say, Santos. Who’s going to sort them out into those that understand and those that don’t? You?

    Who can help us with this thing called “patent law” if the judges are not up to the task? The Congress perhaps. A jury? Or should we all turn to you again?

  133. Justin,

    It will be mighty difficult to overturn (or for that matter to not overturn “ The ruling which struck down business method patents“, since no such ruling exists.

    Given how fundamentally flawed” your understanding of patent law is, perhaps you should be quiet, instead of trying to impress people with the use of such words as “cudgel”?

    Jerry,

    The court of public opinion will have exactly zero impact at the crucial judiciary levels. I think Nihilistic Tendencies has it pegged as to what will have impact. Good ‘ol Quinny isn’t even the one most vocal – you need to check out Patent Docs.

    I also think NWPA might be on to something – this country gave a great shot to the basic research system by inclusion of universities in the patent system and taking that away will create an interesting void.

    EG,

    Are you in cahoots with NAL? You seem to have the same habits of writing boring long posts. And if you are going to start to not “hold soap”, I’m getting out of the shower.

  134. “Sweet! Finally, a judge with some common sense.”–unlikely. More like…another judge who does not understand patent law.

  135. Well thanks for that Jon. The step of isolating the gene from the human chromosome might not have “done” anything to the gene but the gene, isolated, and at the date of the claim, was new and useful.

    Which brings us back to “obvious, or not”.

    Now I await with interest, to see what Jon says to Jane.

  136. Jane Doe,

    And your explanation shows a basic misunderstanding of biology …

    The naturally occurring reference sequence of BRCA1/2 is available in many places including the ‘human genome sequence’ maintained by the National Institutes of Health. The sequence is public. I don’t need myriad to compare my sequence to the known reference sequence, much as I don’t need permission to look in a dictionary for how to spell a misspelled word. Myriad might have a database of sequences that can correlate my sequence to a potential prognosis, but that is not the subject of this patent is it?.

    Modify the BRCA1/2 genes to make them work better, make them do something else, etc, that is patentable. Naturally occurring … I don’t think deserves a patent.

  137. EG: even if it was held eligible for patentability under 101 for purificaition, the way the judge removes it from eligibility is the following:

    >>DNA, and in particular the ordering of its >>nucleotides, therefore serves as the physical >>embodiment of laws of nature—those that define >>the construction of the human body

    Which is Benson.

  138. MaxDrei,

    “Books have sentences. But they are separated by periods, and are written in human-readable form. Your analogy is not exact, is it?”

    Actually, genes do indeed have start and stop signals that are just like capital letters and periods. Almost every gene begins with the bases ATG, which codes for the amino acid methionine. This includes BRAC1 and BRAC2. This is exactly analogous to a capital letter the beginning of a sentence. Almost every gene ends with one of three base pair triplets literally referred to as “stop codons”. This are completely analogous to the period at the end of a sentence. The start and stop signals have been known for 30+ years.

    Myriad’s application of certain techniques to clone a gene might have been new 15 years ago (although I think that is debatable), but they could have applied this technique to isolating any gene. Nothing about the BRAC1/2 gene itself is novel or new. It exists naturally and isolating the gene from the human chromosome did nothing to modify or change it.

  139. Jon,

    Sorry, but your explanation shows a basic misunderstanding of the fundamentals of patent law. Do what you want with your little finger, but once the DNA is no longer in the genome inside the nucleus of a cell inside someone’s body, it is no longer in a condition found in nature. Add to the fact that it has a use, i.e. as a means to identify the presence of the DNA in other individuals so as to identify their risk for cancer and the 101 analysis is done! If this decision were an answer on a law school exam, the student would get an F! This is a feelgood decision for those conspiracy theorists. Boy, I bet all those women who used Myriad’s tests to find out that they had the BRCA genes are jumping up and down about the death of gene patents. Wonder how many would still be here if Myriad hadn’t been granted the patent?

  140. Chris wrote

    “The courts have consistently held that a pure product is different from an un-purified product. See In re Bergstrom, 427 F.2d 1394”

    I agree that this is what the courts have held, and I believe it is bad law that needs to be changed.

  141. Having read some other comments on here, I am in the apparently unusual position of defending business method patents and opposing isolated DNA patents.

    I should say I don’t necessarily support most business method patents, I just do not believe they should be rejected under 101. It’s not as if a bright line exists between technical and business method patents. I think they should be rejected under 102, 103, and 112 where appropriate.

    Isolated DNA patents on the other hand are simply a laboratory recreation of what already exists in nature.

  142. So Sweet says the claimed subject matter is:

    “purification of a product of nature, without more”.

    That surprises me. I wouldn’t myself have thought of using the concept of “purification” here. Thanks EG. I shall have to read the decision. 156 pages. Sigh.

  143. “The court conducted extensive analysis of Supreme Court authority. On its face, it seems persuasive.”

    Ned,

    Not in my opinion. Read my article, now 30 years old, when the topic of patenting purified “products of nature” was a hot topic, as well as whather life forms were patent-eligible under 35 USC 101. Guttag, “The Patentability of Microorganisms: Statutory Subject Matter and Other Living Things,” University of Richmond Law Review, Vol. 13, page 247 (1979). In other words, I’m very familiar with the SCOTUS (and other court) precedent on the patent-eligibility of “products of nature” cited by Sweet in his opinion. Judge Sweets take on what these cases mean doesn’t convey the whole picture, not by a long shot.

    First, Judge Sweet’s opinion suggests that these cases have consistently applied the “products of nature” doctrine in determining whether subject matter is patent-ineligible. But as my article points out, that is far from the truth: “A major difficulty for the courts has not been in stating the [“product of nature”] doctrine, but rather in determining whether there is such a doctrine and how to apply it.” In this regard, I contrasted the General Electric case (where SCOTUS held a patent on substantially pure tungsten to be invalid for covering a “product of nature”) with Judge Learned Hand’s opinion in the 1912 case of Parke-Davis & Co. v. H.K. Wolford Co. (which upheld the patent on adrenalin extracted from glands of animals and which essentially deemed the “product of nature” doctrine irrelevant to patent-eligibility). In fact, Judge Sweet’s dismissal of Judge Hand’s ruling in Parke-Davis as being based strictly on “novelty grounds” is astonishing given that Myriad’s “isolated” BRCA1 and BRCA2 gene sequences are also “novel” as they don’t exist in nature. That Judge Sweet’s suggests that Parke-Davis is “contradicted by subsequent case law” (i.e., Bergy and the 2009 Federal Circuit case of Prometheus Labs. V. Mayo Collaborative Services) is utter nonsense.

    Second, several of these SCOTUS cases don’t rest primarily on “products of nature” being patent-ineligible. For example, in the American Wood-Paper case, SCOTUS ruled a patent covering a purer form of cellulose pulp suitable for manufacturing paper invalid in view of cellulose pulp suitable for manufacturing paper already being in existence (i.e., was an attempt to patent an “old compound” and thus not novel). The holding in Funk Bros. Seed Co. is more properly viewed as an attempt to patent a mixture of non-inhibiting strains of bacteria which was deemed to be unpatentable as being obvious (i.e., under 35 U.S.C. § 103), which Judge Sweet also incorrectly suggests as being based strictly on “patent-eligibility” grounds.

    Third, it is questionable whether the “product of nature” cases such as American Fruit Growers are still good law, especially in view of SCOTUS’s ruling in Diamond v. Chakrabarty. In American Fruit Growers, SCOTUS ruled that fruit impregnated with borax was not a “manufacture.” As my article pointed out, that ruling is bizarre based even on the definition of “manufacture” used in American Fruit Growers. In fact, later cases (including Diamond v. Chakrabarty) have cast the decision in American Fruit Growers (rightly so in my opinion) into oblivion.

    What is most alarming about Judge Sweet’s opinion is his characterization (or more appropriately mischaracterization) of the CCPA’s Bergy case. Judge Sweet makes numerous quotes from Judge Rich’s opinion in Bergy on how 35 U.S.C. § 101 should be interpreted. But what Judge Sweet neglects to point out is that Judge Rich ruled in Bergy that a biologically pure culture was deemed to be patent-eligible under 35 U.S.C. § 101. Why did Judge Sweet neglect to point out this highly relevant fact? Instead, if the holding in Bergy is considered in appropriate context, it supports Myriad’s “isolated” BRCA1 and BRCA2 gene sequences as being at least patent-eligible under 35 U.S.C. § 101 because they don’t exist in nature and cannot exist without significant human intervention.

    To put it succinctly and bluntly (and using my dad’s favorite expression), Judge Sweet’s statement that the “clear line of [SCOTUS] precedent and accompanying lower court authorities, stretching from American Wood-Paper through to [Chakrabarty v. Diamond], establishes that purification of a product of nature, without more, cannot transform it into patentable subject matter” simply doesn’t “hold soap” in my view.

  144. >>doing this to advance science and the public >>interest,

    You may want to spend some time to understand how the system is really functioning. It is true as a researcher it can appear that patents block progress, but when you spend some time looking at the bigger picture, you find that patent provide captial and motivation.

    When I was a researcher, I thought patents were a bad idea too. It wasn’t until I started working in startups and in big corporations that I realized the value of patents.

  145. Jon, forget “transformation” for a minute and, as a biologist, answer me this question.

    Imagine yourself back on the date at which the validity of this claim must be assessed. I don’t know but it might be 10 or 12 years ago. Now imagine reading the specification, on that day. All those years ago, would there have been anything in it at all that you (as a molecular biologist) didn’t already know? Because if there was something, then Myriad back then had indeed contributed something to the state of the art, added something to the stock of knowledge possessed by the interested molecular biological public.

    If there is something, then Myriad has progressed a useful art. They are inherently patentable, have novelty, enablement, sufficiency of disclosure and now just need non-obviousness.

    Books have sentences. But they are separated by periods, and are written in human-readable form. Your analogy is not exact, is it?

    Do not fall into the trap of deciding now what must be decided back then, on the state of knowledge when the “invention” was made.

  146. “What is even more galling when it comes to the Patent Bar is that these lawyers actually try to pretend that they are doing this to advance science and the public interest, rather than very narrow and powerful economic interests built upon coercive monopolies which they wish to preserve at all costs.”

    calm down there lil buddy. you’re gonna run out of moral outrage. also doubt you were jumping up and down like this about lawyers when tort reform was left out of the healthcare package.

  147. I’d like to add a molecular biologist’s take on this and why the Myriad patents are invalid.

    For starters, the methods and techniques used to “isolate” the genes are ubiquitously used day in and day out for a myriad of different genes, excuse the pun.

    As to the idea that the isolated gene is unique, I often like to use a sentence structure analogy when explaining genes and DNA to non-scientists. If we think of the human genome as a book, a long collection of sentences, fragments, statements etc, then a gene can be viewed as a sentence in the book. Whether that sentence is in the book or taken out from the book, an example sentence of “The man drove his car to the store.” has the same meaning. The rest of the book might provide context, but that is not the issue. The issue, as I understand it, is the sentence. “The man drove his car to the store.” It means just that, be it part of the book or taken in isolation.

    If I could add a second example, can I patent a bone in my little finger? Ignoring the usefulness of this for a moment, if I perform surgery, and then cut out/isolate the bone, is the bone patentable? The bone in my finger is not naturally occurring outside my body. I don’t see much difference between this and Myriad’s patents.

    Myriad has done nothing to alter, modify, or improve the naturally occurring genes. They have a database of useful information correlating prognosis to genetic sequence, but this too is not the subject of the patent.

  148. >>this decision is viewed overwhelmingly as >>positive.

    Better step up funding to university research labs as private funding will dry up quickly.

  149. For quick reference, here are two of the invalidated claims:

    1. An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.

    1. A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 12A, 14, 18 or 19 in a human which comprises analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample or analyzing a sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1.

    A quick perusal of the case coverage on the net shows that, at least in the court of public opinion (with the predictable exception of Gene Quinn shatting himself), this decision is viewed overwhelmingly as positive.

  150. >>DNA, and in particular the ordering of its >>nucleotides, therefore serves as the physical >>embodiment of laws of nature—those that define >>the construction of the human body

    A law of nature? This is the same reasoning as in Benson. The adders are an embodiment of a law of nature. Isn’t the body just using a method to manufacture parts of the human body just as a chemist would? Why is that a law of nature? Maybe you could say it is an embodiment of a known method so invalid under 102.

  151. “yes these claims for these patents are gone unless Myriad appeals. But since these patents were set to expire soon (2014 or so), Myriad presumably has a game plan for dealing with it, and other patents to protect their franchise.”

    Myriad is going to appeal. See here:
    link to upi.com

  152. I wish to echo Lionel Hut’z point:

    Isolating soemthing is not an invention and should not be considered one. There is zero creation in an isolated DNA strand.

    There certainly may be creation in the method of isolation and that should be protectable, but the isolated element should not. It is a major flaw in our patent system.

    The argument really is that simple. You can try and “lawyer” it all you want to, but you are never going to convince a growing segment of the public clued into these issues that this was somehow a bad court decision.

    And for those lawyers who worship at the altar of “case law” and “precedent”, you might want to think about the dynamics that brought the Bilski case to the Supreme Court to begin with. I’m sure those who try to justify business method patents also said: ‘Striking down these patents goes against reams of case law, and threatens untold amounts of time and investment that people have put into this industry. It will obviously be overturned and deserves to be!’

    The ruling which struck down business method patents may or may not be overturned, but the point is that “case law” is far less important to the argument than you make it out to be.

    Given how fundamentally flawed the Fed. Circuit’s reasoning has been over broad areas of patent law, I wouldn’t put too much stock in their “precedents” when it comes to anything related to patents.

    Lawyers only use “case law” as a cudgel to try and avoid philosophical arguments that they know they can’t win in terms of convincing others of their position. So instead, they just cite their “authority” and claim that you are ignorant about the subject – so there is no need to try and argue and/or educate.

    What is even more galling when it comes to the Patent Bar is that these lawyers actually try to pretend that they are doing this to advance science and the public interest, rather than very narrow and powerful economic interests built upon coercive monopolies which they wish to preserve at all costs.

    All pretty pathetic if you ask me. This judge deserves high praise.

  153. Money, Lives (life styles) at stake are usually not a primary concern for the Courts compared to case law.

    My the naiveté is abundant this morning.

  154. Malcolm, to clarify, yes these claims for these patents are gone unless Myriad appeals. But since these patents were set to expire soon (2014 or so), Myriad presumably has a game plan for dealing with it, and other patents to protect their franchise.

    So unlike the situation for pharma (where losing fundamental patents can be devastating for the bottom line), Myriad may not need these patents at this point. They have a great head start on everyone else in the industry, and the university hospital labs may find that doing these assays commercially is much more challenging than they expect.

  155. Reading again the piece it all comes down to if an isolated DNA strand is by itself a new invention.
    In the strict sense the answer is no.
    Apparently everything is about the notion that in the DNA sequence to be patented the sequences for the BRCA1/2 genes is CONTAINED. Therefore extra DNA sequences would have been added around the parts of the sequence encoding for the BRCA1/2 genes. This would definitely be patentable since a transformation has taken place (the addition of the extra parts of the sequence).

  156. Money, Lives (life styles) at stake are usually not a primary concern for the Courts compared to case law.

  157. the question remains: are we talking here about a “purified” DNA sequence for the BRCA1/2 genes (which would have an altered sequence) or an isolation in a strict sense comparable to having a sequence of numbers and isolating a subset of it?

    If the sequence would be changed and the DNA would have utility then it would be patentable as an invention (a transformation would have taken place).
    In the second case no patentability would be possible since nothing has been transformed.

  158. the patent act was never written for biological inventions

    The patent act was never written against any sector of invention.

    rene_descartes needs to think this one over again.

  159. Isolating DNA doesn’t transform a fact of nature into something new and worth of patent protection.

    Patent law has as its justification the common good not the protection of inventors’ incomes.

    It’s disgusting to see how business treat these laws with disregard of the reasons why they were created. The limited monopolies allowed by the patent system are not natural rights but a trade off that society is willing to pay for something very beneficial to all.

  160. Well, if that from Doe is perhaps is not quite as crazy as it seems, it might be for the following reasons.

    1. it is no longer a given that the US is better off with its patent system than without it.

    2. The best defence of the patents system is pharmaceuticals. but in that area, in the last 20 years, there hasn’t much that is new and useful.

    3. The American tech companies got to global dominance with no help from the patent system but now argue that they are impeded by it.

    4. The leading American universities got to that status without help from the US patent system.

    5. The US patent system reduces the amount of “soft power” which the USA has, around the world.

    Now me, I think a properly functioning patents system is vital to the promotion of useful arts, which in turn is vital to safeguard all our futures. But the patent system can thrive only when the public gives it due respect. And for that to happen, there should be no “creep” of patent rights into subject matter not fit for patenting. Sorry to mention it yet again but, me, I like the European 101 definition of patentable matter because it produces rational debate, in which both sides are satisfied that their point of view is taken into account by the other side, thereby blocking corrosive creep, with attendant disdain for patent rights.

  161. Um, “containing sequences found in nature” misses the point that practically everything is found in nature.

    =====================

    Which is exactly why NOTHING SHOULD BE PATENTABLE and the PATENT SYSTEM SHOULD BE ABOLISHED!

  162. My interpretation of the opinion is that the court states that isolated DNA is based on analysis on something which already exists (like taking a piece from a puzzle). Invention is synthesis, not analysis, therefore isolated DNA cannot be patented.
    Afaiks the techniques used to isolate a specific part of the DNA could possibly be patented not the DNA itself.

    Scientists can only patent DNA if they think up a DNA sequence for themselves which does not already exist in nature.

  163. For me, what is interesting about this case is that the Decision is a Summary Judgment ie there was no genuine issue of material fact. Now, I’m not a US lawyer, so what follows is just my surmise. Any lawyers out there who can confirm or corerect the next paragraph?

    I had always vaguely supposed that a “Summary” Judgment is proper only when there are no doubts about the case. I take from the present case, however, that my supposition has always been wrong. A 50:50 balance in the jurisprudence is, of itself, no reason to decline the request of the plaintiff for a Summary Judgment.

    One more thought. Myriad was represented by a huge law firm that specialises in big patent cases. There can be no doubt that the judge is an intelligent fellow. So, how can it come to pass that the judge ignores, or fails to grasp the import of, all the relevant legal authority urged upon him by those stellar lawyers?

    Does the judge want to make a name for himself perhaps, as the one who defined the “tipping point” (or should we call it the “Sweet Spot”) on 101 issues?

  164. > Um, “containing sequences found in nature” misses the point that practically everything is found in nature

    You raise a good point. If they allow this, I’m going to patent “isolated stupidity” and point out that I’m “transforming” it by isolating and purifying something which occurs naturally.

    After that, I intend to sue everyone I dislike.

  165. I can remember similar instances where a decision of a wayward district court caused the patent bar to go into a tailspin before the case was ultimately corrected upon review. One that comes to mind is the Transco case, where I believe the ND Ill held that an applicant had to renew his/her best mode even when filing a straight continuatino or divisional application. There were at the time tales of woe how this would result in the invalidation of a spate of patents where, of course, no one had checked whether an inventor had developed a new best mode when a continuation was filed. Another more recent one involved one of the Cal. district courts holding that petitions to revive were only applicable for unavoidably abandoned applications, but not unintentionally abandoned applications, again potentially putting thousands of issued patents in jeapordy. Hopefully this case will be little more than a footnote in twenty years.

  166. Gene patents have been around for about 20 years or so, and it is only now that we have come to finally realise that gene patents are after all not valid!

    Is spotting a muted gene out of the whole thing such an easy task? Or it is only now that it has become an easy task?

  167. In other words we have a new task of defining the invention all over AGAIN. Are we claiming the benefit if hindsight? Appears like a few stabilished standards need to be revisited.

  168. Honestly, I’d be happy to see the whole lot of precedent over what constitutes patentability in relation to genetics overturned. Patents are intended to provide incentive to the advancement and betterment of society, not to fill the coffers of larcenous companies.

    Note that this works both ways. An inventory gains financial advantage for contributing to the progress of society, but conversely, no financial advantage is deserved for an inventory who stifles and harms the progress of society.

    This becomes the crux issue when it is universally understood that competition in industry is always in the interest of society, and the prevention of competition through patent control is never such.

  169. A lot of people here act like the USSC has never made a ruling only to turn around and find their intent perverted far beyond any thing they had intended. Or that the understanding of science has never changed or the public opinions and values.

  170. I feel better after reading Dennis’s comments. This ruling was ridiculous. The judge ought to be demoted to traffic court.

  171. This probably says more about society than the law.

    There is a (large) segment of society that is uncomfortable with this area of patenting, regardless of whether they understand the nuances of the issues (as if we do). Eventually, one of their guys will be on a bench somewhere. It’s probably a healthy outlet, even if it’s expensive for the specific parties involved. They get their pound of flesh in a court of law, and the Fed. Cir. restores order so no real harm occurs.

    I think legislation in this general area might be good, although generally I think legislators screw things up. Courts and lawyers do too, on extremely rare, isolated occasions.

  172. Perhaps some are missing the point of patents: to be beneficial to society. Clearly this patent is not. It stifles innovation to the nth degree.

  173. the patent act was never written for biological inventions; it is time to re-write the statute to seriously consider where biological inventions fit in.

  174. Kevin, agree with your comment except for a couple bits:

    In some ways I think Myriad should not appeal … Walking away from this train wreck will leave one lonely case in one Federal court that is binding precedent on no one but the parties.

    Unless I’ve misunderstood something, the claims that were found invalid here can not be asserted against any other party, unless Myriad appeals.

    invalidation of the method claims are based on Bilski, so that part of the decision has a very short halflife.

    But permanent for Myriad, no? unless they appeal?

  175. Now, Malcolm, we all saw this coming. And the decision is in many ways the best we could have hoped for.

    First, invalidation of the method claims are based on Bilski, so that part of the decision has a very short halflife. Second, the “products of nature aren’t patenable” argument depends on not reading the case law correctly, not understanding the reach of Chakrabarty and not understanding the science at all.

    But the best outcome is dismissal of the constitutional challenge. That was the portion most apt to get the Supreme Court’s attention, and with it gone this is a much less interesting case.

    In some ways I think Myriad should not appeal. Despite Dennis’s provocative title, all gene patents are not invalid – not even all claims of the patents in suit are invalid. Unless Myriad appeals, the plaintiffs have no standing to appeal – they won; you can’t ask the court to rule that you should have won on some other basis when you win. And without the plaintiff patients, doctors and medical groups, PubPat and the ACLU have no standing to appeal.

    Walking away from this train wreck will leave one lonely case in one Federal court that is binding precedent on no one but the parties. If the anti-gene patenting folks want to try to invalidate gene patents one at a time, let them. It will give them something to do.

  176. Sweet dumped the standing issue in an earlier ruling against motions by Myriad and the USPTO to dismiss this case. That told me that Sweet was going to do the “unthinkable” as he did in this ruling which, I’ll say it again, is “inane.”

    Well then this strikes me as an easy reversal for the CAFC if they disagree with Sweet’s standing ruling, unless Myriad was unable to preserve the issue.

  177. “Isn’t there a standing issue here outside of the 101 issue? How does the coalition of scientists and the ACLU have standing to sue here?”

    Willton,

    Sweet dumped the standing issue in an earlier ruling against motions by Myriad and the USPTO to dismiss this case. That told me that Sweet was going to do the “unthinkable” as he did in this ruling which, I’ll say it again, is “inane.”

  178. Mike, there is extensive discussion of Parke-Davis. The court said the issue before Hand was not patentable subject matter, but novelty — whether purified adrenalin was new.

    The court conductive extensive analysis of Supreme Court authority. On its face, it seems persuasive.

    I still lean towards the proposition that one cannot claim a naturally occurring product of nature as a composition of matter. One should, however, be able to claim it in a different form as an article of manufacture, especially if that form does not exist in nature and if that form is made by man.

    It appears that the court was persuaded that “isolated” DNA is also naturally occurring.

  179. ping, many practitioners assume that “radically different” (or sometimes even “different”) automatically equals “unexpected.” It doesn’t. And keep in mind also that it’s unexpected to one of ordinary skill in the art, not a layperson. Ordinary skill in the art of genomics probably requires at bare minimum a Ph.D.

    In other words, would the DNA behave differently, when isolated, than what one of ordinary skill in the art would have expected the DNA to behave, when isolated? If they can prove that statement true, then the isolated DNA is unobvious.

  180. Isn’t there a standing issue here outside of the 101 issue? How does the coalition of scientists and the ACLU have standing to sue here?

  181. isolated DNA has unexpected features when compared with natural DNA. Good luck with that.

    Well, since the snippet is minus end pieces and does things radically different than the full piece, I’d think that “good luck” won’t be necessary (at least with handling that burden.

  182. It seems like someone is conflating 101 with obviousness. The courts have consistently held that a pure product is different from an un-purified product. See In re Bergstrom, 427 F.2d 1394. Thus, the assertion that natural DNA is essentially the same as isolated DNA fails prima facie.

    The claims should be invalid based on obviousness, i.e., purification of a known product does not render the product (purified human DNA) patentable. See Ex parte Gray, 10 USPQ2d 1922. According to that case, the burden is to show that isolated DNA has unexpected features when compared with natural DNA. Good luck with that.

  183. “new alloys and drugs ”

    Maybe new drugs, new alloys do not merely comprise cutting off the ends of something. They are, by definition?, the combination of two+ things.

  184. “So, no squirming here. I would have liked to have been in the room when Noonan saw this decision, though. ”

    That is exactly what I thought. That dude is gonna lose his top!

  185. What? No mention of the landmark “isolation” case of PARKE-DAVIS in all this discussion? Check it out: 189 F. 95 (SDNY 1911) (Hand, J.)

  186. Ooooh it burnses! It freezes!!!!! Surely all progress in such arts will come to a screeching halt!!!!!!!!!!!!!

    lololol

    I will like to see what happens with this at the Fed. Circ.

  187. Can sequence information encoded on a “purified” molecule be patentable under 101, while the same information encoded on a wholly man-made apparatus (e.g., a hard drive) is not?

    In the former case, the “information” itself is not patentable. It’s the new composition of matter with substantial utility that is patentable under 101.

    You say “assume utility for both cases” but the fact is that you can’t patent a DNA sequence that has no known utility except to store the “information” of its own sequence. That would be an insubstantial utility and claims to such molecules have already been found unpatentable under 101.

  188. I think we might have some confusion here. The opinion seems to say that naturally occurring DNA is not patentable per se as a composition of matter. On its face, this seems right.

    But the claim is not to naturally occurring DNA, but to purified DNA. This seems more like a claim to an article of manufacture — like shredded wheat. Now the court holds the claim to purified DNA is effectively a claim to the composition of matter because the DNA remains unchanged.

    Something is wrong with this analysis.

  189. MM,

    Can sequence information encoded on a “purified” molecule be patentable under 101, while the same information encoded on a wholly man-made apparatus (e.g., a hard drive) is not?

    Assume utility for both cases.

  190. “Unless the opinion is a lot more learned than the posted snippet suggests, when it reaches Newman, it’s gonna’ last about as long as a ripe peach in a Gerber’s factory.”

    BB,

    Love your statement! Sweet’s opinion shows his mental age (and bias). If the Federal Circuit doesn’t torch this opinion, we might all need to consider a new line of business, as logic and legal precedent will mean NOTHING.

  191. The sound argument as I see it is:

    – The claimed sequences are not different in their biological significance between the naturally occurring and isolated versions (if they were, the test would be useless as it is the biological phenomenon we are interested in)
    – Isolation “transformation” is a necessary step due to current technical limitations, not fundamental to the “comparison” of sequences. i.e. it is just data collection
    – The “comparison” is an algorithm, which is not patentable.

    With new single-molecule sequencing technology, it is now becoming possible to observe the DNA without the kind of isolation Myriad describes…will they happily let people “compare” the genes without ligitation? Too much money is at stake for them…

  192. squirm MM squirm

    I’m not squirming because, as Dennis notes, this decision will be reversed, at least in part.

    Some of the method claims may actually be invalid under 101, to the extent they involve only looking at sequence information and making a correlation. The Supreme Court’s decision in Bilski may impact that result.

    But there really is no credible distinction that can be made between a purified DNA molecule per se and any other purified substance, at least not under 101.

    The appropriate way to deal with the allaged “problem” of patenting isolated genes is to legislate. I’m not sure there is enough political will to accomplish that, but even if there were, it wouldn’t affect my ability to find inventions to prosecute in the chem/bio arts.

    So, no squirming here. I would have liked to have been in the room when Noonan saw this decision, though.

  193. There is no prohibition against patenting mental steps in the statute.

    The silly insistence that mental steps are somehow appropriately in a realm of the unpatentable has lead to a series of more and more rediculous rulings.

    That fundamental wrong turn in Judicial thinking is what should be reviewed and reversed.

  194. Of the short excerpt of the opinion posted, I would focus on this sentence.

    “Therefore, the patents at issue directed to “isolated DNA” containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 USC 101.”

    Not good.

    Had the learned judge said “. . .directed to ‘isolated DNA’ RESTRICTED TO sequences OF CODONS found in nature. . .” I think the opinion might have a snowball’s hope of surviving review.

    I, personally, do not feel that a naturally occurring sequence of codons or an isolated, unmodified stretch of naturally occurring DNA should be 101 eligible.

    But that’s not what the opinion goes after. According to this excerpt, as long as the DNA stretch CONTAINS naturally occurring DNA, it’s not 101 eligible. Bad call. Every sequence of DNA contains naturally occurring DNA. A single codon is “naturally occurring DNA.”

    You could isolate a sequence and then tag brilliant stuff onto the 3′-end or onto the 5′-end; you could add promoters and inducers and fluorescence markers and any number of cool control elements; you could modify it up one side and down the other — and as long as what you had at the end CONTAINED naturally occurring DNA, it would not pass Sweet’s muster.

    Even if some whiz synthesized a gene completely de novo that would reverse Michael Steele’s bald spot — that completely man-made gene would have to have codons, which are, of course, naturally occurring DNA. There is no such thing as a functional gene — not even a man-made one — that does not “CONTAIN” naturally occurring DNA.

    Unless the opinion is a lot more learned than the posted snippet suggests, when it reaches Newman, it’s gonna’ last about as long as a ripe peach in a Gerber’s factory.

  195. As indicated by casualObserver and crelboyne, the major flaw in this decision is the confusion made by Judge Sweet between a chemical (the nucleic acid, which I believe is patentable) and an information (which is borne by the sequence of chemical). Actually, the information only makes it possible to deduce the sequence of the encoded protein (and only if this is cDNA). Having only a novel DNA sequence in hand (or on the computer screen !) never gave a scientist access to the actual role of the gene without performing some kind of experiments.

    I hope that this decision will be reversed by the CAFC. If not this would jeopardize lots of patents and the business model of a lot of biotechs (Amgen, Genentech…) as well as of Monsanto.

    I believe that these patents (I drafted the opposition brief in Europe) raise the question of the nature of the monopoly that is actually granted by the patent and of the restrictions that could be applied to prevent an abuse of monopoly by the patentee (compulsory licenses and so on). There are some provision in French law about this and the Supreme Court has started to address this issue in recent decisions.

  196. This decision goes against such a boatload of precedent that it’s practically a non-event: There’s no doubt in my mind that the CAFC will overturn this, and I wouldn’t be surprised if the USSC denied cert.

    On the other hand, it does highlight the gulf of understanding between the patent priesthood and the public at large.

    IMHO, this sort of patent protection is vital to promote progress in the development of diagnostics and other biotech products and the ignorance of the general public, lower courts, and legislators will bite us in the ass.

  197. The gist: purified DNA is not a new composition of matter. Utility is not the issue.

    I assume the same is true broadly, far beyond DNA.

    I understand Max to say, that in Europe, one must claim the utility in some manner with the purified element of nature.

    I see nothing fundamentally wrong with this analysis. Perhaps I am missing something.

  198. So, on the issue whether to do away with “absolut Stoffschutz” aka “monopoly rights for a chemical compound, per se” and revert to the status quo ante, we have two counter-arguments, namely:

    1. it is difficult to police infringement and

    2. reduced opportunities for patent attorneys to bill out hours.

    Based on my experience under the EPC, I don’t accept either counter-argument. The EPC gives broad protection for the first medical use, and full protection for every subsequent non-obvious medical use.

    For me, the greatest protection for our profession, long term, is that the public increasingly sees the patent system as a “good thing”. For that to happen, scope of protection must be conformed closely to the magnitude of the inventor’s contribution (to that technical field that is graced by the subject matter of the claim).

    If the technical field is surface treatments for polished wood surfaces, that is one thing. Edible syrups strikes me as a different field. I fail to see where the floor wax company contributed anything to the ready meals industry.

    But James Daily, my compliments, on a delicious hypothetical.

  199. casualObserver is dead-on. You have found the core flaw in Sweet’s analysis (not a trivial task in a 150+ page train wreck of a decision).

    All structure conveys information. From chemicals to stop signs, shapes and chemical/physical interactions convey information.

    Sweet has unfortunately fallen prey to the media-driven upswell of emotion that DNA is unique in biology. These people have given DNA an almost spiritual meaning. They talk about the genome as if it had a mind (“directs the functions of the cell”).

    Sweet will get obliterated at the CAFC. Supreme Court is a closer question.

  200. It doesn’t seem to me that the decision is based on much analysis. Rather, Judge Sweet seems to be quite persuaded by her allegation that gene patents are “a “lawyer’s trick” that circumvents the prohibitions on the direct patenting of DNA in our bodies but which, in practice, reaches the same result.”

    That section of the opinion is telling – the court doesn’t go through a 101 analysis as applied in previous higher court decisions (CAFC,USSCt). Almost like the court is making a policy ruling that ignores precedent.

  201. The court focuses on the high-level encoding function of DNA as its “essential characteristic”, and on that basis is willing to overlook lower-level physical and chemical differences in the isolated form of the material. Different, perhaps, but not “markedly different”. I can’t see this decision surviving an appeal.

  202. If the courts below and above the Federal Circuit keep this up many of us going to have to give up on patent law and get real jobs.

    The Federal Circuit is one day going to be seen as little more than the failed guardian of the patent bar’s interests, and having the same relationship to it that Ben Bernanke’s Federal Reserve and Timothy Geithner’s Treasury have had with Goldman Sachs. Except that the Federal Reserve and the Treasury Department apparently never have to answer to the Supreme Court.

  203. NAL,

    Isolating soemthing is not an invention and should not be considered one. There is zero creation in an isolated DNA strand.

    There certainly may be creation in the method of isolation and that should be protectable, but the isolated element should not. It is a major flaw in our patent system.

  204. Isn’t this decision akin to saying all rubber materials derived from natural rubber (i.e. the rubber tree) are unpatentable under 101 because to get the final rubber material you would be using well known methods/additives into the natural rubber?

  205. MaxDrei: The problems there are manifold. First, some utility must already be shown, even if it need not be claimed as a limitation on the invention. Second, field of use restrictions often open the door to difficult-to-prove contributory infringement.

    For example, if I patent X as a floor wax and a year later Y patents X as a dessert topping, then Y may find it very easy to sell X as a dessert topping knowing full well that many consumers will use it as a floor wax. But I would be essentially powerless to stop it because Y has the good faith excuse that Y is manufacturing and selling X only as a dessert topping. If I had a patent on the compound itself, for all uses, then there would be no such issue.

    Third, most field of use restrictions can be expressed as method patents. For example “A method for treating disease X comprising administering drug Y.” This is common in the US but not allowed in Europe, as I understand it.

  206. “3. If I have a plant vine from the jungle and cut off each end, does the remaining portion meet 101?”

    Yes, a rope (if the vine is pliable) or a spear (if it is not) would pass 101. So would a drug (e.g., aspirin from the bark).

    102 and 103? Nope.

    Yes, I understand your misgivings. But your position, taken to its logical conclusion, would put things like new alloys and drugs on the unpatentable side of 101.

  207. 1. ‘Member in the old days were SNDY pumped out the big brain decisions? Obama’s “change” even got to SNDY. Welcome to the new world, everybody.

    2. “DNA’s existence in an “isolated” form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes.” >>>> Oh, so that is the 101 standard and not some “lawyer’s trick”.

    3. If I have a plant vine from the jungle and cut off each end, does the remaining portion meet 101? If that is the entire gene 101 argument, then it should be easy to use existing patent law attack it via 101 and not have to resort to some “lawyer’s trick” to appease a bunch of cry babies who are not capable of inventing things or want to take other’s hard work.

  208. I look forward to a grand unifying theory of the patentability of claims directed to “Molecule X”. I should like to see them outlawed. Better would be to tie them to a particular utility, like:

    Medicament for disease Y, namely X

    Run faster juice, containing X

    Wrinkle smoother composition containing X

    Means to improve powers of concentration/memory, with ingredient X

    Sedative X

    Party drug X

    Muscle bulker X

    and so on.

    Pipe dream, I know. But one can dream.

  209. NAL,

    I’m with you on this absurd and misguided opinion by Judge Sweet. What Sweet has done here is an absolute travesty and simply caters to the ACLU’s deliberate distortion of what these patents cover. Characterizing “isolated DNA” as being essentially no different from nature simply caters to another popular misconception of the media. That Sweet also rely’s upon the “machine or transformation” test in Bilski takes this opinion from the sublime to the surreal.

    Most significantly, what Sweet has ruled here cannot be squared with what the CCPA (now the Federal Circuit) held in the 1977 case of in In re Bergy: items isolated from nature are not nature and are patent-eligible under 35 USC 101. In fact, Sweet’s ruling cannot be squared with SCOTUS’ ruling in Diamond v. Chakrabarty. I frankly grow weary of “amateurs” (like Sweet) opining on that which they don’t understand. I can only hope the Federal Circuit will trounce this misguided decision.

  210. Lionel,

    The common sense reply would be to ask you if the material that makes up the printed circuits are found in nature. If that direct material is made by man, then ask the same question of that material. Clearly (unless you are Jerry Lawler), I am not saying that circuit boards are but a single step from nature, but all that is required for patentable subject matter is a single step from nature. The step of man’s invention.

    Sooner or later it all comes down to nature and what man makes of nature.

    It’s as simple as that.

  211. NAL,

    Seriously? You’re defending gene patents? Can you please identify where printed circuits are found in nature?

    Common sense and a basic understanding of 101 should tell anyone with common sense isolated DNA is not patentable.

  212. Common sense?

    Um, “containing sequences found in nature” misses the point that practically everything is found in nature.

    It is what happens after finding the raw material that is the object of man’s actions, and it is the ensuing actions that result in things patentable.

    Patent law simply does not recognize “distinct in its essential characteristics from any other chemical found in nature as a valid quarantine of patentable subject matter – this judge has violated controlling authority and will be smacked down.

    This is an application of “common sense” only as it is common for most people to be wrong on things they do not understand.

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