Myriad: Isolated DNA claims from “ball bats in trees,” and “kidneys” to “magic microscopes.”

By Mary Beth Tung
September 25, 2011

The July 29, 2011 Federal Circuit decision in Assoc. for Molecular Pathology et al. v. U.S.P.T.O. and Myriad Genetics has been eagerly awaited by the biotechnology community and by persons concerned with the ethical implications of DNA technology. Although a significant part of the decision involved standing to sue, I will only discuss the scientific portions of the decision that deals with the very real ethical question of whether human genes and/or gene sequences should be patented.

The decision in Myriad was written by Judge Alan Lourie with concurrences-in-part by Judges Moore and Bryson. Judge Bryson also filed a dissent-in-part. Judge Lourie, who has a Ph.D. in chemistry, is well suited to understand all the issues associated with genetic sequence cases and has written some key biotechnology decisions, such as the Regents of the University of California v. Eli Lilly, 119 F.3d 1559 (Fed. Cir. 1997) (Cloned human insulin product did not infringe patented rat insulin.) and In re Deuel , 51 F.3d 1552 (Fed. Cir. 1995) (Settled an issue of obviousness between genetic sequences). Judge Bryson was also part of the Lily decision.

To even begin to understand the issues at stake, beyond the news headlines, the DNA principles behind the technology need to be explained. Genes, the hereditary components of organisms, are made up of four nucleic acid molecules, called “bases”, (adenine (A), guanine (G), cytosine (C), and thymdine (T)) which form chains of polymers with varying sequences of the nucleic acids. One chain of the DNA polymer will bind a complementary chain in that only a C will bind with a G, and a T will only bind with an A. An example:

The two strands occur most frequently as a double helix wrapped around other components in the nucleus to prevent tangling such as occurs with the old coiled telephone cords. The DNA can then be “translated” into proteins using cellular machinery that creates complimentary 3 base RNA molecules that then carry the message to the ribosomes in the cell that use each three-base message to link an amino acid onto a growing protein chain. Thus, all the proteins in our body, from hair to stomach enzymes are translated from the DNA template to form proteins using a “program” that is encoded in the DNA of the nucleus of each cell. Each different type of cell uses different parts of the DNA to make proteins unique to that cell. The unused DNA is shut off. The technology was well explained by Judge Lourie in the Lily case:

DNA functions as a blueprint of an organism’s genetic information. It is the major component of genes, which are located on chromosomes in the cell nucleus. Only a small part of chromosomal DNA encodes functional proteins.

Messenger ribonucleic acid (“mRNA”) is a similar molecule that is made or transcribed from DNA as part of the process of protein synthesis. Complementary DNA (“cDNA”) is a complementary copy (“clone”) of mRNA, made in the laboratory by reverse transcription of mRNA. Like mRNA, cDNA contains only the protein-encoding regions of DNA. Thus, once a cDNA’s nucleotide sequence is known, the amino acid sequence of the protein for which it codes may be predicted using the genetic code relationship between codons and amino acids.

Judge Lourie provided some nice diagrams in both the Lily and the Myriad cases which further describe the process.

The basic argument in Myriad is whether DNA that is isolated from the chromosomes is statutory subject matter, or whether it is a product of nature. The stakes are high in the Myriad case, since the isolated DNA claimed by Myriad encodes mutated BRCA1 and BRCA2 proteins that can be used to detect breast cancer. Myriad has the only test offered in the United States because of its aggressive enforcement of its several patents. The numerous plaintiffs in the case speak to the core of the patent versus non-patent debate: whether patents actually “promote the progress of science and useful arts” as required in the U.S. Constitution. Myriad and other companies heavily reliant on biotechnology patents, would support the argument that strong patent enforcement allows companies which have invested millions or billions in assay or drug development for clinical use to recoup their investment and provide a return for investors. The plaintiffs would argue that such patents not only hinder the useful arts, but also endanger lives and/or drives up the cost of providing potentially life-saving testing and treatment. The anti-patent argument is beyond the scope of this writing, but lies at the core of the plaintiffs’ arguments.

Biotech and DNA patents in particular, evoke strong public and personal sentiment because the genetic material which is built from DNA building blocks encodes who and what we are. DNA is the material that makes up the “genes” that we pass on to future generations and determines that we are human, and not “rat” as aptly demonstrated by the Federal Circuit decision in Eli Lily. The lead biotech case was Diamond v. Chakrabarty, 447 U.S. 303 (1980), a lab-created bacterium that broke down crude was found to be patentable subject matter under 35 U.S.C. 101. The decision, written by U.S. Supreme Court Justice Burger held that “Congress plainly contemplated that the patent laws would be given wide scope” and concluded that Congress had intended patentable subject matter to “include anything under the sun that is made by man.”

Gregory Castanias of Jones Day argued for Myriad and in line with Chakrabarty, asserted that “isolated DNA” is patentable because it is “a non-naturally occurring composition of matter.” To support their contention that isolated DNA sequences are distinct from sequences found in the body, the Myriad attorney used an analogy that a baseball bat is patent-eligible even though the tree it comes from is a product of nature and ineligible under 35 U.S.C. 101. Judge Moore stated that in both the baseball bat and an isolated DNA, man decides what is to be kept and what is to be discarded, and thus both are patentable. This was the first of odd analogies in the colorful exchange between counsel and members of the three judge panel.

Chris Hansen of the ACLU argued that isolated DNA is no more patentable than a kidney removed from his body or that the use of a scalpel is no different than any chemicals used to remove the isolated DNA from a body. Judge Lourie disagreed and pointed out that breaking covalent bonds can result in a compound that has different characteristics and alters the chemical identity of the substance that has been isolated; that DNA wrapped up in a body cannot be tested. Judge Moore in her concurring decision pointed out that diagnostic testing is beyond what nature does with DNA in the body. Judge Bryson stated that merely breaking bonds does not render DNA patentable, whereas Judge Lourie held that the new bonds created a new chemical entity. Judge Lourie distinguished from the dissent by saying that “a covalent bond is the defining boundary between one molecule and another”. Quoting Linus Pauling, she said that the covalent bond is a means to determine an “independent molecular species.” Further, Judge Moore assailed the government’s proposed “chemical alteration” test, which would render a claim patentable under 35 U.S.C. 101 if a chemical alteration of a bioactive molecule” leads to different properties, such as better absorption in the body.” She pointed out that isolation of DNA sequences is not sorting wheat from chaff, but creating a new DNA molecule. She also cautioned that the tests proposed by the government are not limited to just DNA, but could also encompass far broader technologies.

The hypotheticals continued with Mr. Hansen stating that “gold in a mountain” cannot “be made into jewelry”, at which point Judge Louire countered that gold in a mountain is the same mineral as when extracted, but that an isolated DNA is a different chemical composition. Judge Lourie, being the consummate chemist, reminded Mr. Hansen that a 50 base pair DNA sequence is a totally different molecule than a 100 base pair sequence.

Not to be outdone by others in the hypothetical war, the U.S. Department of Justice Acting Solicitor General, Neal Katyal suggested a “magic microscope” test that could “see” into the gene; if the sequence was the same as one found in the body, then the sequence is not patentable. The DOJ position is particularly troubling since the position is in direct opposition to the Patent Office position for over 35 years of issuing such patents and as outlined in the 2001 Utility Examination Guidelines, a point not lost on Judge Moore, who repeatedly questioned Mr. Katyal about the discrepancy with the PTO long standing policy and questioned why the government is not speaking with one voice; later calling the magic microscope test, “kitschy.” Mr. Katyal responded that he thought the position of the Patent Office was “wrong.” It appears that even after the long “high level” discussions that Mr. Katyal indicated occurred between DOJ and the PTO about the allowability of isolated DNA claims, and given that the U.S.P.T.O. did not appeal, the conclusion can be readily drawn that the current administration views isolated DNA as not patentable, except for limited circumstances, such as cDNA.

Judge Moore, in her concurring decision, likewise agreed that a “gene” should not be patentable subject matter, since gene sequences are actually found in the body and she reasoned, genes have no utility for diagnostic assays. However, she continues, since “settled expectations” have arisen from both Congressional action and the “thousands of patents with claims to isolated DNA sequences” then patentability of such claims should not be overturned by the courts. However, science has not yet decided what a “gene” is. A general definition is that one gene encodes one peptide, or protein sequence. However, a publication in 2007 in Genome Research by Mark B. Gerstein of Yale University states that, “A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene.” (emphasis added). The definition, also does not discuss non-genomic regulation of the DNA, such as binding of inhibitors or enhancement factors to the DNA chain that occurs during transcription in the body, but not in a test tube. The difficulty in determining the scope of a claim or any party’s position on patenting of “genes” is uncertain given this definition; an uncertainty which is well-known in the biotech examining corps.

However, in a statement that was woven throughout the Myriad discussions, Justice Burger wrote in Chakrabarty that, “[w]e have cautioned that courts “should not read into the patent laws limitations and conditions which the legislature has not expressed,” which seems to be consistent with Judge Moore’s position. Judge Bryson, while agreeing with the majority on the patentability of cDNA and method claims, dissented on the patentability of gene sequences. Judge Bryson limits Chakrabarty only to “a nonnaturally occurring manufacture or composition of matter,” (citations removed), which was fulfilled with an engineered bacterium not found in nature, but not for genes, since “[t]he only material change made to those [BRCA1 and BRCA2] genes from their natural state is the change that is necessarily incidental to the extraction of the genes from the environment in which they are found in nature.” Bryson then compared an isolated gene to a new mineral discovered in the earth or new plant found in the wild as only being useful once extracted.

Judge Moore bluntly stated that the “Executive’s” position recited by the Solicitor General would “destroy existing property rights.” Judge Moore additionally states that , “[w]e cannot, after decades of patents and judicial precedent, now call human DNA fruit from the poisonous tree, and punish those inquisitive enough to investigate, isolate, and patent it.” Well said, Judge Moore!

The ACLU requested reconsideration of the decision by the same panel based on assertions that Judge Lourie’s explanation of covalent bonds resulting in a distinct DNA molecule was an error because neither side had presented the argument. The ACLU Petition was denied on September 13, 2011, and Myriad’s Petition was denied on September 16. Since an en banc rehearing was not requested it has been waived. It appears that cert. by the Supreme Court is the only option for both parties at this point.

The Author

Mary Beth Tung

Mary Beth Tung

Warning & Disclaimer: The pages, articles and comments on IPWatchdog.com do not constitute legal advice, nor do they create any attorney-client relationship. The articles published express the personal opinion and views of the author and should not be attributed to the author’s employer, clients or the sponsors of IPWatchdog.com. Read more.

Discuss this

There are currently 95 Comments comments.

  1. melvin udall September 25, 2011 12:55 pm

    In the case of Myriad, the isolated nucleic acid claims do not impact testing to identify whether a woman carries one or more mutations associated with susceptibility to cancer. Test is done by extracting and purifying genomic DNA, subjecting it to PCR amplification to amplify the exons of BRCA1/2, and then sequencing the amplicons. Only thing that could possibly be implicated is the 15mer claim, but this claim is certainly invalid due to both 102/103 and/or 112 (claim doesn’t even require that the 15 nucleotides be consecutive!). And even if it’s not invalid due to 102/103 and/or 112, the only way this claim is implicated is if you assume the individual amplicons are “isolated” from the genomic DNA template during the amplification process, which, of course, they’re not. Make no mistake about it, the only claims Myriad really cares about are the diagnostic method claims (particularly those that are not limited to detecting individual mutations). And this particular panel invalidated those. The only disappointing thing in the panel’s decision is that it implied that if the claim had specifically recited the old physical steps of obtaining the DNA sample, etc., the claim would have passed 101, which of course is silliness, but it doesn’t matter because the Supremes are going to address that in Prometheus.

  2. EG September 26, 2011 7:32 am

    “The anti-patent argument is beyond the scope of this writing, but lies at the core of the plaintiffs’ arguments.”

    Beth,

    The plaintiff’s argument (especially as disingeniously espoused by the ACLU) is almost entirely based on anit-patent nonsense. In fact, the positions taken by the plaintiffs essentially takes the view that technology should be free (somewhat like freeware and shareware). and that money grows on trees. Denying patent rights on isolated DNA would rudely awaken these plaintiffs to a world were such technology would no longer be available, or worse yet kept as a trade secret. (Please note that I’m not saying Myriad didn’t make a huge PR gaff by their alleged “aggressive” enforcement of patent rights.)

    I too am a chemist, and I find position postulated by the ACLU that isolated DNA is somehow the same as what’s in “mother nature” absurd in the extreme. In fact, I find it somewhat ironic that the same ACLU that wants to restict any discussion in our schools about intelligent design would turn around and postulate a theory that is essentially “voo doo” science.in the AMP case. Again, the ACLU is hypocritical, two-faced, and fork-tongued, and the AMP case proves this point in spades.

  3. MTung September 26, 2011 9:00 am

    Hello all! An eagle-eye has caught the typo in the first paragraph. Obviously, legal history is important, but Myriad came out in 2011, not 2001.

    EG – unfortunately, the anti-patent sentiment in the public extends way beyond the ACLU and I think has its roots partially in the lack of understanding of the patent system. However, even folks that are very educated about the patent system feel that at the very least, some major overhauls are needed. Some of the recent changes in the patent act also reflects the sentiment. It really is a public policy issue of the interpretation of the Constitutional requirement to promote the progress of the useful arts: does that mean rendering to the public domain as soon as possible, or allowing business to have a monopoly to invest in their invention for profit? The balance betweent these two will always be, and should be a discussion. The Myriad case falls into this category, IMHO.

  4. SM September 26, 2011 9:11 am

    I am a chemist who has been in the IP field for 14 yrs. I see no difference in isolating DNA from a person and isolating a compound from a plant. From a chemist point of view, both are compounds that existed in nature and once extracted and isolated are useful. The only difference is the source of the compound. Seems to me if you argue that you cannot patent isloated DNA, then you cannot patent isolated compounds. Then we would not have Taxol etc. Clearly not logical. You would have to come up with a reasonable rational explanation for the patentablility of a compound which existed in a living plant or tree, over patenting DNA which exists in a living human, that does not lead to the problem described above. Discriminating based on the source does not seem appropriate or logical.

  5. David Koepsell September 26, 2011 11:06 am

    There is no exception from logic for chemistry. The logical law of identity holds for all sciences, and an isolated X is still an X. All the utility arguments in the world don’t change that simple fact.

  6. molecular biologist September 26, 2011 11:57 am

    SM,
    Well articulated and logical for a newbie like me. But, if a compound isolated from a plant is patent-eligible , why not allow minerals to be patented? It too does not exist in pure form in nature.

  7. SM September 26, 2011 3:01 pm

    Molecular Biologist,
    There is a fundemental difference between patenting a compound or a gene then a mineral. Both the compound and the gene which have been isolated have a utility, meaning they have a practical application to a practical problem. The isolated mineral on its own has no use per se.

    SM

  8. EG September 26, 2011 3:18 pm

    “The logical law of identity holds for all sciences, and an isolated X is still an X.”

    Dave,

    May be in your “philosophical” world, but not in my “scientific/chemistry” world. And let’s just “agree to disagree” and leave it at that. As before, neither of us is going to change our opinion here.

  9. MTung September 26, 2011 4:16 pm

    Aside from the philosophical questions here, is the simple fact that DNA patents have been issued for many years (some by me while I was an examiner), and Judge Moore was fairly clear that to overturn years of PTO practice, and the corporate reliance on those patents, is a matter that is best handled by Congress, not the courts.

  10. molecular biologist September 26, 2011 4:22 pm

    “Both the compound and the gene which have been isolated have a utility, meaning they have a practical application to a practical problem. The isolated mineral on its own has no use per se.””

    No object has any utility vallue on its own unless it is utilized. A compound or isolated DNA cannot be patented per se unless a utility method is tied to it. So why is it different for minerals? Trying to educate myself here.

  11. Just visiting September 26, 2011 4:26 pm

    “The logical law of identity holds for all sciences, and an isolated X is still an X.”

    “an artificial tree is still a tree.”

    Both rely upon the incorrect assumption that the second element is a genus and the first element is a species of the genus. The genus of X does not include isolated X. Isolated X has different properties (so say my chemical colleagues). I think the game being played here is a redefinition of “X.” X is really “X in situ,” which is a “natural phenomenon.” By calling it X (instead of “X in situ”), David K is trying to redefine the issue to suit is arguments.

  12. Roland September 26, 2011 7:50 pm

    It seems obvious that naturally occurring DNA sequences aren’t patentable and this is what the (US )government asserts “isolated and unmodified genomic DNAs are not patent eligible, but rather patent-ineligible products of nature, since their nucleotide sequences exist because of evolution, not man.”

    The claim effectively made in the Decision that a segment of DNA undergoes an undefined magical transformation into something un-natural when removed from a cell and isolated is clearly laughable – this really is voo doo science. However the fact that two of the judges failed to see this even when given the more tangible analogy of a kidney gives cause for concern, particularly given the current R&D spend on growing organs for transplant…

    It also seems to be obvious that the processes used on DNA such as those used to isolate, ‘cleave’, duplicate a naturally occurring DNA sequence and splice together DNA segments into a shortened/abridged sequence should be potentially patentable, as would be the inventions that utilise the isolated DNA.

    Reading the Decision it would seem that matters have been confused by lack of consistency and precision in the use of key terms, for example ‘Isolated DNA’ can be read as referring to a single contiguous segment of DNA, but in the discussion it is revealed that it also refers to an abridged sequence. Likewise the names BRCA1 and BRCA2 are used to mean both the natural gene and the abridged version. Obviously, the natural version isn’t patentable, whereas the laboratory manufactured abridged version is (potentially) patentable.

    From a more general patent perspective, a key part of the exchanges were concerned not with “whether patents actually ‘promote the progress of science and useful arts’ as required in the U.S. Constitution” but whether “Myriad’s vigorous enforcement of its patent rights” and by inference patents in general, stifled commercial competition and by implication consumer choice.

  13. Just visiting September 27, 2011 12:52 am

    “but whether ‘Myriad’s vigorous enforcement of its patent rights’ and by inference patents in general, stifled commercial competition and by implication consumer choice.”

    Dude … that is what patents are used for. You cannot focus on an isolated part of the whole (although it certainly makes your arguments look better) — you have to look at the patent system, AS A WHOLE.

    Anytime you give somebody some right you necessary take away a right from somebody else. For there to be a winner, you also have to have a loser. They entire anti-patent movement is based upon the (incorrect) assumption that companies are still going to research just as much as they did before if patent protection isn’t available. The REAL WORLD works on return on investment — not free love, open source, crowding sourcing, communism.

    The goal is to encourage investment in innovation — (i.e., the progress of science and useful arts). Now, in order to encourage that investment in time, money, and/or opportunity, you have to provide a carrot. A patent is that carrot. I keep raising this point, but none of the anti-patent folks want to touch it. The world has a large variety of different economic, political, and legal environments. However, every modern country has a patent system and has had one for a very long time. Why is that?

    A world without patents is a world where the best copiers are the most valued. In contrast, a world with patents is a word where the best innovators are the most valued. I prefer innovators over copies, and it appears that the ROTW does as well.

  14. David Koepsell September 27, 2011 1:45 am

    Just Visitng: nice try, but “isolate”d is not the same as “artificial,” good attempt though at equivocation. Roland is spot on, the isolation does not effect a change in kind, merely context. The net result is defying the case-created exception to patenting products of nature or natural phenomena. Some of the claims in the Myriad case refer simply to isolated, unabridged segments, and those X’s are identical to naturally occurring X’s. But I know the law often defies logic in favor of entrenched interests. And Eric, the laws of logic are true, despite one’s perspective or background.

  15. David Koepsell September 27, 2011 3:54 am

    Just Visiting:

    I see also that in your genus-species argument, you risk conflating product with process. Products can never be species of a genus process and vice versa. So a person artificially-produced (like through IVF) is still a person, and not an artificial person. Your example of “artificial tree” is thus vague. Is it a tree biologically identical to other trees except in its genesis, or is it a plastic tree, meant to mimic a real tree, but qualitatively different as a product? In the case of merely isolated but otherwise unmodified genes or gene segments, the product – the gene segment or gene itself – is identical to the product as found in nature, although the process by which is was created is unnatural, artificial, or otherwise carried out by human intention. Reflecting back on the example of O2 molecules intentionally produced through electrolysis and O2 molecules produced through natural photosynthesis, electrolysis is an artificial process to synthesize and concentrate O2, but the resulting O2 is not artificial. No O2 is artificial as a product. Its structure and existence has nothing to do with human intention. Its structure and its genesis are distinct. X still equals X.

  16. Roland September 27, 2011 6:29 am

    Just Visiting (posting 13):
    Apologies for my final and slightly off-topic comment not being clear. The point I was making was that Mary’s article contained the statement:

    The numerous plaintiffs in the case speak to the core of the patent versus non-patent debate: whether patents actually “promote the progress of science and useful arts” as required in the U.S. Constitution.

    Whereas from my reading of the Decision, there was much discussion of patent enforcement by Myriad and the (negative) effect it had had on the plaintiff’s commercial service offering, but on the few occassions where the discussion touched on innovation (ie. “promote the progress of science and useful arts”), several of the plaintiffs were clear that they were still undertaking non-commercial (ie. research) work on BRCA1 and BRCA2, that would be patent infringing if it were commercialised.

    I personally feel that the quality of the evidence given, helps to inform the debate as to whether we have got the balance right between rewarding the innovator and benefiting the wider society.

    As to your final point “A world without patents is a world where the best copiers are the most valued.” I would agree with you in part; we only need to look at European history in the period 1000~1500 (ie. before patents as we would understand them) where scribes were highly valued (before they were replaced by the printing press) to see that this state of affairs can have significant social value, albeit that many original writers/thinkers were not renumerated for their work.

  17. Roland September 27, 2011 7:22 am

    Just Visiting:

    Sorry my last and slightly off topic comment was poorly put. I was trying to say that Mary’s statement:

    The numerous plaintiffs in the case speak to the core of the patent versus non-patent debate:
    whether patents actually “promote the progress of science and useful arts” as required in the
    U.S. Constitution.

    Didn’t seem to be reflected in the substantive discussions contained in the Decision. The discussions seemed to be more concerned with determining the extent to which Myriad had enforced their patents and the impact this had had on the plaintiffs, namely they had stopped providing a commercial service in an attempt to avoid possible costly patent litigation. However, several plaintiffs were clear that they had continued non-commercial/research work that potentially infringed the Myriad patents and hence implied that they hadn’t been discouraged from innovation in this area.

    In my opinion the quality of the evidence provides good real world case study into the impact of patents and their enforcement and the balancing of interests that the Patent system needs to take into consideration.

  18. EG September 27, 2011 7:42 am

    “the laws of logic are true, despite one’s perspective or background.”

    Sorry Dave, spoken with the “philosopher’s” bent, but not a chemist’s. The laws of chemistry say that when bonds are broken, you have a different molecule. That’s what isolated DNA is: a molecule disconnected from from what “mother nature” produces. And again, let’s just agree to disagree and let it go. Peace.

  19. Bobby September 27, 2011 7:45 am

    “They entire anti-patent movement is based upon the (incorrect) assumption that companies are still going to research just as much as they did before if patent protection isn’t available. The REAL WORLD works on return on investment — not free love, open source, crowding sourcing, communism.”
    Such an arrogant statement. First of all, you’ve conflated a world without patents with communism, which basically screams that you lack a real argument. Double that by your irrelevant mention of free love. You haven’t even picked straw man arguments that are even currently relevant, as your argument would be most effective with the parents of Baby Boomers.

    Furthermore, you indirectly say that the ‘real world’ doesn’t work on open source or crowd sourcing. Open source doesn’t easily translate outside of software, and crowd sourcing is itself not a particularly well defined term, so what is and is not these things isn’t entirely clear. However, both things that fit clearly within those terms and things that might be awkwardly called by those names play prominent roles in the world and in scientific progress. Participating in either may also result in a return on investment.

    You also left out a very important factor for how private resources are allocated to R&D in the ‘real world’: competition. A more competitive market means that a business must better compete to survive, which in itself might result in greater research. The importance of competition is the basis for antitrust laws. Another reality you are forgetting is that patents are not the only manner in which a business can get a return on investment. Being the first to market, having the most experience, and the advantage of an at least temporary trade secret may be more important to getting a return on investment. If I recall correctly, many surveys of businesses often put these factors as being more important than patents.

    Perhaps the biggest flaw is your continued insistence on exaggerating the importance of patents and an appearance of disdain for nuance, to the point of blindly insulting anything that happens to even tangentially conflict with your vision of how the patent system ought to be. Whether the effect of patents is positive or negative, most realistic assessments would put the impact of patents as far more mundane than what conversations lead us to believe. If you hold that patents can have a positive effect and you wish to have at least some root in reality, then patent policy needs to be meticulously crafted and adjusted, while your insistence seems to indicate an ‘up to eleven’ pigheadedness likely caused by an inflated sense of self importance. My apologies for making this too much of a personal matter, but you’ve presented very little of an actual argument, and your post was littered with brutish absolutes.

  20. Gene Quinn September 27, 2011 9:08 am

    DK-

    Actually, “isolated” is exactly the same as “artificial” in thus context because without human activity to isolate it would never exist in that form.

    I have long since given up on you understanding the science, or the law. I am gleefully happy, however, to point out that I was correct and you were incorrect. All your protestations, misrepresentations and mischaracterizations still didn’t matter. You and those who share your views have once and for all contributed to the settling of the law completely against your desired position. You and others conclusively and finally achieved the opposite outcome you desired. For that I say THANK YOU for your assistance and contribution to the greater good.

    -Gene

    Via iPhone from SFO

  21. Allison Williams Dobson September 27, 2011 9:37 am

    Regarding the following from David,

    “Just Visitng: nice try, but “isolate”d is not the same as “artificial,” good attempt though at equivocation. Roland is spot on, the isolation does not effect a change in kind, merely context.”

    This is where the non-scientists are missing something important. The product covered by an “isolated DNA” claim is not in fact isolated in the way you envision. The scientist does not merely separate the DNA segment from other DNA in the cell. Instead, the most common way to obtain “isolated” DNA is to use PCR – where short segments called primers locate the sequence of interest, and then other lab-generated molecules make billions of (non-natural) copies of the same DNA segment.

    The word “isolated” is merely used in the claims to prevent the scope from covering the same DNA sequences as they exist within the human body. Thus, “isolated” corresponds with “artificial” or, more properly, “non-natural.” Nobody has asserted a “gene patent” against a natural DNA molecule within the human body.

  22. MTung September 27, 2011 12:08 pm

    JV:

    “The numerous plaintiffs in the case speak to the core of the patent versus non-patent debate:
    whether patents actually “promote the progress of science and useful arts” as required in the
    U.S. Constitution.

    Didn’t seem to be reflected in the substantive discussions contained in the Decision.”

    I wasn’t saying that the plaintiff or anyone else argued these points in the case, but rather the fact that there were so many plaintiffs in the case exemplifies the patent vs. non-patent debate. Perhaps I wasn’t clear on this. However, the interest in the case and the vigorous debate here shows that the Myriad case is bigger than the court decisions that have arisen or will arise out of it. I’ve been living these debates since I first entered the lab…

  23. Roland September 27, 2011 3:03 pm

    Gene

    Thanks for your clarifying point, however I disagree on the equivalence of terms in this context.

    The word ‘isolated’ needs to be qualified depending upon context, due to the Judges in the section “Composition Claims: Isolated DNA Molecules” of the Decision noting that the “the government asserts, isolated and unmodified genomic DNAs are not patent eligible” and “the government argues that DNA molecules engineered by man, including cDNAs, are patent-eligible” and also note “the PTO’s longstanding position that isolated DNA molecules are patent eligible.”

    I think it is the discussion in the “Composition Claims: Isolated DNA Molecules” section that MTung is referring to in the statement “The basic argument in Myriad is whether DNA that is isolated from the chromosomes is statutory subject matter, or whether it is a product of nature.” Which seems to boil down to the question, is it sufficient to take a knife (physical or chemical) to natural DNA and hence put it in a form where it would not naturally exist or is it necessary to perform some further transformation/alteration to effect this change.

    R

  24. Just visiting September 27, 2011 3:19 pm

    “A more competitive market means that a business must better compete to survive, which in itself might result in greater research.”

    No … it will result in better copiers, not better innovators. If it costs $1 million dollars to innovate a new product while $1 to copy the product, why should anybody innovate? Even if the ratio is just $2 for innovation to $1 to copy, there is little incentive to innovate. In today’s economy, being a first mover gets you very little if everybody else is able to copy because copying can be done (depending upon the subject matter) in anywhere from minutes to just a couple of months.

    The new widget that you unveil in a tradeshow in Chicago on Monday can be on a container ship from China in a week to your competitor. The new piece of software you unveil today can be found in someone else’s software suite tomorrow. The new compound that you’ve isolated for treating X disease can be on the shelves at nearly the same time yours hits the shelves.

    “a world without patents with communism.”
    Sounds like a good analogy to me. In communism, the work of each and every individual member of the commune is shared amongst the commune, and no special rewards are given to those that contribute in a special manner (e.g., creating a machine that allows 1 to do the job of 10). In a world without patents, the intellectual property of individuals/companies are shared with the world with no extra compensation for those that created the intellectual property. As the world has learned with communism, except for the altruistic minority, the incentive is to do as little work as possible, because you maximize your return on investment (i.e., reward divided by effort). As a result, communism as an economic system (albeit seeming fair and just to intellectuals) was a disaster in reality.

    “the isolation does not effect a change in kind, merely context.”
    Let’s take H2O. When the bonds of the H2 are broken with that of the O, the resultant H2 molecule is DISTINCT from the H2 within the H2O molecule. This is a better analogy.

    “So a person artificially-produced (like through IVF) is still a person, and not an artificial person. Your example of ‘artificial tree’ is thus vague.”
    Such a simple example and you mess it up. A blow-up doll is an artificial person – not a personal artificially-produced. The analogy was that just because both elements include the word “tree” does not make them a species/genus or the same species of a common genus.

    “the point of blindly insulting anything that happens to even tangentially conflict with your vision of how the patent system ought to be”
    No … my insults are quite targeted.

    “conflict with your vision of how the patent system ought to be.”
    That should be written “conflict with [the current patent system]”

    “then patent policy needs to be meticulously crafted and adjusted.”
    Sorry … that is not going to happen. We are talking about the government. Meticulous crafting and adjusting means only means more money flowing from lobbyists to Congress and laws that aren’t based upon well-founded logic, but based upon who has more dollars. The current patent system provides incentives for the very big to the very small and does not (mostly) discriminate based upon technology. Your fine tuning would be done by people that care little about the long-term effects and more about the next election cycle.

    “you’ve presented very little of an actual argument”
    And you’ve done nothing to explain why, if a patent system is unnecessary, there are patent systems in every country with a modern economy?

    You’ve written that you want to end all intellectual property. Why should anybody spend tens or even hundreds of millions of dollars producing a movie if your world view prevailed? Explain to me how somebody is going to make money producing a movie? There … an substantive argument for you to chew on — please respond.

  25. David Koepsell September 27, 2011 4:30 pm

    GQ et al,

    Your insistence that “isolated” equals “artificial” proves you continue to fall prey to conflating product with process. You have demonstrated not only that you ignore logic, but fail to comprehend its basics. An isolated X is still an X. Words don’t mean whatever you choose them to mean.

    Enjoy wonderland, folks.

    David

  26. David Koepsell September 27, 2011 4:33 pm

    And, Gene, the law is clearly FAR from settled

  27. MTung September 27, 2011 5:27 pm

    David, a process uses active steps, such as “Isolating a DNA molecule comprising a sequence of SEQ ID NO:1.” A product claim would use the term, “isolated DNA molecule comprising a sequence of SEQ ID NO:1.”

    An isolated X is a product, where “isolating X” would be a process. I don’t think there is a confusion here about the two.

    To tag onto Roland’s comment, an isolated DNA molecule is statutory subject matter IMHO, as the DNA in the body is a complex functioning system of promoters, inhibitors, 3-D struncture and folding, to name a few – which are not present in an isolated molecule. Although the arguments for patentability of an isolated DNA are as complex as the moleule itself, part of the confusion, as I stated in the post is that there is a confusion over the terminology, such as the word, “gene,” which scientists cannot agree on, let alone examiners or judges (I understand that another “Gene,” the owner of this blog site is equally complex!). Isolated “genes” are generally not patentable as not meeting requirements of enablement and/or written description because of all those regulatory components, many of which are not even currently known. So, did I confuse the issue further?

  28. Gene Quinn September 27, 2011 7:20 pm

    David Koepsell-

    Obviously, you are incorrect and I am correct. Perhaps you should re-read the decision.

    Go ahead and keep accusing me of whatever makes you feel good. Perhaps taking erroneous shots at me helps you get out of bed in the morning, I don’t know and I don’t care. All I know is that I am correct, you are incorrect and the law is now VERY settled.

    As far as conflating product with process, your demonstrate your overwhelming ignorance. How you could at all have been involved in following this case and still make such an utterly ridiculous statement is nearly breathtaking… nearly breathtaking. What you have always failed to appreciate, and continue to fail to appreciate, is that this case was about 35 USC 101, which is patent eligibility. The law has been clear since Chakrabarty that the process does matter. Human intervention is the touchtone of patent eligibility. If there is human intervention, which of course we all know there was (yes… even you know that) then there is patent eligible subject matter. What this means, of course, is that YOU are the one that ignores logical and you have never (and likely never will) understand US patent law.

    So I will enjoy reality, you can go visit the wonderland where truth is irrelevant and definitive legal pronouncements that completely contradict your asserted position are meaningless. I just enjoy the fact that your position has been exposed for what it always was… complete and utter nonsense.

    -Gene

  29. Bobby September 27, 2011 8:03 pm

    “No … it will result in better copiers, not better innovators. If it costs $1 million dollars to innovate a new product while $1 to copy the product, why should anybody innovate? Even if the ratio is just $2 for innovation to $1 to copy, there is little incentive to innovate. In today’s economy, being a first mover gets you very little if everybody else is able to copy because copying can be done (depending upon the subject matter) in anywhere from minutes to just a couple of months.

    The new widget that you unveil in a tradeshow in Chicago on Monday can be on a container ship from China in a week to your competitor. The new piece of software you unveil today can be found in someone else’s software suite tomorrow. The new compound that you’ve isolated for treating X disease can be on the shelves at nearly the same time yours hits the shelves.”
    Outside of things that exist completely digitally, where a $400 machine can make and distribute perfect copies around the world, copying isn’t going to happen as quickly as you claim. Also, quite a few surveys indicate that the advantages of being a first mover is often seen as MORE important than a patent, even though a lot of the value in a patent is the defensive ability to not be preyed upon by other patent holders by a lawsuit.

    “Sounds like a good analogy to me. In communism, the work of each and every individual member of the commune is shared amongst the commune, and no special rewards are given to those that contribute in a special manner (e.g., creating a machine that allows 1 to do the job of 10). In a world without patents, the intellectual property of individuals/companies are shared with the world with no extra compensation for those that created the intellectual property”
    Except for the advantages they get by virtue of being the first. Not giving inventors a handout through a legal monopoly doesn’t mean it’s communism. By your logic, the US has communist policies because we don’t offer legal protection for unoriginal databases regardless of the amount of labor put in.

    “Sorry … that is not going to happen. We are talking about the government.”
    Then we’d best drop patents and copyright. These systems are trying to shape matters that depend on an very advanced understanding of economics and psychology (and a remotely modern version of either one was not available to the progenitors of said systems), and crafting a net benefit out of them would be a very difficult task. If we are only going to get is blunt brute force or a system where all nuance is handled by lobbying, then that difficult task can’t reasonably be accomplished.

    “You’ve written that you want to end all intellectual property. Why should anybody spend tens or even hundreds of millions of dollars producing a movie if your world view prevailed? Explain to me how somebody is going to make money producing a movie? There … an substantive argument for you to chew on — please respond.”
    The basic model I see working is that studios sell film to movie theaters, who want people to come and buy popcorn. Since new movies generally get a lot more customers than old movies, theaters have a good reason to pay studios for new films. However, I have no doubts that other models might exist, some of which may be more profitable than the model I see.

    “And you’ve done nothing to explain why, if a patent system is unnecessary, there are patent systems in every country with a modern economy?”
    Because if your country has a patent system and your neighbor doesn’t, your neighbor has a competitive advantage. That means, especially if your patent system leads to a consolidation of industry power, said local industry has incentives to put economic pressure on that neighbor to eliminate that disadvantage. Part of the reason that would be effective is that strong patent systems tend to be more capable of happening in nations with strongly centralized powers. So, basically countries with patents bully countries without patents into having into patents. You’ll also see this in copyright policy around the world. It’s ridiculous to assume that a life+50 or life+70 year term is necessary. The US rose to dominance in the film and music industries without terms like that. The lion’s share of media doesn’t make substantial sums of money outside of 10 years, and even less make money outside of 20 years. However, we have these ridiculous terms of copyright because of said incentive to pressure other nations. So explain why, if a life+ copyright system is unnecessary, there are life+ copyright systems in every country with a modern economy?

    Also, you are operating under the faulty idea that we need any external motivation to be creative, when we have internal drive to do so. External incentives are actually bad at motivating creative and innovative behavior, since they give us tunnel vision. Said tunnel vision is great for motivating us to pull a lever, but not for building a better mousetrap. The only justification that we could really accept in modern terms is one that acts just enough to stop disincentives.

  30. Gene Quinn September 27, 2011 8:12 pm

    MTung-

    You say: “I understand that another “Gene,” the owner of this blog site is equally complex!”

    Complex?!?!?!? Thanks… I think.

    Cheers.

  31. Just visiting September 27, 2011 8:49 pm

    “Outside of things that exist completely digitally, where a $400 machine can make and distribute perfect copies around the world, copying isn’t going to happen as quickly as you claim.”
    You don’t know China very well, do you? I know a lot of people that get things made in China, and they say it is amazing what the Chinese can do if you give them a sample (or just a photograph). Copying is much easier than you think.

    “quite a few surveys indicate that the advantages of being a first mover is often seen as MORE important than a patent.”
    Until you name said surveys, I’m not giving them much credence. Moreover, being a first mover is ONLY important if you don’t have patent protection. It doesn’t matter if you have patent protection. As such, whatever conclusions are being drawn from the survey are flawed. Finally, until I see surveys, what was asked, and of whom, I’m not giving your supposed surveys much credit.

    “Except for the advantages they get by virtue of being the first.”
    Not a whole heck of a lot. For a product that has a lifecycle of 5-10 years, midway through the lifecycle, who really cares somebody came on the market 6 months earlier than the next guy. Also, being the first guy out is a huge risk. If your product has flaws, or the market hasn’t yet been identified, you can waste a lot of time and money putting out a product that doesn’t work the first time or doesn’t meet the market’s needs. On the other hand, the copiers learn from your mistakes and produce the next generation product, and your “first mover” status gets relegated to the “first mover who didn’t get it right” status.

    “the US has communist policies because we don’t offer legal protection for unoriginal databases regardless of the amount of labor put in.”
    Why would there be a lot of labor put into an unoriginal database? Seems like a waste of time – and undeserving of any protection. You need to clarify your arguments.

    “The basic model I see working is that studios sell film to movie theaters.”
    Except that you would have to massively hike the ticket prices to compensate for all the lost revenues streams the studios would be losing. Also, all it takes is a single person to copy the film and upload onto the internet, and who would want to spend $30/ticket, when you can watch the movie at home for free? Oh, I forgot, only the first few movie theaters are going to buy it, and then once the copy gets out, all the others won’t bother to buy it from the movie studios. Great idea — NOT.

    “Because if your country has a patent system and your neighbor doesn’t, your neighbor has a competitive advantage.”
    So, why haven’t all these neighbor countries gotten rid of their patent systems? There are a lot of countries that want to improve their economic standings in the world, if that is such a competitive advantage, why don’t they get rid of their patent systems? Of course, if you are an innovating company, why would you choose to develop your products in a country in which your products are going to be copied without repercussion? A lot of companies have learned that we they take their products to China, it is a deal with the devil. China can produce products very cheaply, but you lose control over your products, and don’t be surprised if the same factory that is producing your product on first shift is producing the same product for your competitor on second shift. Where do you think all those Apple products were coming from that were being sold in the fake stores in China? They were coming from the same product lines that make the “real” Apple products.

    “So, basically countries with patents bully countries without patents into having into patents.”
    Really, the Swiss and the Swedes weren’t bullied into going entering World War II (on either side), yet you think that other countries are capable of bullying them on patent issues?

    “It’s ridiculous to assume that a life+50 or life+70 year term is necessary.”
    Why is it ridiculous? You didn’t create the work, why should you have any rights to it in the first place?

    “Also, you are operating under the faulty idea that we need any external motivation to be creative, when we have internal drive to do so.”
    There is a big difference between you, sitting at home, smoking some dope, strumming your guitar, and coming up with a new riff, and somebody spending thousands, hundreds of thousands, millions, hundreds of millions to create something. You are creative because that is what your addled brain is telling you to do after a couple of hits. Those others are being creative to earn a return on their investment – whether it time, money, brain power, etc. However, they are NOT making that investment if someone can come in and steal it.

    “External incentives are actually bad at motivating creative and innovative behavior.”
    As part of my job, I spend my time around innovative people who are quite happy with the current system of reward. You, on the other hand, are defending the rights of copiers (i.e., those non-innovators). Personally, I’m comfortable that my experience with those that innovate outweighs yours.

  32. Bobby September 27, 2011 9:50 pm

    “Where do you think all those Apple products were coming from that were being sold in the fake stores in China? They were coming from the same product lines that make the “real” Apple products.”
    My understanding was that the products in the fake Apple stores in China did not have actual Apple products but rather products that looked like Apple products. Thus, the product was not truly copied.

    “Why would there be a lot of labor put into an unoriginal database? Seems like a waste of time – and undeserving of any protection. You need to clarify your arguments.”
    Phonebooks are the easiest example of an unoriginal database, and the area in which US case law on the matter was settled in Feist v. Rural. Other databases probably have more economic value, and database can be protected in Europe.

    “Except that you would have to massively hike the ticket prices to compensate for all the lost revenues streams the studios would be losing. Also, all it takes is a single person to copy the film and upload onto the internet, and who would want to spend $30/ticket, when you can watch the movie at home for free? ”
    I believe most films that make profits make profits while in theaters. Also, the studios wouldn’t have to pay licensing fees for existing film clips and music, greatly reducing the cost of making a movie. As for why go to the theater, it because I don’t have a theater in my home, and thus it is an inferior experience to watch the film at home.

    “So, why haven’t all these neighbor countries gotten rid of their patent systems?”
    Because of economic threats from countries with patent systems. Trade with other countries is very important to an economy, and countries with patents threaten trade sanctions against countries without patent systems. As for your example of WWII, bullying could very well result in not only an interrupt of trade, but more trade with the enemy and another army to face.

    “Why is it ridiculous? You didn’t create the work, why should you have any rights to it in the first place?”
    Because in modern democracies, freedom is the norm and a justification has to be provided for a reason to STOP someone from doing something. The notion that one needs a positive right to copy is rooted in the era of oppressive monopolies who used copyright as a means of censorship. Such mindsets do not belong in the modern era. The sole justification for copyright in the US is the belief that it results in a benefit of the progress. However, there’s no good evidence that longer copyright produced more or better works, and there is evidence that a country with weaker copyright law took a dominant position within certain industries. I’m not speaking of copyright itself here, but rather the long terms. You might contend that 28 years of copyright is justified, but life of the author +70 years has no economic support whatsoever. However, it is widespread precisely because of the pattern of economic pressure exerted by the players within industries that benefit.

    “There is a big difference between you, sitting at home, smoking some dope, strumming your guitar, and coming up with a new riff, and somebody spending thousands, hundreds of thousands, millions, hundreds of millions to create something. You are creative because that is what your addled brain is telling you to do after a couple of hits.”
    How about you refrain from relying on personal insults, as they suggest you have a weak argument.

    “However, they are NOT making that investment if someone can come in and steal it.”
    Again, you show your disconnect from reality. Copying is not stealing.

    “You, on the other hand, are defending the rights of copiers (i.e., those non-innovators)”
    A false dichotomy. Being a copier does not make you a non-innovator. Again, a lot of your problems seem to be your repeated insistence on absolutes, when reality has many shades of gray.

  33. David Koepsell September 28, 2011 1:59 am

    KTung and Alison, I am aware of how PCR works, my wife uses it every day. But the sequence itself, the type, if you will, does not represent a new type. It is artificially produced, but not artificial, like my IVF example. The sequence is found in nature, and the act of “isolation” is not creating a new molecule any more than isolating O2 from H through electrolysis produces new, patent eligible O2 ( as some have claimed previously on this site). The sequence patented has developed not through human intention, but through evolution. I forgive the lawyers here or making the same logical and ontological errors as the courts, but these errors should not be tolerated. No realm should be immune from logic and reason. My two examples above and in this comment illustrate the continuing error perfectly, and the only response I’ve seen so far is ” it’s important in the law” if the process is inventive, and so an otherwise natural product is treated in the law, illogically, as somehow new and artificial. That’s not argument, it an appeal to custom, which is fallacious.

  34. David Koepsell September 28, 2011 2:01 am

    MTung not KTung. Apologies.

  35. Roland September 28, 2011 5:06 am

    Thanks to the various contributions (specifically: MTung, Gene, AW Dobson) that have clarified what is actually meant by “isolated” DNA and why the term is used in the claims. Hence why a kidney removed from a body is a different form of isolation to that being referred to in DNA claims.

    It seems that an “isolated” DNA sequence is, to all intents and purposes, a copy or probably more correctly a translation of a natural DNA sequence, produced as the result of following a standard method/lab procedure for copying DNA. ie. given the specifications of the natural DNA sequence, a competent scientist could using the method to produce a corresponding “isolated” DNA sequence.

    So my clarifying query now is what makes this copy/translation statutory subject matter? is it because it is regarded as a “new and useful … composition of matter, or any new and useful improvement thereof”? but then this implies the “isolated” DNA needs to be linked to a useful purpose, such as diagnostic testing, in-order to become patentable.

    R

  36. Roland September 28, 2011 5:34 am

    Just a clarification to my clarifying query in my previous posting (#34). Yes I know that a key part of the discussion in the Decision document in on this very topic. However, I perceive “Isolated” DNA as being the product from a laboratory-based manufacturing process rather than the result of a bespoke trial-and-error process bordering on alchemy. Hence I believe my query to be subtly different but not unrelated.

    R

  37. EG September 28, 2011 9:11 am

    “I forgive the lawyers here or making the same logical and ontological errors as the courts, but these errors should not be tolerated. No realm should be immune from logic and reason.”

    David,

    OK, I warned you about invading our “realm” so now I’m going to invade yours, fair is fair. The problem you have here is that your “perspective/background” is different from our “perspective/background.” (Contrary to your statement above, the “laws of logic” are “true” only if you understand and accept the “perspective” and “background’ from which they come.) You’re obviously not a chemist (as I’m obviously not a “philosopher”), so we don’t speak the same language. As I’ve urged you before, please accept that fact, and move on.

    Your view that we/courts are making “logical and ontological errors” is also based on your “philosophical system” not ours, or even a majority of the public. If you’re suggesting that there is one and only one “philosophical system” that is correct (yours), that’s pretty arrogant and”elitest.” In fact, your suggestion that these “errors should not be tolerated” is, again, based on your “philosophical system,” not ours or the courts, and is also a pretty “intolerant” view of “freedom of speech and thought,” symptomatic of the secular Borg Collective (that’s my expression for left wing secular progressives like you) you’re obviously part of.

    Our “realm” is also “not immune from logic or reason.” It’s just not your ‘logic” or “reason” based on your “philosophical system.” Again, contrary to what you’ve suggested, “perspective” and “background” do matter (for example, why do we call it the “Theory of Relativity”?). You’re also entitled to your opinion, as I’m entitled to mine. The fact is I just don’t accept your opinion, and that’s a perfectly “logical” and “reasonable” for me to do. And again, let’s just “agree to disagree,” there’s not point in debating any further. Peace David.

  38. Allison Williams Dobson September 28, 2011 9:21 am

    So it seems (David) that we are all in agreement that an isolated DNA (as obtained by PCR) is “made by man” and not found in nature.

    I hope you have actually read the Federal Circuit opinion of the Myriad case as well as the more recent Classen opinion. The court is practically screaming at litigants to stop the 101 business – that the other provisions of the Patent Act are appropriate tools for attacking these patents – 102, 103, and 112.

    Once a sequence has been published (the reference human genome, e.g.), it becomes much harder to patent an isolated DNA with that sequence, due to obviousness under 103 (see in re Kubin, e.g.). So your “problem” will gradually fade away, but not for the reasons you give.

    And yes (Roland), such DNA fragments are useful in diagnostic testing, but also in many other ways (both research and medical uses). Your citation of “new and useful… composition of matter” is exactly right.

  39. EG September 28, 2011 9:46 am

    Allison,

    Thanks much for bringing some “sanity” to this subject of patent-eligibility of “isolated” gene sequences under section 101. And I agree thoroughly with your point that Rader in his “additional views” opinion in Classen is “screaming” at us to cease and desist from making so many assertions of patent-ineligibility under 101, and to move on, instead, to sections 102, 103, and 112.

  40. David Koepsell September 28, 2011 11:20 am

    Allison: the sequence itself is not made by man, and even while the tokens (the products of PCR) are produced through an artificial process, the product remains a product of nature (the promoter and stop codons define the gene, not human intention), just as I have argued that “man-made” O2, synthesized from water via electrolysis, is not anything other than a product of nature, and should never be patent-eligible even though it might result in concentrations of quantities of O2 not otherwise available naturally (although a new process for synthesizing a natural product might be). In my O2 example, the concentrated quantity (token) of pure O2 would be an artifact, but the molecules of O2 are not artifactual – their structure depends not upon human intention, but rather upon the laws of nature. Similarly, any creature created through the man-made process of IVF would nonetheless remain a product of nature (unless it were genetically engineered), although the process of creating the token depended entirely upon human intention. And yes, I have read the opinion(s) with some glee since they show the law is not settled, the courts remain divided, and there’s still a chance that SCOTUS will apply logic and get it right, finally. And Eric, the laws of logic apply to everyone everywhere, they are not matters of opinion. Only a hopeless post-modernist would think otherwise. Of course you are free to be a post-modernist, if you wish.

  41. EG September 28, 2011 11:29 am

    “And Eric, the laws of logic apply to everyone everywhere, they are not matters of opinion. Only a hopeless post-modernist would think otherwise. Of course you are free to be a post-modernist, if you wish.”

    David,

    Spoken like a true member of the left wing secular Borg Collective. If you would cease and desist from the “name calling” (“hopeless post-modernist”), I’ll do likewise so we can engage it real debate. It doesn’t lend credibility to your arguments or further the debate. (And as a chemist which you are obviously not, your “O2” analogy “holds no water” as far as I’m concerned.)

  42. Gene Quinn September 28, 2011 12:08 pm

    David K-

    Does O2 exist without the assistance of man?

    Does isolated DNA in its isolate form exist without the assistance of man?

    See, the logic is extremely simple when you break it down to its core. Why you refuse to acknowledge the obvious remains a mystery.

    -Gene

  43. David Koepsell September 28, 2011 3:20 pm

    Louise Brown (and tens of thousands of others since) wouldn’t exist but for the assitance of man, through the marvelous man-made process of IVF. By your logic, except for the explicit prohibition against patenting humans, she would be a patent-eligible product. The process is distinct from the product. An artificial process can be used to (re)produce natural products (products of nature).
    QED

    And BTW, I love that Gene argues that O2 would be patent eligible, it shows the reductio ad absurdum of an untenable position. My work here is done.

  44. Gene Quinn September 28, 2011 3:40 pm

    David Koepsell-

    You say: “I love that Gene argues that O2….”

    It is so typical for you to lie that it is almost expected at this point.

    Of course, anyone who can read understands what I wrote above does not mean what you try and put into my mouth.

    I will remind you of the rules of commenting. Commenting here on IPWatchdog.com is not a right and those who lie are banned.

    I did not say O2 would be patentable. I asked whether it exists. The answer, of course is that O2 does exist in nature in the form of O2.

    I then asked whether isolated DNA in its isolated form exists in nature. The answer, of course, is no it does not.

    So final warning David. If you are going to refuse to lie, misrepresent, manipulate and otherwise display blatant intellectual dishonesty while keeping such an arrogant tone — you will be banned. The choice is yours.

    -Gene

  45. Bobby September 28, 2011 4:13 pm

    Gene,
    I wouldn’t call what David did lying, but rather misunderstanding what you said.

    Also, a question for you. Would the isolated BRCA1 sequence with a bit of additional non-coding DNA at the end of the strand be distinct from the isolated BRCA1 sequence in your view, making it an escape from Myriad’s patents?

  46. Gene Quinn September 28, 2011 4:58 pm

    Bobby-

    I appreciate you jumping in and calming me down. Unlike you, however, I don’t think DK is misunderstanding. He well understands and then twists. That is his MO, both here and elsewhere. He manipulates, takes things out of context and then passes them along with moral indignation. I just don’t need, or want, that kind of ridiculous Monty Python-esque nonsense.

    As for your question, I think the answer is yes. When I delve into the science here on this stuff though I would like to hear what our substantive experts have to say.

    Cheers to you and thanks for continued contributions in the face of tough substantive debate (from me and others).

    -Gene

  47. Partner Emeritus September 28, 2011 5:14 pm

    http://ndpr.nd.edu/news/24118/?id=17005

  48. Breadcrumbs September 28, 2011 5:37 pm

    It has been awhile since I posted, but my friend Blind Dogma wanted to remind folks that Dave Koepsell has donned the clown shoes before to dance the dance ontologic.

    I don’t know if Gene’s archives capture the interchanges (some of the great softwware is maths debates have been lost), but Dave has been put into his place rather forcefully in the past, and I see that his style has not changed. He still enjoys his mental masturbation while not really taking the time to have one foot in each world.

  49. Gene Quinn September 28, 2011 6:19 pm

    Breadcrumbs-

    Welcome back!

    The comments made here on IPWatchdog are all available and you should be able to find them using our Search page:

    http://ipwatchdog.com/about/site-search/

    I suspect the comments are isolated to the Myriad and gene patent articles, which are at:

    http://ipwatchdog.com/category/gene-patents/

    http://ipwatchdog.com/tag/myriad-genetics/

    The comments that were lost, if memory serves me, are the ones that were posted to the PLI blog website. When they did away with the first generation of the blog I wrote the computer folks at PLI didn’t just stop the blog but rather deleted all the posts and comments. A surprise to me I assure you.

    Cheers.

    -Gene

  50. Gene Quinn September 28, 2011 6:26 pm

    Partner Emeritus-

    Thanks for the link, which is to a review of Koepsell’s book written by Professor Chris Holman, an expert in the field of biotechnology and the law.

    One sentence of the review sums up Koepsell’s book nicely: “As yet another example of the misstatements pervading the book…”

    Koepsell likes making provably erroneous legal statements and pretending that they are true because he wishes them to be true. He then claims that those who point out his inaccuracies are somehow incapable of understanding the deep philosophical means. The truth is this — isolated DNA does not exist naturally in isolated form. Whether Koepsell or anyone else wants to pretend, the Federal Circuit has spoken and Myriad prevailed. The ACLU and its like-minded supporters have failed. There was no attempt at an en banc rehearing, so this is either going to the Supreme Court or it is over. Even if the Supreme Court takes the case no one could possibly think this Court would side with the ACLU and throw away tens of thousands of issued patents and billions of dollars in corporate valuation.

    -Gene

  51. Allison Williams Dobson September 28, 2011 8:40 pm

    Bobby, I may take a shot at a few paragraphs to address your question in comment #44, but first please tell me, are you a molecular biologist? It would be helpful to know a bit more about your background before trying to explain. That is not an easy question, and the very short answer is the quintessential lawyer’s answer (for any field – not just patent law): it depends.

  52. Bobby September 28, 2011 11:01 pm

    No, I’m not a molecular biologist. My formal background is simply high school and college bio classes, although I’ve read a little bit about these kinds of things because they are interesting to me. I won’t be insulted if you say things I already know, especially since it might be helpful for other readers and commenters with less or simply different knowledge on the subject.

  53. David Koepsell September 29, 2011 3:36 am

    Gene, there’s no lie in my referring to your direct statement, comment number 10 on April 1, 20101 where above I had raised the question if Priestley’s discovery of O2 should have been patent-eligible: You said “Gene Quinn April 1st, 2010 10:16 am (click my name for the link)

    David-

    Of course that should be patentable. You really should read US Supreme Court cases on patentable subject matter, the 1952 legislative history to the Patent Act and pretty much every non-software patentable subject matter decision from the Federal Circuit. If you do then you would much better understand the law. I would also recommend that you stop listening to scientists about the law. Listen to them about science, not about the law. They know nothing of the law, so their opinions on what does and does not meet legal standards is really uninformed.

    -Gene”

    So Gene, who’s lying?

    As for a reference to a bad review of my book, that is not an argument. There are 3 bad reviews of that book, and 11 good ones, and the reviewers on both sides range from academic to popular, with varying backgrounds, including lawyers, biologists, and others. The three critical ones of which I am aware included two patent attorneys/professors, and one Objectivist-transhumanist. Experts disagree, but relying on one review by someone who still consults for BIO writing amicus briefs would be a poor way to make a judgment. Chances are, if you support gene patents, you won’t like my book. Most people who have reviewed it did like it. I am untroubled by people’s honest opinions.

  54. David Koepsell September 29, 2011 4:12 am

    and Gene, you say: “If you are going to refuse to lie, misrepresent, manipulate and otherwise display blatant intellectual dishonesty while keeping such an arrogant tone — you will be banned. The choice is yours.”

    I assume you flubbed a word or so there (perhaps you meant “insist on” or “continue to”) you’re threatening to ban me unless i lie, misrepresent, etc? Now that’s Monty Pythonesque

    all my best,
    David

  55. Kevin Carson September 29, 2011 4:33 am

    I’m surprised Quinn didn’t throw in the lines “talent on loan from God” and “one lobe of my brain tied behind my back.” Or maybe “Respect my authoritah!” You can almost hear him harrumphing in print.

  56. Allison Williams Dobson September 29, 2011 11:26 am

    So, getting back to the question of what an “isolated DNA” claim encompasses, we must review a few critical patent law concepts. “Claim construction,” which is what we are addressing here, is a complicated subtopic within patent law. The answer to your question is not settled, but make no mistake – that is a VERY different question than whether isolated DNA is patentable subject matter under 101. The 101 question is a threshold inquiry only. It gets you to the REAL tests for patentability under 102, 103, and 112, which are much more stringent.

    Claims are given their “broadest reasonable interpretation in light of the specification.” The analysis is conducted from the viewpoint of a person having skill in the art (PHOSITA for short). The PHOSITA here would typically be a molecular biologist or biochemist (although training in the other advanced medical sciences will usually yield sufficient understanding because molecular biology is useful in a very wide range of laboratory work).

    So the question is, given the quote in the last paragraph, what would a PHOSITA understand the claim to cover, having read the entire specification? The specification, of course, includes all of the lengthy description that accompanies the claims in the disclosure (including any drawings, sequences, etc.). I have not read the specifications for the Myriad patents, nor do I intend to do so (unless someone offers to pay me for the hours it would take to do that). Having said that, I can offer some generalizations.

    The analysis must be done on a claim-by-claim basis, with each word in the claim having significance. There are often 10-20 claims in one patent, but sometimes even more. So if you are still with me (are you?), I’ll try to come back later today or tomorrow and comment again, and perhaps we can take a closer look at one or two of the broader Myriad claims (or hypothetical similar claims involving gene X) and what they do and do not appear to encompass. My guess is you will be surprised as to how little they actually pre-empt the study and use of the gene.

  57. Gene Quinn September 29, 2011 1:36 pm

    David-

    Thanks so much for pointing out the error. I meant to say: “if you continue to lie…”

    Thanks also for putting the context of the question in your comment. Oh wait, you didn’t, which is another misrepresentation. That discussion was about a hypothetical you posed where there was human activity engaged to purify and capture O2. Clearly, if there were human activity associated with bringing about alterations to the state of something then it wouldn’t be in its natural state, which is self evident to everyone but you. We were also discussing whether someone who first allowed for breathable O2 to be self contained could obtain a patent. So your lies and misrepresentations continue.

    You have been warned repeatedly over time, and recently warned again. Notwithstanding your immature antics continue. You are now banned. Enjoy yourself elsewhere, and good luck with that book that reviewers say contains so many inaccuracies and misrepresentations that it is hard to count them all.

    -Gene

  58. MTung September 29, 2011 1:38 pm

    Wow – I go away for a day to do patent stuff and the comments pour in. I think most of you are holding your own on this discussion thread! I do want to make a point about 101 patent eligibility. When I started at the PTO in 1997, we were to use this rejection very sparingly – I would hope the same is true today. Usually, as Allison points out, can be covered under 112/1 or 103. Much of the enablement has to do with whether the translation product has a use – which is a utility issue, but really an enablement issue: can POSITA use the product given the guidance of the specification? A written description rejection can also be made if it is clear that although the sequence claimed is known by the applicant, without any guidance as to how to use the product, the inventor was not in possession. These issues came up a lot with EST application (expressed sequence tags – short sequences of DNA with no known functions for the expression products). Of course 101 can also be used, but the 112/1 arguments seem to be stronger and easier to document and support with evidence.

    The other time it comes up is if the isolated DNA encodes a cellular protein expressed on a cell, but with no other function or assay utility stated in the specification. These types of claims sometimes got very close to the “comparing” claims that were struck down by the CAFC in Myriad. The question becomes, if a particular cell type expressed a marker, but the cell is not known to be involved with any disease, is the marker (and the DNA encoding it) patentable? What if the utility were found out post filing? What if the utility were found out post-issue? Was the inventor in possession of the invention at the time of filing? Should that marker be taken out of the public domain for 20 years when the inventor didn’t even know which disease that the cell would ultimately be associated? I suspect these discussions still grace the halls of the genomic art units of the PTO and of patent practitioners in the field. This has been a good discussion – keep it up!

  59. Gene Quinn September 29, 2011 1:45 pm

    Kevin-

    Thank you so much for the comparisons to Rush Limbaugh. That is a lot to live up to I know, but I appreciate the praise you through my way and tremendous comparison.

    I’m not so much of a South Park fan though.

    To paraphrase another great personality I am sometimes compared with… “wise up!”

    -Gene

  60. Allison Williams Dobson September 29, 2011 1:55 pm

    Mary Beth –

    I’m always interested in hearing from the (former or present) examiner’s perspective. One thing I would like to ask you about is claims to isolated DNA’s with a certain % homology. Drafting a claim to cover a DNA that codes for a polypeptide with a particular sequence already accounts for wobble (degeneracy in the genetic code), and the PTO practice regarding % homology seems to be very inconsistent. I think many of the rejections are based on written description/possession there too.

    Thoughts? Do you know of any precedential case (either BPAI or outside the PTO) that addresses this?

  61. melvin udall September 29, 2011 3:29 pm

    I would like to join David on the banned list. How do I go about ensuring that? Is it just a matter of saying that Ayn Rand is not my hero? OK, Ayn Rand is not my hero. So now can I get banned?

  62. Gene Quinn September 29, 2011 3:51 pm

    Melvin-

    You can become banned by lying and/or repeatedly misrepresenting, as David Koepsell has done repeatedly and after many warnings.

    Alternatively, allow me to offer a suggestion that you probably hadn’t considered. Just don’t comment and go about your life.

    -Gene

  63. MTung September 29, 2011 4:50 pm

    Allison,

    The PTO policy of % homology was somewhat consistent when I was there – unless it was 95% or better, there were 112/1 issues at the least – the claims were rejected. People often claimed around it by putting lengths on the sequence: “at least about 30 consecutive bp” and so forth. None of it really covers gaps, non-contiguous intervening sequences and so forth and it really took a lot of time and effort on the part of the examiner to individualize each sequence search and try to fit the allowable subject matter to the particular DNA sequence. In other words, it all depended upon the encoded protein and what it did. There was a lot of work done in the examination process on whether the coding sequence was claimed, how many mutations were tolerated in the sequence, etc., most of which are not disclosed or even known. % Homology could include a lot of intervening sequences, etc. and it is really hard to know what the applicant is claiming. At some points, % homology language was not allowed at all, and in the earlier days, before I went to the office, the requirements were a little more relaxed. If an applicant really wants the wiggle room, they should draft the claims in such a way that alternative scenarios are disclosed and supported – easier said than done, I understand. An easy one is making sure that “wobble” sequences are included and/or disclosed – which actually is really important in EU applications – the degeneracy of the code is one area everyone should cover. As for case law, the biggest one is Deuell, which really doesn’t discuss % homology as much as some of the reasoning of obviousness of the nucleic acid sequence over the protein sequence. I’ll have to think some more about other case law – I am drawing a blank right now.

  64. MTung September 29, 2011 4:59 pm

    Bobby,

    “Also, a question for you. Would the isolated BRCA1 sequence with a bit of additional non-coding DNA at the end of the strand be distinct from the isolated BRCA1 sequence in your view, making it an escape from Myriad’s patents?”

    As with anything, it depends. If the sequences are commonly-known sequences, such as tags used for isolation in columns, for example, or poly-A tails, etc., they probably would not be an “escape” from Myriad’s patents. I don’t have the claims in front of me, but claims to “an isolated DNA comprising” would likely cover any BRCA1 sequence that had the Myriad sequence in addition to other added sequences. However, if those added sequences fundamentally changed the molecule – such as non-obviousm non-BRCA1 promoter or inhibitor sequences, it might be hard for Myriad to prove their sequences were enabled for the modified “new” BRCA1 sequence. I weould expect them to try to enforce their sequences over the “comprising language, however! Does any of this make sense?

  65. Mike Masnick September 29, 2011 5:20 pm

    Weak move, Gene, to ban David. He’s been nothing but an articulate speaker on these subjects, and nothing if not careful to be accurate in his comments.

    Banning him is childish and suggests that you can’t actually respond to his points. It makes you look really, really petty.

  66. Blind Dogma September 29, 2011 6:22 pm

    been nothing but an articulate speaker

    This would be a hearty call of BS to that. More llike a semantic word game player who had his game exposed.

    I concur with Gene’s ban – the tight ship here makes sure that the place isn’t overrun like the other Patent Blog.

    If you want games and “wordmanship,” I am sure that David can ploy his trade there.

    Oh wait – consider the source….(that explains the “articulate and accurate” butcherings.

  67. Allison Williams Dobson September 29, 2011 6:25 pm

    Thanks for the homology explanation, Mary Beth. And also your next comment.

    Here is one of the Myriad claims (U.S. patent 5,747,282):

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

    Notice that, like the “comprising” example, this claim requires the entire coding sequence to infringe. So actually, several of the various forms of sequencing (there are so many different ways to sequence now that I can’t say any) would likely not infringe if the template was genomic DNA or even a mixture of genomic cDNA.

    Also, if you isolated a DNA molecule that had all but one codon represented (say it is missing the codon from either end), that DNA would not infringe the claim above. This thing is in the range of 5,000 bp long, so leaving one AA off the end would be a small difference.

    Of course, it depends what the putative infringer is trying to do, but notice that either the sequencing OR lopping off a codon at the end and then isolating would likely be sufficient for diagnostic purposes, assuming clinical quality technology. This is a subject of widespread debate, but I have yet to see a good argument as to how the next-gen sequencing methods could infringe.

    Thus, the sequence itself is not covered by this type of claim.

  68. Gene Quinn September 29, 2011 8:20 pm

    Mike-

    Not childish at all, unless you are referring to DK’s lies and blatant misrepresentation. There is no place for lies in an intellectual, substantive debate.

    You can do what you like on your blog, but here lying and mire resenting is not allowed. That keeps the dialogue substantive. Differing opinions are fine, as anyone can plainly see, but I do draw the line to keep a high level of substantive dialogue.

    I would love to have you join in here more. We disagree a lot, but I appreciate your intellectual honesty.

    -Gene — via IPhone

  69. MB September 29, 2011 9:05 pm

    AW Dobson,
    As commented by you above, I think all isoated DNA are patent-ineligible due to obviousness. cDNA cloning has been done since early eighties using RT-PCR. One can patent the utility of the isolated cDNA but not the cDNA itself. I wornder how Judge Lourie and Moore missed this.

  70. Allison Williams Dobson September 29, 2011 10:20 pm

    A newly discovered variant or a new synthetic DNA will always be non-obvious.

  71. Bobby September 29, 2011 11:37 pm

    Allison,
    That’s a rather bold claim, using an absolute like ‘will always be’ for something that is inherently conditional like obviousness. Something can be new and still be obvious. The sequence already exists, and said sequence in isolation seems an obvious composition of matter to me, let alone to PHOSITAs today and in the future. Methods of isolating DNA and applications of isolated genes may be non-obvious. Sequences of DNA that don’t yet exist could very well be non-obvious. But if isolating existing sequences falls on one side of ‘always’ in regards to obviousness, it would seem to favor always obvious over always non-obvious.

  72. EG September 30, 2011 6:56 am

    Hey Beth and Allison,

    Thanks for your posts/dialogue on this subject. We definitely need you folks with molecular biology backgrounds. I’m just a chemistry major (strength in organic) and I do have two books on molecular biology (which so far I’ve only been able to get very part way through). I understand the “patent” issues, but the technology of molecular biology isn’t intuitive to me, even though I’m fascinated by the technology.

    When I was in school, there was no “genome” (just so you know how really old I am!) and biochemistry wasn’t a major, just one course (taught in biology department). I would have liked to take some biology courses, but the entry level biology course was the “screen out” for the pre-meds (sometimes half the incoming class at my school). It was bad enough dealing with the pre-meds in my chemistry courses.

    Again, you’re most welcome on this blog.

  73. Allison Williams Dobson September 30, 2011 7:57 am

    Thank you, EG!

    Bobby, your point is well-taken, and I usually avoid words like “always” and “never.” I was miffed at being badly misquoted, but apparently that is something I will have to get used to if I want to participate in this way.

    Obviousness seems to be a gradually changing thing – something that was novel 20 years ago may now be obvious, and something that is novel today may be obvious in 2031. That is the effect of progress in the state of the art.

    I certainly do not agree with what MB wrote in comment #69. And synthetic biology is opening up a whole new world, the DNA inventions from which should be novel as long as I can imagine into the future.

  74. MTung September 30, 2011 9:27 am

    EG, Thank you as well! This has been a really great discussion and I’ve enjoyed it.

    MB, I have to side with Allison on this one. UC v Eli Lily, 119 F.3d 1559 (Fed. Cir. 1997) is a case, although now “old” by biotech standards, highlighted your exact scenario. University of California researchers has isolated rat insulin, Eli Lily were marketing human insulin. US sued, basically because of commonly known methods existed that could easily isolate human insulin once the rat sequence was known (I think there were only one or two amino acid differences). CAFC held the human insulin was not obvious over the rat insulin – two different inventions (also written by Judge Lourie). Given that only one point mutation can turn normal hemoglobin into the sickle cell form, the Lily decison makes sense: there is just no way we have any means to predict how certain sequence changes will affect the final protein product. So long as the protein folding issue remains the holy grail of science, the unpredicatability of any new DNA sequence and its protein transcript will be non-obvious unless the examiner (or infringer) can find art that basically states that a mutation at a certain location can be predicted with certainty to behave a certain way.

    Allison, Claim 1 of Myriad’s claim includes the word, “having.” I always have to look up the citations – several of them are BPAI decisions – that “having” can either be construed to be totally open, somewhat open or closed. I avoid the word altogether, but there is an argument here that “having” would mean basically the claimed SEQ ID NO:1, plus only non-significant other ingredients, such as carriers, salts, and the like. I have not looked at the court’s reasoning on this, or even if it were brought up in the Myriad cases. I am sure that Myriad would take the position that it is totally open claim language, and thus would include ANY additional seqeunces, but it would still not include mutations. I will look up how the term is currently being interpreted – I avoid it altogether due to the uncertainty… Anyone else that has a take on “having” is welcome to comment!

  75. MTung September 30, 2011 9:30 am

    Correction… one of the holy grails of science, unless of course, one is of the opinion that biotech is the only science that counts! (a side I often take with my non-biotech collegues!)

  76. MB September 30, 2011 10:55 am

    MTung
    Every biologist knows that rat and human insulin perform the same function, although they might differ in few amino acids. Did Eli Lilly prove that their human insulin performed a diff. function over rat insulin?
    Lets look at a similar case, that of Ex Parte Gray 10USPQ2d 1922 (BPAI 1989), Claim was to a human nerve growth factor (b-NGF) produced through cDNA. The prior art disclosed b-NGF purified from human placenta. Board rejected the claims based on product-by-process and the product not having any distinct property/function.
    Given the human genome sequencing, any PHOSITA can isolate cDNA in a matter of munites to any of the 22,000 or so genes. And with degenarate codons, one can obatin a variety of cDNAs, each performing similar function. I still do not see the non-obviousness in isolated DNAs. Just because patents were granted 20 yrs ago on isolated DNAs, it doesn’t mean that we countinue to do the same.

  77. Gene Quinn September 30, 2011 3:52 pm

    Allison-

    You say: “I was miffed at being badly misquoted, but apparently that is something I will have to get used to if I want to participate in this way.”

    Unfortunately, that happens here from time to time, particularly when the topic is related to patentable subject matter. Even more so when the topic is biotech/genes and patentable subject matter. It is unfortunate that so many choose to mischaractize and misrepresent, but there are so many who simply are unable to debate on the merits and choose to go down to that level. That is why from time to time I have to ban those who seek to hijack legitimate and substantive debate in order to keep this a viable and valuable forum for meaningful discussion.

    Thanks for contributing. I hope you stick around. You are adding quite a lot to the discussion.

    -Gene

  78. Mark Nowotarski September 30, 2011 5:32 pm

    It’s a shame DK got banned. I happen to be an expert in oxygen (20 years R&D for an oxygen company) and would have liked to sort out the issues.

  79. Blind Dogma September 30, 2011 7:50 pm

    You can always seek him out (and report back on your excellent results).

  80. Mark Nowotarski September 30, 2011 8:47 pm

    Good idea. I’ve tried here http://c4sif.org/2011/09/gene-quinn-patent-shill-bans-another-articulate-patent-opponent/#comment-5006 but without much luck.

  81. Allison Williams Dobson September 30, 2011 8:57 pm

    He sent me his latest blog which has quite a bit on O2 (surprise). If you really want to know I will help you find it. I’m on linkedin.

  82. Blind Dogma September 30, 2011 9:32 pm

    Gene Quinn, a patent lawyer who insists on having an Opinion, previously banned me from commenting on his joke of a patent shill site, for daring to call a spade a spade.{fn}1 Now this intellectual buffoon has banned the heroic legal philosopher and IP abolitionist David Koepsell. I guess Kevin Carson is next. Purge, purge!

    So much for “intellectual honesty.”

    Kinsella was always more of a joke than even Koepsell.

    Heroic Legal Philospher… not by any stretch of the imagination of word play. He was shut down here cold and hard with his language tinkering without backing.

    Shhh (don’t let it be known that Koepsell is on the Center’s Advisory Board – and guess who else – shockers – Michael Masnick)

    The Center’s Mission: Kook Central:

    “The Center for the Study of Innovative Freedom (C4SIF) is dedicated to building public awareness of the manner in which laws and policies impede innovation, creativity, communication, learning, knowledge, emulation, and information sharing. We are for property rights, free markets, competition, commerce, cooperation, and the voluntary sharing of knowledge, and oppose laws that systematically impede or hamper innovation, especially those enforced in the name of defending “intellectual property,” such as patent and copyright; these should be radically reformed or entirely abolished.”

  83. Blind Dogma September 30, 2011 10:52 pm

    We disagree a lot, but I appreciate your intellectual honesty.

    Check out the link Gene – not much intellectual honesty there.

    And note the board members of the group – Koepsell and Masnick.

  84. step back October 1, 2011 6:14 am

    @MTung
    With regard to “having” (comment #74), the normal canons of claim construction should apply.
    “Having” must have the meaning that one of ordinary skill (in the DNA arts) would ascribe to it in view of other terms found in the claims (i.e. “isolated”) and in view of the spec as a whole. Therefore “having” cannot have a fully open ended meaning in this case because that construction would render superfluous the term “isolated”.

  85. Gene Quinn October 1, 2011 6:19 pm

    BD-

    Thanks for bringing up the Kinsella jab. I tweeted about it the other day.

    I’ll allow readers to come to their own conclusions, but just want to point out that Kinsella was himself banned for lying openly on this forum some time ago. Take a look at:

    http://www.ipwatchdog.com/2009/09/30/responding-to-critics-my-view-on-patents-innovation/id=6421/

    See comment 62 and 64.

    Via prive e-mail I offered to debate him and then he publicly said that he offered to debate me but I never accepted. It boggles the mind that anyone would say things that are so provably false, but the anti-patent crowd seems to feel the way to prevail is to lie. When one has to lie the argument has been lost, and I am just not going to allow this forum to disintegrate like so many other blogs and website. Those that have to lie and misrepresent can go elsewhere.

    -Gene

  86. Mark Nowotarski October 2, 2011 6:27 pm

    Allison,

    Thanks. I found the blog.

  87. Mark Nowotarski October 2, 2011 7:12 pm

    This is somewhat off topic, but I’m it occurs to me that DK’s basic assertion that a substance (e.g. O2) is a substance no matter how it is produced is not true. The properties of a substance are highly dependent on how the substance is produced. I remember from my R&D days one of the senior patent attorneys explaining to me that you can claim a product produced by a new process through a “product by process” claim. The rationale was that even if superficially the product was “the same” as what was already out there, it would, in fact, be different due to the different manner in which it was made.

    US5194124: “Molten salt electrolytic beneficiation of iron oxide-containing titaniferous ores to produce iron and high-grade TiO2” is a good example. This discloses a new way to make TiO2 and iron and claims not only the new process, but also the TiO2 and iron produced by the process.

    Here are the claims.

    16. The beneficiated TiO2 produced by the process of claim 1.
    17. The beneficiated TiO2 produced by the process of claim 15.
    18. The iron produced by the process of claim 1.
    19. The iron produced by the process of claim 15.

    TiO2 and iron are known, but the “TiO2” and “iron” produced by these processes are patentable since the processes used to produce them are new and not obvious.

  88. MTung October 3, 2011 10:10 am

    #76 MB – Ex parte Gray (BPAI 1989) was trumped in 1997 by Lily. There were a lot of arguments in the hallways prior to the decision in Lily coming out. Some folks were making Ex parte Gray rejections. I was in Patent Academy training at the time – a really great time to start at the Patent Office!

    The same function does not equal the same molecule or obviousness. Can you predict that a mutation in a certain place will perform the same function? The DNA art is just too unpredicatable. The argument that Lily was a narrow decision best left to the 1997 era has not really held up as of yet, although a litigator could make the argument with a straight face. Of course, the standards for litigation and for PTO examination are different – a fact that everyone has to understand.

  89. MB October 3, 2011 11:45 am

    ”The same function does not equal the same molecule or obviousness. Can you predict that a mutation in a certain place will perform the same function?”

    MTung, If I understand you correct, an isolated DNA/cDNA with few base changes when compared to prior art DNA is an invention, even though the function is same. Then, for example, can I add few extra stop codons ( for nonbiologists, junk nucleotides) at the end of a prior art cDNA and call it a new molecule?
    My arguement is, isolated cDNA per se is patent-ineligible since the technology of making it is old (obvious). However, its utility can be patented.

  90. mike October 4, 2011 2:14 pm

    The genome is sequenced, the genes are available as prior art. The point is moot, examiners today will not allow a mere gene sequence to be patented because simply isolating the gene from the genome is not sufficient for novelty anymore. The gene must be tied to a utility. There was very little prior art when the Myriad patents were issued, although there was some very good prior art, the specific mutations, locations to amplify and analysis of those mutations as associated with cancer were not available in the art. Therefore the patent issued, the patent expires in a few years, likey before the Supreme Court would grant Cert. Why is the ACLU wasting court resources pursuing this garbage?

  91. mike October 4, 2011 2:41 pm

    MB, many claims contain the “Comprising” language. It has pluses and minuses, a claims to a DNA “comprising” a short DNA sequence will likely be anticipated (not patentable).
    I claim 1) a DNA sequence comprising SEQ 1 (ATCG).
    Since ATCG is found thousands of times in the Genome, in the hundreds of Human Genome Sciences patent applications, and elsewhere in the art, your patent will be rejected.
    I

  92. MTung October 4, 2011 5:38 pm

    #89 MB – the answer in DNA claims is always, “it depends.” Stop codons and other “junk” sequences (I have never thought of stop codons as junk – kind of prevents run-on transcription like the loops I used to get into in computer programming, which is why I am a bioilogist) have a function, many times regulatory in nature. If the stop codon is not located in the position that was engineered, or if the stop codon allows for additional binding of regulatory proteins, or if the stop codon is non-obvious, or has an non-obvious function, then the answer is yes. If, however, the stop codon were inserted just to stop the transcription process, then the answer is that it MIGHT be obvious. Keep in mind too, that there is a lot of case law about this – patent practitioners and the courts try very hard to avoid “hindsight reconstruction” of the claims – reading the inventor’s disclosure into the claims. If what was “obvious” to a scientist (or a judge or practitioner) were used as a standard, there would be hundreds of interpretations of what is obvious, because everyone has a different idea in their heads of what is obvious. So, the term “obvious” has legal definitions that the courts and the patent office have been trying to standardize for years. It is an imperfect set of solutions, but it is better than relying on the opinions of all involved parties, all of whom have completely differing views.

  93. mike October 26, 2011 11:47 am

    This argument is old, boring, and non-productive. The argument itself is dated. Approximately 10 years ago the human genome was sequenced. Mere “Isolation” of human DNA no longer reaches the level of patentability because it is obvious or anticipated. At the time the University of Utah/Myriad identified the mutations in BRCA that were associated with cancer, the feat of isolating a gene (DNA, not the blogger) was much less predictable, let alone associating specific mutations with cancer. Yes it was being developed in universities for the purpose of creating research revenue for the university. This case demonstates that Bayh-Dole promotes commercialization of university research.

    The patents will expire soon, any new patents to an isolated DNA will require either a unique function or unique sequence that has not been publicly available before. A new method of manufacturing an old product is patentable, identifying and isolating a molecule with unique properties is patentable. The fact is the chemical compound that encodes the BRCA1 or BRCA2 gene is a unique chemical compound that had up to that point not been identified publicly. Without prior art it is patentable. Your only argument is, “This isolated DNA is important for cancer diagnosis is SHOULD be free to use!” It is free to use for research purposes and many articles are published each week regarding research on BRCA1 and BRCA2 (check pubmed). What is not free – the development of a commercial screening company that identifies mutations in the BRCA1 and BRCA2. The cease and desist letters that Myriad sent out went to cancer hospitals that ran diagnostic labs for their patients, not research labs. I don’t agree with the way Myriad has managed licensing for the BRCA1 and BRCA2 tests, why not charge a royalty for other labs ensuring their test was the least expensive? I don’t know… Either way, their patent will expire soon and the test will be more widely available. Perhaps someone can open up an offshore testing facility, there are design arounds. The cost of genome sequencing is dropping, maybe getting your genome sequenced is cheaper than going to Myriad. Then you as an individual can look at your genome and determine what BRCA mutations you have. I agree with Kopsell, “An isolated X is still an X” and if no one has seen X before, then it is patentable (whether it is a chemical, mineral, DNA sequence, or cell type). It is just that it would be very hard to isolate a mineral that no one has found before.

  94. LastWord November 1, 2011 11:19 am

    Nowotarski takes on Koepsell re: O2: http://nanowares.wordpress.com/2011/09/30/logic-apparently-off-limits-in-the-law/