This notice in the Federal Register advises that Oregon State University is has requested an exclusive license for a variety of Blackberry from the US Patent office. This is an interesting development. Essentially here it seems to be that under the law, life can be patented. The notice references 35 USC 209 and 37 CFR 404.7. These regulations have existed for some time, but I was not aware of them until reading this notice.
The above references sections of law and regulations deals with the granting of a license to develop and manufacture products based on a patent owned by the US Government. The language in both sections is relatively general and has a few specific items listed in it. The main concern I have with this is that the provision for granting a patent is that it is based on a specific "invention". A new variety of plant, in my opinion, does not fit well with the concept of an invention. While I am sure I am not the first person to put forth these arguments, I think it is worthwhile considering them as an exercise in critical thinking.
A traditional view of an invention is some man-made device used to perform some specific task. To draw upon automotive history, a car and many of its subsystems are specific devices that perform specific functions through a specific implementation of principles. A variety of plant does not fit into this view very well. The differences include the fact that a variety of plant is defined by specific genotypes as opposed to a physical configuration of parts; plants are able to re-produce and are not subject to a manufacturing process; and that a given set of genotypes would be possible to arise naturally rather than being invented by humans.
Species and varieties of plants have been catalogs since Ancient Greece. The basis for distinguishing plant species and varieties was originally careful observation of characteristics of the plants such as shape, size and number of leaves and whether it would reproduce with other kinds of plants or not. When the DNA molecule was discovered by Watson and Crick, the understanding that the expression of characteristics arose out of the specific sequence of amino acids coded in the DNA came to be. Essentially granting a patent on a variety of plant is effectively a patent on specific sequences amino acids in a genome. There is a rule for patents that you cannot patent an idea, you have to patent an invention which is a specific (non-trivial) implementation of an idea. My opinion is that a specific sequence of amino acids in the DNA molecule is much more of an idea rather than an implementation because given the state of biotechnological capabilities, the implementation is relatively non-trivial.
Because life is able to reproduce, control of "manufacturing" is not yet effectively possible. I would grant that for a patentable life form, if the mechanism for reproduction was suppressed, it would nullify this objection. Already there are issues with regards to GMO vs. non-GMO foods where if you have two farmers with adjacent fields and one farmer plants a GMO crop and the other a non-GMO crop, due to the possibility of cross-fertilization, the purity of both crops becomes impossible to guarantee. Traditionally, patents were granted for mechanical devices where, in order to violate the patent, a specific verifiable action had to be taken. With patenting and licensing of species and varieties of plants, violations can occur through simply negligence of someone using the patented or licensed plant. This kind of situation is absurd and calls into question whether life can be patented.
Finally, even the argument that in some cases, genes from completely different plants are being combined to create a new variety or species is suspect. While in the short term, I agree that a gene from an Amazonian bush is highly unlikely to appear in a strain of berry that grows in North America, the reality is that evolution operates on much longer time scales than the human life span. Just because we cannot observe it to happen does not mean that it is not possible and therefore despite there being interventions made to modify genomes, it is not logically possible to argue that these kinds of mutations might not actually not occur given enough time. The human brilliance is in making these changes occur quickly rather than making them occur at all.
Finally, given anything that can be done with plants, these actions can be applied to animals and even humans. To take a pop culture example, in Guardians of the Galaxy, there is a character, Rocket, who is a raccoon upon which bio-engineering and cybernetics have been applied to create a sentient creature. By the rules of the patent office, he could be patentable. An actual example is what has been described in the book "The immortal life of Henrietta Lacks". Ultimately, the logical thing to do is to try and copyright or patent one's own genome. Who knows what specific mutations, immunities or characteristics in your DNA may become marketable. Since these amino acids sequences are really "you", you should have the right to their use.
The Federal Register notice does allow for comments, but these are limited specifically to issues regarding the applicability of the law and regulation on granting a license of a government owned patent to a third party. The bigger picture as to whether characteristics that are due to a specific arrangement of amino acids would really need to be addressed by a change to patent law and regulation.
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