Patent Docs

Lunch with Commissioner Doll

    By Kevin E. Noonan --

John Doll, Commissioner for Patents of the U.S. Patent and Trademark Office, gave a luncheon seminar today concerning the state of the USPTO, hosted by the Boston office of Kirkpatrick & Lockhart Preston Gates Ellis LLP.  As we've said before, Commissioner Doll (at right) is the happy face of the U.S. Patent and Trademark Office:  smiling, self-deprecating, and charming while he espouses the Patent Office mantra that the Office is willing to do everything possible to improve the patenting process in the United States.  Today's offering was no different.

The Commissioner touted a number of programs and policies in the Office intended to address the twin goals of reducing the backlog of unexamined applications and improving the quality of granted patents.  The first initiative Commissioner Doll mentioned was the accelerated examination (AE) program, which he considers an unqualified success.  The statistics he cited bear him out:  110 patents have been granted under the program, and the goal of filing to final disposition (abandonment, grant, or exit from the program for appeal or further prosecution) within a year has "never" been missed.  One unnamed patent was particularly speedy:  allowed within 17 days of filing and granted 58 days thereafter (75 days filing to grant).  Use of the program is accelerating, with 200 applications filed requesting AE in the past month.  Commissioner Doll confessed that his intuition about what would be the most important component of the program - the Examination Support Document, in which the results and detailed analysis of an applicant-performed search are submitted to the Office - was wrong; both applicants/practitioners and Examiners report that it is the interview that makes the greatest difference.

This result has led to a second program initiative, the "interview before first action" program (see "PTO Announces New Program to Reduce Pendency and Improve Patent Quality").  After the Examiner has performed a search, participants can have an interview to discuss the art.  Thereafter, the expectation is that the Examiner will be able to mail an allowance or a first action on the merits, which will be (presumably) the parts of the interview where the examiner and applicant could not reach agreement.  Such interviews have been available for many years.  (For many law firms, one of the purported advantages of a Washington, D.C. office in the old, cooperative days of the Patent Office was the ability to walk down the street and meet with an examiner to discuss an application prior to first action.  This practice was discouraged over the past few years, since it resulted in many instances with a first action allowance and a patent having essentially no prosecution file history.)  The pilot program is limited for now to the computer database arts; the Commissioner referred the curious to the PTO website for more information (alternatively, the curious could refer to the Patent Docs post on this pilot program).

The Commissioner announced a major initiative to bring the Office into compliance with its responsibilities under the Patent Cooperation Treaty, specifically with regard to its status as an International Searching Authority.  The Office currently complies with the time limits for providing a Chapter I search about 4% of the time.  There are currently 17,000 PCT applications unacted upon (i.e., no search has been performed).  The goal is to have these applications searched by the end of the calendar year, and to bring the Office into 80-90% compliance as soon as possible.  While admirable, the way this is being done may be problematic:  the Office has outsourced searching to two professional search firms for the 17,000 "backlogged" PCT applications, and intends to outsource 100% of PCT searching.  While not controversial in and of itself, it seems that these searchers will also be responsible for determining (and denoting on International Search Reports) whether a reference is novelty-destroying (an "X" reference) or precludes inventive step (a "Y" reference) according to the provisions of PCT Article 33.  This raises the question of whether these searchers are competent to make these determinations, and whether the Office has abandoned its responsibility to provide a proper PCT search.  Ironically, the Commissioner also stated that he thought such searches should be "fee neutral" to the Office - raising the possibility that applicants would be charged additional fees under the PCT for searches that may not be PCT-compliant.

Commissioner Doll next addressed the issue of examiner hiring efforts.  The Office has hired 1,200 new examiners each year for the past few years and will be doing so for the next few years, and these efforts will have swollen the examiner ranks to about 6,000 at the end of FY2008; this number is expected to reach 8,000 by the end of FY2010.  Since attrition has been a problem (in the "two steps forward, one step back" sense) with the examiner corps, the Commissioner was happy to say that overall attrition rates are at 8.5%, a number he compared favorably both with Federal government employees overall (11.2%) and employees at high-tech industries.  It also seems that the likelihood of becoming a Patent Office "lifer" goes up dramatically after these first three years; while the attrition rate for "new" examiners (those with less than 3 years on the job) was 15.5%, the attrition rate for years 4 through 30 is only 4%.  To increase the likelihood that examiners stay long enough for these statistics to apply, the Office has instituted a number of financial and lifestyle incentives.  Retention bonuses are the most naked form of gentle coercion (he did not specify the amount of these bonuses); in addition, the Office has instituted overtime and quality bonuses (the latter subject to negotiation with POPA).  There are also programs for "flat goal" work, where the examiner can commit to a certain production level (with, presumably, adjustments in salary for performance below the standard requirements); the Office will pay bonuses of up to $20,000 plus 3% of their base pay for those examiners exceeding the goal.  On the lifestyle side, the Office has a "hoteling" program, where examiners can work remotely.  An impediment to greater use of this program is the requirement (under Federal law) that employees must "report to their station" once a month.  The Commissioner mentioned a bill pending in Congress (S. 1000) that would loosen that requirement.  Finally in this regard, giving laptops to examiners having GS9 seniority or greater has almost doubled the amount of overtime these examiners work.  All of these initiatives are directed, according to Commissioner Doll, to effecting a reduction in the backlog.  Interestingly, another aspect of the Office's focus on the backlog is that the Office is targeting its examiner hiring to those art units most in need of backlog reduction.

A program that the Commissioner ascribes to Director Jon Dudas (who is "aggressively pursuing it") is a "worksharing" program, that is an offshoot of the Patent Prosecution Highway programs currently in place with the Japanese Patent Office and other offices, and soon to be established with the EPO.  The Commissioner drew a distinction between the programs, however, saying that the PPH program was "applicant-initiated" while the proposed worksharing program would be Office-initiated.  Under the PPH, an applicant having an examination in one office can have the results transmitted to a second PPH office, to expedite prosecution in the second office based on (successful) prosecution in the first office.  The worksharing program would also permit examination results to be transmitted between offices, although it can be expected that the offices will not have the applicant's incentive to transmit only positive prosecution results.  Commissioner Doll was particularly hopeful about the economies of scale that could be achieved by having available to the U.S. Office results of a Japanese Patent Office search of Japanese patents and applications (which are rarely a major part of the prior art considered during U.S. prosecution), and envisioned a "common" prior art database that could be used by all offices.  An amusing aspect of this program is the establishment of a PTO "Facebook" so examiners at the different offices can "get to know one another."  The worksharing idea will be further discussed in a meeting between the "Big 5" offices (the USPTO, EPO, JPO, Korean Patent Office and Chinese Patent Office) chaired by Deputy Director of the USPTO Margaret Peterlin, to be followed by a Director level meeting in several months.  Importantly, at least as currently proposed there are no "full faith and credit" provisions for one office to another.

The last part of Commissioner Doll's prepared remarks was a brief encomium to the EFS-Web electronic filing system, which has increased users from 2% to 70% over the past two years.  Calling those not using the program "technology dinosaurs," he offered to do whatever it takes to help those to get with the program.

Commissioner Doll's comments during the Q&A session were not particularly remarkable, except insofar as he stated that the now-enjoined new continuation and claims rules were never viewed as a "silver bullet" for solving the backlog problem.  He reported that the rate of increase in the backlog had slowed (to about 40,000 applications for FY2008), and suggested that the Office had not "given up" on the other pending rules packages (Markush, IDSs, biological deposits) that have been subject to public comment.  He strongly supported provisions of pending legislation that would give the Office fee-setting authority, and hinted that if they got it they would use it to establish disincentives to current continuation practice.  He repeated the Office policy that the "best" application was one where the applicant presented the "best" claims upon initial filing and came to an ultimate resolution in that case, and said the best way for that to happen would be if the Office could impose the Applicant Quality Statement obligation contained in S. 1145.  Using his "crystal ball," he predicted that the growth rate of new filings would be about 5% in FY2008 and at the same level over the next few years.  He characterized this as "healthy," saying that the variances in application filing rates of the last 20 years average about 6.5%, with some years being as high as 25% and others close to zero.  He opined that the Supreme Court's KSR decision might influence filing rates, and defended how the examining corps was applying PTO guidelines on implementing the KSR decision.  He also asserted that the Office had trained "every" examiner on the new guidelines.

With regard to patent reform legislation, Commissioner Doll said Deputy Director Peterlin and USPTO General Counsel John Toupin (at right) were on the Hill "almost daily" working for the legislation, and said the AQS provision was on his "wish list" as the single change that would improve patent quality.  He cautioned against "dumping" too much irrelevant material on the Office in the guise of an IDS, and used two examples.  One was the prosecution history of related applications, where merely filing the entire file history was disfavored.  Also a Patent Office no-no would be filing "boxes and boxes" of material from litigation (seemingly unaware that generating boxes and boxes of material is what happens in patent litigation).  He was similarly unconcerned about the risks of inequitable conduct allegations even for practitioners diligently attempting to comply with Rule 56, and backed Harry Moatz's interpretation of 37 C.F.R. § 10.19 that a practitioner is required to review every page of every reference submitted to the Office.

There was one note of disingenuousness in Commissioner Doll's responses.  He was asked whether a Quality Review official could overrule an examiner.  He said the quality reviewer merely provided a recommendation, because the statute gives primary examiners the authority to decide whether to allow a case, and a Supervisory Examiner (SPE) or even the Commissioner did not have the power to overrule them.  This could be the basis for an important practice tip, except that in the next breath he said that where there was a genuine disagreement with a primary examiner, the examiner could either withdraw the notice of allowability or the SPE would transfer the case.  Even though he said this occurs very rarely (twice in his 33 years, and he was decent enough to admit that in one case the applicant appealed and the Board sided with the applicant), it is perhaps an illustration of his limitations as Commissioner that he obviously didn't see how he had enunciated a distinction without a difference (i.e., that supervisory personnel exercise de facto veto power over the primary examiners).

Not surprisingly (but a little disappointingly), Commissioner Doll is not a big fan of blogs.  While he later backed off his original characterization of bloggers as people without enough to do, in fairness the question was asked with regard to websites that "rate" examiners.  Although understandable in thinking that it was more likely to contain brickbats than kudos, he has obviously not read one lately; there are a surprising number of bouquets among the criticisms, perhaps reflecting real differences between different examiners (which is something you'd think he would want to know).

Commissioner Doll said he valued the kind of face-to-face discussions like today's meeting to discuss how to improve the patenting system.  While that is certainly true, his ardor cannot hide the fact that the actions of the Patent Office over the past few years suggests to many that no one is listening to the patenting community.

An Analysis of the New Written Description Training Materials – Antisense

    By Christopher P. Singer --

Last month, the U.S. Patent and Trademark Office announced that it had updated the training materials to be used by examiners in the examination of patent applications for compliance with the written description requirement of 35 U.S.C. § 112, first paragraph.  The revised training materials supersede and replace the previous set of training materials issued by the Patent Office in 1999.  The new training materials provide seventeen examples, of which fourteen are specifically related to biotech inventions.  In particular, the biotech-specific examples address expressed sequence tags (ESTs) (example 4), a partial protein structure (example 5), DNA hybridization (example 6), allelic variants (example 7), bioinformatics (example 8), protein variants (example 9), a product claimed by its function (example 10), a polynucleotide or polypeptide sequence sharing percent identity with another sequence (example 11), antisense oligonucleotides (example 12), antibodies to a single protein (example 13), antibodies to a genus of proteins (example 14), a genus with widely varying species (example 15), a process claim where novelty resides in the process steps (example 16), and methods of using compounds claimed by functional limitations, methods of identifying compounds, and compounds identified by such methods (example 17). Continuing our review, Patent Docs provides an overview of the example covering aspects of antisense oligonucleotides.

Example 12 – Antisense Oligonucleotides

Example 12 relates to claims directed to an antisense oligonucleotide complementary to an mRNA that encodes a "newly discovered growth factor" (NDG).  This Example is essentially identical to the guidance in the former written description guidelines (presented therein as Example 15).  The exemplary claim in the new training materials recites:

Claim 1:  An antisense oligonucleotide complementary to all or a portion of a messenger RNA having SEQ ID NO: 1 and encoding NDG, wherein said antisense oligonucleotide inhibits the production of NDG.

The hypothetical specification provides the mRNA sequence encoding NDG as SEQ ID NO: 1 and states that the invention includes antisense oligonucleotides that inhibit NDG production.  While no sequences of such antisense oligonucleotide are provided in the specification, it does describe several art-recognized screening methods for identifying target mRNA sequences for candidate antisense molecules (e.g., gene walking, randomized oligo libraries, and DNA arrays).  The specification also describes the use of chemically modified nucleotides that reduce the amount or rate of degradation by nucleases.  While the specification fails to provide any explicit example of an antisense oligonucleotide to SEQ ID NO: 1, the training materials reason that one of skill would understand that complementary sequences that approach the full length of an mRNA (such as SEQ ID NO: 1) are more likely to have antisense activity as compared to smaller sequence fragments.  Therefore, one of skill would acknowledge that the specification does provide one species of the claimed genus, that being the full-length complement to SEQ ID NO: 1.  Moreover, the structure of all possible antisense oligonucleotides falling within the scope of the claim are bound and limited by the full-length complement to SEQ ID NO: 1.  Given the art-recognized correlations between antisense function and structure of the target mRNA (e.g., as provided by certain computer mRNA modeling software packages), certain fragments having antisense activity can be identified and screened to confirm or assess inhibitory activity.  Thus, when the high level of skill and knowledge in the art relating to antisense technology is combined with the disclosure of an mRNA sequence (SEQ ID NO: 1), there exists sufficient written description support for the full scope of claim 1.

For additional information on this topic, please see:

• "Antibodies to a Single Protein & Antibodies to a Genus of Proteins," May 12, 2008
• "ESTs & Partial Protein Structures," May 8, 2008
• "DNA Hybridization & Percent Identity," May 6, 2008

An Analysis of the New Written Description Training Materials – Antibodies to a Single Protein & Antibodies to a Genus of Proteins

    By Christopher P. Singer --

Last month, the U.S. Patent and Trademark Office announced that it had updated the training materials to be used by examiners in the examination of patent applications for compliance with the written description requirement of 35 U.S.C. § 112, first paragraph.  The revised training materials supersede and replace the previous set of training materials issued by the Patent Office in 1999.  The new training materials provide seventeen examples, of which fourteen are specifically related to biotech inventions.  In particular, the biotech-specific examples address expressed sequence tags (ESTs) (example 4), a partial protein structure (example 5), DNA hybridization (example 6), allelic variants (example 7), bioinformatics (example 8), protein variants (example 9), a product claimed by its function (example 10), a polynucleotide or polypeptide sequence sharing percent identity with another sequence (example 11), antisense oligonucleotides (example 12), antibodies to a single protein (example 13), antibodies to a genus of proteins (example 14), a genus with widely varying species (example 15), a process claim where novelty resides in the process steps (example 16), and methods of using compounds claimed by functional limitations, methods of identifying compounds, and compounds identified by such methods (example 17).  Patent Docs continues the discussion of these examples, reviewing Examples 13 and 14 drawn to antibody technology.

Example 13 – Antibody to a Single Protein

Example 13 provides guidance for a single exemplary claim directed to an isolated antibody that binds to an isolated and structurally characterized antigen.  This Example is essentially identical to the prior guidance in the former written description guidelines (presented therein as Example 16).  Nevertheless, the single claim presented in the new training materials recites:

Claim 1:  An isolated antibody capable of binding to antigen X.

The fact pattern of this example states that the specification discloses that "antigen X" was isolated from HIV and is useful for detection of HIV infection.  The specification describes purification of antigen X by gel filtration and discloses its amino acid sequence.  The specification also discloses that antigen X is a 55 kDa monomer, has no disulfide bonds, and has a slightly acidic pI.  While the hypothetical specification discusses antibodies that specifically bind to antigen X and states such antibodies can be used in immunoassays to detect HIV, the specification lacks a working or prophetic example of an antibody that binds to antigen X.  Nevertheless, given the level of skill and knowledge in the art of antibodies at the time the application was filed, production of antibodies against a well-characterized antigen was routine, and therefore the specification satisfies the written description requirement of § 112, first paragraph, with respect to the full scope of claim 1.

While the example fails to provide a specific filing date for the specification, it cites to the 1976 reference of Elvin A. Kabat ("Structural Concepts in Immunology and Immunochemistry," 2nd Ed. (Holt, Rinehart and Winston)) to provide evidence of the knowledge in the art that antibodies can be generated from isolated antigens, that the various isotypes (IgG, IgA, IgM, IgD, and IgE) share certain physical, chemical, and biological properties, and that there is sequence variation in the variable and hypervariable regions of the antibody sequence.  Thus, even though the specification fails to describe (a) any partial physical or chemical properties (e.g., molecular weight, association constant); (b) a partial structure of the claimed antibody by sequence, reference to a deposit, or in the drawings; (c) any functional correlation of antibody structure to binding activity to antigen X; and (d) any method for making an antibody that binds antigen X, the production of such antibodies is so conventional that the amount of disclosure present in this specification is adequate to demonstrate possession of the claimed antibody.

Example 14 – Antibodies to a Genus of Proteins

Example 14 is based on the fact pattern of the 2004 Federal Circuit case, Noelle v. Lederman, 355 F.3d 1343 (Fed. Cir. 2004), and provides guidance for three exemplary claims directed to antibodies that bind to "Protein X" which was isolated from murine tissue and has been structurally characterized.  This Example is new relative to the prior written description training materials.  The three presented claims in this Example recite:

Claim 1:  A monoclonal antibody that binds Protein X.

Claim 1:  The antibody of claim 1 which binds murine Protein X.

Claim 3:  The antibody of claim 1 which binds human Protein X.

The fact pattern of this example states that the specification describes a monoclonal antibody that specifically binds to Protein X isolated from murine tissue, and protocols for producing anti-Protein X antibodies.  Protein X is disclosed as being located on the surface of certain immune cells and is asserted to be useful for treating immune disorders involving cell signaling.  The specification describes purification of murine Protein X and discloses its amino acid sequence.  The specification does not disclose any physical or chemical property for Protein X from any other species (e.g., no disclosure of molecular weight or cross-reactivity of human Protein X with anti-murine Protein X antibodies, and no sequence information for Protein X from any species other than mouse).  The specification does state that human Protein X is expected to have the same in vivo function as murine Protein X, and that antibodies to human Protein X will be useful for treating immune disorders involving cell-to-cell signaling.

Not surprisingly, the written description requirement for claim 2 above is completely satisfied by the disclosure in the specification, essentially for the same reasons provided in Example 13 (adequate description of the purified antigen satisfies written description for antibodies which bind the purified antigen).

As to claim 3, the lack of any physical or chemical description of an antibody that binds human Protein X, along with the lack of any physical or chemical description of human Protein X leads to the conclusion that written description is not satisfied for this claim.  As detailed in the analysis, the specification and prior art fail to provide any evidence that the disclosed properties of murine Protein X are predictive of the properties of human Protein X.  Further, the disclosure of human Protein X in the specification is purely functional and fails to provide any correlation to physical and chemical properties.  As stated in the materials, "Claim 3 is directed to an unknown that is identified only by reference to another unknown."

Similarly, the specification fails to provide written description for the full scope of claim 1, because the claim relates generically to many species of monoclonal antibodies that specifically bind to Protein X from any species.  While the specification adequately describes murine Protein X and therefore an antibody that binds murine Protein X, it fails to provide any physical or chemical description of Protein X from any other organism, and fails to describe a method of making an antibody that binds non-murine Protein X without first having the particular non-murine Protein X in hand.  Thus, because claim 1 is generic to antibodies to Protein X from a variety of organisms, and the specification fails to describe anything other than murine Protein X, claim 1 does not satisfy the written description requirement.  The analysis notes, without further clarification, that if any evidence was presented that murine Protein X was representative of the genus of Protein X molecules from other species, it is possible that claim 1 could meet the written description requirement.

For additional information on this topic, please see:

• "ESTs & Partial Protein Structures," May 8, 2008
• "DNA Hybridization & Percent Identity," May 6, 2008

An Analysis of the New Written Description Training Materials - ESTs & Partial Protein Structures

    By Donald Zuhn --

Last month, the U.S. Patent and Trademark Office announced that it had updated the training materials to be used by examiners in the examination of patent applications for compliance with the written description requirement of 35 U.S.C. § 112, first paragraph.  The revised training materials supersede and replace the previous set of training materials issued by the Patent Office in 1999.  The new training materials provide seventeen examples, of which fourteen are specifically related to biotech inventions.  In particular, the biotech-specific examples address expressed sequence tags (ESTs) (example 4), a partial protein structure (example 5), DNA hybridization (example 6), allelic variants (example 7), bioinformatics (example 8), protein variants (example 9), a product claimed by its function (example 10), a polynucleotide or polypeptide sequence sharing percent identity with another sequence (example 11), antisense oligonucleotides (example 12), antibodies to a single protein (example 13), antibodies to a genus of proteins (example 14), a genus with widely varying species (example 15), a process claim where novelty resides in the process steps (example 16), and methods of using compounds claimed by functional limitations, methods of identifying compounds, and compounds identified by such methods (example 17).  Patent Docs will discuss these examples in a series of articles.  Today, we address examples 4 and 5.

Example 4

Example 4 concerns claims that are directed to an expressed sequence tag (EST), which the training materials define as a cDNA that corresponds to only part of a protein-encoding open reading frame (ORF).  The example is divided into two sections:  one that discusses the effect of open transitional language (example 4A), and one that discusses the effect of closed transitional language (example 4B).  The first section of this example provides a single exemplary claim:

Claim 1:  An isolated DNA comprising SEQ ID NO: 16.

Because this claim uses "open" transitional language (i.e., recites a DNA comprising the recited sequence), the claim encompasses a genus of DNAs in which additional DNA sequences may be attached to either end of the DNA sequence of SEQ ID NO: 16.  The claimed genus would thus include the full-length gene of which the DNA sequence of SEQ ID NO: 16 was a part.  Nevertheless, because the DNA sequence of SEQ ID NO: 16 is a structural feature common to all members of the genus, and the exemplary specification discloses the complete sequence of SEQ ID NO: 16, the specification satisfies the written description requirement with respect to claim 1.  It is important to note, however, that while the above claim would not be rejected under 35 U.S.C. § 112, first paragraph, it would most likely be rejected for failing to comply with the utility requirement of 35 U.S.C. § 101 (see Example 9 of the Revised Interim Utility Guidelines Training Materials).

The second section of Example 4 provides two exemplary claims:

Claim 1:  An isolated nucleic acid comprising SEQ ID NO: 1.

Claim 2:  An isolated nucleic acid consisting of SEQ ID NO: 1.

Because claim 2 uses "closed" transitional language (i.e., recites a nucleic acid consisting of the recited sequence), this claim only encompasses a single species.  Moreover, the exemplary specification discloses the complete sequence of this species.  Thus, the specification satisfies the written description requirement with respect to claim 2.  The analysis of claim 1 in Example 4B is identical to that of claim 1 in Example 4A, and therefore, because the exemplary specification of Example 4A satisfies the written description requirement with respect its claim 1, the exemplary specification of Example 4B likewise satisfies the written description requirement with respect its claim 1.

Example 5

Example 5 concerns claims directed to partial protein structures.  According to the training materials, Example 5 is based on In re Wallach, 378 F.3d 1330 (Fed. Cir. 2004).  This example provides two exemplary claims:

Claim 1:  An isolated protein comprising Protein A,
    wherein said Protein A includes the amino acid sequence of SEQ ID NO: 1 in the N-terminal portion of the protein, and has the same ability to bind to and activate Protein X as Protein A from human urine, and
    wherein said Protein A is purified by subjecting a crude protein recovered from a dialyzed concentrate of human urine to affinity chromatography on a column of immobilized Protein X, and elutes from a reversed-phase HPLC column as a single peak in a fraction corresponding to about 31% acetonitrile and shows a molecular weight of about 22 kDa when measured by SDS-PAGE under reducing conditions.

Claim 2:  An isolated DNA comprising a DNA that encodes Protein A,
    wherein said Protein A includes the amino acid sequence of SEQ ID NO: 1 in the N-terminal portion of the protein, and has the same ability to bind to and activate Protein X as Protein A from human urine, and
    wherein said Protein A is purified by subjecting a crude protein recovered from a dialyzed concentrate of human urine to affinity chromatography on a column of immobilized Protein X, and elutes from a reversed-phase HPLC column as a single peak in a fraction corresponding to about 31% acetonitrile and shows a molecular weight of about 22 kDa when measured by SDS-PAGE under reducing conditions.

According to the training materials, the exemplary specification discloses a sequence of 10 amino acids (SEQ ID NO: 1) that corresponds to the amino-terminal end of Protein A, but does not disclose the complete sequence of Protein A.  The training materials also note, however, that the exemplary specification discloses other relevant identifying characteristics of Protein A (e.g., its ability to bind and activate Protein X, its approximate molecular weight, and the concentration of acetonitrile at which Protein A will elute from a reverse phase HPLC column), as well as a method of isolating Protein A from urine and a working example in which Protein A was isolated from urine using this method.  In view of this disclosure, the training materials conclude that the specification satisfies the written description requirement with respect to claim 1.

Concerning claim 2, the training materials note that the exemplary specification fails to disclose either the complete nucleotide or complete amino acid sequence of Protein A.  In drawing a comparison between the isolated protein of claim 1 and the isolated DNA claim 2, the training materials state that while the exemplary specification provides relevant identifying characteristics for the protein, it does not provide sufficient relevant identifying characteristics for the DNA.  The training materials also state that because the exemplary specification fails to support even one species of DNA in the claimed genus, it is apparent that a representative number of species is not disclosed.  Thus, the training materials conclude that the specification fails to satisfy the written description requirement with respect to claim 2.

For additional information on this topic, please see:

• "DNA Hybridization & Percent Identity," May 6, 2008

USPTO to Appeal Tafas/GSK v. Dudas

    By Kevin E. Noonan --

The U.S. Patent and Trademark Office filed a Notice of Appeal today with the Court of Appeals for the Federal Circuit, challenging the decision of Judge William Cacheris of the Eastern District of Virginia permanently enjoining the continuation and claims rules as being outside the scope of their statutory authority.  The Federal Circuit is expected to notice a briefing schedule, and invite amicus briefing, once it receives the record from the District Court.

It is unlikely that the matter will be finally resolved for several months, and quite possibly not until the change of administration.  Additionally, Judge Cacheris made his decision on only one of several grounds raised by the plaintiffs, Dr. Tafas and GlaxoSmithKline, making it likely that the Federal Circuit will remand the case to the District Court for further proceedings.  It is unlikely that the injunction barring implementation of the rules will be lifted before the District Court has ruled on these alternative grounds for relief.

For information regarding this topic, please see:

• "BIO Responds to Events of the Day," April 1, 2008
• "No April Fool's Joke -- Tafas and GSK Win on Summary Judgment," April 1, 2008
• "PLI's John White Discusses Tafas/GSK v. Dudas," February 11, 2008
• "Judge Cacheris Takes GSK Case under Advisement," February 8, 2008
• "GSK Summary Judgment Hearing Set for Friday Morning," February 7, 2008
• "New Briefing Deadline Set In PTO Rules Case," December 18, 2007
• "Court Sets Summary Judgment Schedule in New Rules Case," December 3, 2007
• "No Discovery in New Rules Case," November 27, 2007
• "Tafas v. Dudas; SmithKline Beecham Corp. v. Dudas (E.D. Va. 2007)," October 31, 2007
• "USPTO Late to Its Own Party," October 31, 2007
• "GSK Secures Injunction," October 31, 2007 (includes links to Court's Order and Opinion)
• "Senator Schumer Sends a Signal," October 30, 2007
• "GSK TRO/Preliminary Injunction Hearing," October 29, 2007
• "AIPLA Supports GSK's Lawsuit Against the Patent Office's New Rules," October 25, 2007
• "GSK Brings Out the Big Guns Opposing the New Continuation and Claims Rules," October 24, 2007
• "Hooray! - (Finally) the Big Dogs Have Joined the Hunt," October 11, 2007
• "Rules Challenger Amends Complaint and Withdraws PI Motion," September 11, 2007
• "Inventor Sues PTO to Prevent New Continuation and Claims Rules from Taking Effect," August 30, 2007

An Analysis of the New Written Description Training Materials - DNA Hybridization & Percent Identity

    By Donald Zuhn --

Last month, the U.S. Patent and Trademark Office announced that it had updated the training materials to be used by examiners in the examination of patent applications for compliance with the written description requirement of 35 U.S.C. § 112, first paragraph.  The revised training materials supersede and replace the previous set of training materials issued by the Patent Office in 1999.  In the updated training materials, the Office explains that the revisions to the materials were necessitated by changes in both the case law and technology since the 1999 training materials were issued.  The Office also notes that to the extent that conflicts exist between the 1999 training materials and the new materials, the new materials will control.

Commenting on the new training materials, Commissioner for Patents John Doll stated that the materials "will improve the quality and consistency of patent examination, as well as provide guidance to practitioners for the drafting of patent applications and responses to examiners."  According to the Patent Office, the new materials are intended to assist patent examiners in applying the "Guidelines for Examination of Patent Applications Under the 35 U.S.C § 112, first paragraph 'Written Description' Requirement," which were originally published in the Federal Register on January 5, 2001, and which are now incorporated in the M.P.E.P. at § 2163.

The new training materials provide seventeen examples, of which fourteen are specifically related to biotech inventions.  In particular, the biotech-specific examples address expressed sequence tags (ESTs) (example 4), a partial protein structure (example 5), DNA hybridization (example 6), allelic variants (example 7), bioinformatics (example 8), protein variants (example 9), a product claimed by its function (example 10), a polynucleotide or polypeptide sequence sharing percent identity with another sequence (example 11), antisense oligonucleotides (example 12), antibodies to a single protein (example 13), antibodies to a genus of proteins (example 14), a genus with widely varying species (example 15), a process claim where novelty resides in the process steps (example 16), and methods of using compounds claimed by functional limitations, methods of identifying compounds, and compounds identified by such methods (example 17).  Patent Docs will discuss these examples in a series of articles.  Today, we address examples 6 and 11.

Example 6

Example 6 concerns claims that are directed to nucleic acid molecules that hybridize to a recited sequence.  This example provides three exemplary claims:

Claim 1:  An isolated nucleic acid that encodes a protein that binds to the NDG [newly-discovered growth factor] receptor and stimulates tyrosine kinase activity.

Claim 2:  An isolated nucleic acid that encodes a protein that binds to the NDG receptor and stimulates tyrosine kinase activity, and consists of the sequence set forth in SEQ ID NO: 1.

Claim 3:  An isolated nucleic acid that encodes a protein that binds to the NDG receptor and stimulates tyrosine kinase activity, wherein the nucleic acid hybridizes under highly stringent conditions to the complement of the sequence set forth in SEQ ID NO: 1.

According to the training materials, the specification, which discloses the nucleotide sequence of SEQ ID NO: 1, satisfies the written description requirement with respect to the full scope of claim 2.  However, because claim 1 encompasses a broad genus of isolated nucleic acids, and the specification fails to disclose any information about the structure or location of NDG receptor binding domains in the protein encoded by the nucleotide sequence of SEQ ID NO: 1, the specification fails to satisfy the written description requirement with respect to the full scope of claim 1.

Concerning claim 3, the training materials acknowledge that "nucleic acids that hybridize to the complement of SEQ ID NO: 1 must share many nucleotides in common with SEQ ID NO: 1," and therefore, that "[t]he disclosure of SEQ ID NO: 1 combined with the knowledge in the art regarding hybridization would put one in possession of the genus of nucleic acids that would hybridize under stringent conditions to SEQ ID NO: 1."  However, the training materials conclude that the specification fails to satisfy the written description requirement with respect to the full scope claim 3 because the specification does not disclose a recognized correlation between the structure of the protein encoded by the nucleotide sequence of SEQ ID NO: 1 and its function, and without this correlation "those of ordinary skill in the art would not be able to identify without further testing which of those nucleic acids that hybridize to SEQ ID NO: 1 would also encode a polypeptide that binds to NDG receptor and stimulates tyrosine kinase activity."

Example 11

Example 11 concerns claims that are directed to a polynucleotide or polypeptide sequence that shares percent identity with another sequence.  The example is divided into two sections, one in which there is no art-recognized structure-function correlation for the claimed sequence (example 11A), and one in which there is an art-recognized structure-function correlation for the claimed sequence (example 11B).  The first section of this example provides two exemplary claims:

Claim 1:  An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.

Claim 2:  An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity X.

Despite the specification's disclosure of only a single species encoding the polypeptide of SEQ ID NO: 2 (i.e., SEQ ID NO: 1), and the lack of any teaching in the specification regarding which amino acid residues in SEQ ID NO: 2 are tolerable to change, the training materials indicate that the specification satisfies the written description requirement with respect to the scope of claim 1.  According to the training materials, this is so because "[w]ith the aid of a computer, one of skill in the art could have identified all of the nucleic acids that encode a polypeptide with at least 85% sequence identity with SEQ ID NO: 2."  However, because the specification lacks any teaching as to which amino acid residues in SEQ ID NO: 2 can be changed while still retaining activity X, and the art lacks any recognized correlation between structure (SEQ ID NO: 2 domains) and function (activity X), the training materials indicate that the specification fails to satisfy the written description requirement with respect to the scope of claim 2.  This would seem to suggest that if claim 3 in Example 6 above were rewritten to exclude an activity limitation, claim 3 would satisfy the written description requirement, since a nucleotide sequence hybridizing under highly stringent conditions would be expected to encode a protein having a sequence identity that is greater than 85%.

The second section of Example 11 also provides two exemplary claims:

Claim 1:  An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.

Claim 2. An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity Y.

The only difference between the hypothetical specification of Example 11A and the hypothetical specification of Example 11B is that the latter identifies two domains that are critical to activity Y (i.e., a binding domain and a catalytic domain).  Not surprisingly, the training materials find that the specification satisfies the written description requirement with respect to the scope of claim 1 of Example 11B.  With respect to claim 2 of Example 11B, the training materials indicate that the specification, which now discloses two domains responsible for activity Y, satisfies the written description requirement.

USPTO News: USPTO and EPO to Implement Pilot Patent Prosecution Highway Program

    By Christopher P. Singer --

According to an April 28, 2008 press release, the U.S. Patent and Trademark Office (USPTO) and the European Patent Office (EPO) will implement a one-year long pilot Patent Prosecution Highway (PPH) program starting in September 2008.  Similar pilot programs with other countries have demonstrated the potential of the program for reducing application backlogs, eliminating redundant work, and leading to more efficient examination of applications.  According to USPTO Director Jon Dudas, the addition of this pilot PPH with the EPO "significantly expands the PPH network in the global patent office community."  Other participant countries in pilot PPH programs include Japan, Australia, Korea, the United Kingdom, and Canada (see links below for Patent Docs reports concerning these other pilot programs).  The program between the U.S. and Japan has moved from a pilot program to a full-time basis program.

The PPH gives applicants the option of requesting a fast track examination of a corresponding EP or US application when they receive a ruling from one or the other of the EPO or the USPTO that at least one claim in their application is patentable.  The prosecution in the second office is based on the patentable results from the first office, and thus, applicants can expect to obtain patents in both offices faster.  The requirements for participation in this pilot program will be published by both the USPTO and the EPO on each Office's website prior to the program's implementation.  We will provide more details concerning the pilot program as soon as they become available.

For additional information of this and other related topics, please see:

• "Patent Prosecution Highway Extended to IP Australia," April 2, 2008
• "Patent Prosecution Highway Network Expands to Canada & Korea," January 29, 2008
• "USPTO Announces Two Additional Partners in the Patent Prosecution Highway Pilot Program," January 17, 2008
• "USPTO and JPO to Implement Patent Prosecution Highway on Full-Time Basis," December 27, 2007
• "USPTO and UK IPO to Collaborate on Patent Prosecution Highway," September 14, 2007
• "Patent Prosecution Highway Pilot Program to Be Extended," June 28, 2007

USPTO News: Patent Office Announces Common Application Format

    By Donald Zuhn --

Last fall, we reported on a memorandum of understanding that the U.S. Patent and Trademark Office (USPTO), European Patent Office (EPO), and Japan Patent Office (JPO) had reached during the 25th Annual Trilateral Conference.  One aspect of this agreement concerned a Common Application Format (CAF), which would allow applicants to prepare a single application that would be accepted by each Office.

At the time of the Conference, the CAF had not yet been disclosed.  The USPTO has now released additional information concerning the CAF.  With respect to the format itself, the USPTO provided an example of a format that complies with the CAF requirements:

Description
    Title of Invention
    Technical Field
        0001
    Background Art
        0002
    Summary of Invention
        Technical Problem
        0003
        Solution to Problem
        0004
        0005
        Advantageous Effects of Invention
        0006
    Brief Description of Drawings
        0007
            Fig. 1
            Fig. 2
    Description of Embodiments
        0008
        Examples
        0009
        0010
        Example 1
        0011
        Example 2
        0012
    Industrial Applicability
        0013
    Reference Signs List
        0014
    Reference to Deposited Biological Material
        0015
    Sequence Listing Free Text
        0016
    Citation List
        Patent Literature
        0017
        Non Patent Literature
        0018
Claims
    Claim 1
    Claim 2
Abstract
Drawings
    Fig. 1
    Fig. 2
Sequence Listing

The USPTO noted that while some of the requirements of the CAF go beyond current Patent Office rules and procedures, the new format was nevertheless consistent with such rules and procedures.  Therefore, the Office announced that it would accept applications that used the new format.  The USPTO also announced that the EPO would be implementing the CAF in early 2009, and that the JPO would be implementing most of the CAF requirements in early 2009 with the remainder of the requirements to be implemented in 2011.

The Patent Office announcement also contains links to information regarding the basic principles of the CAF, common requirements for documents under the CAF, and a comparative table of examples for applications.  With respect to the common requirements, some aspects of the CAF include the following:

• Applicants will not be required to remove National Legends (i.e., cross references to related applications and statements regarding federal funding) from the description.
• A statement of industrial applicability shall be included when it is not obvious from the description or nature of the invention.
• Applicants will not be required to remove any reference citation list from the description.
• Applicants shall use the International System of Units (SI) in the description, but may use additional alternative unit systems as long as SI units are placed in parentheses.
• Paragraphs of the description (but not the title or section headings) shall be numbered consecutively using Arabic numerals.
• Mathematical or chemical formulae shall be preceded by a sign indicating that the formula is mathematical ("Math.") or chemical ("Chem."), followed by a space, and then by an Arabic numeral (e.g., Chem. 1)
• Tables shall be preceded by a sign indicating that the table is a table ("Table"), followed by a space, and then by an Arabic numeral (e.g., Table 1)
• Claims shall be preceded by a sign indicating that the claim is a claim ("Claim"), followed by a space, and then by an Arabic numeral (e.g., Claim 1).

IPO Publishes Letter in Opposition to Proposed Rule Changes to Biological Deposits

    By Christopher P. Singer --

The Intellectual Property Owners Association (IPO) recently published a letter in opposition to the Federal Register Notice outlining proposed rule changes regarding biological deposits (see "Proposed Rule Change to Timing of Filing a Biological Deposit").  In particular, in its letter, signed by President Steven W. Miller, the IPO addresses the reasons why it believes the proposed rules are contrary to existing law and will have an adverse impact on applicants.  The IPO further urges that, in the event that the proposed rules changes are nevertheless adopted, certain additional protective rules be incorporated similar to those existing in the European Patent Office.

Briefly, the proposed rules would enact a requirement that applicants submit a deposit of biological materials prior to the publication of an application, and make it available to the public, without restriction.  In the Federal Register notice, the USPTO stated that its motivation for the rule changes included the AIPA, a desire to promote parity of disclosure across various technology areas, and to move toward international harmonization of rules regarding biological deposits.

The IPO first addresses and refutes the argument that the AIPA essentially requires these changes and that it overrules the CAFC's decision in In re Lundak.  In noting that the language of the AIPA fails to suggest the need for any deposit practice change, the IPO also cites to a GAO report that was commissioned by Congress during consideration of the AIPA.  Quoting from the report's conclusion that "the statute does not require an associated release of a biological deposit concurrent with 18-month publication," Deposits of Biological Materials in Support of Certain Patent Applications, GAO-01-49 (Oct. 2000) at 5, the IPO concludes that Congress was aware of the potential impact that the application publication rule could have on biological deposits.  Noting the lack of any language in the AIPA that addresses the need for changing the existing deposit practice, the IPO concludes that Congress in the AIPA did not overrule the controlling law (i.e., Lundak) for biological deposits.

Moving next to the PTO's argument that the rule changes would provide parity of treatment of inventions and disclosures across various technologies, the IPO again provides a persuasive argument that the proposed changes go too far.  The PTO's argument to this point is that a published application containing a reference to a biological deposit may not be adequately enabled for purposes of its use as a prior art reference under 35 U.S.C. § 102.  While conceding that published applications requiring a deposit of biological material for purposes of § 112 enablement would fail to qualify as prior art to another application with claims directed to the same biological material, the IPO argues that such situations would not be typical.  The IPO argues that the required enabling disclosure of a cited art reference is similar in scope to the enablement requirement of § 112 to support a claimed invention, citing to the PTO's use of non-patent literature and abstracts in art-based rejections.  Many such references fail to contain as much disclosure as a patent application, and fail to provide restriction-free access to the biological materials they describe.  In concluding this point, the IPO states that even with restricted access to a deposit during prosecution of an application, its eventual publication coupled with the existence of the deposit would likely qualify as prior art under 102(g).

As to harmonization, the IPO notes that while the proposed rules would encompass aspects of the deposit rules of the EPO, they completely fail to provide any of the protective rules also encompassed within the EPO's rules.

The IPO also argues that the rules changes would unfairly impact those applicants that make deposits, because a biological deposit effectively provides a mini, self-replicating factory for making an applicant's invention.  The IPO argues that while all inventions must contain adequate description for § 112 purposes, these rule changes would effectively require that a finished sample of the claimed invention be made available to any third party, without restricted use, prior to the issuance of the patent.  This situation creates a burden unique to those applicants making biological deposits.  While acknowledging that such potentially infringing activity could be curtailed by the threat of provisional rights that would provide a reasonable royalty for infringing acts, the IPO notes that such rights would exist only when the issued claim is substantially identical to the published claim.  Further, given that prosecution of a published application is publicly accessible using PAIR, third parties can feely monitor the course of prosecution and base their actions on amendments made to the application.

Hopefully, the USPTO will take the IPO's comments seriously and, if not abandon the changes entirely, consider at least amending the proposed rules to incorporate certain protections for applicants that make a biological deposit.

USPTO Posts Comments on New Rules for Alternative Claiming

    By Donald Zuhn --

Last August, the U.S. Patent and Trademark Office published a notice of proposed rule making entitled "Examination of Patent Applications That Include Claims Containing Alternative Language" (sometimes referred to as the Markush rules).  The Office's proposed rule making would require each claim in an application to be limited to a single invention.  According to the Office's notice of proposed rule making, when alternative language is used to define multiple species in a single claim, such claims would be considered to be limited to a single invention only when at least one of two conditions is met:

1.  "All of the species encompassed by the claim share a substantial feature essential for a common utility."
2.  "[A]ll of the species are prima facie obvious over each other."
The notice defines a substantial feature essential for common utility as being "a common structure, material, or act necessary for at least one shared specific, substantial, and credible utility."

In March, the Patent Office published a supplementary notice concerning its proposed alternative claiming rules.  Despite asserting that the proposed rules "involve rules of agency practice and procedure for which prior notice and an opportunity for public comment are not required pursuant to 5 U.S.C. 553 (or any other law), and thus neither a regulatory flexibility analysis nor a certification under the Regulatory Flexibility Act (5 U.S.C. 601 et seq.) is required under 5 U.S.C. 603," the Office nevertheless decided to "subject the proposed rules to a regulatory flexibility analysis to provide a further opportunity for comment on the small business impact of the proposed rules."  The Office set April 9, 2008 as the deadline to submit comments on the Office's supplementary notice.

The Patent Office has now posted all of the comments it received regarding the August notice of proposed rule making or the Office's supplementary notice.  Among the organizations, corporations and individuals submitting comments to either (or in some instances both) notices were the American Intellectual Property Law Association (AIPLA), the Intellectual Property Owners Association (IPO), the National Association of Patent Practitioners (NAPP), the National Institutes of Health (NIH), Eli Lilly and Company, BIOCOM, the Biotechnology Industry Organization (BIO), Genentech, Inc., GlaxoSmithKline, IBM Corporation, the Pharmaceutical Research and Manufacturers of America (PhRMA), E. I. du Pont de Nemours and Company, Curis, Inc., Wyeth, ZymoGenetics, Inc., David Boundy of Cantor Fitzgerald L.P., Thomas Dodd and Hal Woodrow of Johnson & Johnson, and Harold Wegner of Foley & Lardner LLP.  Earlier this month, we reported on the comments Mr. Boundy submitted regarding the economic impact of the proposed alternative claiming rules (see "Cantor Fitzgerald VP Comments on Markush Rules").  In his submission, Mr. Boundy estimated that Office's alternative claiming rules would impose upon applicants an economic burden of $16 billion per year.

While we plan to review and report on a number of the other comments posted on the PTO's website, we begin today with GlaxoSmithKline's comments (in part because GSK kindly provided us with a copy of its comments prior to today's posting).  In its initial set of comments submitted in October of 2007, GSK argued (as it did in Tafas/GSK v. Dudas) that although the proposed alternative claiming rules were "styled as procedural, the changes to practice mandated by the new rules are in fact substantive."  While recognizing that the Office had a right to exercise control over administrative matters, GSK asserted that "it is not the prerogative of the Office to diminish the patentee's substantive rights for the convenience of its examination policy."

Moreover, GSK criticized the Office for failing to provide any data justifying the proposed rules:

There is no data indicating how many applications are affected by the rules; no data to indicate the scope of the perceived problem; no data to justify limiting "nested" Markush groups to one.  There is also no data to indicate the amount of search and examination time that will be saved by the proposed rules; no data to indicate how many divisional applications will be necessitated by the increased restriction requirements that will likely result from implementation of the rules; and no data to indicate the increased burden upon applicants as they attempt to comply.

GSK also recommended that the USPTO "adopt the unity of invention standard applied by the PCT to evaluate patent applications, and adhere to claiming practices that have found common application throughout the world's patent system," as opposed to creating "yet another system of rules and standards that would be unique to the U.S. and at variance with other major examining authorities."

With regard to specific changes to the rules, GSK contended that the requirement of proposed Rule 75(j)(1) that the number and presentation of alternatives not make the claim "difficult to construe" would create "a new and subjective standard for objecting to a claim."  Predicting that "[d]ifferent examiners are bound to perceive claims with differing degrees of difficulty," GSK argued that:

If a claim particularly points out and distinctly claims the subject matter in accordance with § 112, ¶2, that is sufficient under the law for clarity.  If it does not, then it should be rejected under § 112.  No new criteria are needed.

With respect to the prohibition against the nesting of Markush groups under proposed Rule 75(j)(2), GSK noted that such a limitation "would appear to render many common terms, such as halogen and alkyl, as inappropriate terms within a Markush group -- because each is itself a group of alternatives."  To comply with the proposed rule, an applicant would have to forgo the shorthand for a much longer recitation.  To illustrate its point, GSK noted that the phrase "wherein R is OH, OCH3, C1-6alkyl, or halogen" in the following example:

would have to be expanded to:

wherein R = OH, OCH3, methyl; ethyl, n-propyl, i-propyl; n-butyl, s-butyl, i-butyl, t-butyl; 1-pentyl, 2-pentyl, 3-pentyl, 1-butyl-2-methyl, 1-butyl-3-methyl, 2-butyl-2-methyl, 1-propyl-3,3-dimethyl; 1-hexyl, 2-hexyl, 3-hexyl, 1-pentyl-2-methyl, 1-pentyl-3-methyl, 1-pentyl-4-methyl, 2-pentyl-2-methyl, 2-pentyl-3-methyl, 2-pentyl-4-methyl, 3-pentyl-2-methyl, 3-pentyl-3-methyl, 1-butyl-1,1-dimethyl, 1-butyl-2,2-dimethyl, 1-butyl-3,3-dimethyl, 1-butyl-2,3-dimethyl, 1-butyl-2-ethyl, fluoro, chloro, bromo, and iodo.

Therefore, far from making the examination of such claims less burdensome, Rule 75(j)(2) would actually make the process more burdensome.

GSK also took issue with provisions of the proposed rules that would require an applicant to petition an unfavorable ruling under the proposed rules.  Instead, GSK argued that "the refusal to examine a claim that is clear and distinct should be appealable to the Board of Patent Appeals," noting that "[t]he very due process that was accorded to Weber, Haas, and Harnisch [in cases cited in the proposed rule making], has now been obviated by rulemaking."

In addressing the supplementary notice, GSK again argued "that these proposed rules exceed the boundaries of the PTO's rulemaking authority and, if made final, would be contrary to law."  In contrast with its earlier submission, however, GSK was able to use its recent victory in Tafas/GSK v. Dudas to support its argument (see "No April Fool's Joke -- Tafas and GSK Win on Summary Judgment").  Thus, because the proposed rules will "force an applicant to divide his heretofore permissible claim into multiple claims in an effort to try to obtain the full scope of patent coverage for his invention," the proposed rules will affect an applicant's rights and obligations.  Because the proposed rules affect an applicant's rights and obligations, they are substantive.  And because the proposed rules are substantive, they exceed the Patent Office's authority under 35 U.S.C. § 2.

For additional information concerning this topic, please see:
• "Cantor Fitzgerald VP Comments on Markush Rules," April 10, 2008
• "You Can't Fight the USPTO -- or Can You?" March 11, 2008
• "Patent Office Publishes Notice Regarding Impact of Proposed Markush Claims Rules on Small Entities," March 10, 2008
• "Federal Register Notice Regarding Markush Claims to Publish on Monday March 10, 2008," March 7, 2008
• "USPTO's Bruce Kisliuk Addresses ACI Conference," March 3, 2008
• "IPO Releases Comments on New Markush Rules," October 30, 2007
• "Patent Office Proposes New Rules for Alternative Claiming," August 12, 2007

USPTO News: Pilot Program Begins for Submission of “Complex Work Units” in Electronic Formats

    By Christopher P. Singer --

In an April 14, 2008 pre-O.G. notice the U.S. Patent and Trademark Office made a request for voluntary submission of electronic Complex Work Unit (CWU) files as part of its Pilot Program.  This program became effective on April 14, 2008 and is intended to alleviate the publication burden of applications that contain various CWUs such as structural data for chemical and biological molecules, mathematical formulas, and large data tables.  Importantly, the USPTO considers submissions of a CWU in this program as a supplement (not replacement) to a paper copy submitted by mail or a PDF copy submitted by EFS-Web, of the corresponding CWU (e.g., a protein structure represented in a Figure, supplemented by the supporting structural data).  In particular, chemical structure data can be submitted in IUPAC International Chemical Identifier (InChI) formatted files, protein crystal structure data can be submitted in Protein Data Bank (PDB) compliant format, and mathematical equations can be submitted using Mathematical Markup Language (MathML) format.  Each of these particular formats consists of ASCII text strings that can be effectively submitted as a text file using EFS-Web, in light of the recent upgrade to EFS-Web 1.1.

Alternatively, the voluntary participants in this pilot program can submit the InChI, PDB, and MathML files on CD as a supplement, not a replacement (important to note) to the paper or PDF-based submission of the CWU either by mail or EFS-Web, respectively.  For CDs submitted for the purposes of this pilot program, the PTO is waiving the format requirements of 37 C.F.R. § 1.52(e).  Excluded items from this CWU pilot program are computer program listings, sequence listings, and tables in ASCII format, which must be submitted on CDs in compliance with 37 C.F.R. § 1.52(e), or by EFS-Web in accordance with the legal framework.

The PTO notes that in order to participate in this program, the following requirements must be met:

1.  The patent application submitted on paper or as a PDF file by EFS-Web must include therein at least one CWU (a table, chemical structure, 3-D protein crystal structure, or mathematical formula).

2.  Any CD or text file submitted in accordance with this program must be accompanied by a statement that the CWU file submitted in electronic form is the same as the file used to create the image of the CWU submitted as part of the paper (or PDF format) patent application.  If a discrepancy between the paper or PDF and electronic version of a CWU, the paper or PDF version will be treated as the true version.

3.  Each CD submitted must be labeled "CWU Pilot" and only one copy of each CD is required.  The files on CD must be labeled according to the instructions found here.  The provisions of 37 C.F.R. § 1.52(e) are waived to the extent that they are inconsistent with the CWU pilot program requirements.

This pilot program is expected to last six months, at which time the PTO will determine whether to extend the program, or to enact procedural changes in light of the program's success.  More information, including FAQs, about the CWU pilot program can be found here.

USPTO News: Patent Office Launches Financial Profile System

    By Christopher P. Singer --

In a recent notice, the U.S. Patent and Trademark Office announced that it has launched the "Financial Profile" (FP) system which allows users to access payment history through a secure (and fast) website.  Users of the FP are able to view detailed information for all fees paid to the USPTO.  According to the USPTO's announcement, other options of the FP system include the ability to:

• Create and maintain your unique FP account using a self-registration process;
• Include transactions for multiple payment types (e.g., credit card, USPTO deposit accounts, and USPTO EFT accounts);
• View and print detailed information regarding any particular transaction (e.g., patent/application number, attorney docket number, payment amount, fee code, and fee code description);
• View, print, and download (PDF and CSV files) monthly statements for each registered payment type;
• Search transactions by attorney docket number (i.e., client matter number), application number, transaction type (e.g., sale or refund), and/or payment amount; and
• Transfer funds between existing USPTO deposit accounts, replenish deposit accounts via EFT, and/or select an option to stop receiving paper deposit account statements by mail.

The PTO has created an FP Helpdesk to handle questions and concerns relating to the FP system:  FinancialProfile@uspto.gov.  You can login to (or sign up for) the FP system at this link.

USPTO News: Pilot Program to Allow Law Students to Practice before the Office

    By Christopher P. Singer --

In an April 7, 2008 press release, the U.S. Patent and Trademark Office announced a new two year pilot program that will allow a limited number of law students to practice before the Patent Office.  The program will include opportunities in both patent and trademark branches of the Office, and is intended to give students a real world experience in intellectual property law.  According to the release, a student in the patent section of the program should expect to gain experience with common prosecution-related tasks before the Office, such as drafting and filing a patent application, drafting and filing a response to an Office action, or drafting and filing a brief in an appeal to the Board of Patent Appeals and Interferences.  Similarly, a student in the trademark section should expect to draft and file an application, a response to an Office action, or an appeal to the Trademark Trial and Appeal Board.

The Patent Office plans to choose three to five law schools as participants in the program, based on information provided in an application (available here).  Students applying to participate in this program must meet certain legal and moral qualifications, and those applying for the patent program must have the necessary scientific or technical background required to sit for the patent bar exam.

USPTO News: PTO Announces New Program to Reduce Pendency and Improve Patent Quality

    By Donald Zuhn --

On Monday, the U.S. Patent and Trademark Office announced that it will be initiating a new pilot program that is expected to reduce application pendency and improve patent quality.  The First Action Interview pilot program, which will begin on April 28th and run for six months, will allow applicants of certain applications to interview their cases prior to the issuance of a first Office action on the merits.  The Patent Office believes the pilot program will expedite prosecution of participating applications by enhancing interactions between applicants and examiners and promoting early resolution of outstanding issues.

Under the pilot program, an examiner assigned to a participating application will conduct a prior art search and provide the applicant with a pre-interview communication containing a condensed preview of objections or rejections against the claims of the participating application.  Within 30 days from the issuance of the pre-interview communication, the applicant must either schedule a first action interview or choose not to have the interview.  If the applicant chooses the latter option, the examiner will issue a First Action Interview Office action giving the applicant the longer of one month or 30 days to reply.  If agreement cannot be reached during the first action interview, the First Action Interview Office action will be issued (with the reply period specified above).

To help the Patent Office better gauge the success of the pilot program, it is being limited to two technology areas  -- neither of which is TC 1600.  In particular, eligible applications must be classified in Class 709 (electrical computers and digital processing systems: multi-computer data transferring) or Class 707 (data processing: database and file management or data structures).  However, biotech and pharma patent prosecutors will want to keep an eye on the pilot program, since a successful trial run will likely lead to an expansion of the program to other technology areas.

Additional information regarding the pilot program can be found here, or at the pilot program's website.  In the event that the pilot program becomes permanent, or is expanded to TC 1600, Patent Docs will provide more information regarding the First Action Interview process.

USPTO News: Webcast Regarding Public PAIR Issues

    By Christopher P. Singer --

Recently, the U.S. Patent and Trademark Office announced that it will hold a webcast on April 30, 2008 at 3:00 pm (EDT) in order to address various issues concerning Public PAIR.  In particular, the Office will address the recent access and response time problems that Public PAIR has faced resulting from of downloads of large amounts of data.  The PTO will address its initial efforts to address this problem using the verification code "reCAPTCHA" security measure (see "USPTO e-Commerce Update and Public PAIR Verification System"), and will discuss potential long-term solutions to the problem.

The PTO is explicitly requesting public input regarding this issue in order to be sure that any permanent system solution will still be able to meet the needs of the IP community.  For those interested in viewing the webcast, you only need to enroll (free) for the event at this link.  Public comments and questions regarding the process of gathering information and requirements of the Public PAIR system can be e-mailed to the following address:  PAIR_webcast@uspto.gov.

Cantor Fitzgerald VP Comments on Markush Rules

    By Donald Zuhn --

Last month, we reported on the U.S. Patent and Trademark Office's supplementary notice concerning its Alternative Claims Notice of Proposed Rule Making (frequently referred to as Markush rules).  While the Patent Office asserted that the new alternative claims rules "involve rules of agency practice and procedure for which prior notice and an opportunity for public comment are not required pursuant to 5 U.S.C. 553 (or any other law), and thus neither a regulatory flexibility analysis nor a certification under the Regulatory Flexibility Act (5 U.S.C. 601 et seq.) is required under 5 U.S.C. 603," the Patent Office nevertheless decided to "subject the proposed rules to a regulatory flexibility analysis to provide a further opportunity for comment on the small business impact of the proposed rules."  As we noted in an earlier report, comments on the alternative claims rules were due on or before April 9, 2008.

Yesterday, we received a copy of the comments submitted by David Boundy (at left), the Vice President of Intellectual Property for Cantor Fitzgerald L.P.  In his letter, Mr. Boundy concluded that "[t]he PTO’s rulemaking procedure for the Continuations, Claims, IDS, Appeal and Markush Rules violated the Regulatory Flexibility Act, the Paperwork Reduction Act, 5 C.F.R. § 1320.01 et seq., and Executive Order 12,866," and contended that the still pending IDS, alternative claims, and appeals rules packages "should be withdrawn."

The Regulatory Flexibility Act requires an agency to “make a reasonable good faith effort” to address the costs that a regulation would impose on small entities.  According to Mr. Boundy, "[s]o much is omitted from the [PTO's supplementary notice], and what is considered is considered on such a flimsy basis, as to raise genuine questions whether the PTO can meet even the most lenient standard of 'reasonable good faith.'"

With respect to the Office's obligations under the Paperwork Reduction Act, Mr. Boundy notes that "the entire thrust of the Markush Rule is to compel applicants to file more patent applications, at an acknowledged paperwork cost of about $10,000 each, in an acknowledged minimum number of at least 13,000 per year -- totaling about $130 million per year," and he argues that "[t]he PTO’s refusal to account for the staggering Paperwork costs of the divisional applications required by the Markush Rule is beyond the pale."  In a comment perhaps directed to those members of Congress who would confer additional authority upon the Patent Office, Mr. Boundy challenges the Office to "explain to Congress why [it] has done such a poor job of complying with its Paperwork Reduction Act responsibilities," and "explain to Congress how it can exercise authority under proposed 'Applicant Quality Submissions' any more responsibly than it has exercised authority under existing law."

Executive Order 12,866 requires that the Patent Office account for the economic effects of the alternative claims rules, unless the rules are deemed to have effects that are "not significant."  Mr. Boundy explains that "[t]he designation 'not significant' is reserved for regulations that have only minor consequences and elicit little or no controversy, such as housekeeping actions."  With respect to the alternative claims rules, Mr. Boundy contends that "it seems certain that a minimum of 100,000 additional applications will be required if applicants are to avoid regulatory burdens of lost patent protection," and that at $16,000 per application (the PTO's own estimate), "the burdens of the Markush rule cognizable under E.O. 12,866 are $16 billion per year."  As a result, the alternative claims rules exceed the $100 million threshold for an "economically significant" rule.

Mr. Boundy concludes his letter by addressing information that came to light only as a result of the GSK case.  In particular, he notes that "[w]hen the PTO produced its documents in the Tafas v. Dudas litigation, the absence of any consideration by the PTO of any factor economically-relevant to the public became starkly clear by the absolute absence of any analysis of economic effects on applicants in the administrative record."  According to Mr. Boundy, the omission of such an analysis is an indictment of senior PTO management, who he asserts are "no longer trusted by the PTO’s customer base."  He adds that senior PTO management has:

convinced the patent bar that they have no understanding of the patent system, are unwilling or unable to look at any effect that would occur outside the PTO’s four walls . . . and have too little respect for the rule of law to be able to avoid the legal fiasco that led to the PTO’s defeat . . . in Tafas v. Dudas.

For Mr. Boundy, the ultimate solution is to find "PTO management that can demonstrate sufficient understanding of the issues to earn the trust of stakeholders," rather than to support management that continues to force "economically-irrational rulemaking" upon the patent community.

USPTO News: Patent Prosecution Highway Extended to IP Australia

    By Christopher P. Singer --

In an April 1, 2008 notice, the U.S. Patent and Trademark Office announced that the Intellectual Property Office of Australia (IP Australia) will launch sometime this month a new trial cooperation initiative with the USPTO as part of the Patent Prosecution Highway (PPH) Pilot Program.  The trial program with Australia is set to expire on April 14, 2009.  The list of PPH participants, or trial program participants, continues to expand and now includes Australia, Canada, Korea, Japan, and the UK.  Additional information regarding participation in the Australian PPH program can be found at the following links at the USPTO website and the IP Australia website.

As mentioned in prior posts regarding the other participant Offices (see links below), the motivation behind the PPH is to leverage fast-track patent examination in participant offices so that applicants can obtain corresponding patents faster and more efficiently in each participant country.  Further, the PPH program should allow each office to benefit from work previously done by the initial examining office and consequently reduce examination workload and improve patent quality.

For additional information of this and other related topics, please see:

• "Patent Prosecution Highway Network Expands to Canada & Korea," January 29, 2008
• "USPTO Announces Two Additional Partners in the Patent Prosecution Highway Pilot Program," January 17, 2008
• "USPTO and JPO to Implement Patent Prosecution Highway on Full-Time Basis," December 27, 2007
• "