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Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

supremecourt.gov

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Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#151

Post by dnautics »

daughart wrote: post #140
dnautics wrote: post #133

Earlier quoted context omitted.

You can't just assert that it exists. You'd have to show that it exists.

That should be trivial, if you had a large sample and money for sequencing. The consensus in the listservs I'm on is that cDNA patentability will fall next because of these and other inconsistencies (cDNA existing in nature, being a non-natural transformation).

cDNAs do not "exist in nature" the way you think they do. Viral RTs typically hijack a tRNA for use as a primer, and there is a specific tRNA footprint site that is necessary to initiate RT specifically at the position of interest to the virus. these footprint sites typically don't exist near the gene you care about.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#152

Post by dnautics »

dekhn wrote: post #33
jweese wrote: post #5

Earlier quoted context omitted.

Justice Scalia's concurrence, reproduced here in full: "I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied the opinions below and the expert briefs presented here, that the portion of…

cDNA occurs in nature (reverse transcriptase). In fact DNA intermediates with introns spliced can be reintegrated into the genome. Further, faulty viruses can acquire oncogenes (intron-splicted, mtuated versions of growth factors, like EGF and HER2/neu) and transfer them to other cells via cDNA intermediates. It's not hard to believe that nature has in fact passed BRCA cDNAs around via retroviral intermediates.

RT doesn't work that way, it requires a specific site near its target gene in order to make the DNA strand. There is off-target activity, but it is almost certainly vanishingly rare.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#153

Post by dnautics »

daughart wrote: post #139
dnautics wrote: post #136

Earlier quoted context omitted.

I think I was confused because you meant "patentable", not "patented". But is not isolation by PCR a synthetic modification? If I made a useful machine out of a single piece of wood using a six-axis subtractive tooling device, would you argue that the machine is unpatentable because "it was already there" ? PCR actually goes even further - conceptually it's subtractive procedure but it actually does so by creating co…

Yes, sorry I meant patentable. This ruling specifically says that merely identifying the location of a gene and isolating it is not a patentable transformation. PCR is not transformative because the dsDNA molecule exists in nature. I think in this context isolation is similar in nature to discovery, which is not a patentable activity.

well, no, the supreme court has decided that effectively breaking four covalent bonds is not transformative (your words). I think it's a wrong decision. Even so, if you actually understand it, the act of PCR is an act of creation, not transformation. That dsDNA molecule doesn't exist in nature.

For example, there is a molecule thiostrepton which is an antibiotic compound, that's really quite poor. They have recently discovered that only the core of the molecule is necessary for antibiosis, and removal of the rest of the molecule improves its pharmacological properties. It's a distinct molecule, created by the scission of 3 covalent bonds. Should it be unpatentable? Almost certainly, somewhere in nature, there has a thiostrepton molecule that by accident happened to have been cleaved at exactly the right places to render the molecule. does that change your opinion?

I am not trying to defend the practice - I abhor patents - but a lot of people are letting their emotional reaction to "patenting genes" get in the way of a dispassionate and informed analysis of what actually is going on here.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#156

Post by dekhn »

rcthompson wrote: post #148
dekhn wrote: post #42

Earlier quoted context omitted.

wrong. this happens in retroviral transmission all the time.

To my knowledge, the BRCA1 mature mRNA sequence has not been shown to be reverse-transcribed during any part of the life cycle of any retrovirus.

given that retroviruses are sloppy, basically any any all genes have at some time been reverse transcribed.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#157

Post by dekhn »

dnautics wrote: post #152
dekhn wrote: post #33

Earlier quoted context omitted.

cDNA occurs in nature (reverse transcriptase). In fact DNA intermediates with introns spliced can be reintegrated into the genome. Further, faulty viruses can acquire oncogenes (intron-splicted, mtuated versions of growth factors, like EGF and HER2/neu) and transfer them to other cells via cDNA intermediates. It's not hard to believe that nature has in fact passed BRCA cDNAs around via retroviral intermediates.

RT doesn't work that way, it requires a specific site near its target gene in order to make the DNA strand. There is off-target activity, but it is almost certainly vanishingly rare.

"almost certainly vanishingly rare event" * "incredibly high rate of reproduction of viruses" = almost certainty.

See the first 4 chapters of "Biology of Cancer" by Weinberg.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#158

Post by daughart »

dnautics wrote: post #153
daughart wrote: post #139

Earlier quoted context omitted.

Yes, sorry I meant patentable. This ruling specifically says that merely identifying the location of a gene and isolating it is not a patentable transformation. PCR is not transformative because the dsDNA molecule exists in nature. I think in this context isolation is similar in nature to discovery, which is not a patentable activity.

well, no, the supreme court has decided that effectively breaking four covalent bonds is not transformative (your words). I think it's a wrong decision. Even so, if you actually understand it, the act of PCR is an act of creation, not transformation. That dsDNA molecule doesn't exist in nature. For example, there is a molecule thiostrepton which is an antibiotic compound, that's really quite poor. They have recently…

Your perspective is confusing. You say that a modified form of thiostrepton should not be patentable, even though the patent protects the molecule as well as the process of chemical synthesis or purification, which often requires significant innovation, and in this case the natural molecule is also significantly modified. On the other hand, when you PCR something you are generating a dsDNA molecule that is identical to the original molecule. I understand PCR quite well, and doing PCR is not innovative or transformative. You are creating something, sure, but it's an exact copy of something that exists in nature. The Supreme Court clearly states here that merely finding out where a genetic sequence is and isolating it is not patentable. The process of PCR itself is an invention, and is patented (Cetus, Mullis).

It seems preposterous to say that you are strongly against patents, and then say you think the patent should be much more restrictive. I have no emotional reaction to patenting genes. I think patenting a significant modification of a naturally occurring substance is completely reasonable as it protects the investments involved in inventing and applying the modifications, while at the same time allowing others to use and understand the development. Without patents biotech would become full of trade secrets, holding back progress in the field.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#159

Post by dnautics »

daughart wrote: post #158
dnautics wrote: post #153

Earlier quoted context omitted.

well, no, the supreme court has decided that effectively breaking four covalent bonds is not transformative (your words). I think it's a wrong decision. Even so, if you actually understand it, the act of PCR is an act of creation, not transformation. That dsDNA molecule doesn't exist in nature. For example, there is a molecule thiostrepton which is an antibiotic compound, that's really quite poor. They have recently…

Your perspective is confusing. You say that a modified form of thiostrepton should not be patentable, even though the patent protects the molecule as well as the process of chemical synthesis or purification, which often requires significant innovation, and in this case the natural molecule is also significantly modified. On the other hand, when you PCR something you are generating a dsDNA molecule that is identical…

Yeah, i'm against patents, but i think if we have them they should be applied fairly and according to a clear set of rules instead. It's like saying, I'm opposed to government being involved in marriage, but if we are going to have it then homosexuals should be allowed to be married.

The only reason why the perspective seems confusing is because you're conflating process with molecules. In general any given claim of a patent can protect the molecule or the process. Myriad did not choose to claim the process, because the process is obvious. But having a process that is obvious does not necessarily make the molecule obvious.

Doing PCR is not innovative. But the process DOES transform one molecule into another, unless your primers are exactly flush with the end of the dsDNA - in which case it is merely a straight copying operation. OK? The molecule that comes out at the end has a different covalent structure than the molecule that you start with. Is that not true? if you don't believe that, then you would make the claim that octane 'is the same as' dodecane, because it's just a truncated version.

Also, it is not an exact copy of something in nature, unless that 'thing' is a data fragment. It is an original molecule, that copies the data, but the molecule is distinct. That is an important point. Molecule patents don't care about the abstract qualities of something (beyond proving that it's useful). Molecule patents only care about the structure of the molecule.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#160

Post by dnautics »

dekhn wrote: post #157
dnautics wrote: post #152

Earlier quoted context omitted.

RT doesn't work that way, it requires a specific site near its target gene in order to make the DNA strand. There is off-target activity, but it is almost certainly vanishingly rare.

"almost certainly vanishingly rare event" * "incredibly high rate of reproduction of viruses" = almost certainty. See the first 4 chapters of "Biology of Cancer" by Weinberg.

molecular biology can deal with probabilities that are lower than 1/the number of particles in the universe.
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