Measuring Uncertainty

measuring tape
measuring tape

               Current subject matter eligibility jurisprudence is often criticized for increasing uncertainty. However, this raises the question: how can we measure uncertainty to know that it has increased? Until very recently, I thought that the uncertainty criticisms were based on conflating uncertainty with incomprehensibility. I always thought this was wrong, since the two are different concepts. That is, I felt it was relatively easy to predict whether an invention would or would not be treated as ineligible, but that the justifications given for the eligibility/ineligibility determinations were basically gibberish. Recently though, I learned that the patent office purported to have a quantitative measurement of uncertainty for subject matter eligibility, and so I decided to take a look.

In an article published in April of 2020, the patent office quantified uncertainty as a measurement which would be made on the level of individual U.S. patent classes, and defined the uncertainty for any particular class as that class’s inter-examiner variance in proportion of first office actions which included subject matter eligibility rejections. While I applaud this effort to make some kind of objective evaluation of uncertainty, I think an inter-examiner variance-based approach is fundamentally flawed, because it ignores the fact that any rejection based on subject matter eligibility is a sign of underlying uncertainty. To illustrate, consider an example of a subject matter eligibility question where there really is no uncertainty: whether you can patent a literary work. In this case, the answer is clearly no, and the result is that authors protect their literary works with copyrights, not patents. This is only to be expected. Preparing, filing, and prosecuting a patent application is an expensive and time-consuming proposition, and so, if something clearly can’t be patented, people (assuming they are constrained by time and/or money) won’t try to patent it. Thus, even if the proportion of applications treated as ineligible is consistent across examiners, every application treated as ineligible represents a case where two people (i.e., the examiner and the applicant) operating in good faith came to different conclusions when applying the same rules, and therefore where those rules produced uncertainty.


               A more accurate measure of uncertainty would consider the behavior of both applicants and examiners, and would account for all circumstances in which their actions reflected uncertainty, not just first office actions.  In this approach, each initial filing of an application, as well as every response which addressed rejections under section 101 should be treated as reflecting the applicant’s conclusion that the claims complied with the relevant rules as of the time of filing, including those of subject matter eligibility. Similarly, because the patent office follows the policy of compact prosecution, but can adopt a new ground of rejection any time before patent issuance, each substantive communication from the patent office would be treated as communicating a conclusion that the claims either do (if there were no rejections under section 101) or do not (if there were rejections under section 101) comply with the then current rules of subject matter eligibility. The level of uncertainty could then be calculated as the number of times the patent office and a patent applicant, looking at the same application and applying the same rules of subject matter eligibility, reached a different conclusion, divided by the total number of times patent applicants and the patent office, looking at the same application and applying the same rules, expressed (either implicitly or explicitly) any conclusion regarding eligibility at all.


               Ultimately, I don’t think there is a perfect measurement of the uncertainty in subject matter eligibility law. For example, while the approach I propose here improves on the patent office’s approach by considering the actions of both applicants and the patent office, it misses entirely the uncertainty determinations made by people who decided that subject matter eligibility is too unpredictable, and so decide not to file at all. Similarly, any approach will necessarily omit the uncertainty in whether a claim issued by the patent office will be upheld by the courts, since only a tiny fraction of patents are litigated, and courts use different rules for evaluating eligibility. However, regardless of the limitations, the level of uncertainty in subject matter eligibility determinations is an important topic, and so any effort to measure it should reflect both the actions of the patent office and applicants, as well as the fact that any section 101 rejections are a reflection of differences in opinion, and therefore of uncertainty in the system.


Disclaimer – “The statements and views expressed in this posting are my own and do not reflect those of my law firm, are intended for general informational purposes only, and do not constitute legal advice or a legal opinion.”

In re Killian: Defining “Abstract Idea” and “Inventive Concept”

In re Killian is interesting because the Federal Circuit used that case to respond to the frustration many patent applicants feel regarding the amorphous and unpredictable nature of analysis under 35 U.S.C. § 101. Killian made that frustration quite plain, leading off his appeal with the argument that

the standard promulgated in Alice and Mayo is indefinite—so poorly defined that it renders all court and Board decisions finding a claim patent ineligible under the Alice/Mayo standard arbitrary and capricious under the Administrative Procedure Act (APA), 5 U.S.C. § 706(2)(A), and the Due Process Clause of the Fifth Amendment.

While there was basically no chance that the Federal Circuit would agree to an argument premised on the proposition that the standard laid out by its reviewing court (and applied by it) was incomprehensible, I think the Federal Circuit choosing to address that argument with a precedential opinion rather than affirming the board under rule 36 is interesting in and of itself. Even more is that the Federal Circuit acknowledged and responded to “Mr. Killian’s desire for ‘a single noncapricious definition or limiting principle’ for ‘abstract idea’ and ‘inventive concept.’” Thus, In re Killian not only shows that the Federal Circuit feels the need to respond to criticisms of the Alice/Mayo framework, it also shows what the Federal Circuit feels is the closest it can come to concrete definitions of the phrases “abstract idea” and “inventive concept” which are at the heart of the eligibility determination.


                Turning first to “abstract idea,” the Federal Circuit began by acknowledging that there is no single rule which could distinguish what was and was not an abstract idea.  It explained that such a rule did not exist because there were at least three different types of abstract ideas: (1) methods of organizing human activity, (2) claims to mental processes, and (3) claims to results rather than means of achieving them. It also said that it had provided guidance as to what constitutes an abstract idea in the form of cases which said that the abstract idea determination was made based on the claimed advance over the prior art, and cases which said that the intangibility of information meant that advance in the specified content of information were abstract. It finally turned specifically to software inventions, stating that, for that kind of invention eligibility “often” turns on whether the claims focus on “the specific asserted improvement in computer capabilities” or “on a process that qualifies as an ‘abstract idea’ for which computers are invoked merely as a tool.”


                The treatment of “inventive concept” was similar, with the Federal Circuit indicating that it had provided guidance, but stopping short of elaborating a clear definition. With respect to guidance, there was actually very little on offer, with the examples of guidance laid out by the Federal Circuit largely restating principles already laid out as “guidance” for what was an abstract idea. For instance, the first example of guidance in the discussion of “inventive concept” was that “methods that ‘improve[] an existing technological process’ include an inventive concept at step two.” However, the discussion of abstract ideas had already stated that the lack of “any particular assertedly inventive technology” would doom a claim to an invention where the improvement was information of specified content, and so it isn’t clear what would be added by treating an improvement to “an existing technological process” as an inventive concept.


                Ultimately, I don’t think the Federal Circuit’s explication of its “guidance” would be particularly satisfying to someone who, like the appellant in Killian, is frustrated by the current state of 101 caselaw. Indeed, the fact that the Federal Circuit could do no better than provide a non-exhaustive list of types of abstract ideas, then point to various past cases as “guidance” seems to confirm the ad-hoc and nature of contemporary subject matter eligibility analysis. I suspect that the Federal Circuit realized this, since it ended its discussion of “abstract idea” and “inventive concept” by explaining that, even if it was “persuaded by Mr. Killian’s argument that the Alice/Mayo framework is insolubly unclear, both this court and the Board would still be bound to follow the Supreme Court’s § 101 jurisprudence as best we can as we must follow the Supreme Court’s precedent unless and until it is overruled by the Supreme Court.” Hopefully, the Supreme Court will view this as an invitation to come up with a standard that a court couldn’t even hypothetically be persuaded is “insolubly unclear,” as otherwise I think the frustration felt by Mr. Killian (and many others) is likely only to get worse.


Disclaimer – “The statements and views expressed in this posting are my own and do not reflect those of my law firm, are intended for general informational purposes only, and do not constitute legal advice or a legal opinion.”

3 Anti Alice Responses to Overcome §101 Rejections in Molecular Biology

Patent lawyers love the overused quote from Diamond v. Chakrabarty, “everything under the sun invented by man.” Forty years later, this remains good law in most situations. However, Mayo v. Prometheus and AMP v. Myriad Genetics went on to make clear that not everything under the sun is patentable when it comes to biology. Most recently, Alice, and the associated 2019 PEG have come to dominate how examiners and attorneys approach subject matter eligibility arguments, even when it comes to inventions within the life sciences.

Even with the most conscientious claim drafting, rejections under §101 are not unlikely when the claimed subject matter centers on organic molecules or other “products of nature.” Given the dynamic state of legal arguments in this field, it can be particularly helpful to look at successful responses prepared by other attorneys facing similar rejections.

If you are dealing with §101 rejections involving molecular biology, or other technology classes where “natural phenomena” are frequently cited, you may want to consider taking a prong, (or better, two), from the winning arguments we’ve selected,  below:

Molecules Created Through Human Efforts Can Lay a Path

If the subject matter is artificial, it does not fall under a judicially-created exception to §101 and, therefore, constitutes patent-eligible subject matter.

In biology cases, the examiners typically rely on the “natural phenomena” judicial exception in their §101 rejections. The Patent Office does not want to be responsible for issuing a patent on a biological matter that occurs naturally. This would potentially turn every living organism into an infringer.

To overcome this rejection under the Alice test and the 2019 examination guidelines, you must show the subject matter does not fall into the “natural phenomena” category or the claims include substantially more than a natural phenomenon. Where the claimed subject matter is artificial and the hand of an engineer or scientist is needed to produce it, the invention is legitimately the product of human ingenuity and human effort must be made to infringe the claims.

This argument succeeded in an application for a “Vesicular Linker and Uses Thereof in Nucleic Acid Library Construction and Sequencing” This case was filed in 2017 and issued in 2020.

The examiner issued a rejection under §101 citing the judicial exception for “natural phenomena.” In response, the applicant amended the claims to clarify the claimed kit did not contain a naturally occurring molecule, but rather an engineered product.

With respect to claim 3 as currently amended, the claim now recites “a first primer, having the same sequence as at least a portion of the first strand of the vesicular non-paired region of the oligonucleotide vesicular adaptor” and “a second primer, specifically paring with the second strand of the vesicular non-paired region of the oligonucleotide vesicular adaptor”. Thus, it would be appreciated by the one skilled in the art that the structures of the first primer and the second primer tightly depend on the oligonucleotide vesicular adaptor which is not a naturally occurring product and is instead is a novel and non-obvious presentation for constructing a nucleic acid library and of which specific nucleotide sequences are artificially selected in accordance with actual needs.

Specifically, the claims recited an oligonucleotide vesicular adaptor that connected to a first primer at one location and a second primer at another location. The first primer and second primer are molecules that can occur in nature. But the applicant argued the claimed kit was not a natural phenomenon for two reasons.

  1. The oligonucleotide vesicular adaptor does not occur naturally. Rather, the inventors developed this molecule.
  2. Although the molecules that make up the first primer and second primer occur in nature, a scientist must select and artificially design the first primer and second primer claimed in the application based on the application of the invention. As a result, the primers were not randomly assembled, as would occur in nature, but deliberately created, as would occur in an engineered molecule.

The examiner found these claim elements established that the claimed molecule could not occur naturally. The examiner withdrew the §101 rejection and allowed the claims.

The lesson drawn from this case is that your claims can include molecules that may occur in nature. But make sure that your claims either include non-natural molecules with them or make clear that the molecules are not the naturally occurring variety.

Kudos to Z. Peter Sawicki from Westman, Champlin & Koehler for exemplary work in drafting winning office action responses!

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A Combination of Humanized and Natural Molecules Can Save the Day

This argument is a close corollary of the first argument. If the subject matter contains molecules that are arguably naturally occurring, you may be able to argue that the combination cannot occur in nature. This moves you out of the judicial exceptions for “products of nature” and “natural phenomena” and allows you to escape the second prong of the Alice test.

Avoiding Alice’s second prong can substantially improve your chances of allowance. The test’s second prong, which asks whether the invention includes substantially more than the ineligible subject matter, is highly subjective. Therefore, qualifying under the first prong should be your first, strongest, and best thought-out argument.

This argument was used in an application for “Humanized Antibodies” This application was filed in 2016 and issued in 2020. Prior to allowance, the applicant received a rejection under §101 on the ground that the claimed invention comprised products of nature.

The antibody or antigen-binding fragment thereof of the pending claims exhibit “markedly different characteristics” as compared to a naturally occurring counterpart in at least two ways. First, one of ordinary skill in the art would understand that the non-human donor antibody is itself “man-made” … Second, … the antibody, or antigen-binding fragment thereof of claim 1, and those dependent thereon, is eligible subject matter because it exhibits structurally distinct characteristics as compared to a naturally occurring counterpart by comprising both non-human donor and human donor residues, introduced into the claimed antibody by the “hand of man.”

In response, the applicant amended the claims to clarify that the claimed invention included a humanized antibody from a non-human donor. This gave the applicant three strong arguments in the office action response:

  1. The humanized antibody behaved differently from naturally occurring antibodies. It did not behave like the non-human donor antibody because it had been humanized. And it did not behave like a human antibody because of its non-human donor origins.
  2. The humanized antibody was not naturally occurring because artificial processes were needed to humanize a non-human donor antibody.
  3. The final product, a humanized antibody, could not occur in nature because it contained both human and non-human residues.

The examiner allowed the claims. Although the examiner did not identify which of the arguments ultimately persuaded the examiner to allow the claims, all three of the arguments are powerful.

The lesson to be drawn from this case is that your chances for allowance improve if you can claim and argue for the non-natural creation, structure, and behavior of the claimed molecule.

Kudos to Elizabeth M. Rohlfs from Pfizer Inc for exemplary work in drafting winning office action responses!

A Real-World Application Can Carry You Through

Although you would prefer to satisfy the Alice test’s first prong rather than battling over the more subjective second prong, you should not limit your arguments to the first prong. If an examiner disagrees with your arguments under the first prong, you will need to present something under the second prong to try to satisfy the Alice test.

This occurred in an application for “Predicting the Ability of Atlantic Salmon to Utilize Dietary Pigment Based on the Determination of Polymorphisms” This application was filed in 2016 and allowed in 2020, although it has not yet issued as a patent because the applicant has not paid the issue fee.

The application claimed a process for sequencing the genes of an Atlantic salmon to detect cytosine at a particular location in the gene sequence. The examiner rejected these claims as directed to a natural phenomenon.

[A]lthough nature-based product limitations are recited by claim 15, analysis of the claim as a whole indicates that claim 15 is focused on a process of detecting the presence of a specific nucleic acid sequence in a sample from a salmon, and is not focused on the nature-based product per se. Id. at 11. For example, as amended herein, claim 15 recites, in part:

a) obtaining a nucleic acid sample from a salmon; and

b) assaying the nucleic acid sample to detect a presence of one or more alleles in the nucleic acid sample;

c) detecting the presence of a cytosine at position 36 in SEQ ID NO: 14.

In response the applicant amended the claims and presented two arguments:

  1. Under the first prong of the Alice test, the applicant argued that the claims were not directed to a natural phenomenon. Specifically, the applicant pointed out that the process of obtaining a DNA sample from the fish, sequencing it, and looking for a particular gene was an artificial process even though it worked on a naturally occurring molecule. As stated by the applicant, the claims were focused on the process of detecting the naturally occurring product and not the naturally occurring product per se.
  2. Under the second prong of the Alice test, the applicant argued that the claims were not merely directed to detecting the naturally occurring product. Instead, the results of the process were used to guide the selective breeding of the fish tested so that the desired characteristic was passed to the offspring. Thus, the claims recited “substantially more” than the process of detecting the naturally occurring product. Specifically, the test results had a real-world use in improving fish husbandry.

The examiner allowed the claims. But the examiner did not identify which of these arguments was found persuasive.

The takeaway from this case is that you should always present arguments on both prongs of the Alice test. In this case, while each argument was powerful independently. the applicant took measures to avoid prolonged prosecution, by presenting both sets of arguments in the office action response.

Kudos to Bradley W. Thomas from Shook, Hardy & Bacon LLP for exemplary work in drafting winning office action responses!

Overcoming §101 Rejections in Molecular Biology Cases

Although some patent practitioners might view Chakrabarty as dated, the “made by man” phrase remains one of the most powerful arguments you have to secure allowance of artificially-created biological inventions.

But you should not limit yourself to “hand of man” arguments. The chances for allowance increase as you present more ways that the claimed molecule differs from its natural counterparts. Look for specific differences in structure and behavior between the claimed molecule and naturally occurring molecules and recite these differences in the claims.

Finally, do not ignore the second prong of the Alice test. Even if you feel optimistic about your arguments that the claims do not embody a natural phenomenon or a product of nature, an examiner might disagree. As a result, you should also present arguments that the claimed invention includes substantially more than a natural phenomenon or product of nature. You can do this by reciting in the claims a real-world application for the invention.

These arguments were found using Arguminer. Visit IP Toolworks to learn more about using Arguminer to find proven arguments for your office action responses.

Disclaimer – “The statements and views expressed in this posting are my own and do not reflect those of my law firm, are intended for general informational purposes only, and do not constitute legal advice or a legal opinion.”