Denialism

SCOTUS decision on gene patents is bad biology, and bad for science

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by

MarkH
in

I’m pleased the Supreme Court has decided to reject the idea of patenting genes, as such case law would be restrictive to scientific discovery and also just feels fundamentally icky. From a legal perspective, as far as I understand patent law (not a lawyer here), it also seemed to fail on the more basic level of novelty and obviousness. The methods used to discover such genes were not what was invented. And one could conceive of “gene trolls” that would seek out gene aberrations and sit on them, just like other patent trolls, waiting for a payout and hindering scientific and medical progress.
Unfortunately, the second half of the SCOTUS decision makes little sense to me from a scientific perspective, or my unsophisticated understanding of the law. From the NYT coverage:

The price of the test, often more than $3,000, was partly a product of Myriad’s patent, putting it out of reach for some women. The company filed patent infringement suits against others who conducted testing based on the gene. The price of the test “should come down significantly,” said Dr. Harry Ostrer, one of the plaintiffs in the case decided Thursday. The ruling, he said, “will have an immediate impact on people’s health.”
The court’s ruling will also shape the course of scientific research and medical testing in other fields, and it may alter the willingness of businesses to invest in the expensive work of isolating and understanding genetic material.
The decision hewed closely to the position of the Obama administration, which had argued that isolated DNA could not be patented, but that complementary DNA, or cDNA, which is an artificial construct, could. The patentability of cDNA could limit some of the impact on industry from the decision.

This strikes me as completely undermining the nature of the first part of the decision, and scientifically and legally unsound. Now, most of us understand the basics of molecular biology, but all you need to know to understand the significance of this is that DNA is transcribed into RNA, which is then translated into protein. In the process of transcription of DNA to RNA, large sections of the RNA are spliced out (the introns) and the remaining pieces (exons – which are expressed) are what get translated into the final protein sequence by little machines called ribosomes. Scientists are usually more interested in the final, mature RNA sequence after splicing, since that’s what results in function (for now ignoring regulatory elements in introns etc.). To study these sequences, they harvest RNA from cells, and reverse transcribe that information using an enzyme called a “reverse transcriptase” to turn that sequence into cDNA, which is more stable, can then be made double stranded, variously manipulated, cloned into plasmids or amplified by techniques like the polymerase chain reaction.
The Supreme Court has decided that since cDNA is artificial (is it really? We make it with enzymes stolen from viruses so viruses make cDNA too right?), cDNAs can be patented. But the exact same information from the mature RNA is in the cDNA! What’s the damn difference? This is like saying you couldn’t patent a recipe on paper, but if you transfer it word for word onto sheepskin, it becomes patentable. Does this make sense to anyone? Am I taking crazy pills or is this basically saying you can’t patent genes, unless you copy the information into a new format? Unless the cDNA is truly novel, and not isolated or cloned from a human or other organism, this strikes me as simply sleight-of-hand.
This decision is terrible and not the victory science advocates would like to believe, at least to my understanding of what has been done. I’ll read the actual decision once I’m home from work, but just from the news coverage, I’m disturbed.
**Update** As I read the decision it appears that our esteemed Justices don’t really understand biology, and as a result, have made a frankly stupid decision. Sentences that make me cringe include, “cDNA is not a “product of nature
,” so it is patent eligible under §101.” Umm, no, cDNA is found in nature. We use natural enzymes to make it! Viruses make their reverse-transcribed genes all the time. Also, check out this boneheaded statement, “cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments. Its creation results in an exons-only molecule, which is not naturally occurring.” Agggh! What about the mRNA that is was copied from? Are they saying cDNAs are the only form of “exons” only molecule? This is either bad biology, or poor sentence construction. Or maybe they think cDNA comes from stitching together sections of genomic DNA by some other process?
Then they appear to reject the idea you should be able to patent the only type of DNA that arguably should be patentable:

This case, it is important to note, does not involve method claims, patents on new applications of knowledge about the BRCA1 and BRCA2 genes, or the patentability of DNA in which the order of the naturally occurring nucleotides has been altered.

So, copy the information from mRNA to a cDNA and you’ve created something “new” (bullshit) but change that DNA sequence yourself for potentially novel and interesting results and that won’t necessarily be patentable? Idiots!
Check out this nonsense:

That may be so, but the lab technician unquestionably creates something new when cDNA is made. cDNA retains the naturally occurring exons of DNA, but it is distinct from the DNA from which it was derived. As a result, cDNA is not a “product of nature” and is patent eligible under §101, except insofar as very short series of DNA may have no intervening introns to remove when creating cDNA. In that situation,a short strand of cDNA may be indistinguishable from natural DNA.

The mere fact that they describe this as a mere technical process should be a hint. The human adds nothing. The justices seem to suggest that by taking advantage of the cell’s splicing apparatus, you have created something new, but you have not! You have merely copied the information from the mRNA onto a new media.
Add to this the bizarre rejection of the first section of the decision by Scalia, which only describes facts about biology (he rejects basic science that’s been established for 50 years!) , and I have to ask, why do we let these 9 non-experts decide anything related to technology? How was their extensive education so flawed with regards to biology? Who is educating them on biology now in preparation for a case such as this? Whoever it is needs to be fired. They have written law based on such a flawed conception of basic biology (and one actually abstains from acknowledging the existence of molecular biology!), that we now have this stupid idea that mere transcription of genetic information to a new media should be protected under patent! The source of this idea seems to come from the opinions of the lower court judges who seemed to think that any cutting or synthesizing of DNA to make a “new” molecule should be patentable. That would suggest using any restriction enzyme that cuts genomic DNA creates millions of new patentable molecules. It is equivalent to suggesting that by cutting a wire made up of 4 recurring metals fused together in some order, one is creating new patentable wires because their chemical composition is different from the original wire, but that’s nonsense, because what makes DNA a molecule of any patentable interest is not it’s simple chemical composition or the changes in chemical composition when subjected to enzyme treatments or synthesis reactions, it’s the information contained within the order of the chemicals in the chain. The chemical composition, in terms of the absolute quantity of each of the base-pairs is unlikely even change by such a process. The only thing that matters is the information contained in the code.
The Supremes, and I guess whichever clerk wrote this for Clarence Thomas (not that I esteem his intellect, but that’s how these things work right?) have failed Bio 101. As a result this decision is stupid, unscientific, and worse, bad law. This should not have been reported as any kind of victory for science, but rather is a muddled, ignorant, and unhelpful decision that awards patent protection to the mere transcription of information from one media to another using methods in existence for the last 30 years.

Comments

14 responses to “SCOTUS decision on gene patents is bad biology, and bad for science”

  1. Mu

    Does the body actually produce cDNA as a molecule? You’re mixing method and material patents in your argument. You cannot patent the method if it copies a natural process, but if that process in nature never produces cDNA as a molecule you can. Emphasis is on never. If you can show that there’s free cDNA floating in the body you can have that patent invalidated based on the same decision that (for now) validated the cDNA part.

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  2. Mark

    Mu they’re not talking about patenting the process of making cDNA! If that were the case, that would make perfect sense, because it involves taking various natural enzymes to make a product that would not normally occur. But this is not the case, cDNA synthesis is a technique that’s been in existence for the last 30 years.
    What they’re suggesting is that by taking an existing mRNA molecule, and using a 30-year-old technique, you render a natural product (mRNA) patentable because the resulting cDNA would not otherwise occur in nature.
    That’s not novel. That’s not non-obvious. That’s what we do a billion times over every time we run a reverse-transcriptase reaction. One could argue thousands of people beat them to this as every time anyone ran a RT on a breast cancer cell line with BRCA mutations, they make that cDNA thousands and thousands of times over (the reverse transcription is performed non-specifically on all the mRNA isolated from a sample)
    They are saying by subjecting natural molecules to an existing, known, and simple biologic enzyme the resulting molecule is novel and patentable. In reality, all you have done is copy information from RNA to DNA (think VHS to DVD) using an existing process. I strongly disagree with the court decision and it strikes me as fundamentally ignorant of basic molecular biology.

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  3. makeinu

    Biology in university and grade school education is, for any field outside of biology, the “dump stat” of the education process.
    Basically, if you’re not working in the field of biology, no one expects you to learn jack sqat about it to graduate from school.
    This is especially true of non-science degree programs. At least in a science program, you’re expected to take something beyond a “let’s disect a frog!” level of coursework in biological sciences. In fact, at most universities, in most non-science degree programs, you’re not actually required to take any serious science courses for graduation at all. All too frequently, majors outside the sciences have special “X for non-majors” science courses that dumb down the material so far as to be essentially non-educational.
    This may not be true outside the US, and may not be true at all universities within the US even, but it’s true enough to be a generalism.
    So, it’s completely unsurprising that a bunch of lawyers know absolutely nothing about basic science.

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  4. Pseudonym

    The decision makes more sense if you read the amicus briefs and the transcript of the oral argument, and also read the opinion carefully. The court was only talking about eligibility under section 101, and explicitly declined to make a decision as to whether or not cDNA is patentable under the other rules.
    What SCOTUS decided was the cDNA is legally not a “product of nature”. What they explicitly did not decide is whether or not cDNA, where the sequence is dictated by nature and not by a scientist or technician, is unpatentable on other grounds, and in particular, whether or not it passed the “obviousness” test.
    It seems to me that cDNA which we know occurs naturally in a cell, but can’t be extracted from the cell (mRNA is a pain to work with because it folds itself up and reacts with other mRNAs before you have a chance to get hold of it) is indeed an artificial human creation. But it’s also obvious to anyone skilled in the art, which should make it unpatentable on those grounds.
    However, SCOTUS did not make a decision as to whether or not cDNA is patentable on those grounds and explicitly said so in the opinion. They did not decide this for the simple reason that they didn’t need to decide that question to resolve the case (and, if I’m reading it correctly, they seemed to feel that they had insufficient evidence before them to decide it anyway).
    Unfortunately, the only way that question will be settled is with another court case. I think it’s better for biology and for science that the court doesn’t make a decision (if making a decision is not required to decide the case before them) than that they make a bad decision. In that sense, it’s a good decision.

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  5. Your genes cannot be patented, but it is too early to celebrate | Science, I Choose You!

    […] also seems weird to me. The technique used to generate cDNA has been around for a few decades (HT Mark Hoofnagle for mentioning this in his blog post). So, the technique itself is definitely not […]

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  6. Mark

    @Pseudonym,
    This is where I get into trouble writing about law and not being a lawyer.
    If that is indeed the interpretation, then that pulls this back from total disaster. However, since they still allowed Myriad to patent the BRCA cDNAs according to this opinion this still strikes me as awful.
    I guess the failure of the court that upsets me here is that they don’t address the real issue when it comes to genomic research and testing. DNA and RNA and cDNA or whatever format the biological molecule is in doesn’t matter. It’s the information that’s critical. Creating the distinction over cDNA because you can make mRNA into cDNA through an unnatural process, seems like a real shady move. It’s still the same information as was in the mRNA, so if you allow that to be patented, you are still allowing companies to patent natural information! Only you force them to transcribe it to an unnatural medium first.

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  7. Kagehi

    This is what you in fact get when you have either a) experts on a field, who don’t know how to translate that into something normal people can comprehend, or b) lawyers, writing briefs for other lawyers. I tend to suspect both happened in this case.
    The best analogy I can come up with would be that you can’t patent a mathematical equation just because its expressed as a + b = c, on the basis that the “original” version was written as:
    “If you assume a is apples, and add b, which is bananas, you would get c, which we will call ‘canned fruit.”
    The form of the damn equation isn’t what is relevant. cDNA is nothing more or less than parsing the above sentence, and replacing it with a more direct version of the same basic data. So, yeah.. Its a kind of WTF decision, but not surprising, especially given how some of SCOTUS have a habit of making decisions, “based on what I believe”, without having the slightest damn clue what they are talking about (and, being proud of doing so).

    Reply
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  9. Virgil H. Soule

    I don’t understand the SCOTUS gene decision. The Court said “genes” can’t be patented. Is it referring to the genes themselves or the genetic code that describes those genes? Of course genes themselves can’t be patented. They’re natural phenomena. The data describing a gene, however, should be patentable. The information describing sequences of bits of DNA in a gene would be intellectual property that its discoverers would want to protect. Knowing what elements are where in the gene sequence would be what chemists would use to develop tests and medical procedures for finding and fixing a given gene in a person’s genome. The code ought to be patentable seeing as how considerable expense and technology was needed to find it.
    I could write a book describing my adventures on Mars. The book would be protected by copyright law. Mars, however, is not. Anyone else could go there and make their own discoveries.
    A prospector finds gold in Alaska and draws a map showing where that gold deposit is located. The prospector has every right to hide that map so as to protect his discovery and prevent other prospectors from jumping his claim.
    I think the Court’s decision is flawed.

    Reply
  10. Nat Scientist

    If cDNA is a pcr copy of the segment of DNA gene as developed in nature’s lab, it is patentable when used as part of the “winners” process, but equally available to an other than proprietor’s process being the un-patentable Made in Nature label that even QE the second can’t tap.

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  11. ilya shmulevich

    Mark, you are absolutely correct to say that it is the information that’s central. In the 1990s, the undertaking of the Human Genome Project marked a fundamental shift in the conceptual framework of biology, from one that was centered on energy and matter to a framework rooted in information. Sydney Brenner, speaking to Horace Freeland Judson at Cambridge in 1971, put it this way:
    If you went to a biologist 20 years ago and asked him, How do you make a protein, he would have said, Well, that’s a horrible problem, I don’t know… But the important question is where do you get the energy to make the peptide bond. Whereas the molecular biologist would have said, That’s not the problem, the important problem is where do you get the instructions to assemble the sequence of amino acids, and to hell with the energy; the energy will look after itself.

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  12. Links 6/19/13 | Mike the Mad Biologist

    […] Very Waspy Beetle SCOTUS decision on gene patents is bad biology, and bad for science PETA’s Mixed Martial Assault on Scientists SCOTUS: DNA is information, not a chemical Ancient […]

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  13. Jenny F. Scientist, PhD

    Even when the patent rulings were originally issued on patenting naturally occurring gene variants/SNPs/ etc, I think most biologists saw it as obvious and not patentable.
    I got the impression that the SC was trying to make something patentable to encourage innovation (or something), or else they are tragically misguided and think every plasmid ever is a patentable product under the law. But to a biologist, it does read like “if you print things out on an inkjet and glue them together and xerox them onto a different color paper then that can be patented.” It makes me wonder exactly how they’re going to enforce it. Is it, as Mike mentions, the gene’s (naturally occurring) information that is now patented as ‘cDNA’, in which case this is no better, or if I cut it with a different RE or put on a different tag or promoter, does that count?

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  14. Pseudonym

    Jenny F Scientist, I do want to repeat what I said above: SCOTUS did not rule on the question of obviousness, and explicitly left it open (see footnote 9 in the opinion). This was the legally right thing to do because a) the question didn’t need to be decided to decide the case, and b) the court was not presented with enough evidence to decide it anyway.
    SCOTUS are not experts on biology and they know it. So it’s absolutely right for them to pass on a question that they can’t answer, especially if they don’t need to answer it right now.
    I agree with you cDNA which is dictated by nature or by the process used to determine it should be unpatentable. I also think you’re 100% right that it’s the fact that it’s “obvious” is what should make it unpatentable. However, I don’t blame SCOTUS for leaving that question open, under the circumstances.

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