On the 13th of June the US Supreme Court handed down it's
decision in the case of Association for Molecular Pathology et al v Myriad Genetics., Inc et al.
A lot of the commentary in the conventional news media has been to the effect that the Supreme Court has banned the patenting of human genes. That's not necessarily so. The Court specifically held:
“A
naturally occurring DNA segment is a product of nature and not patent
eligible merely because it has been isolated, but cDNA is patent
eligible because it is not naturally occurring.”
Myriad Genetics, as is clear from
the statement about the case on their website, see the decision largely as a victory in two respects -
- Firstly although the Court struck down the company's claimed ownership of the naturally occurring DNA segments that are the BRCA1 and BRCA1 genes, they upheld Myriad's patent claims relating to complementary DNA, cDNA. (Note cDNA is called complementary DNA by experts, not 'composite' DNA, the term used by Justice Thomas in the decision). So Myriad has the exclusive right to synthetically create BRCA1&2 cDNA.
- Secondly, though the case was not reviewing Myriad's method patents – patents relating to the way the company does genetic testing, biotech research and other processes – the company are interpreting some of the remarks of Justice Thomas in Part III of the ruling as re-inforcing all of their method patent claims.
The Association for Moleular Pathology
seems equally pleased:
"The decision helps to lay the foundation for continued research and application of diagnosis and
treatment of diseases at the molecular level. "AMP applauds the U.S. Supreme Court on their ground
breaking, unanimous decision. There is no question that this is a critical and right decision for the
future of medicine and science. Biomedical researchers, clinicians, and most importantly patients will
see great benefit from this development," said
Jennifer L. Hunt, MD, MEd, AMP President."
Which of the two parties has the most right to claim victory only time will tell. What does appear clear is that the reasoning of the Court in striking down the DNA claims and upholding the cDNA claims was effectively unanimous but confused.
Justice Scalia wrote a separate short concurring opinion disassociating himself from Justice Thomas's efforts to explain the science, and implying that doing science was not the business of the Court. He would not put his name to what he did not understand.
"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 DNA isolated from its natural state
sought to be patented is identical to that portion of the
DNA in its natural state; and that complementary DNA
(cDNA) is a synthetic creation not normally present in
nature."
The fact that the Court has decided that a naturally occurring DNA segment is not patentable is clear. The attempted logic they use to get from there to the patentability of cDNA is flawed. Justice Thomas goes to great pains to emphasise that the Myriad patents under review are information patents not chemistry patents (see p14):
...extensive effort alone is insufficient to satisfy the demands
of §101.
Nor are Myriad’s claims saved by the fact that isolating
DNA from the human genome severs chemical bonds and
thereby creates a nonnaturally occurring molecule. Myriad’s claims are simply not expressed in terms of chemical
composition, nor do they rely in any way on the chemical changes that result from the isolation of a particular
section of DNA. Instead, the claims understandably focus
on the genetic information encoded in the BRCA1 andBRCA2 genes"
Merely doing chemistry and breaking a chunk of gene out of a DNA chain is not enough to grab ownership of that gene. That makes sense. We shouldn't be allowed to cut up products of nature and say we now own the offcuts.
DNA chains have useful functional sequences of crossbars called exons and less useful sequences called introns.
On the route from DNA -
- to RNA where the DNA unwinds into single strands from the original double helix
- to the removal of the useless introns
- to mRNA where the exons spliced back together in their original sequence
- then on to the production amino acids and proteins in cells
the naturally occurring information content of the DNA does not change. So breaking down BRCA1&2 genes, stripping out the introns and putting the genes back together as cDNA without the introns
does not change the information content of the genes. So if the DNA is not patentable the equivalent cDNA cannot be patentable, from an information perspective.
Let's put it another way. The collections of genes inside living cells are a bit like the cells' recipe books. When a cell needs to do something like manufacture a protein it consults the gene recipe book and follows the instructions there. BRCA1&2 DNA and cDNA have the same information content, in the same order, the same recipes. The BRCA1&2 cDNA recipe book might be shorter and neater, stripped of the waste intron pages, but it contains the same instructions, methods, recipes.
Not only has the Supreme Court
not banned patenting human genes, in this case it has granted Myriad Genetics
control of the most functionally useful naturally occurring information in BRCA1 and BRCA2 genes.
So as I understand the reasoning, it goes something like this -
- BRCA1 & BRCA2 genes are naturally occurring DNA segments
- As naturally occurring DNA segments (with their naturally occurring exon recipe books) they are not patentable just by cutting them out of the DNA chain they form part of
- Chemistry doesn't cut it - excuse the pun - to earn patent control
- BRCA1&2 cDNA, however, (with their naturally occurring exon recipe books with the same natural recipes) are patentable because they are different without the introns and there's more chemistry (you have to cut out the genes, cut out the introns, put the exons back together in the same order)
The Supremes themselves, in page 2 of the summary of the decision, say:
"Myriad did not create or
alter either the genetic information encoded in the BCRA1 (sic)and
BCRA2 (sic) genes or the genetic structure of the DNA. It found an important and useful gene, but groundbreaking, innovative, or even
brilliant discovery does not by itself satisfy the §101 inquiry."
Neither has Myriad created or altered the functional genetic information encoded in the BRCA 1 and BRCA2 cDNA. It makes little sense, therefore, that the DNA is not patentable but the cDNA is. Justice Scalia may have been honest in noting he could not sign up to the fine details of molecular biology in the opinion. All nine justices may have had a variable grasp of the science but it seems none of the nine had a proper handle on the information science.
Casual readers should probably call a halt there. I look at some extracts from the decision below.
Justice Thomas in Part I, Section A, pp1-4, attempts to explain the science in the case. I can't help feeling the inclusion of pictures/illustrations could have helped his task enormously here. I wonder when courts looking at science and technology are going to embrace science and technology beyond text to help deliver their reasoning. In section B he describes Myriad's discovery.
"Myriad discovered the
precise location and sequence
of what are now known as
the BRCA1 and BRCA2 genes. Mutations in these genes
can dramatically increase an individual’s risk of developing breast and ovarian cancer...
Myriad identified the exact location of the BRCA1 and
BRCA2 genes on chromosomes 17 and 13. Chromosome
17 has approximately 80 million nucleotides, and chromosome 13 has approximately 114 million...
Within
those chromosomes, the BRCA1 and BRCA2 genes are
each about 80,000 nucleotides long. If just exons are
counted, the BRCA1 gene is only about 5,500 nucleotides
long; for the BRCA2 gene, that number is about 10,200. Knowledge of the location of the BRCA1 and BRCA2
genes allowed Myriad to determine their typical nucleotide sequence. That information, in turn, enabled Myriad to
develop medical tests that are useful for detecting mutations in a patient’s BRCA1 and BRCA2 genes and thereby
assessing whether the patient has an increased risk of
cancer.
"
Once they found BRCA1&2 they headed for the patent office. Nine claims from 3 of those resultant patents were under consideration here - claims 1, 2, 5, 6 and 7 of
US Patent No. 5,747,282; claim 1 of
US Patent no. 5,693,473; and claims 1, 6 & 7 of
US Patent no. 5,837,492. From Section C, page 6 of the decision:
"Myriad’s patents would, if valid, give it the exclusive
right to isolate an individual’s BRCA1 and BRCA2 genes
(or any strand of 15 or more nucleotides within the genes)
by breaking the covalent bonds that connect the DNA to
the rest of the individual’s genome. The patents would
also give Myriad the exclusive right to synthetically create
BRCA cDNA"
The italics above are mine. Not only did Myriad want control of the 80,000 nucleotide strings in BRCA1 or BRCA2, they wanted control of
any 15 nucleotide strand within the 80,000. Any 15 piece nucleotide string that could be chopped out of BRCA1&2 would belong to Myriad.
Justice Thomas then goes on to explain (p7) that once the patents were granted Myriad sued or threatened to sue "entities that performed BRCA testing" ending up with a monopoly as a result. One of the doctors on the receiving end of the Myriad's legal action along with a number of others returned the compliment several years later declaring Myriad's patents invalid. That case eventually reached the Supreme Court via the District Court which ruled against Myriad and the Federal Circuit appeal court which ruled in favour of Myriad (see pp 9-10 for an outline of the decisions in those courts).
In Part II Section A, Justice Thomas describes the provisions of §101 of the Patent Act.
“Whoever invents or discovers any new and useful . . .
composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.”
He follows up with an important exception:
We have “long held that this provision contains an important implicit exception[:] Laws of nature, natural phenomena, and abstract ideas are not patentable.” ... Rather, “‘they are the basic tools of
scientific and technological work’ ” that lie beyond the
domain of patent protection... the Court has explained, without this exception, there
would be considerable danger that the grant of patents
would “tie up” the use of such tools and thereby “inhibit
future innovation premised upon them.”
...
The rule against patents on naturally occurring things is not without limits, however,
for “all inventions at some
level embody, use, reflect, rest upon, or apply laws of
nature, natural phenomena, or abstract ideas,” ...patent protection strikes
a delicate balance between creating “incentives that lead
to creation, invention, and discovery” and “imped[ing] the
flow of information that might permit, indeed spur, invention.”
Part II Section B gets onto the meat of the decision.
"It is undisputed that Myriad did not create or alter any
of the genetic information encoded in the BRCA1 and BRCA2 genes. The location and order of the nucleotides
existed in nature before Myriad found them. Nor did Myriad create or alter the genetic structure of DNA. Instead, Myriad’s principal contribution was uncovering the
precise location and genetic sequence of the BRCA1
and BRCA2 genes within chromosomes 17 and 13. The
question is whether this renders the genes patentable."
On page 12 Justice Thomas compares Myriad's work to the
Chakrabarty case in 1980 where the US Supreme Court held that a modified bacterium used to break down components of crude oil was patentable.
"In this case, by
contrast, Myriad did not create anything. To be sure, it
found an important and useful gene, but separating that
gene from its surrounding genetic material is not an act of
invention.
Groundbreaking, innovative,
or even brilliant discovery
does not by itself satisfy the §101 inquiry." {My emphasis}
...
Myriad found the location of the BRCA1 and
BRCA2 genes, but that discovery,
by itself, does not render
the BRCA genes “new . . . composition[s] of matter,” §101,
that are patent eligible." {My emphasis again}
From page 14 onwards Justice Thomas tackles Myriad's patent claims.
Many of Myriad’s patent descriptions simply detail
the “iterative process” of discovery by which Myriad narrowed the possible locations for
the gene sequences that it sought.6
[Note 6: Myriad first identified groups of
relatives with a history of breast
cancer (some of whom also had developed ovarian cancer); because
these individuals were related, scientists knew that it was more likely
that their diseases were the result of
genetic predisposition rather than
other factors. Myriad compared sections of their chromosomes, looking
for shared genetic abnormalities not found in the general population.
It
was that process which eventually
enabled Myriad to determine where
in the genetic sequence the BRCA1
and BRCA2 genes reside.]
Myriad seeks to import
these extensive research efforts into the §101 patent
-
eligibility inquiry. Brief for Respondents 8–10, 34. But
extensive effort alone is insufficient to satisfy the demands
of §101.
Nor are Myriad’s claims saved by the fact that isolating
DNA from the human genome severs chemical bonds and
thereby creates a nonnaturally occurring molecule. Myriad’s claims are simply not expressed in terms of chemical
composition, nor do they rely in any way on the chemical changes that result from the isolation of a particular
section of DNA. Instead, the claims understandably focus
on the genetic information encoded in the BRCA1 and BRCA2 genes. If the patents depended upon the creation
of a unique molecule, then a would-be infringer could
arguably avoid at least Myriad’s
patent claims on entire
genes (such as claims 1 and 2 of the ’282 patent) by isolating a DNA sequence that included both the BRCA1 or
BRCA2 gene and one additional nucleotide pair. Such a
molecule would not be chemically identical to the molecule
“invented” by Myriad. But Myriad obviously would resist
that outcome because its claim is concerned primarily with
the information contained in the genetic
sequence
, not
with the specific chemical composition of a particular
molecule."
In essence this section of the decision amounts to two things - firstly the sweat of the brow or hard work is not enough to make something patentable; and secondly Myriad's specific patent claims are not about chemistry, they are about information. Myriad's claims are "
concerned primarily with
the information contained in the genetic
sequence
, not
with the specific chemical composition of a particular
molecule." {My emphasis} That key point is crucial when the Court later distinguishes the patentability of naturally occurring DNA from that of cDNA.
Another small but important point on page 15 related to Myriad's argument that the US PTO's past practice of awarding gene patents was "entitled to deference". Justice Thomas for the Court simply said "We disagree". The notion that decisions of a patent office should not be subject review in the courts is unsustainable. And even the US government had argued in the Federal and Supreme Courts that isolated DNA was not patent-eligible.
That was it on the patentability of isolated DNA. Yet the Court goes on to make the following enormous (il)logical leap in sanctioning cDNA as patent eligible in Part II Section C on page 16-17 of the decision:
"cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments. As
already explained, creation of a cDNA sequence from
mRNA results in an exons-only molecule that is not naturally occurring.
Petitioners concede that cDNA differs
from natural DNA in that “the non-coding regions have been removed.” Brief for Petitioners 49. They nevertheless argue that cDNA is not patent eligible because “[t]he
nucleotide sequence of cDNA is
dictated by nature, not by
the lab technician.”
Id.,
at 51. 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."
Remember that Myriad's claims are "
concerned primarily with
the information contained in the genetic
sequence
, not
with the specific chemical composition of a particular
molecule." Yet the lab technician doing chemistry "unquestionably creates something new when
cDNA is made"? The lab technician doing chemistry may well be breaking up gene molecules, clearing out the intron rubbish and rebuilding the molecules with the clean exon components but s/he does
not create new genetic information. So are we dealing with information patents or chemistry patents here?
Well in Part III the Court says "It is important to note what is not implicated by this decision" but this short conclusion doesn't help deal with the confused interpretation of the information science. It does, however, explain Myriad's
confidence that their methods patents have received some re-enforcement.
"It is important to note what is
not
implicated by this
decision. First, there are no method claims before this
Court. Had Myriad created an innovative method of
manipulating genes while searching for the BRCA1 and
BRCA2 genes, it could possibly
have sought a method patent.
...
Similarly, this case does not involve patents on new
applications
of knowledge about the BRCA1 and BRCA2
genes. Judge Bryson aptly noted that, “[a]s the first party
with knowledge of the [BRCA1 and BRCA2] sequences,
Myriad was in an excellent position to claim applications
of that knowledge. Many of its unchallenged claims are limited to such applications.” 689 F. 3d, at 1349.
Nor do we consider the patentability of DNA in which
the order of the naturally occurring nucleotides has been
altered. Scientific alteration
of the genetic code presents a
different inquiry, and we express no opinion about the
application of §101 to such endeavors. We merely hold
that genes and the information they encode are not patent
eligible under §101 simply because they have been isolated
from the surrounding genetic material."
So there is a hint not only that Myriad's method patents may be ok but that the company is in a strong position to claim such patents. Though they approve cDNA patents where the order of the exons is not altered from the DNA from which they are derived, the Court didn't consider the patentability of naturally occurring DNA where the nucloetides have been shuffled.
To conclude, then, let's return to the heart of the decision where the Court has held that:
"A naturally occurring DNA segment is a product of nature and
not patent eligible merely because
it has been isolated, but cDNA is
patent eligible because it is not naturally occurring."
The case is specifically about information encoded in genes not chemistry. Myriad's claims are "
concerned primarily with
the information contained in the genetic
sequence
, not
with the specific chemical composition of a particular
molecule."
The naturally occurring DNA segments that are the BRCA1&2 genes are products of nature and
not patent eligible merely because they have been isolated. The isolation and lopping of a gene out of a DNA chain is not sufficient to engender ownership rights over that gene. Fair conclusion.
However, somehow breaking up those genes, throwing away the useless bits (introns) from the cellular recipe book perspective and putting the functional bits (exons) back together in the same order with the same, naturally occurring, information - doing chemistry which is specifically excluded by the Court (pp14-15) as the focus of this decision - such that they provide the same cellular recipes as those naturally occurring in products of nature,
does facilitate (patent time limited) ownership rights over BRCA1&2 cDNA. That, in the words of certain fictional Vulcan of Star Trek fame, is illogical.
The upshot is that Myriad can control the useful information in BRCA1 and BRCA2 genes but not the naturally occurring DNA kind. They are "limited" to controlling the same information except in synthetic cDNA form, once some chemical magic has been deployed, to extract the functionally information free introns. (Remember the introns don't make it into the cellular recipe book).
In summary the Court's decision effectively reads:
- The dispute is concerned primarily with
the information contained in the genetic
sequence
- Myriad cannot control the information in the naturally occurring DNA segments that are the BRCA1 & BRCA2 genes; because these are products of nature and
not patent eligible merely because they have been discovered/isolated
- Myriad can control the same information after some chemistry has tidied up the naturally occurring DNA and turned it into synthetic cDNA
In other words -
It's not about chemistry.
It's about information.
The information cannot be commercially controlled.
If you do some chemistry the same information
can be commercially controlled.
QED.
This not the kind of "logic", I suspect, that Paul Otlet, Henri Le Fontaine or Claude Shannon would recognise as such (and Otlet and Le Fontaine were lawyers!).
I'm tempted to launch again into my diatribe on the absence of scientific and technical understanding of the
legislature, the
executive, and the
judiciary but to those who have made it this far, it's probable you have suffered enough.
Update: On the advice of a much more informed scientist friend, the wonderful Jo Davis, I've tweaked the bullet points under the
diagram describing the sequence from DNA through RNA to mRNA and onto amino acids and proteins. Apologies for any confusion.
Lucian,
Whilst agreeing with your broad theme – on disproportionate societal fear, the consequent attraction of simplistic paternalistic securocratic governance and our undermining of fundamental liberties through e.g. trading privacy for convenience with modern communications technologies – I don’t completely subscribe to the notion that the biggest threat to liberty is ourselves.
At the moment a bigger issue is that the interests of the state and corporate establishments happen to be aligned in relation to big data. The collection and processing of personal data is [wrongly] perceived to be a silver bullet route to solving a range of political issues in the case of the state (e.g. terrorism as you mention) and to financial success in the markets in the case of the private sector. Simplistic and ill-informed though these mindsets are – computers do not magically solve complex political, social, economic, environmental, security or market problems just by chucking money at them or by making them bigger/faster or capable of collecting & processing more data – they fundamentally undermine privacy/liberty interests of the individual.
Whilst the state is subject to significantly tighter formal checks and balances than the private sector in relation to mass surveillance – the rule of law theoretically precludes the engagement in indiscriminate fishing expeditions in the hope of finding smoking gun evidence – the arguments rolled out by politicians, under the pressure of the modern 24/7 news cycle, relay a persuasive if misleading message to the contrary on preferred policy. We can, it is said, have liberty OR security; security OR privacy; or in more subtle form, we have to BALANCE privacy and security. This is a false dichotomy. As you rightly point out, security and liberty are mutually dependant not opposing forces.
Additionally we have the powerful but false and, frankly, poisonous ‘nothing to hide, nothing to fear’ meme repeated by William Hague and others in response to the PRISM revelations recently. When you cast the apparently small privacy need of the individual against the national security gain of the state which will seemingly benefit society as a whole, it is impossible to argue the needs of the individual outweigh the common good.
The ‘nothing to hide…’ argument, however, is based on two huge and erroneous foundations.
The first is that it assumes all privacy is only about hiding bad things. Yet without personal privacy/liberty our society would be suffocating – privacy, liberty and the common good are inextricably interlinked and mutually dependent.
The second is that decimating privacy is the solution to the problem du jour – security, terrorism, serious crime, benefit fraud, NHS patient care etc. It’s possible to prove this thesis wrong mathematically but for the present purposes think of terrorist detection as a needle in a haystack problem. You don’t make it easier to find the needle by throwing more electronic data hay on the stack. Mass data collectors can dig deeply into the digital persona of anyone but don’t have the resources to do so with everyone. The resultant pursuit of false positive leads mean the real bad guys often get lost in the noise, as happened with the 9/11 attackers who were known to US authorities but not considered sufficiently important to intercept.
There is no magic computer solution to the rare terrorism problem.
Don’t get me wrong. Law enforcement and security services need to be able to move with the times, use modern digital technologies intelligently in their work and through targeted data preservation regimes – not a mass surveillance regime – engage in technological surveillance of individuals about whom they have reasonable cause to harbor suspicion. That is not, however, the same as building an infrastructure of mass surveillance.
This brings us back to the current alignment of state and corporate interests in relation to the architectures of our digital communications technologies. We could architect systems that enhance privacy and facilitate anonymity and net neutrality. We don’t.
The organisations that construct and operate these technologies have no market or regulatory incentives to build or run them this way. We, I agree, contribute enormously to this state of affairs by trading our privacy for the convenience/ attraction/gratification/access/community/conformity of the services that we use on the internet. We additionally contribute by failing to engage in a meaningful and persuasive way in the public debate on these issues. Our much maligned politicians are busy generalists subject to the constant glare of the media spotlight who really do not understand the technology and we have to be better at explaining it to them.
The state, likewise, has no incentive either to direct its vast purchasing power towards or to pass regulations to require the building and operation of liberty respecting network architectures. [Neither, in relation to regulations, has it got the required understanding of the technology to do so.] The state establishment, at the highest levels of its requisite parts, has largely bought into the belief that big data is good and their unfettered access to it even better.
We have to be more active/persuasive/engaged as individuals, citizens, employees, consumers or prosumers in convincing ourselves, our organisations, communities, society, the market and the state that an infrastructure of mass surveillance is not conducive to the public good. As long as the most powerful actors in this calculus, however, the state and the corporate sector, continue to share the belief that the continued building and operation of such an infrastructure of mass surveillance is in their mutual interest, it will be a difficult argument to win.
Regards,
Ray
PS Aside from the Snowden story, on the positive side, if the earlier Bradley Manning Wikileaks leaks revealed anything it was the huge numbers of dedicated US government officials and diplomats working day to day, above and beyond the call of duty, to uphold the values of the US Constitution and Bill of Rights. Having worked yourself at senior level in the civil service, you’ll no doubt be aware of equivalent commitment to democratic values on the part of UK government officials. There are a multitude of similarly dedicated individuals in the the state and corporate establishment across the globe. So it can’t be beyond us to evolve the surveillance state that is the internet of 2013 into something more respecting of democratic values and freedoms.