DETAILED ACTION
Applicant’s response, filed Oct 14 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim Status
Claims 1-2, 4, 6-14, and 16-23 are pending.
Claims 3, 5, and 15 are canceled.
Claim 21 is objected to.
Claims 1-2, 4, 6-14, and 16-23 are rejected.
Priority
The instant Application claims the benefit of domestic priority to US provisional application 62/635,536, filed Feb 26 2018.
Applicant's claim for the benefit of a prior-filed application, PCT/US2019/019530, filed Feb 26 2019, is acknowledged.
Accordingly, each of claims 1-2, 4, 6-14, and 16-23 are afforded the effective filing date of Feb 26 2018.
Claim Objections
Unless otherwise indicated, the outstanding objections to the claims are withdrawn in view of the amendments submitted herein.
The claims are objected to because of the following informalities. The instant objection is maintained from the previous Office Action.
Claim 21, limitation 7, recites “a first differences”, which should be amended to recite “[[a]] first differences” or similar. The objection is maintained from the previous Office Action.
Response to Applicant Arguments
At p. 11, par. 2, Applicant submits that the claims were amended to obviate the claim objections. However, claim 21 has not been amended to address the outstanding objection.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claim 13 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. The instant rejection is newly stated and is necessitated by claim amendment.
Claim 13 recites “wherein determining an amount of impact of the candidate substitution on the Gibbs free energy change…”. It is unclear whether the wherein clause is intended to require performing the determination of an amount of impact within the metes and bounds of the claimed invention, or if it is only further limiting the method such that determining the amount of impact is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of the determination of an amount of impact, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the determination is intended to be performed and the claim should either recite “further comprising determining…” or depend from claim 11 rather than claim 10, which recites actively determining an amount of impact. The rejection may be overcome by clarifying what steps are required to be performed.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2, 4, 6-14, and 16-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to methods and a system, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong 1
With respect to Step 2A, Prong 1, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong 1 evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claim 1: creating… a data set including the amino acid sequences, the first values, and the second values; and
determining… a candidate substitution indicating a modification of the amino acid sequence of the base protein at a respective position;
Independent claims 1, 10, and 21: determining… using the data set, a first additional data set that corresponds to a first group of the number of proteins that includes the candidate substitution, the first additional data set including first amino acid sequences of the first group of the number of proteins, a first set of the first values that correspond to the first group of the number of proteins, and a second set of the second values that correspond to the first group of the number of proteins;
determining… using the data set, a second additional data set that corresponds to a second group of the number of proteins that does not include the candidate substitution, the second additional data set including second amino acid sequences of the second group of the number of proteins, a first additional set of the first values that correspond to the second group of the number of proteins, and a second additional set of the second values that correspond to the second group of the number of proteins;
performing… comparisons between individual first positions of individual first amino acid sequences of the first group of the number of proteins and individual second positions of individual second amino acid sequences of the second group of the number of proteins;
determining… based on the comparisons, first differences between the individual first amino acid sequences and multiple groupings of the individual second amino acid sequences;
determining… based on the comparisons, second differences between the individual first amino acid sequences and the individual second amino acid sequences;
determining that a portion of the first differences is minimized with respect to the second differences for a subset of the groupings;
based on the determination that the portion of the first differences is minimized with respect to the second differences for the subset of groupings, generating… a modified data set that (i) represents individual groupings of the subset of groupings as a single protein having a first normalized value of the Gibbs free energy change and a second normalized value of the unfolding temperature based on the values of the Gibbs free energy change and the values of the unfolding temperatures of the respective proteins included in the individual groupings and (ii) indicates associations between individual second proteins of the second group of the number of proteins and one or more single proteins corresponding to one or more individual groupings;
determining… using the modified data set, additional differences between the first normalized values and the first additional set of values for the Gibbs free energy change that correspond to the second group of proteins;
determining… based at least partly on the additional differences, that the candidate substitution produces a statistically significant effect on values of the Gibbs free energy change of the first group; and
determining… based on the candidate substitution producing the statistically significant effect on the values of the Gibbs free energy change, one or more of the first group of the number of proteins that have a measure of stability that is greater than an additional measure of stability of the base protein.
Dependent claim 2: determining that at least one of yield or stability increases based at least partly on the statistically significant effect produced by the candidate substitution.
It is noted that the limitation is interpreted under the BRI as encompassing in silico assays or actions to determine the stability, as supported in the instant specification at least at [0028].
Dependent claim 4: determining… further differences between the second normalized values and the second additional set of values for the unfolding temperatures that correspond to the second group of proteins.
Dependent claims 6 and 11: performing an analysis of variance or a t-test to determine an amount of impact of the candidate substitution on the Gibbs free energy.
Dependent claim 12: determining, based at least partly on the comparison, that differences between (i) a first amino acid sequence of the individual first amino acid sequences and (ii) a second amino acid sequence of the individual second amino acid sequences and a third amino acid sequence of the individual second amino acid sequences are less than a threshold number.
Dependent claim 23: determining, based at least partly on an amount of impact on the candidate substitution on the Gibbs free energy change, that the candidate substitution has an effect on yield of the protein.
It is noted that the limitation is interpreted under the BRI as encompassing in silico assays or actions to determine the yield, as supported in the instant specification at least at [0028; 0065].
Dependent claims 8-9, 13, 19-20, and 22 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claims 8 and 19-20 further limit the candidate substitution of claims 1 and 10; claim 9 further limits determining how the candidate substitution produces the statistically significant effect in claim 1; claim 13 further limits determining the amount of impact to including determining a probability; and claim 22 further limits determining that the candidate substitution produces the statistically significant effect.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine whether a candidate substitution in a protein sequence has a statistically significant effect on the Gibbs free energy change in comparison with the base protein. Without further detail as to the methodology involved in “creating”, “determining”, “performing”, “generating”, and “comparing”, under the BRI, one may simply, for example, use pen and paper to record values and sequences of proteins to create a data set, sort the proteins into groups that have and do not have a candidate substitution, determine differences between proteins in different groups, determine minimized differences between subsets of the groupings of individual amino acid sequences, generate normalized values from those minimized groupings, use that information to determine that the candidate substitution has a statistically significant effect on the property, and determine values for the modified proteins using in silico processes. Some of these steps, such as “determining… that the candidate substitution produces a statistically significant effect”, and those recited in the dependent claims, require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0042; 0064; 0080; 00107; 00127].
Therefore, claims 1, 10, and 21, and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong 2
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong 2
With respect to the instant recitations, the claims recite the following additional elements:
Claim 1: physically expressing a number of proteins with amino acid sequences that have been modified to include one or more substitutions with respect to an amino acid sequence of a base protein;
performing one or more first analytical tests to determine first values for Gibbs free energy change of the number of proteins; and
performing one or more second analytical tests to determine second values for unfolding temperatures of the number of proteins.
Claims 10 and 21: obtaining… a data set that includes (i) amino acid sequences of a number of proteins that have been modified to include one or more substitutions with respect to an amino acid sequence of a base protein, (ii) first values for Gibbs free energy change of the number of proteins, and (iii) second values for unfolding temperatures of the number of proteins.
Dependent claim 14: generating a user interface that includes at least one user interface element to capture a value for the Gibbs free energy change with respect to the base protein.
Dependent claims 7 and 16 further limits the base protein and the number of proteins physically expressed in claims 1 and 10 to being antibodies.
Dependent claim 17: comprising one or more analytical tests to determine the first values for the Gibbs free energy change of the number of proteins and to determine the second values for the unfolding temperatures of the number of proteins.
Dependent claim 18 further limits what values are determined by performing the one or more analytical tests of claim 17.
Claims 1, 10, and 21 and those claims dependent therefrom include non-abstract computing elements. Claim 1 includes one or more computing devices and one or more user interface elements. Claim 10 includes one or more computing devices. Claim 21 includes a system comprising: one or more processors; and one or more non-transitory computer-readable media storing computer-readable instructions that, when executed by the one or more processors, perform operations.
Considerations under Step 2A, Prong 2
With respect to Step 2A, Prong 2, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to insignificant extra-solution activity to the judicial exception, such as “physically expressing a number of proteins with amino acid sequences that have been modified at a number of positions with respect to an amino acid sequence of a base protein” and “performing” analytical tests in claim 1, perform activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim. The expressed proteins are not required to be acted upon by the remainder of the limitations, which are each performed by a computing device based on an actions performed on the in silico sequences of the proteins. Insignificant extra-solution activity does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Further, those steps directed to data gathering and outputting perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application, and insignificant extra-solution activity is not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The limitations directed to additional non-abstract elements of a system as recited above do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)). Further, the computer system contains the recited instructions (i.e., software) that are used for performing the operations which are considered to recite judicial exceptions as described above. Thus, the limitations only generically link the use of the judicial exceptions to the technological environment of a computer.
The specification does not provide a clear explanation for how the additional elements improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the prior art review to Wrenbeck et al. (Current Opinion in Structural Biology, 2017, 45:36-44; previously cited) discloses that physically expressing a number of proteins, including antibodies, with amino acid sequences that have been modified at a number of positions with respect to an amino acid sequence of a base protein, and then examining the proteins under different conditions (such as temperature, etc.) to generate multiple fitness landscapes, and performing crystallography to determine the structure of proteins are insignificant extra solution activities that are routine, well-understood and conventional in the art. Said portions of the prior art are, for example: the abstract; p. 36, col. 1 through col. 2, par. 2 and par. 4; p. 38, col. 1-2; p. 39, col. 2, par. 1; p. 40, col. 1, par. 2-4, col. 2, par. 1 and par. 3; and Figures 1-2. Further, the prior art to Kumar et al. (Nucleic Acids Research, 2006, 34:D204-D206; newly cited) discloses ProTherm and ProNIT, which are thermodynamic databases for proteins where researchers can deposit thermodynamic data including changes in Gibbs free energy (ΔG), thermal denaturation, and secondary structure (abstract; Table 1). Kumar discloses that ProTherm contains 17,113 entries from 1497 scientific articles at the time of publishing (2006), demonstrating the widespread practice of measuring Gibbs free energy and unfolding temperatures. As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The insignificant extra solution activity as recited in the instant claims constitutes a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 1, 10, and 21 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (see MPEP 2106.06(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at [0067-0068]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 11, par. 5, through p. 12, par. 2, Applicant requests that the pending claims be examined according to the framework and analysis set forth in Enfish, LLC v. Microsoft Corp., 822 F.3d 1327 (Fed. Cir. 2016) and McRO, Inc. v. Bandai Namco Games America, Inc. 837 F.3d 1299 (Fed. Cir. 2016). Applicant submits that the analysis in both Enfish and McRO takes place with the first step of the patent eligibility analysis set forth in the Alice Corp. v. CLS Bank Int'l. 573 lJ.S. 208 (2014) decision, which corresponds to the MPEP, Step 2A, Prong 1 analysis. Applicant submits that Enfish is not directed to Step 2A, Prong 2 and Step 2B additional element analysis, but instead performed before at Step 2A, Prong 1 to determine if there is an improvement related to the functioning of a computer or a technological field. At p. 12-14, Applicant summarizes the Enfish and McRO framework.
It is respectfully submitted that this is not persuasive. The claims are examined according to the framework and analysis set forth in MPEP 2106, which organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B and incorporates Enfish, McRO, and Alice. MPEP 2106.04(II) discusses that improvements were afforded by a “means for configuring” interpreted under 35 USC 112(f) that required a four-step algorithm and precluded the claims from reciting a judicial exception at Step 2A, Prong 1. However, the instant claims are not analogous to these considerations in Enfish because they do not recite any such limitations which preclude the claims from being interpreted as reciting a judicial exception at Step 2A, Prong 1, more similarly to the example of Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1147-49, 120 USPQ2d 1473, 1480-81 (Fed. Cir. 2016), where the courts interpreted the claims as encompassing nothing other than pure mental steps.
At p. 14-17, Applicant submits that the claims improve the field of identifying variants of proteins that have increased stability with respect to base proteins, as well as improving the functioning of a computing system that implements the claimed operations. Applicant points to various portions of the specification for support. Applicant submits that the computer functioning is improved because differences are only determined between coupled proteins, thereby minimizing processing and memory resources. Applicant submits that the state of the field, as disclosed in the specification, may require synthesizing and testing hundreds up to thousands of protein variants for improved stability, which can be obviated by using balanced data sets or the invention to couple proteins for statistical analysis as described in the instant invention. Applicant submits that the claim is directed to a specific process for producing the unbalanced dataset and analyzing said dataset.
It is respectfully submitted that this is not persuasive. As set forth above, the claims are examined according to the framework and analysis set forth in MPEP 2106. At Step 2A, Prong 1, the limitations of the claim are examined limitation by limitation to identify whether the claimed concept (the specific claim limitation(s) that recite an exception) aligns with at least one judicial exception (see MPEP 2106.04(I)) under the broadest reasonable interpretation of the claims as a whole (see MPEP 2106.04(II)). Contrary to Applicant’s assertions, the claims recite limitations which are merely mental processes which include observations, evaluations, and judgments of data, as well as limitations which encompass or require mathematical concepts. That the claims are performed using a computing system does not change the mental or mathematical nature of the limitations. Conversely, the performance of the limitations on the computing system do not affect the performance of the computing system as alleged by the Applicant.
Because the claims include limitations which recite judicial exceptions, the analysis proceeds to Step 2A, Prong 2, where the additional limitations of the claim are identified, and the claim as a whole is examined to determine whether the additional elements, either alone or in combination with the judicial exceptions, provide a practical application. The additional elements of the instant claims are only those limitations which either generate the data being analyzed in claims 1 and 17 or provide the generated data in claims 10 and 21, along with computer elements to perform the judicial exceptions. Data gathering limitations do not provide a practical application (see MPEP 2106.05(g)), and neither do instructions to apply the judicial exception to a computer environment (see MPEP 2106.05(f)). The improvement purported by Applicant is provided merely by the judicial exceptions and is therefore not an improvement which can provide a practical application at Step 2A, Prong 2, because judicial exceptions cannot apply themselves. It is further noted that the function of the computer is not altered by the performance of the judicial exceptions. That the judicial exceptions down select the amount of data required to be analyzed does not actually alter how the computer functions, it merely provides less data to the computer, similarly to selecting one type of content or function for a computer hardware to perform (Affinity Labs of Tex. v. DirecTV, LLC, 838 F.3d 1253, 1264, 120 USPQ2d 1201, 1208 (Fed. Cir. 2016)).
Further, “identifying” proteins having improved stability is not a technical field which can be improved, because identifying proteins is itself a judicial exception. Applicant’s arguments regarding the specific process for analyzing the data are similarly not convincing.
Regarding Applicant’s arguments of avoiding the synthesis of large numbers of proteins and improving screen methods, it is noted that Applicant’s arguments are not commensurate with the scope of the claims. The claims do not limit the number of proteins being physically expressed and analyzed. Additionally, claim 21 is a system claim and does not require the physical expression and analysis of any proteins. If Applicant intends for these arguments to be considered, then the claims must be amended to reflect these arguments.
At p. 17, par. 3 through p. 23, Applicant submits that the Office Action did not explain why the claim elements were categorized as mathematical concepts and mental steps and asserts that the limitations should not be categorized as judicial exceptions. Applicant submits that Examples 38-39 of “applying transformations to digital facial images or generating random numbers” should be considered because they are hypothetical examples only which are intended to be illustrative.
Regarding Applicant’s assertion that no reasoning for why the claim elements were considered to recite judicial exceptions was provided, Applicant is directed to the last paragraph of p. 11 and the first paragraph of p. 12 of the previous Office Action, which describe that the actions are considered to be able to be performed mentally or with pen and paper as an aid, and explains that determining a statistically significant effect is considered to require a mathematical concept as its only embodiment. Applicant has provided no reasoning for why a statistical effect does not require or encompass a mathematical concept, besides asserting that the limitation does not require math but is merely based on math. However, MPEP 2106.04(a)(2) notes that a mathematical concept need not be expressed in mathematical symbols, because “[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula”. Therefore, the claim explicitly recites a mathematical concept by reciting “determining… that the candidate substitution produces a statistically significant effect”, and does not merely rely on a mathematical concept. The concepts of determining subsets of data, performing comparisons between the data, and determining differences between data, as is encompassed by the limitations pointed to by Applicant, merely recite observations, evaluations, judgments, and opinions, which MPEP 2106.04(a)(2)(III) describes are mental processes.
Applicant submits that these actions could not practically be performed mentally because that one of ordinary skill in the art would recognize so, and provides an example where at least 10 or 30 or more proteins would be required in an unbalanced dataset to perform the claimed method, describing that as each protein includes hundreds to thousands of amino acids, a determination of the differences between the sequences would not reasonably be performed in the human mind. Such an argument is not convincing because the criteria for whether an action can be performed practically in the human mind is not the scale of the number or required actions, but the nature of the action itself. A human mind is perfectly capable of comparing data and identifying differences. That the claims encompass large comparisons of data does not negate the mental nature of those actions. It is further noted that the courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (See MPEP 2104(a)(2), III: e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674 (noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016) (holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper")). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind." Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015). See also Intellectual Ventures I LLC v. Symantec Corp., 838 F.3d 1307, 1318, 120 USPQ2d 1353, 1360 (Fed. Cir. 2016) (‘‘[W]ith the exception of generic computer-implemented steps, there is nothing in the claims themselves that foreclose them from being performed by a human, mentally or with pen and paper.’’); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016) (holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer"). If a claim recites a limitation that can practically be performed in the human mind, with or without the use of a physical aid such as pen and paper, the limitation falls within the mental processes grouping, and the claim recites an abstract idea. See, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674 (noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, 839 F.3d at 1139, 120 USPQ2d at 1474 (holding that claims to the mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). That the claims encompass a large number of comparisons does not change the mental nature of the limitations, but merely recites the application of a computer to carry out the judicial exception on a large number of sequences. It is further noted that the claims recite no limit on the number of protein sequences being compared, and Applicant’s arguments are therefore also not commensurate with the scope of the claims.
Regarding Examples 38-39, those examples are not considered to be analogous because the instant claims do not recite methods for applying transformations to digital facial images or generating random numbers as set forth in the previous Office Action. While those examples are considered to be hypothetical and illustrative, they are not analogous to the instant claims because the instant claims merely recite steps for the manipulation and analysis of data, whereas Examples 38-39 recite transformations of images or an actual generation of numerical data, and are specific examples outside the scope of purely numerical data analysis and actions which a human mind is incapable of performing. MPEP 2106.05(c) explicitly sets for that for data, mere “manipulation of basic mathematical constructs [i.e.,] the paradigmatic ‘abstract idea,’” has not been deemed a transformation (CyberSource v. Retail Decisions, 654 F.3d 1366, 1372 n.2, 99 USPQ2d 1690, 1695 n.2 (Fed. Cir. 2011) (quoting In re Warmerdam, 33 F.3d 1354, 1355, 1360, 31 USPQ2d 1754, 1755, 1759 (Fed. Cir. 1994))). By extension of the same logic, mental process manipulations of data also do not provide a transformation. Therefore no transformation exists in the instant claims, and they are not analogous to Examples 38-39.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached on (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/J.N.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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