Friday, November 5, 2010

Superficial Appeal of DOJ Brief Proves Illusory

I can understand why many people find the position advanced by the US government in AMP v. PTO (the DOJ amicus brief, discussed in an earlier post) quite appealing. On its face, it seems to offer a reasonable compromise: patent eligibility for "engineered" cDNA, but not for genomic DNA merely "excised" from a human chromosome. However, the distinction is superfical, and does not in my view withstand closer scrutiny.

In particular, the DOJ conveniently ignores the fact that in almost all cases isolation of genomic DNA involves amplification, either through laboratory techniques such as PCR, or by replication in recombinant cells. This distinguishes DNA and RNA from other biomolecules. Prior to the development of recombinant molecular biology in the 1970s, isolation of a naturally occurring biomolecule, such as a protein, involved removing the biomolecule produced in a naturally occurring from other biological constituents. Importantly, all of the purified biomolecule originated in the natural source, and was purified by separating it from other cellular constituents.

In contrast, because DNA can serve as a template for its own replication, DNA is normally isolated by amplifying it many times ("million-fold" is the term used in the amici brief filed by BIO and AUTM). As a result, a typical preparation of "isolated genomic DNA" actually consists primarily of synthetic copies of the genomic DNA molecule.

The DOJ makes much of the fact that a cDNA molecule does not contain the introns, which exist in most human genes, and implies that molecular biologists have "engineered" the introns out. In fact, the introns are naturally removed in the body when genomic DNA is transcribed into mRNA. There is no human engineering involved; production of a cDNA molecule simply entails making a DNA copy of a naturally occurring mRNA and then amplifying it.

In most instances a preparation of isolated genomic DNA comprises synthetic DNA molecules, produced in the laboratory by amplification, that correspond in sequence to a naturally occurring genomic DNA. A preparation of cDNA comprises synthetic DNA molecules, produced in the laboratory by amplification, that correspond in sequence to a naturally occurring mRNA. Considered in this light, I think that the distinction DOJ makes between "excised" genomic DNA versus "engineered" cDNA proves largely illusory.

True, a cDNA molecule has a slightly different chemical structure than the mRNA on which it is based, but the differences are small. The sugar group (ribose) in DNA is lacking an oxygen atom (hence the “deoxy”), and one of the four base groups in RNA (uracil) is slightly different than the corresponding base in DNA (thymine), due to replacement of a methyl group with a hydrogen atom. But mRNA and its corresponding cDNA both encode the same information, and both hybridize to the same complementary strand.

In many instances, a synthetic copy of a genomic DNA molecule is also chemically different from the original. Most naturally occurring genomic DNA is methylated, a form of epigenetic modification, while synthetic copies are often not methylated.

In short, the minor structural difference between cDNA and mRNA is not so qualitatively different than the difference between amplified genomic DNA and genomic DNA of natural origin to warrant using this distinction as the basis for drawing a line between patent eligible and patent ineligible subject matter.


David said...

Chris, for once we agree, except this is why I argue cDNA ought not to be patent-eligible. As for you brief, you seem to be arguing: sure the claims are too broad, but no court will ever enforce them so broadly. Which is an awkward position to take. It is like saying: true, separate is inherently unequally, but no court will ever let separate accommodations stand if challenged, so let's wait for Congress to pass the civil rights act.

Anonymous said...


I am entering this conversation very late but as I read Chris' brief I understood his point to be that there are other legal avenues to deal with the patents at issue and, therefore, why invent a new doctrine.

The law of nature doctrine was fabricated by the courts and finds no support in the statute or the US constitution. Whether something is or is not a law of nature is not the relevant question from a societal or economic point of view. The question is whether the inventor has added to the "storehouse of knowledge" (to quote Funk) that it otherwise did not enjoy. If the answer is yes, then a patent should be granted provided the other requirements are met. If not, it was never novel in the first place and not patentable (rather than not patent eligible).

David said...

Dear anonymous,

Judicially-created law is still law, just as Brown vs. Topeka bd. Of ed. Was law that overturned bad prior, judge-made doctrine. Legislatures too are free to amend or change the law. I happen to think the Diehr, Chakrabarty exceptions to patent-eligibility are quite logical. O2 made by photosynthesis is morphologically identical to O2 made through electrolysis. The products are identical, even while a new, patent eligible process is devised to separate the natural products. So patent the inventive process, don't devise artificial distinctions among products. This seems like a fine solution to me that will promote inventiveness. Cook-deegan's study showed clearly that Myriad's claims encompass too much, and the solution is to not pretend that a "synthesized" version of a natural product is something different. In metaphysics and ontology, the principle of sparsity is violated if we populate the world with things that are not distinct. Taking the reasoning of those who support patents on synthesized copies of otherwise naturally occurring products (rather than allowing patents on the process, which I think is fine if new and non obvious) then O2 made by photosynthesis is a different sort of thing than o2 made by human-generated electrolysis. This is maddening, illogical, and what I have long argued for overturning.

David said...

also, the law of nature and physical phenomena exceptions do have societal relevance if, as I argue, these things belong to the commons-by-(logical)-necessity. Some things simply cannot ethically be monopolized. I argue that E=MC^2, and natural phenomena like naturally-occurring molecular structures (isolated or not) belong to these sorts of commons.

Ken Chahine said...


Review the examples that you are using - O2, E=MC2, etc. and ask yourself "was the public benefiting from those so-called product and laws of nature prior to any discovery?" The answer in both instances is yes. Therefore, I would agree with you that neither deserves protection ... but not because it is not eligible but because they are not new. We were using O2 and the E=MC2 prior to any discovery. Under patent law, a discovery for how something works has never been per se patentable, even if the public didn't appreciate it.

Second, in law there must always be a judicial underpinning for the decision. The court cannot simply say it does or does not "like" something. Under Brown there was a judicial underpinning to the ruling - the Constitution and Bill of Rights. What is the legal underpinning for ruling that laws of nature are not eligible?

Ken Chahine
Professor of Law
University of Utah.

David said...

Hi Ken

So, you too would do away with the exceptions the Supreme Court has drawn?

My arguments are not based upon utility, but rather upon an expanded view of the commons, which I argue includes parts of the universe that cannot be enclosed, as I have argued that enclosure, scarcity, rivalry, and exclusivity are the hallmark of just property law. I think that the Diehr/Chakrabarthy exceptions to patent-eligibility are perfectly logical and just in light of the fact that commons-by-necessity can never be justly enclosed, or even logically so. In fact, we have all also been benefiting from the BRCA1 and 2 sequences too, or suffering from the presence of their mutations long before their discovery.

The courts' reasoning about not patenting "too far upstream" has always been based upon utility, as this can foreclose useful inventiveness downstream, create thickets, etc. But my ethical arguments have nothing to do with utilitarian arguments, but rather relate to the injustice of allowing monopolies over parts of the commons-by-necessity.

I think that SCOTUS got this right most recently with Chakrabarthy, which I cite for this very principle, and which both Judge Sweet and the DoJ also cite for the same principle.

Sometimes, utility must lose to deontological principles. This is such a case.

Ken said...


Let's leave the legal theory aside - I will get to that later.

I am a consequentialist - what is the society getting in return? If the invention does not take something society already enjoyed and its new utility significantly improves the human condition, then I would completely disregard the structural differences.

In that vein, I would be very interested in your point of view on how ethically we justify granting rights to real property (i.e., land - a finite resources not created by man) in perpetuity versus a limited exclusivity over a non-made isolated gene?


David said...


As a deontological ethicist, I cannot argue against a utilitarian in the same context. We don't share foundational principles. Utilitarianism is a weak theory, prone to abuses, shown throughout history to be sometimes catastrophic. You must accept that losses of rights (which you cannot believe in as a utilitarian) are justified by a greater good for a greater number. I simply do not accept the hedonic calculus.

Property rights in scare resources stem from labor and improvement, as Locke, Smith, and others have argued. They also stem from our need to prevent violence, and the categorical immorality of violence. In order to dispossess someone of a scarce resource, violence must be committed, or mutual agreement must be reached. In the one case, in the case of violence, the categorical duty to respect the autonomy and bodily integrity of one is violated. In the case of mutual agreements or contract, that same autonomy is respected. Just laws thus recognize claims to property based upon prior, peaceful possession, labor, and improvement.

Because the subjects of IP are non-scarce, non-exclusive, non-rivalrous, the law of IP is entirely positive, and not grounded in natural law, rights, or other deontological principles. However, if IP laws conflict with natural law, they too can be unjust. Because I argue that our collective, mutual, free access to abstract ideas, laws of nature, natural phenomena, and other commons-by-necessity are impeded by attempts to grant monopoly rights over un-modified, but merely 'isolated' genes, I argue that all such patents are immoral.

Science proceeds apace, investigating and uncovering facts about nature, generally through publicly-subsidized research. I have no fear that future discoveries of medical import will not occur if we stop granting these sorts of patents.

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