Showing posts with label cDNA. Show all posts
Showing posts with label cDNA. Show all posts

Wednesday, June 19, 2013

Philosophy and Public Policy: Metaphysics Matters!

It has been nearly a week now since I received word about the outcome of the Myriad case. I was travelling at the time and suddenly started getting congratualtory emails and Facebook messages, so I went online via free wifi at the coffee shop I was at in the US, and quickly found the news that the Supreme Court had unanimously rejected Myriad's arguments. I was so excited I hit my best friend in the chest... sorry Justin. Now that a week has passed, and the airwaves and blogosphere have been awash with a plethora of incriminations, congratulations, and musings about what it all means, I want to address what is to me a central lesson: philosophy matters.

Sure, some will claim this decision was a legal one, having no relation to philosophy, but such claims betray a complete ignorance about what philosophy is. My book and the writing and speaking I have done on the subject of gene patents ever since have focused upon the ontology of the underlying objects. I have long felt that before we can approach ethical questions we need to clarifying what we are dealing with. I did this first for software, then genes, then nanotehnology. While I have taught medical and bio-ethics, the thesis of Who Owns You is not guided by standard bioethical principles, but rather founded upon uncovering the nature of the objects involved in the debate. Thus, my arguments about the nature of the "commons-by-necessity" and the status of genes as part of that commons confused some who expected typical applied ethics arguments, or legal anti-commons claims. For the past four years, what I have tried to do is show by recourse to basic ontological concepts, that unmodified but merely isolated genes are not different in kind from the genes claimed by Myriad and others as found in nature.

In the course of these arguments, the illogic of those who pursued the course of maintaining gene patents as they existed was laid bare, perhaps never more clearly than in debates about the nature of another naturally-occurring product: O2. When it became clear through those arguments that patent attorneys and others who supported gene patenting must also endorse patenting O2, the necessity of ontology was also revealed. Despite their claims otherwise, a world in which individual O2 molecules are distinguished from each other based upon their origins makes little sense ontologically, forget the ethics. One needs to confuse process with product, a basic ontological error, to support such a view. The Supreme Court, whether they realized it or not, sided with sound ontology. Although lacking the language that philosphers use when engaging in ontology, the Supreme Court's opinion makes both logical and ontological sense.

The Court has reasoned that the BRCA mutations claimed in Myriad's patents, even though "isolated" from the surrounding genome, remain "natural phenomena." An explanation for how this is so resides in ontology. In each case, the molecules described by the nucleotide sequences identified are not the result of man's design. They are nature's own products. Similarly, even when synthesized, O2 is never the product of man's design.  The process of creating isolated BRCA mutations in the lab may well be man-made, but will never result in anything other than a natural product because the product is one designed by evolution, not human ingenuity. We could call lab-made O2 or BRCA genes "synthetic natural products," and explain this by understanding that the process of making something cannot be confused with the resulting product. To be non-natural, both the intention of creating the product and the design of the product must come from minds. This is why I am more or less comfortable with the court's holding that cDNA is patent-eligible, because in producing cDNA (when, as the Court notes it does not exactly mirror sequences found in nature), one must combine intention with design.

At one of my recent talks, someone asked why in making my arguments I relied on ontology rather than ethics. My response was that courts are typically unmoved by ethics. This may be suprising, but it is true. The Court's decision in Myriad is about the nature of the underlying objects, not about what is right or wrong. Perhaps there is an ethical dimension to the general prohibition against patenting abstract ideas, natural phenomena, and laws of nature. Or perhaps not. Perhaps this restriction is about the nature of the objects too, as I have claimed when I argue they are simply materially and logically (and thus maybe also ethically) "unencloseable." But the Court's decision is guided, whether knowingly or not, but an ontology, and one which is coherent if understood as I am describing it. It provides guidance for those who conduct basic research, and those who wish to commercialize inventions. It offers some clarity where the law had deviated from logic. It illustrates that philosophy is not divorced from other subjects, and can indeed be relevant in numerous spheres. Indeed, metaphysics matters a great deal, and we engage in its practice every day to greater or lesser degrees, and sometimes public policy is significantly affected by its improper or proper uses. Philosophers would do well to point out the role of philosophy, as illustrated by the Myriad case and its implications, in the real world, and those who fail to see this as an implementation of philosophical reasoning should review the role and nature of philosophy historically. It really is the meta-science.

Tuesday, April 16, 2013

JUSTICE KAGAN: "And the PTO seems very patent happy"

I love that quote from Justice Kagan because it pinpoints the root of the issue. She said it when Myriad's attorney tried to justify the practice of patenting isolated genes by referring to the Patent and Trademark Office's past practice of doing so. She is right, and that office, run as it is by patent attorneys, much like the CAFC is dominated by them, is a poor guide for what ought to be the case. They are "patent happy." (see, e.g., the Peanut Butter Sandwich patent).

One should never try to predict what the Supreme Court will do in any given situation. Nonetheless, a brief analysis of the transcript of the oral argument in the Myriad case is revealing. The Justices seem inclined to hold in a way that readers of this blog will be familiar with: isolation of a gene is not enough, only changing the gene suffices to make it patentable. The questioning from the Court right from the start revealed their discomfort with the current "isolation" regime, which is unsurprising in light of their recent decision in Prometheus.

Mr. Hansen did an excellent job in his argument, under some difficult questioning, steering the discussion back to the question of whether a product of nature, merely isolated, should be eligible under Section 101. He cited all the best examples, arguments, and precedent. He also conceded as he should that recombinant DNA is eligible, and that the patents at issue in the Myriad case are not recombinant. He also left the door open for the Justices to do as they seem inclined to do, and follow the lead of the Solicitor General, ruling that the isolated genes alone are ineligible subject matter but that cDNA is. This is also the position I have maintained all along in my book and since. The attorney for Myriad had a tougher time of it, and the questioning of the Justices seemed to have him in a corner a couple times. Instead of recapping the arguments, I urge you read them yourself here. Also, I am providing links to some excellent in-depth and plain English analyses here, at Patently-O and at ScotusBlog. What I wish to do here is highlight sections from my book that made the same argument that seems likely to win the day, a conservative position I have maintained all along, arguing that mere isolation is insufficient to warrant patent, that some degree of intention (and design) is necessary to make something inventive, and that while engineered genes ought to be patent eligible, isolated genes alone ought not to be. Here are some relevant passages:

"Each instance of the un-engineered human genome is a naturally occurring object. Its existence as an abstracted ideal which is instantiated in you, me, and every other human, in its present form has no element of the type of expression described above. There is no mixing of labor with any present human genome’s form, nor is there any human intention involved." (Who Owns You? p. 111-12)
"All copyrightable and patentable objects are intentionally produced man-made objects and they are not merely ideas. Your DNA, or mine, or any other non-engineered being, is not an expression according to this description of intellectual property, and neither is any naturally-occurring subset of a genome (such as a gene or a SNP)." (Ibid, p. 112)
"Chemical formulas, for example, or natural laws, cannot be copyrighted or patented. The seminal Supreme Court case Diamond v. Diehr, specifically excluded from patentability “laws of nature, natural phenomenon and abstract ideas.” (Ibid, p. 113)
"Many gene patents are perfectly valid both legally and ethically. All valid patents use products of nature in some form, but they do not extend to protect the naturally-occurring parts of the invention. Most patents on new chemicals involve not just a patent on the new compound, but also a patent on the process of synthesizing the compound.These sorts of patents provide guidance for how gene patents can legally issue and still also promote innovation. New genes could of course be patented if they are man-made. New combinations of genes can also be patented if they are the products of human intention." (Ibid, p. 114)
"Many gene patents issue now in which the current use of the gene is in merely finding the same gene. This is quite absurd. It is like patenting the element iron, and then claiming that the use of iron is in finding iron, or patenting the Rock of Gibraltar and then claiming that the utility of the patent is in locating the Rock of Gibraltar." (Ibid., p. 115)

I quote these sections because they show that the arguments I made anticipated the same ones made in the Myriad case which began a couple months after my book was published. These same arguments have been to a large degree echoed by the questioning of the Justices. Together with Myths About Who Owns You the past year at least has demonstrated just how conservative my arguments have been and how they echo the thinking of at least some Supreme Court Justices as well as precedent, and that perhaps initial claims about how wildly inaccurate, off-base, or whacky my arguments were, were themselves wildly inaccurate, whacky and off-base, or perhaps merely ideologically-motivated.

Now of course, the Court may still rule that all gene patents are just fine, but at least I take comfort in having my arguments made in public court, in language and with examples similar to that I used in 2006 when I first confronted these issues from a philosophical perspective. I'm comforted that now my arguments seem firmly in the mainstream and persuasive to many if not all.

Monday, November 9, 2009

Stop Lying about the Myriad Patents on BRCA 1 and 2

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. Isolating a gene is accomplished in nature in the process of cellular metabolism. Protein synthesis is accomplished without human intervention, much less, human invention, because various forms of RNA read the beginnings and ends of genes, omit the introns, and construct proteins from the remaining (exon) codons. So, merely finding the beginning and end of a gene is, as I have analogized in my book and elsewhere, equivalent to reading a map, and noting a geographical feature therein. Nature made the feature, and defined its borders, and we simply find it and model it. So that's the "isolation" and it doesn't warrant patent.

The "purification" part is part of nature's bag of tricks too, as mRNA skips the introns (the non-protein coding regions), and in fact some laboratory methods for creating cDNA (thus "purifying" DNA) use mRNA to accomplish this. Again, nothing at all inventive.

Finally, the Myriad patents on BRCA1 and 2 claim un-modified genes -- mutations in the BRCA1 and 2 gene that occur naturally. Their sole inventive claim is "isolation." See the patent yourself, and look at the claims (pp. 153-156). Look specifically at this:

"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."


Now, note: these are not method claims, they are not claims for cDNA, but rather over naturally-occurring mutations to naturally-occurring genes. As I discuss above, and in my book, and elsewhere in this blog, this is not inventive at all. Rewarding for discovery of laws of nature goes beyond the scope of patent, and it inhibits research, and access to the "commons by necessity" that is the human genome and laws of nature in general.

It is like saying that since detached bird wings do not exist in nature, one ought to be able to patent detached bird wings. It's madness, and everyone except patent lawyers and others getting wealthy off this insanity can see that.