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« USPTO Releases Performance and Accountability Report for FY 2012 | Main | Supreme Court Grants Cert in AMP v. Myriad »

November 29, 2012

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We'll know as early as later today if SCOTUS will grant cert.

I'll comment on only one aspect of your analysis--the assertion that PacBio or Oxford nanopore sequencing would not infringe. I don't understand the logic of that assertion. There is nothing in the COM claims that calls for amplification, separation, purification, targeted excision or any other step. The claims are on "isolated" molecules of the specified sequences. In a PacBio machine or Oxford Nanopore USB device, the molecules are just as "isolated" as they are in other methods. I realize there is disagreement and many in patent law think there is a settled understanding of what "isolated" means, that the target sequences are enriched or separated from other DNA, but that is reading into the claims and probably wrong. The molecule being read out by a PacBio or Oxford Nanopore instrument is a particular "isolated" DNA by definition. If it weren't the instrument could not produce the sequence data. By my reading of the claims--which is equally open to challenge, I freely concede--most of the 8,000 articles by those 18,000 authors, only 2.5% of which had any direct relation to Myriad, involved work that infringed.

Dear Bob:

Unless I am mistaken, these devices never produce a full-length molecule in an isolated state, i.e. at the end of the process there isn't a tube containing a DNA molecule encoding the entire BRCA gene. If you have a basis for your understanding that differs from mine (as set forth here as a definition) then let me know.

As for the publications, isn't the point you make the point - 18,000 researchers performed work resulting in 8,000 publications (and an untold amount of work that was not published, plus all the grant proposals funded and unfunded that were submitted on this work) and the overwhelming majority don't infringe. How then does Myriad's patents inhibit research?

Thanks for the comment.

Kevin "mutations in the BRCA1 and BRCA2 genes could be detected that would not infringe Myriad's claims (without accentuating for the Court that these technologies could not be so used if Myriad had not identified the mutations in the first place)."

Not sure what you're driving at with respect to the parenthetical, Kevin. Are you suggesting that this fact should have been accentuated, or complimenting Myriad on understating that fact?

"It remains to be seen whether the Court will be able to resist the siren song of this politically charged question, or will dive headfirst into another foray of trying to be the final arbiter of the scope and direction of American innovation."

LOL. Maybe we should let each citizen vote on whether another person should be allowed to control which of their nucleic acids they are "permitted" to "isolate".

You really should consider toning it down, Kevin. The loss of the right to patent "isolated" DNA is not that big of deal. A much bigger problem is the development of some over-arching, ill-considered "theory" that attempts to explain when any composition of matter is an ineligible "product of nature."

You know what I find funny? That the PTO had to establish rules that genes were claimed within 101 and 112. As a general rule the courts should take note that this occurred, and infer that it is just patent protectionism by the office, and strike the whole lot of whatever is covered by those "guidelines" down.

Dear Keep:

"Tone it down?" What's the fun in that?

I totally agree with you that the risk here is an broad "product of nature" ban. I think it unwise for the Court to venture into these waters (as it did today) but we can develop strategies to try to limit the scope of the scope of the damage they do.

Thanks for the comment.

6:

You misunderstand. The utility and written description guidelines did not establish than genes are patent-eligible. They established what the Office required in the specification to support the claims. This addressed two issues: how to incorporate the Federal Circuit's Regents of the University of California v. Eli Lilly case into the Office's examination practices, and to ensure that the flood of Human Genome Project sequences were not patented in the absence of any evidence of the utility of the encoded proteins.

But now that the Supreme Court has granted cert we can see what they decide.

Kevin,

I'm not sure why you reject my claim that we could distinguish products of nature and those of man by looking at whether the claimed invention is the result of both man's intention and design? This would fix the embarrassment of the O2-as-patentable corner you have boxed yourself into (by way of the overbroad 'isolation' line of reasoning dating back to Parke-Davis) and it makes logical and practical sense. I'd love for you to explain why you think otherwise. Show me a good counterexample, for instance.

best,
David

David: "we could distinguish products of nature and those of man by looking at whether the claimed invention is the result of both man's intention and design"

Sure, we could do that. Then you would undoubtedly agree that Myriad's claimed compositions are not "products of nature." The claimed compositions did not exist prior to Myriad's discovery and they can't be created without man's "intention and design."

Or is there something else you want to add to your test?

Also, if I allow an organism to be exposed to mutagens for the purpose of generating a variety of sequence mutations in its massive chromosome, have I "designed" all the resulting sub-sequences (i.e., the ten base stretches of the chromosome with new mutations in it)? Or did "nature" do that?

What if I engineer an organism so that it its DNA-damage repair functions are impaired, which causes it to mutate its chromosome in certain stretches with great rapidity? Did I "design" every sequence that ever will be created in this organism? Or is "nature" doing that?

What if I simply discover an organism that naturally has a high mutation rate? Did I "design" every sequence that ever will be created in this organism? Or is "nature" doing that?

I know these are obvious questions and I'm certain you have the answer ready in hand, David. I just had to ask, though.

MM states "The claimed compositions did not exist prior to Myriad's discovery and they can't be created without man's 'intention and design.' " and misses out on the lesson from Prometheus. My paraphrase from the sister thread fits here:

But to transform an unpatentable product of nature into a patent eligible application of such a product, a patent must do more than simply state the product of nature while adding the words “isolate[d].” It must limit its reach to a particular, inventive application of the product, one different in kind from what is available to all from Nature’s warehouse.

Actually, KIR (or MM) the claimed sequences did exist before man discovered them, their use is in finding their occurrence naturally in humans. Their prior existence is precisely what makes them diagnostically useful. There has been no alteration and thus no design by man. The finding of endpoints for genes is aided by nature's own delineation of genes via stop and promotor codons. Again, no design by man. I think design mus be more than urging mutation, to answer that question, and in Chakrabarthy it was a form of directed evolution, which might well suffice. In the case of Myriad, the researchers identified a naturally-occurring sequence, and included that sequence in their claims. No part of that sequences was designed by man, but rather is a mutation found regularly in nature associated with a higher incidence of cancers. Regarding the discussion of utility in the other thread, I find it highly amusing to claim that the use of a naturally-occurring product is in identifying the presence of that same product. Does no one else see the humor of that?

the claimed sequences did exist before man discovered them

This is a lie. There is no "claimed sequence." There is a claimed composition of matter that is defined, in part, by a sequence of nucleotides and, in part, by its purity relative to other compositions. The claimed composition did not exist "before man discovered it."

"KIR (or MM)"

Last time I checked it's KIR. If you want me to make some other name to call you, I'm happy to do that. Just let me know, David.

I will be stunned if the Supreme Court is going to approve of this lie. I expect the Supreme Court to refute the lie in very clear terms.

Is there a reason that you won't answer the questions I aaked you, David? Are you going to play the same game that Skeptical does and pretend that simply repeating gibberish over and over makes your position more persuasive?

David: "Regarding the discussion of utility in the other thread, I find it highly amusing to claim that the use of a naturally-occurring product is in identifying the presence of that same product"

It's actually a serious point and it'd be nice if you treated it that way. For starters, the claimed composition is not a "naturally occurring product" in any meaningful sense of the term "naturally occurring product." I can go on from there but why waste time if you're just going to babble on and on?

Let's try another hypothetical, David. Say that I synthesize a novel, non-obvious chemical and demonstrate that the chemical successfully reverses Alzheimers in 100% of patients. I claim a 95% pure composition consisting of the chemical and some stabilizers (typical composition claim). Five years after my patent is granted, Professor Skip Tickle is researching mating swarm behavior of African desert bullfrogs. During the course of performing mass spectroscopy on the sticky mixture of frog semen and clay, he discovers that for every 100 gallons of frog semen and clay created during the mating swarm, one molecule of a very similar chemical is created (it's a dimer, instead of a monomer).

Please apply your "theory" of subject matter eligibility to this situation. If you need any other facts, just say so. Please let me know first, however: is it your opinion that my claimed composition is "naturally occuring"? If not, please explain why not. Thanks.

DK "The finding of endpoints for genes is aided by nature's own delineation of genes via stop and promotor codons"

Right. And in every case that "delineation" is so crystal clear it's no different than driving down an empty street and seeing the traffic lights. Remind me again, David: where did you get your Ph.D. in molecular biology?

Also, so I'm perfectly clear on where you're coming from, your position is that polynucleic acid composition claims are eligible as long as they don't include start and stop codons? I mean, why else would you bringing that up?

"design mus be more than urging mutation"

Just answer the questions that I actually asked David. Yes or no. It's that easy. Are you afraid of doing so for some reason? It seems that you like spouting things like "design must be more than urging mutation" than you do actually considering the implications of what you are saying.

Are you sure that your position isn't simply that all polynucleic acid compositions should be ineligible for patenting? It really seems that way. Same with Skeptical. It seems that way because every time I ask you to extend your position into logical and inevitable situatoins both of you start (1) answering questions that I didn't ask and (2) repeating the same garbage.

What's going on, David?

Wow MM, that is some rant.

Are you even capable of a civil discourse?

I am...

KIR: try to follow... the sequences are not the result of human design. We could choose any even arbitrary beginning and end point and in no case will the sequence of nucleotides have become the result of man's design. Unlike chipping away stone to create a statue, copying a string of nucleotides (like copying a string of text) is not per se inventive, it doesn't create a product not already found in nature. In none of your examples have you pointed to a case of designing a product. Directed evolution might arguably be different, because you are purposely pushing the evolution of an organism to tolerate some environment, but your example seem to be of random mutation, which is not purposive and thus not designed. Try, for instance, selecting a random bit of my text here, copy it, paste it elsewhere, and then ask yourself: have I "created" something new in the process? What is it's use? I contend the only use and one analagous to the uses claimed in these diagnostic patents is in identifying that same string.

In my book and elsewhere I have maintained consistently that genetically engineered organisms are patent-eligible under sec 101 because they are products of man's design. I actually did answer your questions above, just not the way you wanted me to. For that, I can offer no sincere apology.

David: "I actually did answer your questions above, just not the way you wanted me to."

LOLOLOLOLOLOLOLOLOL!!!!

You should run for Congress, David. Thankfully I've interacted with enough online "philosophers" already so I know to expect very little from them.

Anyway, the questions and your non-answers are up thread, preserved for all to see. We can return to them later when the case is decided (I know that I will!). I'm pretty sure when the Supreme Court justices will be expecting better answers than the ones you (didn't give). You never even tried to address the 4:09 hypo or answer the question I posed there, as far as I can see.

"I contend the only use and one analagous to the uses claimed in these diagnostic patents is in identifying that same string. "

First, David, claims at issue here don't recite any "uses". They claim compositions of matter. So now in addition to not answering questions, you are just flubbing the basics. In addition, the point you appear to be clumsily trying to make is a very old one and widely recognized by everyone in the field (including myself, the courts, and the USPTO) in the situation where (as in your "analogy") (1) the structure of the target *to be detected* is public knowledge and (2) the *claimed composition* is an obvious choice for detecting that structure. Nucleic acid composition claims are routinely rejected under 35 USC 103 when the above facts apply. Nobody blinks, nobody ever has.

Those aren't the facts of the Myriad case, however, as you certainly know. So your analogy isn't very well-considered. This is why I ask you again: is your position simply that nucleic acid compositions should remain ineligible ... just because? Can you answer at least that question "yes" or "no"? Right now it seems your position is that a composition that is "designed" is eligible ... except when it's shown later that "nature" might have made it before (even when there is no evidence that nature did make it before).

"In my book"

You wrote a book? LOL. I'm going to do you one better, David: you're IN my book. Along with a few other characters who insist on wading into the deep end of the pool without their flotation devices.

I won't dignify your incivility with any more attempts at responses. As you should know, sequence claims must have clearly expressed uses under guidelines from the USPTO to prevent willynilly sequence claims. None of your examples presented any purposive mutation, and thus no design, which is what I claim ought to be the distinguishing feature setting apart natural products from artifacts. My position is clear, on record, logical, and soundly based on principles enunciated by the Supreme Court. I wish you well, and hope you are a better person in real life than you appear online.

Best,
David

KIR, just so the record is spotless on my responses... Regarding your 4:09 hypo, the chemical you created was the result of design and intention, and the patent would be justified, you didn't discover it, you invented it, even though we might later find a natural equivalent. Regarding the "composition of matter" vs. sequences issue, the claims recite compositions of matter defined by specific sequences, which sequences were discovered, not designed. I think the distinction between design and discovery is pretty rudimentary, and none of your counterexamples seem problematic in that regard. Some more examples: I toss a bunch of gears and such in the air and they fall to earth in the form of some useful machine, just by happenstance. I did not design that, it was chance. I cut and paste random sequences of letters and end up with a pleasant poem somehow, I didn't design that and cannot claim to have created it nor should I be granted some monopoly rights over it. I identify some mineral in the ground and find that it works nicely to write on slate, I didn't design the mineral and ought not to get some monopoly over the mineral which is a product of nature. I think in each case where there is a clear difference between products of nature and those of man, there must be some mixing of intention with deliberate design to result in a new product for there to be a product of man. Some other examples that I believe help bolster this point: we create all sorts of accidents all the time that end up being products of man but not inventive. Excretions (use your imagination), footprints from our walking, garbage piles, etc., none of which is the product of design though they may in some cases be the product of intentional action. Those accidents are not products of nature, nor are they "inventive" warranting some monopoly protection, they are accidental products of man. This is why I think design is critical to cross the threshold of patent-eligibility. I doubt any rational person supports granting monopolies over even useful excretions, etc., even though they are sometime the intentional products of man. I am doing my best to bring some order to this problem, consistent with principles embraced by the courts, and I happen to think in the case of diagnostic gene patents, because the claimed compositions of matter are sequences of nucleotides that are not the result of both man's intention and design, they ought not the be patented. As I said before, consistently and repeatedly, genetically engineered organisms are typically the products of both intention and design and thus meet the threshold, are not products of nature, and should be patentable.

Anyway, that should sum it all up and I think close any loose ends in the thread.

all my best,
David

David:

"the chemical you created was the result of design and intention, and the patent would be justified, you didn't discover it, you invented it, even though we might later find a natural equivalent."

Okay, that's an extremely important point that you should make a greater effort to make.

So really your position is not that novel nucleic acid compositions shold be ineligible in every case where the composition consists of a sequence of nucleotides that appears in a "natural" organism's un-engineered genome. Rather, your position is that the eligiblity of novel nucleic acid compositions should be determined according to the manner in which those novel nucleic acid compositions were conceived and reduced to practice.

Thus, if I use my genius and certain design principles to create a novel non-obvious isolated nucleic acid composition encoding a novel protein that catalyzes the conversion of X->Y, my composition remains eligible even when it is discovered 5 years after my patent grant that an identical gene exists in a thermophylic archaebacteria. Do I have that right, David? I assume the answer doesn't change if the gene is found in a human but let me know if I'm mistaken.

"I identify some mineral in the ground and find that it works nicely to write on slate, I didn't design the mineral and ought not to get some monopoly over the mineral which is a product of nature. "

What about if the mineral is really rare and only works nicely to write on slate if it is purified in large quantities, which requires extensive and novel man-made processes, and you claim the mineral composition so that it encompasses the purified mineral in chunks of a certain size that do not exist in nature? Is that composition claim ineligible? Can you explain the policy behind your rule, and how that policy jives with your answer to my 4:09 question?

"As I said before, consistently and repeatedly, genetically engineered organisms are typically the products of both intention and design and thus meet the threshold, are not products of nature, and should be patentable."

I hope you're being to understand, David, that repeating these vague statements achieves very little when you are talking to someone who has years of experience in the area you are seeking to "achieve order."

The substrate for the natural product doesn't matter at all, as I've said, the issue isn't about "human" genes but products of nature. That is where the supreme court draws the line.

I'd say patent the processes for purification but purifying something nature designed doesn't suddenly make it man made, see, e.g my arguments about O2. The policy behind the rule is to reward invention and not mere discovery of natural laws, products, or abstract ideas. I didn't make that policy, the supreme Court did. I think it's sensible.

Actually David, the Supreme Court didn't make the policy either (at leas they don't own up to it, at least not fully).

They claim the authority for the policy comes from the implicit words of Congress (the branch of government constitutionally sanctioned to come up with patent law).

As I mentioned to EG though, whether the Supreme Court could really keep their fingers out of the pie, well, I'm...

David: "The substrate for the natural product doesn't matter at all"

I do recall using the term "substrate" and I do not want to guess that the term means to you or why you are making this statement. Are you addressing something that I wrote? If so, please reproduce the statement you are responding to so we are not talking past each other. I suspect it is likely that you are misreading something I wrote so I would advise not jumping to conclusions before making strange statements about "substrates."

Better still, why not simply respond directly to the straightforward questions I asked you in my 12:43 pm comment? Again, it's a bit mystifying trying to understand your position, the basis for that position, and its logical ramifications if you refuse to answer questions about it.

"the issue isn't about "human" genes but products of nature."

Well, the question certified is most definitely about "human genes", but let's not quibble about that.

I'm still mystified as to why you seem so intent on avoiding directly answering questions. It appears that the quoted statement of yours is an attempt to resspond to one aspect of the first hypothetical in my 12:43 comment. But you ignored the more important and interesting question which was an attempt to clarify your earlier-stated position about "design" versus "discovery" and see how you would apply it to the eligibility of nucleic acid composition claims. My 12:43 comment is very clear so I will let you re-read it and hope to see you address the questions I asked and confirm that I understand your position on these straightforward, practical scenarios. As you know, I've been prosecuting in this field and thinking about these issues for many, many years. I, too, would like "order" to be brought to the area. That is why I believe it worthwhile to think these issues through carefully and understand precisely how subject matter eligibility is determined and, equally importantly, why.

I look forward to your thoughtful answers to the questions and requests for clarification in my 12:43 comment.

At the beginning of my previous comment, I wrote: "I do recall ..."

I should have written: "I do NOT recall..."

I apologize for the confusion.

I answered 12:43 completely at 4:34. To clarify my use of the term "substrate" I meant it colloquially to refer to the underlying conditions in which something lies. The air is one substrate in which O2 molecules are found, so is a tank of O2. In each case, the O2 molecules are not the result of man's design. Thus "purified" O2 or a purified mineral remains undesigned even while processes developed to make each more useful might be designed. Similarly, "isolating" some naturally occurring nucleotide sequence from its substrate (the rest of the genome) does nothing to change the fact that the sequence has evolved and not been designed.

And actually, KIR, or MM, I know nothing about you. Who are you? Besides, the appeal to authority is a fallacy. Only arguments and reason matter to me.

Looking forward to seeing how it plays out in SCOTUS, where it matters.

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