Andrew Nicholas John Brojer. Phillips et al.

Patent Trials and Appeals Board

Aug 9, 2019

12552829 - (D) (P.T.A.B. Aug. 9, 2019)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/552,829 09/02/2009 Andrew Nicholas John Brojer Phillips 215786-0096-00-US 5371
141674 7590 08/09/2019
Drinker Biddle & Reath/Microsoft
1500 K Street, N.W.
Suite 1100
Washington, DC 20005
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
08/09/2019 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
DBRIPDocket@dbr.com
usdocket@microsoft.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte ANDREW NICHOLAS JOHN BROJER PHILLIPS and
MICHAEL DAVID PEDERSEN
____________

Appeal 2018-001191
Application 12/552,829
Technology Center 1600
____________

Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.

Opinion for the Board filed by Administrative Patent Judge FREDMAN.

Opinion Dissenting filed by Administrative Patent Judge NEW.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal1,2 under 35 U.S.C. § 134(a) involving claims to a
method of creating a genetic device. The Examiner rejected the claims as

1 Appellants identify the Real Party in Interest as Microsoft Technology
Licensing, LLC (see Br. 3).
2 We have considered and refer to the Specification of Sept. 2, 2009
(“Spec.”); Final Office Action of Jan. 25, 2017 (“Final Act.”); Appeal Brief
of Aug. 9, 2017 (“Br.”); and Examiner’s Answer of Sept. 15, 2017 (“Ans.”).
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directed to patent-ineligible subject matter. We have jurisdiction under
35 U.S.C. § 6(b). We reverse.
Statement of the Case
Background
“Synthetic biology aims to design and create novel genetic devices to
carry out some desired and well-defined function. For example, micro-
organisms may be genetically engineered to improve crop yields, fight
bacterial infections, detect pollutants, or convert sunlight into energy” (Spec.
¶ 1). “The design and construction of a genetic device is a difficult task that
is typically achieved through trial-and-error, which can be time-consuming
and costly” (Spec. ¶ 1).
The Specification describes an automated approach for design of
genetic constructs composed of parts such as “promoters prom, ribosome
binding sites rbs, protein coding regions pcr and terminators ter” (Spec.
¶ 22). This approach may also provide positive or negative regulation of the
genetic construct (see Spec. ¶ 23) and address information necessary to
direct the expressed genetic construct to a particular biological location
(Spec. ¶ 25). The Specification realizes the automated approach using a
specialized programming language and syntax for coding and compiling the
genetic construct (see Spec. ¶¶ 26–32) along with other constraints
necessary for biological function (see Spec. ¶ 34). After a genetic device
has been designed, the Specification teaches “it can be implemented in a
living cell such as a bacterium using a genetic device manufacturing system”
(Spec. ¶ 33).
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The Claims
Claims 1–6, 9–12, 15–19, 22, and 23 are on appeal. Independent
claim 1 is representative and reads as follows:

1. A method of creating a genetic device including a
deoxyribonucleic acid (DNA) sequence that encodes genetic
parts that function together when introduced into a host cell to
satisfy a specified set of constraints, the method comprising:
establishing a connection to a database of genetic parts,
an entry in the database comprising a part type and at least one
part property;
receiving, by a program editor, input specifying a
plurality of part designs at least some of which comprise the at
least one part property expressed in terms of a logical variable
and constraints on the logical variable without exact
specification of a DNA sequence to be used;
resolving, at a compiler, the constraints using a constraint
resolution engine to provide at least one sequence of the genetic
parts from the database of genetic parts, wherein the sequence
of the genetic parts satisfies the constraints, the constraints
being one or more biological behaviors, chemical reactions, or a
combination thereof, wherein the resolving includes:
identifying a genetic part,
identifying an empty device template and an empty part
substitution,
binding a module name to a function given one or more
parameters,
looking up the module name,
invoking the function bound to the module name,
producing a part sequence, producing a union of two part
sequences,
producing a sequential composition of the two part
sequences,
creating a compartment-specific part sequence,
substituting a new variable for the logical variable, the
new variable not occurring elsewhere in the sequence of genetic
parts,
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creating a set of context-sensitive substitutions,
ignoring compartment names in transport reactions,
identifying substitutions that satisfy a numerical
constraint, and
combining context-sensitive substitutions arising from
the numerical constraint;
presenting the at least one sequence of the genetic parts
which satisfy the constraint; and
manufacturing the at least one sequence of genetic parts
which satisfy the constraint.

The Rejection
The Examiner rejected claims 1–6, 9–12, 15–19, 22, and 23 under
35 U.S.C. § 101 as directed to non-statutory subject matter (Final Act. 3–4).
The Examiner finds that the claims “do not amount to significantly
more than an algorithm designs a genetic device using a genetic parts and a
‘compiler’ or ‘constraint resolution engine’” (Final Act. 3). The Examiner
further finds that a “series of data processing steps or algorithm is a court-
established abstract idea, and further is similar to other court-established
abstract ideas such as mathematical operations and procedures for
organizing information” (id.).
Appellants argue that:
None of these assertions by the Examiner is sufficient to show
that the claims are “directed to” an abstract idea. In other
words, is not relevant that the Examiner stated that he has
identified mathematics in a claim, that the claims recite features
that “constitute” mathematical relationships, that the alleged
abstract idea “is” a mathematical construct, that the claims
recite “using” a mathematical function, or that there is
discussion of mathematical nature of the innovation in the
specification.
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(Br. 18). Appellants contend that “the claims recite a substantial practical
application rather than mere mathematical operations” (Br. 20). Appellants
contend “this practical application is found not only in connection with a
digital computer, but via the language of the claims being directed to the
manufacture of genetic devices which are tangible items made using
biological molecules (i.e., nucleotides and proteins)” (Br. 22).
The Alice Test
To determine whether a claim is invalid under § 101, we employ the
two-step Alice framework. In Alice step one, we ask whether the claims are
directed to a patent ineligible concept, such as an abstract idea or law of
nature. Alice Corp. v. CLS Bank Int’l, 573 U.S. 208, 217 (2014). Although
system claims are generally eligible subject matter, claims that are directed
only to abstract ideas and/or natural phenomena are directed to patent
ineligible concepts. Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d
1371, 1376 (Fed. Cir. 2015). In Alice step two, we examine the elements of
the claims to determine whether they contain an inventive concept sufficient
to transform the claimed judicial exception into a patent-eligible application.
Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66,
71–72 (2012) (quoting Alice, 573 U.S. at 217).
2019 Guidance
The PTO recently published revised guidance on the application of
§ 101. USPTO’s January 7, 2019 Memorandum, 2019 Revised Patent
Subject Matter Eligibility Guidance, 84 Fed. Reg. 50–57 (2019) (“2019
Guidelines”). Under that guidance, we first look to whether the claim
recites:
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(1) any judicial exceptions, including certain groupings of abstract
ideas (i.e., mathematical concepts, certain methods of organizing
human activity such as a fundamental economic practice, or mental
processes); and
(2) additional elements that integrate the judicial exception into a
practical application (see MPEP § 2106.05(a)–(c), (e)–(h)).
See 84 Fed. Reg. 54–55. Only if a claim (1) recites a judicial exception and
(2) does not integrate that exception into a practical application, do we then
look to whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not
“well-understood, routine, conventional” in the field (see MPEP
§ 2106.05(d)); or
(4) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of
generality, to the judicial exception.
See 84 Fed. Reg. 51.
Analysis
Applying Alice step one, we look to see if the claim recites any
judicial exceptions. First, we find independent claims 1, 12, and 16 recite
methods or systems that use a compiler with a constraint resolution engine to
generate a genetic device that results in a particular biological function. The
Specification explains that the compiler “comprises two components; a
parser and a corresponding translator” and that the “translator invokes a
prolog engine (or other suitable constraint resolution engine) for solving the
input constraints” (Spec. ¶ 32). The Specification explains that the
“compiler is arranged to resolve the constraints in such a manner that
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interactions between possible DNA sequences are taken into account during
the constraint resolution process” (Spec. ¶ 34). In resolving the constraints,
the Specification teaches the compilation yields a device template (see Spec.
¶ 37). The Specification teaches that the “device template is computed by
in-lining module invocations, introducing fresh variables where part
identifiers have been omitted and disregarding everything but the part
identifiers/variables and their sequential/parallel compositions” (Spec. ¶ 38).
These computations used to generate the device template, along with
the use of arithmetic operations during the generation process (see Spec.
¶ 30), reasonably support the Examiner’s finding that the claims recite the
judicial exception of a mathematical concept. See SAP America, Inc. v.
InvestPic, LLC, 898 F.3d 1161, 1166 (Fed. Cir. 2018) (“The court concluded
that the claims . . . are directed to ‘performing statistical analysis,’ specified
using words in the claims and using more technical, mathematical notation
in the written description”). Therefore, we determine that the claim recites a
mathematical concept which falls within the abstract idea category of
judicial exceptions.
Second, we find that claims 1, 12, and 16 recite methods and a system
for comparing and analyzing biological data associated with biological parts.
While these methods and system are ordinarily performed by a computer
(see Spec. ¶ 5), they ultimately represent mental processes that a biochemist
would undertake to generate a new construct.3 As explained by our

3 For example, a biologist might create a construct composed of a heat shock
promoter linked to a BCR/ABL kinase that contains a nuclear localization
signal in order to create a temperature-regulated kinase located in the nuclear
compartment. The biochemist would perform the steps recited in the claims
where the compiler would be the scientist’s own mind.
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reviewing court, “analyzing information by steps people go through in their
minds, or by mathematical algorithms, without more, [are treated] as
essentially mental processes within the abstract-idea category.” Elec. Power
Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016). Because
claims 1, 12, and 16 recite collection and analyzing information by
mathematical algorithms, we find claims 1, 12, and 16 recite a mental
process which falls within the abstract idea category of judicial exceptions.
A claim that recites a judicial exception requires further analysis to
determine if any additional elements integrate the judicial exception into a
practical application. See 84 Fed. Reg. 54. The 2019 Guidelines explain
that additional elements that integrate the judicial exception into a practical
application include applying the judicial exception in some meaningful way
beyond generally linking the use of the judicial exception to a particular
technological environment. (See 84 Fed. Reg. 55, citing Diamond v. Diehr,
450 U.S. 175, 184 (1981)). As Appellants correctly note (Br. 18–19), the
claims in Diehr recited a method for operating a rubber-molding press
including the step of “opening the press automatically when a said
comparison [of calculated cure time vs. elapsed time] indicates
equivalence.” See Diehr, 450 U.S. 179 n.5.
While this is a very close case, when we apply the Diehr reasoning
consistent with the 2019 Guidelines, we find that claims 1, 12, and 16 at
issue recite a practical application of “manufacturing the at least one
sequence of genetic parts which satisfy the constraint.”
We determine that the manufacturing step integrates the judicial
exceptions into the practical application of “creating a genetic device” as
required by claims 1, 12, and 16. This integration occurs because, as in
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Diehr, the mathematical concepts and abstract ideas recited in claims 1, 12,
and 16 result in a physical construct, a DNA sequence that when inserted
into a cell results in a particular expression product or product(s).
Specifically, the claimed methods and system are analogous to the Diehr
step of opening the press because both require a specific, practical physical
act in a particular technological environment that extends the methods
beyond mental steps or mathematical analysis. In the instant case, the
method and system do not merely inform the artisan about possible genetic
devices that might be made, but actually require the generation of a
particular DNA sequence that satisfies the desired constraints. Because we
conclude that the judicial exceptions recited in claims 1, 12, and 16 are
integrated into the practical application of methods and systems for creating
genetic devices, we conclude that claims 1, 12, and 16 are directed to patent-
eligible subject matter.
We recognize the Examiner’s point that the claims use “generically-
recited manufacturing technology that is used according to practices that
were well-understood, routine and conventional in the art prior to the time of
invention” (Ans. 7). However, we agree with Appellants that simply
because “a mathematical equation is required to complete the claimed
method and system does not doom the claims to abstraction.” Thales
Visionix Inc. v. United States, 850 F.3d 1343, 1349 (Fed. Cir. 2017). The
instant claims seek to protect the detailed, and presumably unobvious,4
method and system for creating a genetic device using the database, program

4 We note that while the Examiner cited numerous related references (see
Ans. 3), no prior art rejection is currently of record.
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editor, compiler, constraint resolution engine, in order to obtain a DNA
sequence that is then manufactured using conventional processes.
Therefore, rather than claiming an abstract idea that merely “designs a
genetic device using descriptions of genetic parts and automated constraint
resolution” (see Ans. 2), the claims specify a particular unobvious approach
to such design that results in unconventional genetic devices. See Thales,
850 F.3d at 1349 (“The claims specify a particular configuration of inertial
sensors and a particular method of using the raw data . . . . Far from claiming
the equations themselves, the claims seek to protect only the application of
physics to the unconventional configuration of sensors as disclosed.”)
We understand the claimed invention as a new laboratory technique
that transforms known genetic part information into a physical and
functional genetic device. This distinguishes the concern in Cleveland
Clinic about an invention that “does not purport to derive new statistical
methods to arrive at the predetermined or control levels of MPO that would
indicate a patient’s risk of cardiovascular disease.” Cleveland Clinic Found.
v. True Health Diagnostics LLC, 859 F.3d 1352, 1362 (Fed. Cir. 2017).
Here, Appellants assert, and the Examiner does not rebut, that “prior to
Appellant’s contribution, genetic devices were not designed in this way”
(Br. 26).
Alice Step Two
We are persuaded by the Appellants’ position that the Examiner does
not establish sufficiently that the claims on appeal satisfy Alice step one. As
such, we need not proceed to Alice step two in order to conclude that, on the
record before us, it has not been established sufficiently that the claims on
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appeal fail the Alice Test for patent eligibility.
Conclusion of Law
We conclude that claims 1, 12, and 16 are not directed to patent-
ineligible subject matter.

SUMMARY
In summary, we reverse the rejection of claims 1–6, 9–12, 15–19, 22,
and 23 under 35 U.S.C. § 101.

REVERSED

12
UNITED STATES PATENT AND TRADEMARK OFFICE
____________
BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________
Ex parte ANDREW NICHOLAS JOHN BROJER PHILLIPS and
MICHAEL DAVID PEDERSEN
____________
Appeal 2018-001191
Application 12/552,829
Technology Center 1600
____________
Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.
NEW, Administrative Patent Judge, Dissenting.
I concur with the majority’s finding that independent claims 1, 12, and
16 are each directed to a process or method and, consequently, to a category
of generally patent-eligible subject matter. See supra at 6. Furthermore, I
concur with the majority’s findings that the claims recite a nonstatutory
judicial exception to Section 101, i.e., an abstract idea. Id. at 8. However, I
part ways with the majority’s reasoning with respect to their finding that the
abstract idea recited in the claims is: “integrated into the practical
application of methods and systems for creating genetic devices.” Id. at 9.
Claim 1 recites a series of limitations, staring with: “establishing a
connection to a database of genetic parts, an entry in the database
comprising a part type and at least one part property…” and concluding
with:
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presenting the at least one sequence of the genetic parts
which satisfy the constraint; and
manufacturing the at least one sequence of genetic parts
which satisfy the constraint.
Of these limitations, the first through the penultimate recite the
judicial exception. The final limitation merely directs the user of the claim
to take the results obtained from the execution of the abstract idea upon a
generic computer and to: “manufacture the … sequence of genetic parts” in
a manner consistent with the output of the algorithm, i.e., the abstract idea.
The manner of manufacturing is not specified by the claim, nor is it defined
in the Specification, which discloses merely, by way of example, that: “Once
a device 112 is produced by the system this may be realized using a genetic
device manufacturing system 116.” Spec. 5; see also Fig. 1. It is thus
evident that any genetic device manufacturing system, past, present, or yet to
come will satisfy this limitation of claim 1.
Moreover, there is nothing in the limitations that precede this final
step that integrally ties the abstract processes recited to the manufacturing
step, either expressly or inherently. To the contrary, the language of the
claim is such that the computer process recited could be used to generate,
and present to the user, the derived genetic sequence and then, at another
time, and in another place, and by another user, the generated sequence
could be manufactured. In my opinion, there is nothing in the claim that
directly integrates the manufacturing step into the practical application of
manufacturing the desired genetic sequence. Rather, the two steps: (1) using
a generic computer to generate a sequence; and then (2) manufacturing that
sequence by means unspecified, do not represent an integration of the
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abstract idea into the practical application; rather, the manufacturing step is
simply a subsequent step that can be performed once the genetic sequence is
derived.
The USPTO’s 2019 Revised Patent Subject Matter Eligibility
Guidance, 84(4) Fed. Reg. 50 (2019) (the “Guidance”), states that:
A claim that integrates a judicial exception into a practical
application will apply, rely on, or use the judicial exception in a
manner that imposes a meaningful limit on the judicial exception,
such that the claim is more than a drafting effort designed to
monopolize the judicial exception. When the exception is so
integrated, then the claim is not directed to a judicial exception
[…] and is eligible.
Guidance 54. The question before the panel, therefore, is whether claim 1”
“appl[ies], rel[ies] on, or use[s] the judicial exception in a manner that
imposes a meaningful limit on the judicial exception, such that the claim is
more than a drafting effort designed to monopolize the judicial exception.”
Our reviewing courts have provided some meaningful guidance in
determining whether a claim imposes a meaningful limit upon a judicial
exception. In Mayo Collaborative Serv’s v. Prometheus Labs., Inc., 566
U.S. 66 (2012), the Supreme Court affirmed the proposition that: “[S]imply
appending conventional steps, specified at a high level of generality, to laws
of nature, natural phenomena, and abstract ideas cannot make those laws,
phenomena, and ideas patentable.” 566 U.S. at 82. In other words, the
Court held: “To transform an unpatentable law of nature into a patent-
eligible application of such a law, one must do more than simply state the
law of nature while adding the words ‘apply it.’” Id. at 72 (citing Gottschalk
v. Benson, 409 U.S. 63, 71–72 (1972)); see also Ariosa Diagnostics, Inc. v.
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Sequenom, Inc., 788 F.3d 1371, 1377 (Fed. Cir. 2015); Genetic Technologies
Ltd. v. Merial L.L.C., 818 F.3d 1369, 1379 (Fed. Cir. 2016).
In my opinion, the claims do no more than recite an abstract idea, i.e.,
a judicial exception to Section 101, and then, in its final limitation, merely
directs the user to apply that judicial exception by appending a conventional
step (manufacturing the derived genetic sequence), at a high level of
generality (by any means past, present, or future). As such, I am not
persuaded that the claims in question integrate the judicial exception into a
practical application.
Nor do I agree with the majority’s reasoning that Diamond v. Diehr,
450 U.S. 175 (1981) compels reversal of the Examiner’s rejection. In Diehr,
an algorithm, the Arrhenius equation, was applied by a computer to a
continuous series of temperature measurements inside a rubber mold cavity,
so as to constantly recalculate the cure time and to then signal the computer
to open the press when the optimal cure time was reached. Diehr, 450 U.S.
at 179. The Court held that: “When a process for curing rubber is devised
which incorporates in it a more efficient solution of the equation, that
process is at the very least not barred at the threshold by § 101.” Id. at 188.
By contrast, in the present appeal, all of the limitations of claim 1,
save the final one are directed to an abstract idea, with the final limitation
saying, in effect, “go apply this result.” I do not agree that this final step is
integral to the claim, but, rather, it is my opinion that the latter is merely
appended to the proceeding portion of the claim, which recites a complete
process, and merely for the purpose of adding an additional practical step
and to thus transform a patent-ineligible claim into a patentable invention. It
is, in my opinion, little more than: “a drafting effort designed to monopolize
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the judicial exception.” Guidance 54. Furthermore, I do not think, for
practical reasons, that this is either a reasonable or desirable form of patent-
drafting alchemy. I therefore respectfully dissent.