Fired Up: Challenging the Constitutionality of the Patent Act

Thomas Jefferson, the first US patent examiner

Thomas Jefferson, the first US patent examiner

The Plaintiffs allege that because human genes should not be patented.  Hardly something that anyone can argue.  The only trouble is that this is not what the US Patent Office allows, and it is not what Myriad Genetics has been granted a patent on.  Nevertheless, the frivolous ACLU lawsuit that seeks to use the US Constitution to declare patent claims invalid is allowed to proceed regardless of the facts and in spite of there being no justifiable statutory theory for the plaintiffs to purse.  Instead, Judge Sweet is allowing the plaintiffs to cite generalized Constitutional harm, in direct and open violation of well establish standing principles.  They seek to challenge patents because they want others to be able to use the Myriad Genetics techniques for free and without paying.  They claim that patents control thoughts, and therefore violate the First Amendment.  How ridiculous!

Under this rational no patents are Constitutionally justified and we should simply stop issuing patents.  Better yet, by this decision by Judge Sweet sets precedent for anyone who doesn’t like patents or wants to use a patented technology to file a lawsuit claiming some unidentified, non-existent Constitutional rationale for invalidating patent claims.  For those who hate patents now is your chance to run to the Southern District of New York and file a lawsuit seeking to invalid patent claims.  Judge Sweet obviously doesn’t read the patent claims, at least not on a Motion to Dismiss, so you should be able to survive through to Summary Judgment.  So lets all race to Judge Sweet’s courtroom with frivolous complaints and cause the entire patent system to grind to a halt, killing the US economy in the process!  You better act fast before the Courts or Congress react.  Be sure to ask for Judge Sweet by name at the time of filing!

Can you tell I am fired up?  I am and the assaults on the patent system and war on the private sector need to stop here and now.  There will be no end to the challenges filed against all patents now because by its very nature a patent grants an exclusive right.  Never mind that the same Congress who included the Intellectual Property Clause to the US Constitution (i.e., Article I, Section 8, Clause 8) also included the First Amendment.  Do you think our founding fathers did so knowing that the granting of patents specifically authorized by the IP Clause would violate the First Amendment?  I don’t know, they were awful bright men.  I cannot imagine they would have done something so carelessly stupid.  I also cannot imagine the conservative majority of the US Supreme Court would ever rule that patents violate the First Amendment.  Call me crazy, but I don’t see Justices Scalia, Thomas, Alito and Roberts finding that persuasive.  I also cannot imagine Justice Kennedy would accept such a radical proposition, and Justice Sotomayor is known to believe strong intellectual property rights are a good thing, which shouldn’t be a surprise given she was once married to a prominent patent attorney.  So this case will not end good for the ACLU, we all know that.  Nevertheless, that attacks on innovators and the patent system are increasingly ridiculous.  Someone needs to stand up and say the Emperor has no clothes, and I am happy to oblige.

[Bio-Pharma]

Judge Sweet in his opinion stated the plaintiff’s position as follows:

According to the Plaintiffs, these genes exist as naturally occurring products of nature, and Myriad did not invent, create, or in any way construct or engineer the genes. Rather, Myriad located them in nature and described their informational content as it exists and functions in nature. According to the Plaintiffs, Myriad did not invent, create, or in any way construct the differences that may be found when a patient’s BRCA1/2 gene sequences are compared to the normal BRCA1/2 gene sequences or the correlations between certain mutations in BRCA1/2 and an increased risk of breast and/or ovarian cancer.

Later Judge Sweet again picked up on this, saying:

The Complaint further alleges that the information encoded in the BRCA1/2 genetic sequences, rather than being the result of an inventive process, exists in nature. -See Compl. ¶¶ 34, 46, 51, 55-60. The Complaint also alleges that the existence of certain mutations in BRCAI/P and their correlation with an increased risk of breast and/or ovarian cancer constitutes nothing more than a naturally occurring phenomenon. -See Compl. ¶¶ 61-80. Based on these factual allegations, the Plaintiffs assert that the patents-in-suit grant Myriad ownership rights over products of nature, laws of nature, natural phenomena, abstract ideas, and basic human knowledge and thought in violation of the First Amendment’s protections over freedom of thought. Compl. ¶¶ 52, 54. In addition, the Plaintiffs assert that Myriad’s ownership of correlations between certain BRCA1/2 mutations and an increased risk of breast and/or ovarian cancer has inhibited further research on BRCAl/P as well as genes that interact with BRCAl/Z. See, e.g., Compl. ¶¶ 96-98, 101. As a result, the patents-in-suit are alleged to violate Article I, section 8, clause 8 of the Constitution which directs Congress to “promote the Progress of Science and useful Arts . . . .” Compl. ¶¶ 52, 54.

The facts alleged in the Complaint are plausible, specific, and form a sufficient basis for Plaintiff’s legal arguments. Consequently, the pleading requirements as set forth in Iqbal are satisfied.

The only trouble is Judge Sweet is wrong and it is obvious that he did not read the claims in question. This is obvious because had he read the claims in question it would be obvious in light of the US Supreme Court ruling in Diamond v. Chakrabarty that there is in fact sufficient innovation to result in a patentable invention. In Diamond v. Chakrabarty the Supreme Court recognized that human intervention is all that is required to alter something from its natural state into a state made by man. Had Judge Sweet read Diamond v. Chakrabarty and read the patent claims in question he could not have possibly issued this ruling unless he was engaging in judicial activism to forward his own personal beliefs and agenda.

US Patent No. 5,693,473 is being challenged, and claim 1 states (in relevant part):

1. An isolated DNA comprising an altered BRCA1 DNA…

US Patent No. 5,709,999 is being challenged, and claim 1 states (in relevant part):

1. A method for detecting a germline alteration in a BRCA1 gene…

US Patent No. 5,710,001 is being challenged, and claim 1 states (in relevant part):

1. A method for screening a tumor sample from a human subject ….

US Patent No. 5,753,441 is being challenged, and claim 1 states (in relevant part):

1. A method for screening germline of a human subject…

US Patent No. 6,033,857 is being challenged, and claim 1 states (in relevant part):

1. A method for identifying a mutant BRCA2 nucleotide sequence…

You see, had Judge Sweet actually looked at these patent claims in question there is absolutely no way he could have reached this decision.  There is simply no way that anyone who is being fair, honest and impartial could find the facts as alleged by the plaintiffs to be “plausible,” yet that is what Judge Sweet did.

Allow me to state the obvious at the risk of being vilified for being correct.  Isolated and altered DNA does not naturally occur.  Methods for detecting, screening and identifying do not naturally occur.  Diagnostic methods and screening techniques are carried out by people, and the presence of a human actor makes these claims patentable under Diamond v. Chakrabarty.  That is the law, and filing a lawsuit and having an activist judge ignore the law does nothing but impose unjustified and unwarranted costs on those who can read, understand the law and know what it means.

Share

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 as of the time of publication and should not be attributed to the author’s employer, clients or the sponsors of IPWatchdog.com. Read more.

Join the Discussion

30 comments so far.

  • [Avatar for Gene Quinn]
    Gene Quinn
    January 5, 2011 06:52 pm

    canavan disease-

    Why would people not get the cure? If you are suggesting they get it for free regardless of ability to pay or insurance coverage, then I guess they wouldn’t get the cure, but that isn’t any different than currently exists. Medical care, like all other scarce resources, are rationed.

    -Gene

  • [Avatar for canavan disease]
    canavan disease
    January 5, 2011 05:55 pm

    What the heck? Why would we want to restrict what people can do to help others get well? So does this mean if someone finds a cure for, say, canavan disease that those who need it might not get it?

  • [Avatar for Gene Quinn]
    Gene Quinn
    April 3, 2010 02:26 am

    George-

    I will take a look to see if I missed a claim, but clearly the use of “isolated” in the claim provides the requisite human activity required by the Supreme Court. Unfortunately, Judge Sweet interpreted “isolated DNA” to mean “DNA” including DNA in it’s natural state. But isolated DNA does not occur naturally, and he is wrongvon the law and wrong on the facts. He will be reversed without doubt.

    Not sure what you mean by straw man argument. I know the concept, but no straw man here. I just point out the lies of the ACLU. Facts and reality should matter.

    -Gene

  • [Avatar for George White]
    George White
    April 3, 2010 01:02 am

    I think there is somewhat of a straw man argument in the article. In the list of patents & claim number 1’s that you lay out above you missed one: 5747282 whose claim 1 is:

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

    Unlike the claim you did cite, this one does not recite “altered”. From what I read in the press the judge decided that in the case of DNA, “isolated” and un-isolated are the same thing, unlike insulin I suppose. I do not know enough to have an opinion on the ruling but your readers should get to see the claim that does not have the limitation of “altered” .

    I enjoyed your talk at NAPP in San Diego.

    —George White

  • [Avatar for Mike]
    Mike
    November 16, 2009 01:40 pm

    The issued claims in US5747282 are:
    1. An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.

    2. The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.

    3. The isolated DNA of claim 1 which contains BRCA1 regulatory sequences.

    4. The isolated DNA of claim 2 which contains BRCA1 regulatory sequences.

    5. An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

    6. An isolated DNA having at least 15 nucleotides of the DNA of claim 2.

    Yes, they have great claims. An isolated DNA, and a half dozen methods of detecting BRCA mutations.

    They also have a plethora of mutations described:
    (i) C and T at position 2201,
    (ii) T and C at position 2430,
    (iii) C and T at position 2731,
    (iv) A and G at position 3232,
    (v) A and G at position 3667,
    (vi) T and C at position 4427, and
    (vii) A and G at position 4956;

    Isolated genes, i.e. not in a human body, are not found floating around in nature. Yes, they are isolated by the hand of man and fifteen years ago when the genes were isolated, it took a lot of work and investment to identify the genes that correlated to a specific disease. The claims expire in ~5 years and are available without restriction in the public domain.

    Others were working on the same or similar problems. I have not reviewed the genes involved or DNA sequences used, but the DNA markers used for detection in “Screening of inherited breast cancer with DNA markers,” Lancet. 1993 May 29;341(8857):1422, may provide some prior art. You would have to do a detailed analysis of the sequences provided, complete alignment, and identify any mutations and/or amplified sequences that are available in the prior art (if Lalle, et al. had the right gene). I do not have a full day to devote to this analysis.

    Myriad Genetics currently has 172 assigned patents and applications with the USPTO. I do not have time to review each and every claim of each and every application. IT is clear to me that if someone were to use the Lalle markers to sequence the BRCA gene, they should be in the prior art. It would take much more time and analysis to ensure DNA sequencing using the Lalle markers would be outside each and every one of the Myriad Genetics claims.

    Arguing that the excact sequence, SEQ ID NO. 1, would spontaneously end up isolated in a microtube without the hand of man is not a logical argument. That is an emotional statement that you feel Myriad’s work is outside of patent scope because in your professional opinion they don’t deserve a patent. The question of whether or not Myriad deserves a patent is a legal question based on the state of the art at the time the patent was filed, the content of the patent application, and the discussion between the examiner and the patentee. Courts may review the examiner’s decision, especially in light of new prior art. Any sequence existing greater than 1 year prior to the filing of their first application is in the prior art and may be used without fear of infringement.

    Claims 5 and 6 should be easy to invalidate because prior art DNA seqeunces of 15 nucleotides are fairly easy to find, if you have the time. Legally, they may already be invalid because they are broader than the claim from which they depend (that’s a “No! No!”). That would have to be flushed out in a legitimate court case.

    All of this began through University of Utah and Cancer Institute research. They either are or at one point made money off of this invention and received financial support for their research. The may have some form of licensing agreement to continue research and there may have been US government funding allowing some institutions to research as well.

    This is a very long and detailed case, with a lot of patents and pending applications. I cannot review each and every avenue out, but I have shown several paths (prior art, limits on the definition of BRCA gene, and possible licensing) to free up use of the BRCA gene. It would take money and time to clear a path through this patent thicket, a legal, legitimate, fact-based, non-infringing path.

    Right now I would use a primer encoding a 20 aa tag sequence to amplify 90% of the BRCA coding region, that would be outside the literal scope of claims 1 – 4. Claims 5 & 6 may be much more difficult to enforce, and more easily invalidated.

    Best regards and good luck with your design-around,

    Mike

  • [Avatar for Stop Lying About the Myriad Patents on BRCA1 and 2]
    Stop Lying About the Myriad Patents on BRCA1 and 2
    November 15, 2009 01:58 am

    […Numerous defenders of Myriad often claim that the patents do not cover naturally-occurring genes, but rather only “methods” created by humans, or “isolated and purified” genes, which they allege can only be created by man. After all, they claim, isolated genes do not appear in nature, and it takes the work of humans to create them. This is, of course, hogwash….]

  • [Avatar for David Koepsell]
    David Koepsell
    November 14, 2009 02:50 pm

    Mike,

    Claims 1, 2, 5, and 6 say nothing about detection… dowload the patent from my blog, or read here verbatim:

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

    2. The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.

    5. An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

    6. An isolated DNA having at least 15 nucleotides of the DNA of claim 2.”

    which is why Myriad has enforced their patent against anyone daring to replicate the BRCA1 or 2 genes, no matter what the purpose.

  • [Avatar for Gene Quinn]
    Gene Quinn
    November 12, 2009 02:39 pm

    All-

    In the Medtronic Bilski amici brief an excellent point was made regarding diagnostic methods and screening predating treatments by years or even decades. It seems incredibly short-sighted to lament the patenting of screening and diagnostics. You have to be able to identify an ailment before you can treat it, so if we give disincentive to screening and diagnostics that will set back treatment advances. I can’t understand how that would be for the greater good or at all help society. This is particularly true here were the testing is to let the individual know whether they are at a higher risk and MAY suffer from cancer later on in life.

    -Gene

  • [Avatar for Mike]
    Mike
    November 12, 2009 01:48 pm

    Jon,

    Whether it’s detecting the genotype, diagnosing a disease, or prescribing a treatment regime, there claims are still hinged on the “method of detecting,” “method of treating a disease,” or “method of identifying a propensity for cancer.” There are some claims directed to the combined detection and subsequent treatment, or selecting a different treatment. Either way, the claims require some physical test, or administration of a product, or the like.

    If you have problems with a specific claim, I will analyze it for you and identify the physical aspects of the claim required for patentability. If the claim is directed wholly to a law of nature, physical phenomena, or abstract idea, I will provide support for invalidating that claim.

    Best regards,

    Mike

  • [Avatar for Jon Merz]
    Jon Merz
    November 12, 2009 01:32 pm

    Mike, I tend to think the key words to the scope of the claim have not to do with ‘detecting’, because what is being detected may be well known (and we know that the methods of detecting are all extremely well known and many are free to practice by anyone skilled in the art), but rather with drawing conclusions, observations, or whatever the claim drafter cares to call the actual recognition step that the resultant genotype is associated with some phenotype.

    These diagnostic patents are predicated purely on the discovered meaning of the test result.

    jon

  • [Avatar for Mike]
    Mike
    November 12, 2009 12:52 pm

    David,

    The claims are directed to detecting naturally-occurring mutations of naturally-occurring genes. The operative word is detecting (diagnosing, etc.).

    Claims that are directed to naturally-occurring mutations of naturally-occuring genes as they exist in nature are not valid.

    The terminology in a claim must be carefully construed because it a very precise excercise to determine exactly what is claimed. The same precision is required when analyzing claim scope as is required when reviewing and analyzing a property survey, title of ownership or other property contract. There is a very big difference between even the simplest of terms (i.e. “hereby” vs “agrees to” assign). Because patents describe complex inventions using the limitations of the written language, each and every word of a claim must be properly construed in light of the claim terms, definitions in the specification, prosecution history, and the meaning of terms as they were used at the time of filing by one of ordinary skill in the art.

    Provide any one claim that you feel reads on a naturally-occurring gene and I will provide a detailed analysis of the claim scope. If it does actually read on a naturally-occurring gene, I will provide support for invalidating that claim.

    Best regards,

    Mike

  • [Avatar for David Koepsell]
    David Koepsell
    November 11, 2009 06:58 am

    Actually, the challenged claims include claims to naturally-occurring mutations of naturally-occurring genes. Click above for my blog-post clarifying this, and providing a link to the patent at issue.

  • [Avatar for Mike]
    Mike
    November 10, 2009 11:24 am

    Jon,

    First, I hate writing blog responses and losing the text when I post.

    A technology ban is not the most constructive way to achieve your goals. If patents are the greatest hinderance to academic research, legislation should be put forward to clarify the research exemption that is currently available. The scope of the academic research exemption has not been vetted in court making it difficult to advise universities and foundations regarding the research exemption. It is clear that purely academic research would likely receive a research exemption, unfortunately most universities are business entities with patents and licensing agreements. Thus a university with commercial aspects to their research should respect patent protection and be more patent savvy.

    Currently, research scientists and the public in general do not understand patent claims or the true scope of a patent. I have personally designed gene sequences for a variety of pharmaceutical companies that avoid patent claims and allow research to continue. Unfortunately, claim construction is biased – every patent owner thinks they can stop everyone from using their research while each researcher inists they don’t infringe the patented technology. A proper analysis of the claims would clarify what is protected, what is marginally protected, and what is free to use. A good analysis of patent scope would benefit many researchers prior to entering into any agreements or beginning research with patented technology. Ironically, often times people over-pay in licensing agreements for technology they are not using.

    Finally, all systems have excesses and poor examples. I do not necessarily agree with Myriad, their licensing decisions, or have a complete understanding of how much patent protection they deserve. They do have very strong patents to a series of different BRCA assays and diagnostics. They have also been very aggressive with enforcing those patents. They are one example of someone who continues to do the speed limit in a blizzard. They are not breaking the law, but the may not be living by the spirit of the law. That said, they have a business that needs to earn money, satisfy investors, and pay off any debt they may have incurred developing the test. That is their business decision.

    Changing the laws for each technology area, banning diagnostic assays, would have unintended consequences. It would limit more expensive and complex assays from being commercialized. The patents you are worried about have a 20 year lifetime from the priority date and they will expire in time. Currently, patents are not granted to simple and obvious assays. The entire human genome has been sequenced, simply identifying an ORF and possible function is not sufficient for patent protection today. To revise the entire system, a system that continues to evolve, based on several examples of aging patents would be short sighted and will have unintended consequences.

    If you feel that academic research is inexorably hindered by patents, you should first discuss the importance of patents with the university technology transfer office. Next you should investigate the true scope of the patents that hinder research, remember everything available in expired patents is guaranteed free for public use. Finally, you should develop a design around or cross-licensing agreement for each issued patent (published applications pose different problems).

    There is a lot of animosity in patent discussions. Some patents are overly enforced, but the overall picture is not the David and Goliath saga you paint. Patents are far more essential to smaller start-up companies than they are to the industrial beasts who own the majority of the patents (IBM uses patents like trading cards, averaging about 10 issued patents a day). Patent practitioners must work to discuss and educate researchers about the value of patents, the true scope of a patent claim, and the overall benefit of a strong patent portfolio to universities and research foundations.

    Please advise if there is a more constructive way to explain the benefits of all patents. A way to quantitate commercialization of university research and place value on the end results, a new commercial product with a limited monopoly for innovation.

    Thanks for your time,

    Mike

  • [Avatar for Jon Merz]
    Jon Merz
    November 9, 2009 01:45 pm

    A few thoughts:

    First, the labcorp claim at issue was not attacked in the lower courts on the product of nature issue, and the case was essentially dismissed by the supremes because the issue wasn’t preserved below. the issue i raised, whether these sorts of observations comprise patentable subject matter, remains open. Further, the claim at issue cannot be designed around. Sure, there are various assays folks can use to measure homocysteine levels but there’s absolutely no way around the observation claimed.

    Second, i’ll just note that the chip manufacturers are almost alone amongst biotechnology companies in not supporting this sort of patenting. imagine a chip that has a million snips, that costs, say $100 for its purchase and use. the marginal cost of looking at any particular snp could be a fraction of a cent. but patentees on these “inventions” may block use, or charge whatever they wish, and experience shows that the royalties demanded (when licensing is used instead of, like myriad, attempted monopolization of the test service itself), have been fixed sums per test. An example for you: one laboratorian we interviewed had developed a jewish panel that tested for a few alleles in CF, Tay Sachs, Gaucher, Neimann Pick, and Canavan disease. his marginal cost of running this assay was under $100. at the time, royalties demanded included $2 for CF, $5 for Gaucher, $12.50 for Canavan, and NP was not being actively enforced. see Merz et al. Nature 2002; 415:577-9. so the royalties stacked on this test accumulated to some 20% of the cost of performing the test. as the marginal cost of performing a test drops to zero, the royalties stay the same. so if everyone held patents on all the known genetic disease assocations out there, the micro chip technology would be simply unaffordable. thankfully, those who hold these patents have largely chosen not to enforce them, and it is the exceptions such as Myriad, Athena Diagnostics, and a handful of others that have driven the discord.

    Third, regarding stifling research, Myriad threatened the research community some years ago and did file suit against Penn (which was doing research and maybe some clinical testing), and the NCI negotiated a good deal (sequencing the two genes for somewhere around $800) with the company to do testing for NCI funded projects around the country. The research may take place, but Myriad gets to do the testing and decide what to charge for it. Whether more or less research takes place because of the patents is not, and arguably can not be, known.

    jon

  • [Avatar for Mike]
    Mike
    November 9, 2009 10:54 am

    Both of your examples, Apo-E and LabCorp, demonstrate how the patent system works very well. Anyone can manufacture the tests for Apo-E and LabCorp for any reason except to measure specific levels for one assay for the respective diseases, alzheimer’s or vitamin B deficiency. The claims in the patent and the scope of the invention are established.
    Admittedly, by today’s standards, those patents would be difficult to prosecute because technology has advanced. At the time the applications were filed, the association may have been more difficult. Like technology, patentable subject matter advances. Initially a protein sequence and coding region were patentable subject matter. Now, more is required including a function, activity, or other invention. Although Millenium and other gentics companies slapped together thousands of sequences and applied for numerous patents, very few issued without a requirement for sequence function- many to a single sequence with a very specific function. Because sequencing became easier and more commonplace, the level of patentability was raised for these patents.
    The same thing happens with patents in all industries, as the technology front advances so does the level of sophistication in the patents. All patents are judged by the same standards, electronic, biotech, business methods, chemical, etc., therefore some patents may issue based on a novelty that is not clear to those outside the prosecution. The patents, when enforced, should be valued based on that novelty. That may be the disconnect, multi-million dollar awards for a calendar tool were not justified. The system adjusts over time. If there are hard and fast rules excluding certain technologies by limiting patentable subject matter, future advances may not be protected from copying. Because patentable inventions are by definition novel, we will not be able to predict what technology we would be sacrificing in the future. As inventions progress in the information age, more and more activities are conducted on the computer, more diseases are tracked and treatments customized, new methods to accomplish different tasks may be developed and they may be excluded from patent protection simply because they use a computer (like a wrench) to accomplish those tasks. By denying protection to some “minor” diagnostic assays, you may forever block future microarray assays, or complex chemotherapy treatments, or the like that are not as simple.
    The fact that the LabCorp patent stood up in court says something about the underlying invention. Because the invention is a very simple diagnostic assay, it can be easily designed around or avoided until it expires in a few years. They Myriad BRCA tests are not easily designed around. These assays are better characterized and more developed than the Vitamin B deficiency assays. Although this patent is more substantial than the LabCorp patent, it has not stifled academic research as research continues and new papers are published almost daily on BRCA research.
    Exclusion of different technologies from patentability will have unforseen consequences, especially when future technological advances are unknown at this time.

  • [Avatar for Jon Merz]
    Jon Merz
    November 6, 2009 05:39 pm

    hi, i figure i’ll weigh in here a bit… i’m not a party or expert to the myriad suit, but i’m a close collaborator with some of the plaintiffs and experts, and i’ve published a lot on genetic diagnostic patents. to my mind, they in fact violate the proscription on patentability of mental steps. and they’re also detrimental to medicine.

    take as an example the patents covering diagnostic and prognostic uses of Apo-E. we carry 2 copies of this gene in our body, and it comes most frequently in 3 alleles, E2, E3, and E4. duke researchers recognized that if a person carries at least 1 copy of E4, then s/he is at increased risk for developing late onset alzheimers disease. US Pat. No. 5,508,167 claims characterizing one’s Apo-E status (by one of many methods available to the field, none of which methods are unique or first taught by the patent) and ‘observing’ that the patient is at increased risk because of the presence of at least one copy of E4. now, they also realized that if a patient is homozygous in E4 (carries 2 copies), s/he will be less likely to respond to a certain class of drugs, so they patented the identification of patients likely to be responsive to cholinomimetic drugs by determining how many copies of E4 a person has note that the test is the same test, but the interpretation and use of the test result is different. Another patent (to Pitt if i recall) claims the interpretation of the same test result as relates to the risk of prostate cancer, but that is of questionable scientific validity. Also of note, Apo-E status is a risk factor for cardiovascular disease, so the test may be done for cardiovascular indications and the physician who orders or performs the test is not infringing unless s/he recognizes (i.e., that mental step i mentioned above) that the result may have Alzheimer’s implications.

    unlike the bald assertion that it is the “method” that is being patented, the truth is that it is the observation of an association between a genetic difference and a phenotypic difference that is claimed. which leads me to ask Gene (aptly named, BTW): what did you think of Metabolite v. Labcorp, substantively, not procedurally. and, if you think the patent claim there, which claimed the observation that a high homocysteine level meant the patient was suffering a B vitamin deficiency, is valid subject matter. note that there are numerous methods for measuring homocysteine levels in the blood, but only 1 way to observe what that result means.

    if you think these are valid, then is the ‘mental step’ proscription dead?

    for a somewhat dated exposition of my concerns about these diagnostic patents, see Merz, Clinical Chemistry 1999; 45:324-330. (email me for a copy).

    jon

  • [Avatar for Mike]
    Mike
    November 5, 2009 11:48 am

    “altered” includes all mutations, either induced or naturally occuring. They also have claims to many different methods of detecting/diagnosing those mutations. That said, the claims never read on any naturally occuring DNA. They do read on diagnosing a propensity for cancer based on the presence of those mutations.
    The problem is not with the claims, the problem is a moral dilemma – protection for the inventor vs a persons right to identify and treat a disease. Unfortunately it is a slippery slope from “diagnosing a disease” to free use of any safety related device. I believe it’s agreed that Myriad should have (and may have) compassion for those who wish to test for BRCA mutations. It is a business decision on Myriad’s behalf, not a public decision. Alternatively, we may want to make some decisions for insurance companies, bankers, and other large corporations, they make life or death decisions based on monetary gain as well.
    This all boils down to Hatch-Waxman and whether or not it works. Look at university tech transfer offices before 1980 and after 1990 to see if more patented inventions are being tranformed into active businesses. The University of Wisconsin, Stanford University, MIT and many others have been very successful at converting professors patents into successful (and unsuccessful) businesses. Most biotech companies come from these fertile grounds. Applied Biosciences purchased its PCR technology and strictly enforced its patent protection. A statistical analysis of university patent applications and licensing before and after Hatch-Waxman may be a very quantitative way to measure the effectiveness of patents. In this time of outsourcing, a strong patent system is required to ensure quality medications, treatments, and equipment is available. Countries without strong patent systems can attest to the value of “branded” medications that are authentic and from the US. IF you prefer no patent controls or enforcement, I encourage you to order your prescribed medications from countries without strong patent protection.

  • [Avatar for Gene Quinn]
    Gene Quinn
    November 5, 2009 11:29 am

    Passerby-

    I will have to take another look. I would agree with you though, even if “altered” means mutated there is still isolation that would require some human intervention. The other method claims would also seem to require human intervention as well.

    Thanks.

    -Gene

  • [Avatar for passerby]
    passerby
    November 4, 2009 11:47 pm

    Gene,

    For clarity, are you positive that the claim limitation “altered” implies any human intervention? Looking at the specification, it seems like “altered” is used synonymously with “mutated”, and is referencing the naturally occuring mutations of the gene, rather than a manipulated alteration. I only skimmed the patent, so correct me if I’m mistaken. And ultimately, my understanding is that this wouldn’t change anything about the patentabliity because “isolated” still implies human intervention beyond a state that occurs in nature.

  • [Avatar for Mike]
    Mike
    November 4, 2009 05:19 pm

    POP,

    To answer your question, the patent may stifle some research and encourage other research.

    Investment in biotechnology is required, expensive, and risky. Patents are used to measure the innovation of a company and encourage independent funding. Especially funding for phase I/phase II clinical trials. W/o patents there would be very little investment.

    Companies that want to do independent research, especially for FDA approval/submission, have protection under the law allowing them to research. Similar protection is available for BRCA research. There are thousands of research papers on BRCA (the gene in the patent), over 30 published in the last month. University research continues.

    What has been stopped by the cease and desist letters are the basement test labs. Labs doing the same diagnostic tests as Myriad. A university lab, without the FDA standards and requirements, could do the same assay for a lot less. Myriad sends them cease and desist letters and is very strict about enforcing their patents.

    The ACLU wants the tests to be freely available (Myriad charges ~$3000.00). It is unclear if Myriad has assistance available for those who can’t afford their test. The ACLU also wants to get a “2nd opinion” thus requiring at least one other lab to provide the test other than Myriad. That is currently not available. Part of Myriads costs are ensuring FDA compliance. The tests and equiment must be certified and use certain FDA practices to ensure good protocols are followed. This will always drive up the costs of an assay. Many of the tests must also be managed by skilled labor, especially since PCR tests and binding assays are sensitive to contamination. It would be very hard if 3000 people found out the lab tech was positive for cancer causing BRCA mutations. In conclusion, it is unclear if $3000 is unreasonable for this highly technical, FDA approved assay.

    The test is expensive, there is no 2nd opinion available, but research continues and other assays will be available. The test can be conducted in one of the 130+ countries where there is no patent protection, or a new test can be designed “around” the Myriad test. Unfortunately new FDA approval would be required for design around tests.

    I hope this helps clarify the research aspect of your question.

    Mike

  • [Avatar for Karl Enevold, PhD]
    Karl Enevold, PhD
    November 4, 2009 05:10 pm

    Gene:

    I was arguing from the claims and Table 12a where somatic mutations in the human that occur naturally are associated with patient numbers, confirming their presence in nature. The fact that these gene mutations only predispose an individual to an increased chance of getting breast cancer infers that in others these gene sequences function normally and points to environmental factors or other factors that define the incidence of the disease. This is unlike Sickle Cell Anemia where a single nucleotide change or gene mutation is directly associated with disease incidence. The fact that “something that is isolated and altered by man” is covered by obviousness and infers naturally occuring in the human population. The statement “By definition the steps of isolating and altering are not steps that occur naturally”, are again steps that were derived prior published technologies and supported by public funding. The statement that “Even if the ultimate result is equivalent to nature, the process by which man modifies nature from one form into another form” is not supported by the prior identification of a sequence found naturally occuring in the human population and is only predisposing to an increased incidence in the occurance of the disease. This should not “be patentable under all existing understandings of method patents”.
    I was one of the first people to propose, in my postdoctoral grant applications, mismatch hybridization as a method for deducing gene function and correcting gene mutations by replacing, deleting, or inserting nucleotides in any specific area of a gene in 1984. I was awarded funding by the NIH, American Cancer Society, and McKnight Foundation, so the creation of an altered DNA sequence is also obvious. The only bonafide claims should cover a kit for detecting sequences contaning somatic mutations that could predispose an individual to getting breast cancer and not be allowed to prevent further research in an area or extract exorbidant fees from a captive population at risk of death I do not see what you are alluding to, but patent validity is cetainly up for discussion as these gene sequences occur in nature, only predispose an individual to getting a disease, and involves technologies published in the public domain and supported by public funding. The only merit is the kit and this should not prevent anyone from coming up with a better or cheaper version using alternate proceedures.

  • [Avatar for Mike]
    Mike
    November 4, 2009 05:00 pm

    POP,

    I appreciate your open mind. Patents in software are difficult because it is a quickly advancing field with an exponential growth in the amount of information available. Software patents are also only applicable (in many cases) for about 2 years from the time the technology is developed to the time when new technology is available to replace it. Thus by the time a patent issues, technology has often left it behind.

    Software patent lawsuits would be less problematic if everyone did an extensive prior art search to identify anticipating prior art before the suit was filed.

    That said, if you worked to solve a video compression problem for software (i.e. packaging a picture to be viewed on a cellphone) and current solutions were not working You develop software to simplify the image and it is very unique (not MP3 or JPEG) and entirely new. 10 fold better than anything available today using a completely independent system. IF you commercialized that system without a patent and license, everyone would copy your software, few if any would credit you for that software and Adobe or Microsoft would sell it as a plug-in for their new PDA systems. Alternatively, a patent would allow you to license your software, include your name or patent number w/in the software and ensure you got credit for your work.

    Unfortunately, some have taken this to the opposite extreme. They get a weak patent, with a minor improvement (if any) and they sue everyone with money (Microsoft, AT&T, etc.). Because the infringement award is not based on the quality of the patent/invention awarded damages ($$$) have gotten too large. This problem is unique to electronics and is brought on because of the fast pace of the field. Better prior art searches would get rid of this problem and reduce the number of bad patents issued.

    In other fields the cost of development is much greater and copying is a lot easier. In the ACLU v Myriad case, developing a genetic assay was very difficult. Many, many, many genes had to be assayed. Once identified the gene had to be put through clinical trials ($$$$). Now that the work has been done, anyone can copy the assay protocol and do the test for ~$50.00 worth of materials. Myriad stands to lose a lot if emotion rules over facts in this case.

    There are legitimate reasons for patents, even in electronics. Many times the courts will adjust correctly. It is a constantly moving target between over- and under-protection. Most solutions that try to single out one technology or another typically are short-sited solutions that do not treat all inventions fairly. The current law protects anything under the sun by the hand of man that is not an idea or law of nature. It’s a good standard that has been around for a long time and is well understood by practitioners and the courts.

  • [Avatar for Pissed Off Programmer]
    Pissed Off Programmer
    November 4, 2009 04:01 pm

    -Gene

    I think you hit upon the core split in your reply to Karl. A person’s opinion about patents rests pretty firmly on if they believe they promote innovation or take away from it. Like I said before I’m not going to pretend that I understand the effects on other industries, but I am not surprised to see a biologist comment on here as well. Biologists and other medical professionals seem to be the other loud anti-patent group next to computer people.

    It’s easy to say we should just find other ways of doing things, or that the patents don’t mean what what they seem to mean, and another thing practice, especially when it comes to finding alternate ways of doing the same thing. There are more patents issued than any person can possibly read, much less understand, so knowing about all the things you have to avoid is impossible. Another thing is, just because there is another way to do the same thing doesn’t mean it’s any good. It isn’t like we go to write a new program and sit down with a stack of patents to copy off of, which is how some people make it sound. Sometimes the best solutions or at least good solutions are obvious because there really aren’t that many ways to solve a given problem.

    Another thing I have a huge problem with is when a second person/entity comes to the same innovation/invention/research/etc… independently at a later date, they are still subject to live under the patent! When person X figures out a way to do A he is treated like a hero and given a monopoly over it, but when person Y figures out how to do A a year later, not knowing anything about X, he is treated like he might as well have ripped it off! It gives the impression that a thing is only worth doing if it hasn’t been done already. Is it any less amazing just because somebody else did before you without you knowing about it?

    I think that sort of thing happens in software A LOT more than people give credit for. There are a few truly deserving innovations like RSA public key encryption, but the majority are just run of the mill junk. If you keep your source code closed, and nobody reads your patent, and a bunch of people are writing their code the same way, it suggests to me that there really isn’t anything special about it, and that people would be doing it without patents.

    I think some good examples where patents should work are Apples iTunes database format, which is a secret, except to approved partner developers. That is a unique way to store data and it keeps their iPod products from being used with unauthorized programs. Nobody was using it before, and even though people try, nobody can really figure it out now. I don’t see any harm in that because they can use it go after people who are only trying to use it cheat them by undermining their iPod software.

    At the same time, if somebody independantally came up with a similar enough process or technique that Apple uses and had no intention of using for reading iTunesDB files, then I don’t think they should be punished either. They came up with it fair and square just like Apple did. Determining something like that is hard to say I’m sure since it’s largely word of mouth, but I could see something more restrictive to particular uses like they have in trademarks, where the same trademark can exists in different fields since they don’t conflict.

  • [Avatar for Gene Quinn]
    Gene Quinn
    November 4, 2009 02:28 pm

    Dale-

    Thanks for the praise. Glad you liked it. Sometimes when I get going I just pound the keyboard into submission.

    I enjoyed chatting with David via Skype, and wish I could have made it to NY. There will be other opportunities though, I am sure.

    I hope all is well.

    -Gene

  • [Avatar for Gene Quinn]
    Gene Quinn
    November 4, 2009 02:20 pm

    Karl-

    Thanks for joining the discussion.

    I don’t understand how you can say that something that is isolated and altered by man occurs naturally. By definition the steps of isolating and altering are not steps that occur naturally, but are imposed by man. Even if the ultimate result is equivalent to nature, the process by which man modifies nature from one form into another form would still be patentable under all existing understandings of method patents.

    I am not going to dispute what you say about the science. Notwithstanding, I have tried to point out to those who hold opposing views (such as David Koepsell) that the problem with the arguments they make are that it would require a complete and total re-write of the patent laws. That is why many who are against patents in a particular area are believed to have a hidden agenda. I am not saying you do, but a radical shift in patent law is not something that is going to happen. For better or worse (and I think worse) we have a one-size-fits-all patent system. So a change here causes ramifications there, and so on. I think we need to have a 1952-like re-write of the patent laws that focuses on rules that make sense for different technologies.

    I sense what you and others are trying to articulate may be that patents in this area fundamentally inhibit innovation because there is no other way from point A to point B. If that is true that should be considered in fashioning a solution that makes sense for all interested. But when statements are made that patents prohibit innovation, knowledgeable individuals stop listening because there is no credible evidence that is the case throughout history. In fact, the patent system is built on the premise that if an exclusionary blocking right is given others will be forced to engineer around and innovation jumps, rather than crawls.

    The thing you have going against you here is that many computer programmers incorrectly argue that patents prohibit innovation. They do not concern themselves with understanding the law, or reading patent claims. They base their views on titles of patents and abstracts, and on erroneous legal assumptions. Software patents do not prohibit innovation because there are hundreds or thousands of ways to get from point A to point B. Software patents force you to think about what you are doing and do something different.

    -Gene

  • [Avatar for Pissed Off Programmer]
    Pissed Off Programmer
    November 4, 2009 12:41 pm

    -Mike

    On the contrary, I have read all the patent codes, read patents from time to time, and generally try to keep up to date on patent court decisions. I wasn’t commenting specifically on the ACLU case, which I haven’t read, just on the general viability of patents affecting innovation, which was brought up in this case.

    I’m glad you agree that people don’t copy by reading patents, because they don’t. Patents are used to teach about as often as sofa beds are used to make toast. Patents are only used to enforce monopolies. The real question then becomes, how does this encourage innovation and research? If the disclosure of the patented process/claim/innovation/etc written in the patent doesn’t help anybody, because nobody reads them in order to take advantage of them, then what are they good for? The only decent answer is the carrot of a monopoly. People assume that companies will see research as a waste of money if their competitors can just rip them off without paying for the research costs, and so they will stop doing research.

    Not only do you have to believe that A) that is true, which I don’t, at least when it comes to software, but I won’t stretch outside my field, and B) That even if it were true, the benefits outweigh the costs associated with reducing competition and restraining the free market, which I also don’t.

    If you can give me a better argument or show that I am wrong, then I will listen, I am not closed minded, but so far I am not convinced. In a way I don’t care about the ACLU case because the real issue for me is, does it discourage more research and innovation? I can’t answer that question, but if the answer is yes then the patent should be thrown out no matter what the law says, and the law should be changed.

  • [Avatar for Mike]
    Mike
    November 4, 2009 11:59 am

    POP (Pissed off programmer),

    It is clear that you don’t read patents. Your experience with patents may be negative because you have not reviewed what can be patented, what the purpose of a patent is, or how the ACLU v Myriad case is incorrect.

    Genes themselves as they exist in the human body cannot be patented. ACLU arguing that Myriad has the “gene” patent is incorrect and not based on fact.

    You feel that only patent lawyers read patents – what about the inventors who entrusted their invention to a patent for protection. Copying rarely comes from the patent, it comes from money making products. Someone sees a product that makes money and they copy it without regard for patent protection. The patent merely lets the inventor enforce the rights they have for creating an invention.

    Software patents are a bad example of patent protection simply because there is no consolidated database of software methods. Software programmers frequently re-invent the wheel and seek patent protection for their re-invented wheel. Unfortunately, without a consolidated database, it is very difficult for software patent examiners to identify existing technology. If an examiner cannot present previous technology, they must by law allow the patent. That said, a patent can never read on previously existing technology or it is invalid.

    There are many misconceptions in the public about patents and it is our jobs as patent professionals to educate the world on what patents protect.

  • [Avatar for Karl Enevold, PhD]
    Karl Enevold, PhD
    November 4, 2009 11:52 am

    Gene,

    I always enjoy reading your articles, but I believe there are several other issues at work here. First, as a scientist from the biotechnology industry and an inventor of a live cell artificial pancreas laid to waste by the frivolous expenditure of funding pursuing the clueless whims of a biotech management, I have a major complaint with your statement ” Isolated and altered DNA does not naturally occur. Methods for detecting, screening and identifying do not naturally occur. Diagnostic methods and screening techniques are carried out by people”. With >300,000 SNP’s clearly identified by researchers and 10,000,000 thought to exist in the human genome, we are talking about DNA sequences that are known to exist naturally and technologies known to exist previously. Obviousness rules should have been utilized to invalidate these claims. Breast cancer and altered Brac sequences are naturally occuring in the human population and have been with us for 1000’s of years and not discovered in 2009, 1999, 1989, or even 1979. Molecular biology and specifically nucleic acid hybridization technologies, as well as sequencing technologies owe their existence to academic researchers from the 1970’s and maybe the 1980’s with the development of PCR; all supported by public funding. I know as I was there, as a graduate student. Myriad took advantage of previous know how’s to get where they are today. Though a second issue has to be the costs of the tests. At the heart of this discussion is Myriads cease and desist commands and, from an earlier posting, “marking up the costs of this test to $3800. It costs a lab only about $400 to do this test without a patent”. We really need to re-examine our priorities and a companies right to recoup expenditures, when I know the frivolous whims of a clueless managment are at play in this arena. A third issue, from a previous posting, Celera is also an opportunist and built on the hype of its founder, as it borrowed much of its technology from academic researchers supported by public funding. It’s only real value was for its founder, as they sequenced his DNA, and only real benefit was for him and the rest of the Venters in this world today. Hospitals and insurance companies control the reimbursement issues surrounding allowed tests, yet the public is expected the cough up the money for tests that could very well make the difference in life or death consequencies. But, as a scientist, these are my non-legalese opinions!

  • [Avatar for Dale B. Halling]
    Dale B. Halling
    November 4, 2009 11:30 am

    Gene, excellent article. The best analysis of the issues I have seen. I hope you don’t mind that I created a post, giving you full credit, about this issue. It is too bad that you were sick and could not be at the debate with David Koepsell.

    Thanks

  • [Avatar for Pissed Off Programmer]
    Pissed Off Programmer
    November 4, 2009 11:05 am

    -Gene

    I think what you are failing to understand here is the spirit of the law. Just to start things off, let me remind you that the majority of the founding fathers never wanted future generations to live by their rules. They firmly believed that every generation should make their own decisions about what was right for them, a reasonable conclusion considering they were upset about living under a monarchy.

    The “IP” clause in the constitution is hardly representative of Intellectual Property. It doesn’t even mention copyright or patents explicitly. There is a famous saying in the sciences, “if the model doesn’t fit the data, throw out the model”. The goal here is to promote and encourage progress in the sciences and arts, so no matter what the patent law currently says, if it goes against that end goal, it needs to be changed or thrown out.

    There is are few things on this planet that are more anti-competitive and anti-collaboratory than patents. You people always act is if the entire world would come to a halt if patents were gone tomorrow. Suddenly without the carrot from the patent office dangling over them all research and innovation would stop. The cold hard sobering fact is that most of the truly valuable research is done by governments, universities, and grant funded projects.

    You would argue that companies would stop paying for research because their competitors would be able to use it without paying for it, but there is a fatal flaw in this line of thinking. Let’s consider all the possible combination’s.

    With Patents
    ——————
    Competitors figure out how to duplicate the patented claims without reading the patent, which is almost always since nobody reads patents except for lawyers. In this case, what was the point of the patent? The claim is either obvious because anybody can figure it once they have the idea, which is not patented.

    Competitors can’t figure it out, don’t get a license, and go out of business due to competition from the patent holder. The patented company becomes a monopoly that nobody can compete with and all the research money falls into the hands of a few individuals who control the market. People who could be doing good research are crowded out and forced to wait for 20 years. Other people will find alternatives in the mean time but eventually there will be deadlock when all the plausible solutions have been discovered, and useful collaboration will have to wait until all the patents expire.

    Competitors do get a license but fork over most of their profits to the patent holding company and make almost no profits themselves. Again, as with above, all the research power is held by a single entity.

    Without patents
    ————————

    People will do research anyways because there is a demand for it. Every company will have access to every innovation. Some may benefit more than others, but competition will be based on the quality of the products and services and upon the merits of the companies. The only way to get an advantage is to innovate and stay on the cutting edge. Just like with evolution, an arms race will constantly drive people to come up with better, cheaper, safer ways to do things in order to gain an edge. Lots of books are out of copyright, but there is a lot of choice out there. Cheap paperbacks, leather bound tomes, famous introductions, and a whole host of other features to give the consumer more bang for their buck.