DoEPHETAN: Applying the “merely tangential” exception to the “prosecution history estoppel” limitation of the “doctrine of equivalents” expansion of the definition of infringement

by Dennis Crouch

Ajinomoto Co., Inc. v. ITC; CJ CheilJedang Corp. v. ITC (Fed. Cir. 2019)

Some aspects of patent law are unduly complicated.  Here is one: Prosecution History Estoppel (PHE) as applied to the Doctrine of Equivalents (DOE).

The DOE finds infringement when someone is practicing something very similar (albeit different) than what is literally claimed.  Although the doctrine is court-created, courts are also wary of the potentially unmoored doctrine and thus have created a number of major limitations on the doctrine that have severely limited its scope.  Prosecution History Estoppel is one such limitation and arises when patent claims are narrowed during patent prosecution (something that happens in the vast majority of cases).

Under PHE, a narrowing limitation during prosecution is “presumed to be a general disclaimer of the territory between the original claim and the amended claim.” Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722 (2002).  In Festo though, the Supreme Court identified the disclaimer as rebuttable upon proof that “the amendment cannot reasonably be viewed as surrendering a particular equivalent.”  The high court particularly identified three mechanisms of such proof:

  1. The equivalent was unforeseeable at the time;
  2. The reasons for the amendment bear only a “tangential relation to the equivalent”; or
  3. “some other reason.”

The Federal Circuit has noted in the past that these exceptions are “very narrow”  Cross Med. Prods., Inc. v. Medtronic Sofamor Danek, Inc., 480 F.3d
1335, 1342 (Fed. Cir. 2007)). Further, proof of the exceptions and the patent applicant’s intent must be “objectively apparent” and “discernible from the prosecution history record.”

Like I said, unduly complicated.  The easiest way to state this (recklessly ignoring the various burdens) is that PHE applies to cut-of DOE when there is a narrowing amendment reasonably related to the equivalent at issue.

I also have to say that this is a really poorly written opinion by Judge Taranto in that it muddles together various facts over many pages — often without spelling out which facts are relevant for what purposes.  The dissent by Judge Dyk is much more clear-headed as written.

= = = =

Ajinomoto’s patent claims E. coli bacteria genetically engineered with the yddG gene to increase L-amino acid production (including tryptophan) and also claims the method of making the amino acids by cultivating the aforementioned bacteria.  Ajinomoto filed a complaint against CJ CheilJedang in the USITC, and the Commission eventually sided with the patentee — finding infringement under the doctrine of equivalents.

The claim structure here is odd.   Claim 20 is the claim at issue and is couched as a multiple dependent method claim — the method of producing the L-amino acid by cultivating bacteria “according to any one of claims 9-12, 13, 14, 15-18, or 19.”  The appeal here focuses only on claim 20’s L-amino acid production according to claim 9.

The dissent explains why CJ does not literally infringe:

Claim 9 covers a recombinant bacteria having [sic] a “protein consist[ing] of the amino acid sequence of SEQ ID NO: 2.” Id. col. 22, ll. 56–57. This corresponds to the amino acid sequence of E. coli YddG protein (a membrane-bound protein involved in the cellular export of aromatic amino acids). [CJ’s] Strain B does not
literally infringe claim 9 because it produces a protein with an amino acid sequence that differs from SEQ ID NO: 2. Instead, Ajinomoto asserts infringement under the doctrine of equivalents, arguing that Strain B’s non-E. coli YddG protein is equivalent to the E. coli YddG protein (SEQ ID NO: 2) in claim 9.

Although not literally the same as what was claimed, the ITC found that it was the equivalent and therefore infringing.  On appeal, the Federal Circuit agreed — that DOE applies generally, but then focused on whether it was limited by PHE.

The original claim language covered SEQ ID NO: 2 along with modification such as “deletion, substitution, insertion or addition of one or several amino acids” of SEQ ID NO: 2. That claim was narrowed after an anticipation rejection to get around a different naturally occurring protein (YfiK).  By narrowing the claim, it also now excludes the particular YddG protein variation used by CJ.

On appeal, the Federal Circuit held that the purpose of the appeal was to get around the YfiK prior art, not the YddG prior art.  As such, the reasons for the amendment were merely tangential to the equivalent in question.

Judge Dyk writing in dissent argued the other side:

Originally, the claim covered proteins with amino acid sequence variations from SEQ ID NO: 2, which would have included the non-E. coli YddG protein at issue here. The examiner rejected the original claim based on anticipating prior art, and the patentee responded with a narrowing amendment. Instead of continuing to define the covered proteins in terms of amino acid sequence variations from SEQ ID NO: 2, the patentee deliberately chose to redefine the claimed proteins in terms of the ability of their encoding nucleotide sequences to hybridize with SEQ ID NO: 1 under the claimed conditions. The amended claim language excluded the prior art protein (Livshits) because it was made based on a nucleotide sequence that did not meet the newly added hybridization requirement. The accused equivalent is similarly not covered by the amended claims because it is produced based on an encoding nucleotide sequence that does not hybridize with SEQ ID NO: 1 under the claimed conditions. Thus, I do not see how the reason  for the narrowing amendment is tangential to the accused equivalent. . . .

In my view the tangential exception cannot apply. The equivalent is directly related to the reason for the amendment—to exclude those proteins made by an encoding nucleotide sequence that does not hybridize with SEQ ID NO: 1 under the specified conditions.

The majority disagreed with this analysis and affirmed the infringement holding.

28 thoughts on “DoEPHETAN: Applying the “merely tangential” exception to the “prosecution history estoppel” limitation of the “doctrine of equivalents” expansion of the definition of infringement

  1. 3

    I once had an applicant amend *his spec* and his claims to exclude the exact art I had cited against him, essentially saying “When I say genus, I mean a genus that doesn’t include [the prior art species the examiner cited].”

    I think it is clear how, if that kind of act was valid, the entire patent system would break down.

    And yet the majority allows the exact same rose by another name. If one is allowed to change the scope to exclude anything cited against the claim without moving the filing date, the inventor is not the applicant, but the examiner. The invention would be not what the inventor posited, but everything that had not come before. If so, simply make the next claim “All subject matter not rendered obvious by any combination of prior art” and be done with it.

    It seems ridiculous to me that the applicant can obtain through inaction and boilerplate disclaimer that which the law would expressly exclude him from if explicitly sought, but the CAFC has never been a paragon of consistent intellect.

    1. 3.1

      think it is clear how, if that kind of act was valid, the entire patent system would break down.

      Break down? My, that sounds exactly like how MaxDrei describes how the EPO does work.

      1. 3.1.1

        The jurisprudence of the Boards of Appeal on disclaimers is tough for outsiders to grasp if only because it serves the provision in the EPC that excludes secret prior art from inclusion in obviousness attacks. here a Link to representative Enlarged Board of Appeal Decision G1/16:

        link to epo.org

        1. 3.1.1.1

          Thanks MaxDrei – you introduce the disparate treatment of the legal fiction known as PHOSITA in regards to obviousness and secret prior art as a way of “explaining” the oddity that Random Guy jibes with, as if two wrongs makes a right.

          This is just too easy to pull your strings.

    2. 3.2

      Indeed, RG. That’s why this decision is a hot disgusting mess. Maybe it will be cleaned up en banc.

      1. 3.2.1

        That’s why this decision

        Because of Random’s completely different “fact pattern,” THIS decision is how you feel…?

        Any Means at all to get to your desired Ends, eh Malcolm?

    3. 3.3

      Agree fully Random. Especially with your last para. The CAFC is out of its depth, adjudicating a Statute that over the years has evolved into an omnishambles.

      1. 3.3.1

        You do realize that over the last several years that the major driver to that inconsistency has been our Supreme Court and their fire-hose training of the caged CAFC simian judges, eh MaxDrei?

    4. 3.4

      There is some conflating going on here. Amended his spec? What?

      If you can write a narrower set of claims that pass 112, then there is nothing unseemly about those claims. You, RandomGuy, make it sound like some new material has been added and somehow gotten the earlier filing date.

      There is nothing wrong with narrowing claims to avoid prior art.

      1. 3.4.1

        Nor is there anything wrong — per se — with amending claims to get around particular prior art AND such amendments simply do not automatically doom the Doctrine of Equivalents (as the cognitively dissonant, “any Ends that is bad for the patent holder Malcolm” so eagerly jumps to — in error).

        And rather unsurprisingly, look how Malcolm’s minion, the court jester Shifty, attempts to jump in with his “gotcha” games…

  2. 2

    This was a major fail by this panel. Dyk got it right. That said, this isn’t the first time this sort of result has obtained under these circumstances. It’s a flaw in the system and if “unpredictability” is a major concern for you then it’s time to complain loudly.

    The better reasoning here is that the DOE should not be available to expand the scope to cover mutations in SEQ ID NO:2 because the clause in the claim that literally covered such mutations was deleted by amendment to get around the prior art. That’s the end of the analysis. Everything else is just hand-waving gobbledyg00k.

    1. 2.1

      You know, it’s rather humorous given your recent claim to being SO knowledgeable on the subject that you would make such an egregious error of over-simplification and altogether rather unsurprising that your error would be against a patent holder (given your highest ever recorded history of cognitive dissonance).

      1. 2.1.1

        an egregious error of over-simplification

        In fact, the majority made an “egregious error of over-complication” because … who knows why? Probably Taranto liked the lawyer’s hair or something equally arbitrary.

        1. 2.1.1.1

          Says the guy who says the concept is NOT complicated (because he is so smart) AND gets its wrong.

          Absolutely stultifying.

          1. 2.1.1.1.1

            “AND gets its wrong.”

            Get’s DOE wrong? That accusation is void for vagueness. What is the wrong, specifically? In your opinion.

          2. 2.1.1.1.2

            What is “wrong” about I wrote?

            Nothing. Taranto’s decision is absurd and to the extent it’s reasoning can be followed, it leads to sh-tty results.

  3. 1

    Three additional thoughts unrelated to the DoE issue:

    (1) Whenever I send out an order to an outside counsel for them to draft an app for me, and they send me back a claim set, one of the first things I think about as I read through the draft claims is to ask myself—word-by-word—“why is this word in here?”. In other words, each word of the claims had better be serving an important function, or else it is coming out. If I find a word that I do not believe to be strictly necessary, I call up the outside counsel who drafted it and ask them to explain to me what function the word is meant to serve, and if they cannot explain to me why it is necessary that the word in question be there, then I tell them to strike that word.

    Why do I mention this, because the patentee quite nearly lost here because of a totally unnecessary clause in the claims. The claim here recited

    A recombinant Escherichia coli bacterium, which has the ability to accumulate aromatic L-amino acid in a medium, wherein the aromatic L-amino acid production by said bacterium is enhanced by enhancing activity of a protein in a cell of said bacterium beyond the levels observed in a wild-type of said bacterium,

    [1] and in which said protein consists of the amino acid sequence of SEQ ID NO: 2

    [2] and said protein has the activity to make the bacterium resistant to L-phenylalanine, fluorophenylalanine or 5[-]fluoro-DL-tryptophan,

    [3] wherein the activity of the protein is enhanced by [3a] transformation of the bacterium with a DNA encoding the protein to express the protein in the bacterium, [3b] by replacing the native promoter which precedes the DNA on the chromosome of the bacterium with a more potent promoter, [3c] or by introduction of multiple copies of the DNA encoding said protein into the chromosome of said bacterium to express the protein in said bacterium.

    Note that clause 2 (“said protein has the activity to make the bacterium resistant to L-phenylalanine”). This clause is totally superfluous. If the protein has the sequence of SEQ ID NO:2 (as required in clause 1), then it will necessarily be able to “make the bacterim resistant to L-phenylalanine.” The property of conveying L-Phe resistance is inherent in the structure of SEQ ID NO:2. However, so long as those words remain in the claim, then this is one more element that the plaintiff has to prove up when enforcing. Clause 2 is doing nothing to make the claim more defensible to invalidity challenge, but it makes it just that much harder to prove infringement. Don’t do that.

    1. 1.1

      This is good advice. The caveat is that clause (2) (along with other “limitations” in the claim) is probably a vestigial clause that was initially doing some work in the claim as filed (properly or improperly) but, as you point out, it became superfluous when the limitation regarding SEQ ID NO:2 was inserted.

    2. 1.2

      (3) I suppose that this is a close case, but I would have gone the other way on the written description challenge here. The universe of promoters that are “more potent” than the “native promoter” is quite possibly infinite (literally). I cannot see how we can conclude that the patentee has provided either a “representative sample” of species lying with the genus “more potent than the native promoter.” Nor can I see how one might conclude that the patentee has described structural features that are common to the whole genus (but not common to all DNA sequences, whether or not they work as promoters). If I had been on this panel, I would have dissented from the written description and held the claims invalid for want of adequate written description.

      1. 1.2.1

        My point #2 is evidently still trapped in the filter. Maybe it will eventually come through (sometimes they do, and sometimes they never do).

    3. 1.3

      Just to be clear, if you read the case, there was a challenge to the adequacy of the plaintiff’s proof for the clause 2 claim limitation. The plaintiff eventually won that fight, but they could have avoided even having the fight if the attorneys drafting the claims had removed clause 2 before the end of prosecution. Once they added clause 1, clause 2 became a pointless vestigial organ that should have been excised.

    4. 1.4

      (2) Another easily avoidable flaw in this claim is the product-by-process limitation in clause 3b. The defendant actually escaped liability for certain imported products because instead of “replacing” the promoter in their bacteria, they had simply introduced a point mutation into the promoter.

      That is only a problem because the patentee had claimed “wherein the activity of the protein is enhanced by… replacing the native promoter which precedes the DNA on the chromosome of the bacterium with a more potent promoter… .” If—instead of this product-by-process limitation—the patentee had described the DNA structure (“… wherein the DNA comprises a more potent promoter than the native promoter, and wherein the more potent promoter is operably linked to the DNA encoding the protein to express the protein in the bacterium”) then the claim would have covered the materials that were found not to infringe in this case.

      Do not use product-by-process unless it is truly impossible otherwise to define the boundaries of the claimed invention.

    5. 1.6

      The property of conveying L-Phe resistance is inherent in the structure of SEQ ID NO:2. However, so long as those words remain in the claim, then this is one more element that the plaintiff has to prove up when enforcing. Clause 2 is doing nothing to make the claim more defensible to invalidity challenge, but it makes it just that much harder to prove infringement.

      The clause may have relevance in getting the claim initially granted, though. One still needs a reference to prove inherent features, and most prosecutors view “requiring the examiner to assert another reference” as a move toward patentability. (Because they may perceive that it de facto is) Conversely it may be, as MM suggests, vestigial from an initial genus claim that was later narrowed to a species.

      I do question this though – How can you make this statement: Clause 2 is doing nothing to make the claim more defensible to invalidity challenge, but it makes it just that much harder to prove infringement.

      I agree that if something is inherent it has no legal effect on an invalidity challenge, but for the same reason it has no legal effect on an infringement challenge, either. Inherency is inherency. It would be just as trivial to prove the inherency for infringement as for invalidity.

      1. 1.6.1

        Inherency is inherency. It would be just as trivial to prove the inherency for infringement as for invalidity.

        Every time you need an expert, that is just one more occasion for a Daubert motion to exclude the evidence. Proving the identity between the bacterial protein and SEQ ID NO:2 is one piece of expert testimony. Proving that the protein of SEQ ID NO:2 convey’s L-Phe resistance is another piece of expert testimony.

        The merits of the Daubert challenge to the first are not the same as the merits of the challenge to the second, even though the scientific fact of L-Phe resistance is inherent in the structure of the first. It is very much possible for the plaintiff to win against the Daubert challenge that seeks to exclude the expert testimony as to Clause 1, but lose against the Daubert challenge that seeks to exclude the testimony as to Clause 2. If so, then one the testimony on Clause 2 will not come into evidence. At that point, the plaintiff will—as a matter of law—have failed to prove infringement, even though scientifically it is impossible to a bacterium to satisfy Clause 1 without simultaneously satisfying Clause 2.

        1. 1.6.1.1

          Yes I agree with all of the above. What I’m confused about is why it isn’t equally applicable to an invalidity situation?

          Obviously every time you put in any limitation, that makes it harder to prove infringement. The counter is, of course, that every time you put in any limitation, that makes it harder to show invalidity. They’re two sides of the same coin. So how do you arrive at a non-mirrored statement like

          Clause 2 is doing nothing to make the claim more defensible to invalidity challenge, but it makes it just that much harder to prove infringement.

          By definition any difficulty borne by the plaintiff to show the scientific inherency for their infringement burden must be joined with an equal or greater (because of the clear and convincing standard) difficulty borne by the defendant to show the scientific inherency for their invalidity burden, right? I sense I’m wrong here but I don’t know why.

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