A Myriad of Natural Product Claims May Be Toast, With Extra Mayo: The USPTO issues new Examiner Guidance documents expanding the scope of patent-ineligibility

On March 4, 2014, the USPTO issued a document entitled “Guidance For Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products” (“Guidance”). The new Guidance document can be found here. The accompanying “Quick Reference Sheet” can be found here.

This document expressly supersedes the June 13, 2013 memorandum to the Examining Corps, to some extent, subsumes and amplifies on the interim guidance for examination of process claims involving “laws of nature” provided in the July 3, 2012 memorandum in view of the Supreme Court decision in Mayo Collaborative Services v. Prometheus Laboratories Inc. The new Guidance document does not change the examination procedures regarding claims reciting an “abstract idea” set forth in the 2012 guidance, because the Supreme Court is scheduled to hear Alice v. CLS Bank in 2014, a case involving the abstract idea judicial exception, which may settle some current ambiguity.

The Guidance document presents three questions to be asked after establishing the broadest reasonable interpretation of the claim, as set forth in the following flow chart:

Question 1: Statutory Category?
This is the usual analysis (nothing new).

Question 2: Judicial Exception Recited (e.g., Natural Product)?
In additional to the longstanding “laws of nature/natural principles and natural phenomena” judicial exceptions to patent-eligible subject matter under 35 USC 101, the Guidance document now expressly clarifies that the USPTO is interpreting the holding of Myriad to apply to “subject matter eligibility determinations of all claims … reciting or involving … natural products” (underlined emphasis in the original, and bold emphasis added), and not just examining claims to DNA sequences. “Natural products” are defined as including, but not limited to:


… chemicals derived from natural sources (e.g., antibiotics, fats, oils, petroleum derivatives, resins, toxins, etc.); foods (e.g., fruits, grains, meats and vegetables); metals and metallic compounds that exist in naturemineralsnatural materials (e.g., rocks, sands, soils); nucleic acidsorganisms (e.g., bacteria, plants and multicellular animals); proteins and peptides; and other substances found in or derived from nature.


The Examples make it expressly clear that purified natural products per se are patent-ineligible, without moreThis applies, for example, to claims of the familiar form “An isolated (or purified) [natural product X].” If the claim is determined to be directed to a natural product, a further question must be asked to determine whether the claim recites a significant difference from the natural product.

Question 3: Significantly/Markedly Different? There is very little guidance provided in the Guidance document regarding what is meant by “significantly different” or “markedly different” in the natural product judicial exception:


A significant difference can be shown in multiple ways, such as: (1) the claim includes elements or steps in addition to the judicial exception that practically apply the judicial exception in a significant way, e.g., by adding significantly more to the judicial exception; and/or (2) the claim includes features or steps that demonstrate that the claimed subject matter is markedly different from what exists in nature (and thus [is] not a judicial exception).


What constitutes a “significant difference” (or “markedly different” as the above statement essentially tautologically defines a “significant difference”) is not further defined. However, the USPTO takes the position that eligibility requires more than the “hand of man”, and that to be eligible, the claimed product must be both non-naturally occurring and markedly different from naturally occurring products. What is of interest to note is that the “markedly different” concept comes not just from Myriad but by reaching back to Chakrabarty:


Myriad relied on Chakrabarty as “central” to the eligibility inquiry, and re-affirmed the Office’s reliance on Chakrabarty’s criterion for eligibility of natural products (i.e., whether the claimed product is a non-naturally occurring product of human ingenuity that is markedly different from naturally occurring products). Id. at 2116-17. Myriad also clarified that not every change to a product will result in a marked difference, and that the mere recitation of particular words (e.g., “isolated”) in the claims does not automatically confer eligibility. Id. at 2119. See also Mayo, 132 S. Ct. at 1294 (eligibility does not “depend simply on the draftsman’s art”). Thus, while the holding in Myriad was limited to nucleic acids, Myriad is a reminder that claims reciting or involving natural products should be examined for a marked difference under Chakrabarty.


However, Chakrabarty did not define what “markedly different” means, but only used the term to distinguish the invention in contrast to the patent-ineligible combination of bacterial cultures in Funk:


Judged in this light, respondent’s micro-organism plainly qualifies as patentable subject matter. His claim is not to a hitherto unknown natural phenomenon, but to a nonnaturally occurring manufacture or composition of matter – a product of human ingenuity “having a distinctive name, character [and] [447 U.S. 303, 310] use.” Hartranft v. Wiegmann, 121 U.S. 609, 615 (1887). The point is underscored dramatically by comparison of the invention here with that in Funk. There, the patentee had discovered that there existed in nature certain species of root-nodule bacteria which did not exert a mutually inhibitive effect on each other. He used that discovery to produce a mixed culture capable of inoculating the seeds of leguminous plants. Concluding that the patentee had discovered “only some of the handiwork of nature,” the Court ruled the product nonpatentable:

“Each of the species of root-nodule bacteria contained in the package infects the same group of leguminous plants which it always infected. No species acquires a different use. The combination of species produces no new bacteria, no change in the six species of bacteria, and no enlargement of the range of their utility. Each species has the same effect it always had. The bacteria perform in their natural way. Their use in combination does not improve in any way their natural functioning. They serve the ends nature originally provided and act quite independently of any effort of the patentee.” 333 U.S., at 131.

Here, by contrast, the patentee has produced a new bacterium with markedly different characteristics from any found in nature and one having the potential for significant utility. His discovery is not nature’s handiwork, but his own; accordingly it is patentable subject matter under 101. [emphasis added]


This description of the phrase “markedly different characteristics” does not help the USPTO to establish a bright line that distinguishes what the term means. Therefore, the USPTO provides a list of factors weighing towards eligibility (significantly different) and factors weighing against eligibility, and Examples A-H, which attempt to apply those factors and explain what they mean.

The Guidelines state that a significant difference can be shown in multiple ways, such as: (1) the claim includes elements or steps in addition to the judicial exception that practically apply the judicial exception in a significant way, e.g., by adding significantly more to the judicial exception; and/or (2) the claim includes features or steps that demonstrate that the claimed subject matter is markedly different from what exists in nature (and thus not a judicial exception). The memo then lists a dozen factors, six that weigh toward eligibility and six that weigh against eligibility:


For Question (3)
Factors that weigh towards
eligibility (claim does recite something significantly different)
Factors that weigh against
eligibility (claim does not recite something significantly different)
1. Product claim that initially appears to be a natural product, but after analysis is determined to be non-naturally occurring and markedly different in structure from something naturally-occurring. 1. Product claim recites something that appears to be a natural product and has a structure that reflects that.
2. Claim recites elements/steps that impose meaningful limits on claim scope beyond the judicial exceptions. (Claim is narrow enough so that others are not precluded from using idea entirely). 2. Claim recites elements/steps that impose meaningful limits on claim scope beyond the judicial exceptions, but are too generalized and overly broad.
3. Claim recites elements/steps in beyond the judicial exceptions that are more than nominally related to what is being claimed. 3. Claim recites elements/steps in addition to the idea/objecting being claimed that must be used or taken by others to be applied.
4. Claim recites elements/steps that are more than just general instructions to apply or use the idea/object being claimed. 4. Claim recites elements/steps that are well-understood and conventional.
5. Claim recites elements/steps that include a particular machine or perform a transformation of a particular article. 5. Claim recites elements/steps in addition to the idea/object being claimed, but add no meaningful limiting steps.
6. Claim recites one or more elements/steps in addition to the idea/object being claimed that add a feature that is well-understood and conventional. 6. Claim recites elements/steps that amount to nothing more than a mere field of use.


Examples A-H:


  1. A naturally occurring plasmid is not patent-eligible, nor is a naturally occurring bacteria; however, a bacteria which does not naturally contain the plasmid but is engineered to contain it is patent-eligible. (Chakrabarty)
  2. A purified naturally occurring compound is not patent-eligible, but a methylated version which creates a functional difference is patent-eligible. A functional difference is not per se necessary, but makes it more likely that a small structural difference will be deemed a significant difference. Also the guidelines suggest – without explaining in detail – that narrowing limitations may be necessary in order to convert method claims using patent-ineligible natural products into patent-eligible claims.
  3. A firework comprising a combination of naturally occurring compounds in a cardboard tube with an ignition source is patent-eligible because the compounds form a structure that is “physically integrated” and does not foreclose others “from using the natural products in other ways.”
  4. A combination of naturally occurring bacteria that have not been changed is patent-ineligible. (Funk)
  5. A pair of DNA primers are patent-ineligible, because “the first and second primers have the same function as their natural counterpart DNA, i.e., to hybridize to their complementary nucleotide sequences,” while the method of using them to amplify DNA, comprising specific steps of combining with Taq polymerase and thermal cycling is patent eligible, because the natural products can be used in other methods.
  6. A method for determining whether a patient has disease X, by using a novel antibody that does not exist in nature in an immunoassay is patent eligible.
  7. Three method claims for treating a mood disorder with light; the first uses natural light and is patent-ineligible; the second uses a synthetic light source, but is still patent ineligible because “the step of exposing a patient to synthetic white light for the purpose of affecting a mood disorder is just an attempt to limit the use of the natural principle to a particular technological environment (use of artificial light as opposed to sunlight)”; while the third method, which specifies with more particularity specific wavelengths of light (UV) and not others (white light), and the positioning of the patient, is deemed patent eligible.
  8. This example recites in essence the method claim from Myriad for identifying a mutant of the BRCA2 gene, which was found patent-ineligible, because it recites an abstract idea, and is to be “analyzed under the existing guidance in MPEP § 2106(II).”

Unfortunately, these Examples leave much to be desired in the way of clarity for Applicants, especially for the types of claims that they will be using to work around these expanded definitions of patent-ineligible subject matter. On March 19, 2014, the USPTO published a slide presentation which comprise the training materials used to provide further guidance to the Examiners for applying the new Guidelines, which lays out the step-by-step process that the USPTO will use to evaluate claims for compliance with these new patent-eligibility guidelines.

What is the immediate effect of these new examination guidelines?

There is no effect on issued patents. The examination guidelines have no force or effect on granted patents. Under pre-AIA law, neither ex parte nor inter partes reexamination can be granted on the basis that the patent claims patent-ineligible subject matter. A patentee might consider having his patent reissued, but it would likely be premature to do so, and certainly could put their claims at risk. Unless the patentee is already in litigation, and does not have any claims which are clearly and distinctly directed to patent-eligible subject matter, it is presumed that this procedure is unlikely to be used by many patentees. There are essentially no post-AIA patents yet which might be subject to the applicable Post-Grant Review procedures. While parties in litigation opposing patents on natural products might be able to use the legal arguments in the Guidelines, based on the underlying cases such as Myriad and Chakrabarty, the Guidelines themselves are in no way binding on the courts.

Obviously, applications currently in prosecution are being examined under the Guidelines. In fact, we have seen them applied in rejections that have already been received that were dated prior to the issuance of the Guidelines.

Will these Guidelines be challenged, and if so, how?

There was some initial suggestions in the patent bar that the Guidelines were issued improvidently, as they should have been an opportunity for public comment under the Administrative Procedures Act, for failing to allow public comment on these substantive changes in patent examination, as was done for earlier changes, e.g., in accordance with the implementation of the decisions in KSR v. Teleflex, In re Bilski, and the changes to examination guidelines for determining compliance with 35 U.S.C. 112. However, so far, we are not aware of any such challenge being launched.

A more likely possibility is through these arguments being presented during current litigation, and working their way through appeals to the Supreme Court. It is noted that under these guidelines, claims covering many commercial products currently on the market would not have been granted, and competitors and licensees may be emboldened to infringe or repudiate their licenses. This could conceivably happen before or concomitant with challenges arising from rejections at the USPTO rising through the Patent Trial and Appeals Board, through the CAFC and then to the Supreme Court.

Yet another possibility, theoretically faster, but less likely, is that businesses, professional organizations such as AIPLA and IPO, and/or trade associations such as BIO and PHARMA could reach out to legislators to inform them of the serious consequences of this overly broad expansion of the already troubling Supreme Court decisions in Mayo and Myriad.

How can Applicants overcome/avoid the broadened exclusions of patent eligibility of these Guidelines?

These issues have already been extensively discussed by many patent practitioners, legal scholars, business people and other parties having an interest in the situation since both cases were decided, and long before these Guidelines were published, and in the practical application of at least the initial versions of the interim Guidelines for both Mayo and Myriad to diagnostic, screening and DNA claims. Clearly, in most cases, there are workarounds to the Guidelines available to protect commercial aspects of our clients’ inventions. Of course, the ease of applying these workarounds depends on how presciently the applications were written prior to these decisions being published, and whether there is written description to support claims which exclude the now patent-ineligible subject matter. Thus, for example, DNA sequences can be claimed as being operably linked to a heterologous promoter, or within a heterologous cell. Therapeutic proteins can be claimed as having non-naturally occurring glycosylation, or in sterile pharmaceutical compositions, as can other naturally occurring therapeutic molecules, which distinguish them from their natural form.

However, it is troubling that even these simple and obvious types of workaround claims, which were logically commercially relevant forms for enormously important therapeutic inventions that could and should have been more clearly addressed by the USPTO in these Guidelines, were not. Diagnostic-type claims have been similarly if not more difficult to address, with the guidance being provided by the USPTO often being to amend the claims to commercially irrelevant forms, such as including a step of treating the patient after the clinical laboratory-performed diagnostic tests, which make the claim unenforceable because they cannot be infringed by a single party. New applications of existing assays for different diagnoses, prognoses or theranostics assays, as well as screening assays may be similarly precluded, at least without much more limitations to the claim, as the recitation in Example F that the assay and reagents used were new suggest.

In fact, rather than positively addressing what the Supreme Court characterized with disapproval in Mayo as “interpreting patent statutes in ways that make patent eligibility ‘depend simply on the draftsman’s art’ without reference to the ‘principles underlying the prohibition against patents for [natural laws],'” these new Guidelines appear to encourage that kind of strained interpretations and exercise of “draftsman’s art” of claim drafting to create convoluted claims that attempt to cover a reasonable scope of protection for Applicant’s inventions, while avoiding the quicksand of the growing number of (often post-hoc) judicially created exceptions.

While these Guidelines are being implemented and we become familiar with how they will be applied in practice, as well as while the cases challenging them and/or their underlying principles wind their way through the courts and/or legislature, we will carefully follow these events, and provide practical advice to our clients for avoiding these problems to the extent possible, as well as maintaining the flexibility to protect their inventions a broadly as possible as the patent landscape continues to change and evolve.


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