By Adam S. Braegelman, Ph.D. Adam is a first-year law student at the Sandra Day O’Connor College of Law at Arizona State University. Currently, Adam serves as a Scholarship Fellow at the McCarthy Institute. Prior to law school, Adam earned his Ph.D. in Bioengineering at the University of Notre Dame and was a practicing patent agent for over two years.
On September 18, 2025, the United States Patent and Trademark Office (“USPTO”) welcomed its new director, Under Secretary of Commerce for Intellectual Property John A. Squires.[1] Since taking office, Director Squires has made the expansion of patent eligibility a central goal of his leadership.[2] 35 U.S.C. § 101 establishes patent eligibility for “any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof.”[3] However, several recent Supreme Court decisions have significantly narrowed patent eligibility in ways that lack clarity and predictability. Today’s patent eligibility framework is based primarily on Mayo Collaborative Servs. v. Prometheus Labs., Inc. (2012) and Alice Corp. v. CLS Bank Int’l. (2014).[4]
In Mayo, the U.S. Supreme Court analyzed the eligibility of patent claims directed to the use of thiopurine drugs to treat autoimmune diseases.[5] The claims comprised an “administering” step of dosing a patient, a “determining” step of measuring levels of metabolites in the patient’s blood, and “wherein” steps of informing whether the metabolite concentrations are too low such that the drug is rendered ineffective or too high such that harmful side effects may likely occur.[6] The Court held the patent claims invalid and unpatentable, concluding that the relationship between drug metabolite concentrations and the probability of ineffective treatment or harmful side effects is a law of nature, and the additional steps recited in the claims are merely instructions to apply that law of nature.[7] The Court held such despite the Constitution’s use of the word “discoveries” in setting forth patent subject matter and the fact that the Prometheus Laboratories researchers first discovered the relationship of drug toxicity/ineffectiveness based on measured metabolites.[8]
Then, in Alice, the U.S. Supreme Court focused on eligibility of patent claims directed to mitigating settlement risk (i.e., the risk that not all parties will pay their agreed upon obligation) by using a third-party intermediary.[9] Importantly, the claims required electronic implementation of intermediated settlement, which the Court held to be “a fundamental economic practice long prevalent in our system of commerce.”[10] The Court reasoned that requiring a generic computer to implement an otherwise abstract idea, such as intermediated settlement, is insufficient to transform that abstract idea into a patent-eligible claim.[11] Moreover, in a succinct concurring opinion, and joined by Justices Ginsburg and Breyer, Justice Sotomayor emphasized her adherence to the view that any “claim that merely describes a method of doing business does not qualify as a ‘process’ under §101.”[12]
Following these decisions, the USPTO updated its Manual of Patent Examining Procedure (“MPEP”) § 2106 with a flow chart summarizing the Alice/Mayo framework (alternatively, the Mayoor Alice test).[13] The Mayo test is a two-step, two-pronged approach.[14] Step 1 asks whether the patent claims statutory subject matter of “a process, machine, manufacture or composition of matter.” If not, the claim is invalid. If the claim recites statutory subject matter, the analysis continues to Step 2A, which asks: Is the claim directed to one or more of the judicially-created exclusions of laws of nature, natural phenomena (products of nature), or abstract ideas? If not, the claim is patent eligible and further assessment is conducted under, among others, 35 U.S.C. §§ 102, 103, and 112. If the claim is directed to one of the three exclusions, the analysis proceeds to Step 2B, which asks: Does the claim recite additional elements that amount to significantly more than the judicial exception? Step 2B is sometimes referred to as the “inventive step.” If not, the claim is invalid. If the claim recites significantly more than the judicial exception, then the claim passes § 101 eligibility and may be further examined.[15]
Director Squires has focused on Step 2A. Limiting the reach of Step 2A will permit broader patent eligibility for new technologies, or fields of technologies, previously excluded from patent eligibility.[16]
In particular, Director Squires emphasized a “return-to-basics” approach to patent eligibility, citing to broader interpretations of the past, summarized as “anything under the sun made by man.”[17] Director Squires also noted the Mayo and Alice decisions have been “widely misinterpreted” and “wielded as bludgeons to exclude entire classes of invention.”[18] Instead, according to Director Squires, “eligibility should turn on whether an invention integrates abstract ideas into something more – something inventive, practical, and transformative.”[19] Director Squires identified nascent fields of technology, including artificial intelligence (“AI”) and machine learning (“ML”), along with established fields, such as medical diagnostics, that face restricted (if not entirely prohibited) patent eligibility under the current framework. Director Squires has instructed patent examiners to look for concrete results and demonstrable improvements in technology, even if those improvements are not as tangible as previously required, such as reduced memory requirements or reduced computing time.[20]
The rationale for expanding patent eligibility is largely underpinned by concerns of “national security, economic growth, and global leadership,” wherein fields like AI, clean energy, and biotechnology are “at once a commercial opportunity and a national security imperative.”[21] Commercially, Director Squires emphasized that patent eligibility provides strong economic incentives in the development of new technologies, and the broad-stroke exclusion of fields like AI and ML as unpatentable algorithms hinders development of key technologies useful in building the US economy. He referred to the USPTO as “the Department of Commerce’s Central Bank of Innovation” where every new issued patent is a “potential job, a new business, a competitive advantage, or an investible asset” that contributes to strengthening the nation as a whole.[22] Regarding AI, he explained that “AI start-ups cannot secure the venture capital needed to compete against state-backed giants in China and elsewhere” and that eligibility “is the difference between an ecosystem of American innovators and a future where leadership in AI is ceded abroad.”[23]
Director Squires also highlighted national security: “Nations that dominate in emerging technologies wield not just economic power, but diplomatic and military leverage,” including important defense and counter-terrorism tools.[24] He posited that, in the wake of the September 11 attacks, “[p]atents became our shield and sword – tools to create, protect, attract capital and deploy technologies to monitor, track, and counter the financing of terrorism in real time.”[25] He also referenced his personal experience of patenting methods “to detect and deter illicit financial activities and suspicious transactions.” Partnering with the Federal Bureau of Investigation (“FBI”), Director Squires said he used patents, and the attendant innovations, as instruments of war, “operational tools” of counter-terrorism, and “our best weapon and inexhaustible resource.”[26] Director Squires concluded: “to say that such inventions should be ineligible for protection under our patent laws – is not only doctrinally wrong. It is cowardice.”[27]
Director Squires also demonstrated his focus on the patentability of fields such as AI, ML, and medical diagnostics prior to his Congressional testimony. Director Squires publicly signed two patents on the first day of his tenure.[28] The first, U.S. Patent No. 12,419,201, is directed to an antibody fragment. The independent claims are compositions of matter, while several dependent claims and the patent specification detail the antibody fragment’s use in methods of cancer diagnosis.[29] The claims appear well within the scope of patentability under the existing Alice/Mayo framework. However, granting this patent in the signing ceremony signals Director Squires’s interest in biotechnology innovation and the bolstering of diagnostic methods which were previously seen as excluded from patenting. The second, U.S. Patent No. 12,419,202, is directed to network architecture and distributed ledger technology, encompassing aspects of machine learning, artificial intelligence, blockchain protocols, and crypto technologies.[30] Previously, the label of “algorithm” in such inventions would be pointedly avoided, as such a label was often a death knell for similar technologies during patent examination.
Director Squires has also influenced examination procedures. The week after his confirmation, the USPTO issued a landmark decision in Ex parte Desjardins.[31] In a review mechanism known as the Appeals Review Panel (ARP), the Director may sua sponte order and personally participate in the review of a previous Patent Trial and Appeal Board (PTAB) decision. In Ex parte Desjardins, Director Squires drafted and issued a decision in which claims directed to “a computer-implemented method of training a machine learning model” were found patent eligible.[32] This is only the second ARP since the review mechanism was instituted in 2023.[33] In the decision, the Panel confined their discussion to Step 2A of the Alice/Mayo framework, which is itself a two-pronged inquiry.[34] The first prong asks whether the claim recites “an abstract idea, law of nature, or natural phenomenon?”[35] The second prong asks whether the claim recites “additional elements that integrate the judicial exception into a practical application?”[36] The Panel held that the Step 2A prongs must be analyzed sequentially, and that the Prong One analysis “requir[es] a claim to recite (i.e., set forth or describe) an abstract idea in Prong One before proceeding to the Prong Two inquiry” and “[i]f, at Prong Two, the claim as a whole is not directed to a judicial exception, the eligibility analysis is concluded” without proceeding to Step 2B.[37] Using this approach, the Panel found the computer-implemented method of training a machine learning model patentable, reasoning “that although independent claim 1 may recite an abstract idea, it is not directed to an abstract idea,” and “when considered as a whole, [claim 1] integrates an abstract idea into a practical application.”[38] (Contrast Ex parte Desjardins with Mayo, stating: “to transform an unpatentable law of nature into a patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words ‘apply it’” (emphasis in original).[39])
Beyond showcasing the USPTO Director’s willingness to be personally involved in such decisions, the Panel in Ex parte Desjardins signaled to examiners and the patent practitioner community their intent to proceed under an expanded interpretation of patent eligibility:
Under a charitable view, the overbroad reasoning of the original panel below is perhaps understandable given the confusing nature of existing § 101 jurisprudence, but troubling, because this case highlights what is at stake. Categorically excluding AI innovations from patent protection in the United States jeopardizes America’s leadership in this critical emerging technology. Yet, under the panel’s reasoning, many AI innovations are potentially unpatentable – even if they are adequately described and nonobvious – because the panel essentially equated any machine learning with an unpatentable “algorithm” and the remaining additional elements as “generic computer components,” without adequate explanation. Dec. 24. Examiners and panels should not evaluate claims at such a high level of generality.[40]
On November 4, 2025, the decision in Ex parte Desjardins was designated precedential.[41] In a memorandum to the Patent Examining Corps issued December 5, 2025, the Deputy Commissioner for Patents indicated that MPEP guidance on patentability has been updated to incorporate the Ex parte Desjardins decision.[42] The memorandum also asserted that the updates were “meant to be consistent with existing USPTO guidance.”[43] This language attempts to soften the introduction of this new interpretation of Step 2A and the resultant broadening of patent eligibility. This notably contrasts the tone of Director Squires’s statements and the ARP’s direction to examiners in their Ex parte Desjardins decision.[44]
Patent practitioners should take note of the evolving interpretation of Step 2A in the Alice/Mayo framework. Director Squires emphasized that “the proper statutory tools for limiting the scope of patents are §§ 102 (novelty), 103 (obviousness) and 112 (written description and enablement).”[45] It seems this broadened interpretation will functionally shift the statute governing patent eligibility from 35 U.S.C. § 101 (patentability) to 35 U.S.C. § 112 (written description and enablement). Rather than emphasizing the inventive concept of new inventions, particularly within the fields of AI, ML, and diagnostics, practitioners will need to draft claims with clear and significant practical improvements. It is likely that supporting data evincing such clear and significant improvements will take a more prominent role in examination within these fields of technology. (Again, however, contrast Statement by Director Squires with Mayo: “[we] decline the Government’s invitation to substitute §§ 102, 103, and 112 inquiries for the better established inquiry under § 101.”[46])
However, practitioners should keep in mind that the USPTO Director’s sphere of influence has its limitations. The Director may shift interpretations of examining procedures and significantly affect the granting of new patents, but he must also sway the perspective of the courts to codify the influence of his chosen interpretation.[47] The tension between the USPTO and federal courts regarding patentability was present long before Mr. Squires assumed his directorship.[48] For example, in the patent infringement suit Aviation Capital Partners, LLC v. SH Advisors, LLC, the U.S. District Court of the District of Delaware stated, regarding the examiner’s determination of patent eligibility, that “[d]espite having a practical application, the claims of the patent offer no new insights or improvements for implementing their abstract idea…I again give no weight to the conclusions of the PTO.”[49]
The Court of Appeals of the Federal Circuit (“CAFC”), which serves as the primary appellate court for U.S. patent jurisprudence, also appears unlikely to readily accept Director Squires’s reinterpretation of patent eligibility. The Ex parte Desjardins decision predominantly relies on Enfish, LLC v. Microsoft Corp., in which the CAFC held that “[s]oftware can make non-abstract improvements to computer technology, just as hardware improvements can,” and that patent eligibility inquiries should ask “whether the claims are directed to an improvement to computer functionality versus being directed to an abstract idea.”[50] More recently, however, the CAFC held in Recentive Analytics, Inc. v. Fox Corp. that “patents that do no more than claim the application of generic machine learning to new data environments, without disclosing improvements to the machine learning model to be applied, are patent ineligible under § 101.”[51] This rationale was extended in Longitude Licensing Ltd. v. Google LLC, in which the CAFC held that claims directed to “using data to identify an image’s subject and modifying image data based on that subject” are ineligible, as the claims “functionally describe[] a mere concept without disclosing how to implement that concept.”[52] Director Squires’s increased reliance on § 112 (written description and enablement) does not directly oppose the patentability requirements indicated by the CAFC, but whether the CAFC will accept the merging of § 101 with § 112, and to what extent the courts will further amend the boundaries of patentability, is yet to be determined.
Current guidance about the boundaries of patent eligibility provides a complex mosaic for inventors and patent practitioners. Director Squires seeks to simplify complex patentability analyses that have been built-up piecemeal by decades of case law and judicial interpretations. The interpretation of patent eligibility put forward by Director Squires acts to broaden the fields of technology eligible for patent protection, including artificial intelligence, machine learning, and medical diagnostics. For now, this approach will likely shift the primary filter of patentability from § 101 to § 112, and thus require applicants to show clear and significant improvements beyond existing technology in an era where innovation is becoming more intangible.
[1] John A. Squires, United States Patent & Trademark Office, https://www.uspto.gov/about-us/john-squires (last updated Sept. 23, 2025).
[2] Statement by Director Squires before the United States Senate Subcommittee on Intellectual Property Committee on the Judiciary, United States Patent & Trademark Office (Oct. 10, 2025), https://www.uspto.gov/about-us/news-updates/statement-director-squires-united-states-senate-subcommittee-intellectual (last accessed February 1, 2025).
[3] 35 U.S.C. § 101 (West, Westlaw through Pub. L. No. 119-59).
[4] Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66 (2012); Alice Corp. v. CLS Bank Int’l, 573 U.S. 208 (2014).
[5] Mayo, 566 U.S. at 72.
[6] Id. at 74-75.
[7] Id. at 79-80.
[8] Id. at 75-76; U.S. Const. art. I, § 8.
[9] Alice, 573 U.S. at 212.
[10] Id. at 219.
[11] Id. at 225-26.
[12] Id. at 227.
[13] MPEP § 2106 (9th ed. Nov. 2024).
[14] Id.
[15] Id.
[16] Statement by Director Squires before the United States Senate Subcommittee on Intellectual Property Committee on the Judiciary, supra note 2.
[17] Id. (referencing Diamond v. Chakrabarty, 447 U.S. 303, 309 (1980)).
[18] Id.
[19] Id.
[20] Id.
[21] Id.
[22] Id.
[23] Id.
[24] Id.
[25] Id.
[26] Id.
[27] Id.
[28] Patent Signing Ceremony, United States Patent & Trademark Office (Sept. 24, 2025), https://www.uspto.gov/about-us/news-updates/patent-signing-ceremony.
[29] U.S. Patent No. 12,419,201.
[30] U.S. Patent No. 12,419,202.
[31] Ex parte Desjardins, No. 2024-000567, 2025 WL 3095778 (P.T.A.B. Sept. 26, 2025).
[32] Id.; U.S. Patent Application No. 16/319,040.
[33] Martin Gomez, et al., Watch Out Section 101, the USPTO Has a New Sheriff in Town, Goodwin (Oct. 17, 2025), https://www.goodwinlaw.com/en/insights/publications/2025/10/alerts-lifesciences-ip-watch-out-section-101-the-uspto.
[34] Ex parte Desjardins at 3; MPEP § 2106.04(II)(A) (9th ed. Nov. 2024).
[35] MPEP § 2106.04(II)(A)(1) (9th ed. Nov. 2024).
[36] MPEP §2106.04(II)(A)(2) (9th ed. Nov. 2024).
[37] Ex parte Desjardins at 3.
[38] Ex parte Desjardins at 5.
[39] Mayo, 566 U.S. at 72.
[40] Ex parte Desjardins at 5.
[41] Charles Kim, Advance notice of change to the MPEP in light of Ex Parte Desjardins, United States Patent & Trademark Office (Dec. 5, 2025): https://www.uspto.gov/sites/default/files/documents/memo-desjardins.pdf.
[42] Id.
[43] Id.
[44] Statement by Director Squires before the United States Senate Subcommittee on Intellectual Property Committee on the Judiciary, supra note 2.; Ex parte Desjardinsat 5.
[45] Statement by Director Squires before the United States Senate Subcommittee on Intellectual Property Committee on the Judiciary, supra note 2.
[46] Mayo, 566 U.S. at 91.
[47]Supra note 32.
[48] Jack T. Carroll, et al., Alice Patent Eligibility Analysis Divergence Before USPTO and District Court, Foley (Sept. 10, 2024), https://www.foley.com/insights/publications/2024/09/alice-patent-eligibility-analysis-divergance-before-uspto-and-district-court/.
[49] Aviation Capital Partners, LLC v. SH Advisors, LLC, No. 22-1556-RGA, 2023 WL 5333187 (D. Del. Aug. 18, 2023) at 5.
[50] Ex parte Desjardins at 4; Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1335 (Fed. Cir. 2016).
[51] Recentive Analytics, Inc. v. Fox Corp., 134 F.4th 1205, 1216 (Fed. Cir. 2025).
[52] Longitude Licensing Ltd. v. Google LLC, No. 2024-1202, 2025 WL 1249136 (Fed. Cir. Apr. 30, 2025) at 3, 5.