SYNTHETIC GENOMICS, INC.

Patent Trials and Appeals Board

Jul 2, 2020

2019006121 (P.T.A.B. Jul. 2, 2020)

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.
15/052,781 02/24/2016 Clyde A. Hutchison III SGIDNA1450-2 9786
95432 7590 07/02/2020
Synthetic Genomics, Inc.
c/o DLA Piper LLP (US)
4365 Executive Drive
Suite 1100
San Diego, CA 92121-2133
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
07/02/2020 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):
gtdocket@dlapiper.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte CLYDE A. HUTCHISON III,
MICHAEL G. MONTAGUE, and HAMILTON O. SMITH1
____________

Appeal 2020-006121
Application 15/052,781
Technology Center 1600
____________

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

NEW, Administrative Patent Judge.

DECISION ON APPEAL

1 We use the word Appellant to refer to “applicant” as defined in 37 C.F.R.
§ 1.42(a). Appellant identifies the real party-in-interest as Synthetic
Genomics, Inc. App. Br. 4.
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SUMMARY
Appellant files this appeal pursuant to 35 U.S.C. § 134(a) from the
Examiner’s Final rejection of claims 1, 3–5, and 15–17 as unpatentable
under 35 U.S.C. § 112(b) as being indefinite.
Claims 1, 3–5, and 15–17 also stand rejected as unpatentable under 35
U.S.C. § 101 for being directed to non-statutory subject matter.
Claims 1, 3–5, and 15–17 stand further rejected as unpatentable under
35 U.S.C. § 103(a) for being obvious over the combination of Wong et al.
(US 2003/0219756 A1, November 27, 2003) (“Wong”) and W. Ludwig et
al., ARB: A Software Environment for Sequence Data, 32(4) NUCLEIC ACIDS
RES. 1363–71 (2004) (“Ludwig”)
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

NATURE OF THE CLAIMED INVENTION
Appellant’s claimed invention is directed to methods and apparatus
for encoding human readable text conveying a non-genetic message into
nucleic acid sequences with a substantially reduced probability of biological
impact, and decoding such text from nucleic acid sequences. Abstr.

REPRESENTATIVE CLAIMS
Claim 1 is representative of the claimed subject matter, and recites:
1. A method of generating a sequence of codon identifiers
corresponding to a sequence of human readable symbols, and
assigned according to a coding scheme to convey a non-genetic
message in a human reference language, the method comprising:
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(i) receiving the sequence of human readable symbols at a
memory module;

(ii) loading a human readable symbol map within the
memory module, wherein the human readable symbol map is
configured to determine a codon identifier that maps to each
human readable symbol within the sequence, wherein the human
readable symbol map is further configured to map a human
readable symbol with a frequency of occurrence that is less than
one percent within the reference language to a start codon, and
wherein the symbol map is further configured to map a human
readable symbol with a frequency of occurrence that is greater
than five percent within the reference language to a stop codon
and no symbol is coded for by ATG; and

(iii) using a transcoder to map a sequence of codon
identifiers corresponding to each human readable symbol within
the sequence according to the human readable symbol map and
outputting the sequence,

(iv) synthesizing a nucleic acid with the sequence of step
(iii).

App. Br. 15.

ISSUES AND ANALYSES
We adopt the Examiner’s findings, reasoning, and conclusion that the
claims on appeal are indefinite under 35 U.S.C. § 112(b). However, we
decline to adopt the Examiner’s reasoning or conclusion that the claims are
directed to non-statutory subject matter or are prima facie obvious over the
cited prior art. We address the arguments raised by Appellant below.

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A. Rejection of the claims under 35 U.S.C. § 112(b)
Issue
Appellant argues that the Examiner erred in finding that the claims are
indefinite because languages define sets of symbols but do not define a
“frequency of occurrence” of those symbols, and that since a body of
documents can be variable, the symbol frequency will also vary and,
furthermore, that symbols are shared among languages but have different
frequencies of occurrence among languages. App. Br. 6 (citing Final Act.
3–4).

Analysis
The Examiner finds that the claims do not particularly point out which
symbol(s) constitute(s) “a human readable symbol with a frequency of
occurrence that is less than one percent within a reference language” and “a
human readable symbol with a frequency of occurrence that is greater than
five percent within the reference language.” Final Act. 3. The Examiner
finds that languages define sets of symbols, but do not define a “frequency
of occurrence” of those symbol. Id. The Examiner reasons that the
frequency of occurrence of symbols can be determined from a specific body
of one or more documents, but since a body of documents is a variable
object, the symbol frequency will vary from one body of work to another.
Id. (citing MPEP § 2173.05(b)(II)). The Examiner notes that Appellant’s
Specification tacitly admits that symbol frequencies are not set, and instead
vary depending upon the input – the Specification discloses “a symbol
frequency analyzer for determining how frequently certain symbols appear
within one or more input symbol streams.” Id. (quoting Spec. ¶ 127).
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The Examiner next finds that symbols (e.g., letters, numbers and
punctuation marks) are shared among languages, but have different
frequencies of occurrence among languages. Final Act. 3. The Examiner
notes that English, French, Italian, Portuguese, and Spanish share most of
their alphabets, but estimates of letter frequency from bodies of documents
in each language will be substantially different. Id. at 3–4. For example,
the Examiner finds, “h” has a relatively high frequency of occurrence in
English, but not in any of the other four languages, and “v” is less common
in English than in the others. Id. at 4.
The Examiner therefore reasons that, given two symbols, a person of
ordinary skill in the art would not be able to determine with certainty
whether those symbols fell within the scope of the limitation of independent
claim 1 reciting “a human readable symbol with a frequency of occurrence
that is less than one percent within a reference language” or the limitation “a
human readable symbol with a frequency of occurrence that is greater than
five percent within the reference language,” since neither the language nor
the body of work that establish the symbol frequency are defined by the
claims. Final Act. 4. The Examiner concludes that the claims are indefinite
because they fail to inform a person of ordinary skill in the art of the metes
and bounds of the invention, and that a skilled artisan would not be able to
determine what sets of symbols infringe the claims. Id.
Appellant argues that claim 1 recites that the method involves loading
within a memory module a human readable symbol map that maps a human
readable symbol with a frequency of occurrence that is less than 1% within
the reference language to a start codon and maps a human readable symbol
with a frequency of occurrence that is greater than 5% within the reference
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language to a stop codon. App. Br. 7. Similarly, argues Appellant,
independent claim 15 recites a data structure configured to map a human
readable symbol with the recited frequencies of occurrence. Id.
Appellant contends that a person of ordinary skill would readily
comprehend that the frequency of occurrence of a symbol differs depending
on which reference language is used. App. Br. 7. In support of this
contention, Appellant points to the Declaration of Dr. Michael Montague
(the “Montague Declaration” filed February 24, 2016). In the Declaration,
Dr. Montague states that the frequency of occurrence of human readable
symbols in various reference languages is well known in the art and is easily
ascertainable from public sources, i.e., a simple Internet search on letter
frequency or linguistic resources at a public library. Id. (citing Montague
Decl. ¶¶ 4–5).
Appellant notes that, by way of example, Dr. Montague determined
the frequency of occurrence of the letter “E” is about 13% in English, about
15% in French, about 16% in German, and about 12% in Spanish. App. Br.
7 (citing Montague Decl. ¶¶ 4–5). Conversely, Dr. Montague attests, the
letter “J” occurs with a frequency of less than 1 % in English, French,
German, or Spanish. Id. Appellant also asserts that Dr. Montague states that
the same information is readily available for the other letters in many
reference languages, Portuguese, Esperanto, Italian, Turkish, Swedish,
Polish, Dutch, Danish, Icelandic, Finnish, Czech, and others. Id. (citing
Montague Decl. ¶ 5).
Therefore, argues Appellant, a person of ordinary skill in the art could
easily ascertain the reference language of the message (e.g., English or
French or German, etc.), and the frequency of occurrence of a particular
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symbol in the particular reference language. App. Br. 7. Even if such were
not available from public sources in an obscure language, the frequency
could be determined without inventive work or undue experimentation since
persons of ordinary skill in the linguistic arts clearly know how to make such
calculations. Id. at 7–8.
Appellant argues that, despite the Examiner’s finding that a body of
documents is a variable object, a person of ordinary skill in the linguistic arts
know what type of document they are reviewing (e.g., a scientific document,
conventional text, etc.). App. Br. 8. Therefore, argues Appellant, and
regardless of nature of the body of work, a skilled artisan could readily
calculate the frequency of occurrence of various letters symbols without
undue experimentation, and in the same manner that such values are
calculated in the sources. Id. (citing Montague Decl. ¶¶ 4–5). Appellant
asserts that a person of ordinary skill in the art would understand that this is
a statistical calculation and further understands how to perform it. Id.
Appellant alleges that the Examiner has applied an incorrect legal
standard in requiring an “absolute precision” that the Federal Circuit has
held is not attainable, and that is greater than “reasonable certainty” with
respect to the subject matter. App. Br. 8 (citing Bancorp Servs., LLC v.
Hartford Life Ins. Co., 359 F.3d 1367, 1369 (Fed. Cir. 2004); see also
Nautilus Inc. v. Biosig Instruments, Inc., 572 U.S. 898, 910 (2014) (holding
that “‘the certainty which the law requires in patents is not greater than is
reasonable, having regard to their subject matter’” (quoting Minerals
Separation, Ltd. v. Hyde, 242 U.S. 261, 270 (1916))).
The Examiner responds that numerous online and print resources do
provide letter frequency tables for many languages, including English, but
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these tables are not consistent because the letter frequencies are estimated
from different bodies of work. Ans. 11. The Examiner refers to six letter
frequency tables, acquired from public sources on the Internet and submitted
as evidence of record during prosecution, that demonstrate that the limitation
reciting “a human readable symbol with a frequency of occurrence that is
less than one percent within the reference language” might or might not
include the letters “K” and “V”, and the limitation reciting “a human
readable symbol with a frequency of occurrence that is greater than five
percent within the reference language" might or might not include the letters
“H,” “R,” and “L.” Id. The Examiner points out that these exemplary tables
are English-language tables, but Appellant’s Specification discloses that the
recited “reference language” can be any natural language and need not
match the language of the “sequence of human readable symbols.” Id.
(citing Spec. ¶ 87),
The Examiner concludes that the claim is indefinite because the same
“human readable symbol map” might not infringe the claim when using a
letter frequency table estimated from one body of work, but might infringe
the claim when using a letter frequency table estimated from a different
body of work. Ans. 11.
By way of example, the Examiner suggests a case in which a
practitioner could start with a letter frequency table in which “V” has a
frequency of greater than 1% percent, and then generate a symbol mapping
in which the letter “V” is the only symbol that maps to a start codon. Id. at
11–12. The practitioner would thus reasonably expect that that symbol
mapping does not infringe the claim, because it does not “map a human
readable symbol with a frequency of occurrence that is less than one percent
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within the reference language to a start codon.” Id. at 12. In this
hypothetical, however, the Examiner posits that a party, in trying to show
infringement of the claim, could use a different letter frequency table in
which the letter “V” has a frequency of less than 1%. Id. In such an
instance as this, the Examiner finds, the practitioner’s symbol map does
“map a human readable symbol with a frequency of occurrence that is less
than one percent within the reference language to a start codon” and
consequently would infringe the claim. Id.
The Examiner reasons that a claim that is infringed in some
circumstances, but not in others, that is, a claim having a scope that changes
based on some variable quantity - does not distinctly claim the invention,
even with reasonable certainty. Ans. 12.
We are not persuaded by Appellant’s arguments. Section 112(b)
“require[s] that a patent’s claims, viewed in light of the specification and
prosecution history, inform those skilled in the art about the scope of the
invention with reasonable certainty.” Nautilus, 572 U.S. at 912. The
Examiner has concluded that the claims are indefinite because, depending
upon the given frequency table used by a hypothetical practitioner, the
practice of the claimed method may or may not be infringing upon
Appellant’s claims.
The Examiner relies upon evidence of record to demonstrate that, for
example, depending upon the English language-source use, the frequency of
the letter “V” used is either 0.98%, 1.11%, 1.01%, 1.06%, 0.98%, or 1.05%.
See Non-Patent Literature, filed October 12, 2018. Similarly, the letter “H”
has a frequency of, respectively, 6.09%, 5.92%, 3.00%, 4.96%, 6.24%, or
5.05%, depending upon the table consulted. Id. It is evident, therefore, as
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the Examiner explains, that mapping the letter “V” as a start codon, or the
letter “H” to a stop codon, would infringe in some instances and not in
others, depending upon the frequency table employed by a given
practitioner.
Because claims delineate the patentee’s right to exclude, the
patent statute requires that the scope of the claims be sufficiently
definite to inform the public of the bounds of the protected
invention, i.e., what subject matter is covered by the exclusive
rights of the patent. Otherwise, competitors cannot avoid
infringement, defeating the public notice function of patent
claims.

Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1249 (Fed. Cir.
2008). Furthermore, “[e]ven if a claim term’s definition can be reduced to
words, the claim is still indefinite if a person of ordinary skill in the art
cannot translate the definition into meaningfully precise claim scope.” Id. at
1251.
Appellant argues that a skilled artisan in the linguistic arts would
know what type of document they are reviewing (e.g., a scientific document,
conventional text, etc.) and, regardless of nature of the body of work, could
readily calculate the frequency of occurrence of various letters symbols
without undue experimentation, and in the same manner that such values are
calculated in the sources. See App. Br. 8 (citing Montague Decl. ¶¶ 4–5).
Specifically, the Montague Declaration states that:
Persons of ordinary skill in this field know that the frequency of
occurrence of various human readable symbols in a particular
language varies depending on the language. Such persons also
know that the frequency of occurrence of particular human
readable symbols in various languages can be readily determined
by resort to publicly available information. An online search on
letter frequency quickly reveals charts that set out the frequency
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of occurrence of human readable symbols in various languages,
and this information is available to the public – whether from
internet sources or from public libraries. This permits a person of
ordinary skill to quickly ascertain the frequency of occurrence of
such symbols in various languages of interest. This information
was available prior to 2009, also from publicly available sources
and has been of interest to the sciences, e.g.[,] in the field of
linguistics.

Montague Decl. ¶ 4.
We do not find this argument persuasive. As an initial matter, the
Montague Declaration does not define, or provide evidence supporting, the
qualifications and knowledge of a person of ordinary skill “in this field,” or
even what “this field” may happen to constitute.
More importantly, the Montague Declaration does not rebut the
Examiner’s evidence that English language-letter frequency tables show
variation in letter frequency, when derived from different, non-specialized
sources. Moreover, in addition to the subject matter of the body of work,
whether specialized or non-specialized, from which such a frequency table is
derived, factors such as sample size are almost certain to affect the
frequency of letters in the table. Furthermore, Appellant’s Specification
discloses that the reference language “reference language” refers to “any
language on the planet.” Spec. ¶ 87. We find that, given the necessary
variability that such a broad definition implies, it would be dauntingly
difficult for a skilled artisan to know with reasonable certainty whether a
claimed letter, mapped to a start or stop codon, would be infringing or no-
infringing of the claimed method.
As such, we conclude that the claims do not, when viewed in light of
Appellant’s Specification and prosecution history, inform a person of
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ordinary skill in the art about the scope of the invention with reasonable
certainty, because a skilled artisan could not know, with reasonable
certainty, whether practicing the method recited in the claims is infringing or
not. See Nautilus, 572 U.S. at 912. We conclude, consequently, that the
claims are indefinite under Section 112(b), and we affirm the Examiner’s
rejection upon this ground.

B. Rejection of the claims under 35 U.S.C. § 101
Issue
Appellant argues that the Examiner erred in concluding that
Appellant’s claims do not amount to significantly more than the abstract idea
of a procedure for organizing information by “generating a sequence of
codon identifiers corresponding to a sequence of human readable symbols.”
App. Br. 8 (citing Final Act. 5).

Analysis
The Examiner finds that components of the claimed method recited in
the claims include a “sequence of human readable symbols,” a “human
readable symbol map[ ] configured to map a human readable symbol … to a
start codon, and [ ] configured to map a human readable symbol … to a stop
codon” and a “sequence of codon identifiers corresponding to each human
readable symbol within the sequence.” Final Act. 5. The Examiner fids
that, considered as a whole, the invention is directed to an abstract idea
because the series of steps in which information is organized is essentially
the innovative aspect of the invention. Id. (citing, e.g., Spec. ¶¶ 17–21, 89–
154). However, the Examiner finds, Appellant’s Specification discloses
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only a de minimis description of how that information is organized using
generic technology. Id. (citing Spec. ¶¶ 32–36, 58–63). Therefore, the
Examiner concludes, the claims appear to monopolize the abstract idea
itself, rather than confining the use of the abstract idea to a particular
technological application, or integrating it into a particular inventive
concept. Id. at 5–6. Consequently, the Examiner reasons, the claims are not
patent eligible. Id. at 6 (citing MPEP § 2106.05).
Appellant argues that the steps or structures recited in the claims
allow the user to synthesize a nucleic acid sequence containing a non-genetic
message that does not have a biological impact on an organism carrying the
nucleic acid. App. Br. 9. Appellant points to the Specification’s explanation
that this means that there is a low probability that a nucleic acid synthesized
by the method will be transcribed or translated by a cell’s internal biological
processes, due to the prevalence of stop codons. Id. (citing Spec. ¶ 17).
According to Appellant, a message-carrying sequence encoded according to
the claimed method will therefore be unlikely to be transcribed due to the
scarcity of start codons, and any sequences that happen to begin
transcription are likely to be cut off by the prevalence of stop codons. Id.
Appellant asserts that that the message can therefore be safely and
innocuously carried and replicated by cells and can be decoded to provide
the message carried therein with a low probability of unwanted transcription.
Id. (citing Spec. ¶ 18). Consequently, argues Appellant, the claims recite
significantly more than the alleged abstract idea of a procedure for
organizing information, and do not tie up an abstract idea. Id. (quoting Final
Act. 5).
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Appellant contends that, contrary to the Examiner’s findings, the
claims recite specific requirements for what symbols can be mapped to a
start codon or a stop codon, and which every sequence must contain. App.
Br. 9. Appellant argues that, because the claims require that a symbol with a
frequency of occurrence of greater than five percent is mapped to a stop
codon, the sequences encoded will have a relatively high number of stop
codons. Id. Similarly, argues Appellant, because the claims require that a
symbol with a frequency of occurrence of less than one percent is mapped to
a start codon, the sequence will have a low number of start codons. Id. at 9–
10. Appellant asserts that these rules permit the nucleic acid generated to
have a low biological impact on an organism carrying the sequence. Id. at
10. Therefore, argues Appellant, the claims recite additional elements
demonstrating that the claims as a whole do not seek to tie up the abstract
idea and are not wholly directed to subject matter encompassing a judicially
recognized exception. Id. (citing MPEP § 2106.04(a)(l)(II)).
Appellant likes the claims on appeal to those in McRO, Inc. v. Bandai
Namco Games Am. Inc., 837 F.3d 1299 (Fed. Cir. 2016). App. Br. 10. As in
McRO, argues Appellant, the claims on appeal involve methods of
generating a sequence of codon identifiers according to limited rules,
reflecting a specific implementation that would not have been used by a
person of ordinary skill in the art. Id. Appellant therefore asserts that the
specific method does not preempt the use of rules of other processes or
techniques and is integrated into a practical application. Id.
Appellant argues further that the claims on appeal include additional
steps or structures that show the subject matter of the claims is integrated
into a practical application, and adds something significant to, the natural
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principle itself and impose meaningful limits on the claim scope. App. Br.
11. Appellant points to the claims’ requirement that a nucleic acid is
synthesized carrying a non-genetic message that does not have a biological
impact on an organism carrying the nucleic acid. Id. (citing Spec. ¶ 17).
In performing an analysis of patentability under 35 U.S.C. § 101, we
follow the framework set forth by the Supreme Court in Mayo Collaborative
Servs. v. Prometheus Labs., Inc., 566 U.S. 66 (2012). We are also mindful
of, and guided by, the United States Patent and Trademark Office’s 2019
Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50
(January 7, 2019) (the “2019 Guidance”).
Appellant’s independent claim 1 recites, inter alia: “A method of
generating a sequence of codon identifiers corresponding to a sequence of
human readable symbols, and assigned according to a coding scheme to
convey a non-genetic message in a human reference language….”
Following the first step of the Mayo analysis, we find that the claims are
directed to a method or process and therefore fall into one of the broad
statutory categories of patent-eligible subject matter under 35 U.S.C. § 101.
In the next step of the Mayo analysis, we determine whether the claim
at issue is directed to a nonstatutory, patent-ineligible concept, i.e., a law of
nature, a phenomenon of nature, or an abstract idea. Mayo, 566 U.S. at 70–
71. If the claim is so directed, we next consider the elements of the claim
both individually and “as an ordered combination” to determine whether
additional elements “transform the nature of the claim” into a patent-eligible
application. Id. at 78–79; see also Ariosa Diagnostics, Inc. v. Sequenom,
Inc., 788 F.3d 1371, 1375 (Fed. Cir. 2015). Specifically, the Supreme Court
considered this second step as determining whether the claim recites an
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element or combination of elements that is “sufficient to ensure that the
patent in practice amounts to significantly more than a patent upon the
[ineligible concept] itself.” Mayo, 566 U.S. at 72–73.
More specifically, in this second step of the Mayo analysis, we look to
whether the claim recites one of the judicially-created exceptions to 35
U.S.C. § 101, i.e., an abstract idea, a law of nature, or a natural phenomenon.
See 2019 Guidance 54 (Step 2A, Prong 1). If we determine that the claim
recites a judicial exception, we then determine whether the limitations of the
claim reciting the judicial exception are integrated into a practical
application. Id. (Step 2A, Prong 2).
Finally, if we determine that the claim is directed to a judicially-
created exception to 35 U.S.C. § 101, we evaluate the claim under the next
step of the Mayo analysis, considering the elements of each claim both
individually and “as an ordered combination” to determine whether
additional elements “transform the nature of the claim” into a patent-eligible
application. Mayo, 566 U.S. at 78–79; 2019 Guidance 56 (Step 2B).
Claim 1 recites the steps of: (1) receiving a sequence of human
readable symbols at a memory module; (2) loading a human readable
symbol map within the memory module, in which the human readable
symbol map is configured to determine a codon identifier that maps to each
human readable symbol within the sequence; (2a) the human readable
symbol map is further configured to map a human readable symbol with a
frequency of occurrence that is less than one percent within the reference
language to a start codon; (2b) the symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is greater than
five percent within the reference language to a stop codon; (2c) no symbol is
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coded for by ATG; (3) using a transcoder to map a sequence of codon
identifiers corresponding to each human readable symbol within the
sequence according to the human readable symbol map, and (4) synthesizing
a nucleic acid with the sequence of step (3).
More simply put, Appellant’s claimed method comprises using a
generic computer to compose a map in which human readable symbols (e.g.,
letters, numbers) correspond to a codon of nucleotide bases, and in which a
symbol with low frequencies of occurrence (>1%) in the language
correspond to a start codon and one with a higher frequency (>5%)
corresponds to a stop codon (and no symbol coded for the codon ATG). A
transcoder is then used to map a sequence of codons such that the
corresponding symbols in a sequence that corresponds to a desired
“message,” and a DNA sequence is then synthesized from that template.
Claim 1 is thus directed, at least in part, to a series of computational
steps by which human readable symbols are mapped onto codon sequences,
subject to various rules (viz., steps 2a-c, supra). These steps can be mapped
using a generic processor. Appellant’s Specification discloses:
[T]he terms “processor,” “microprocessor,” and “digital
processor” include all types of digital processing devices
including, without limitation, digital signal processors (DSPs),
reduced instruction set computers (RISC), general-purpose
(CISC) processors, microprocessors, gate arrays (e.g., FPGAs),
programmable logic devices (PLDs), reconfigurable compute
fabrics (RCFs), array processors, and application-specific
integrated circuits (ASICs). Such processors may be contained
on a single unitary IC die or distributed across multiple
components.

Spec. ¶ 63. A series of abstract steps (i.e., mapping one set of symbols to
another), performed upon a generic processor is, by itself, not generally
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patent eligible. Annotated Figure 3 of Appellant’s Specification illustrates
the general mapping process:

Figure 3 of Appellant’s Specification (amended) depicts an
exemplary symbol map 220

We find that these processes recited in these computational steps
could be performed equally either mentally or with a pencil and paper and,
as reflecting mental processes, are not patentable subject matter. See
CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1373 (Fed. Cir.
2011) (holding that:
Methods which can be performed entirely in the human mind are
unpatentable … because computational methods which can be
performed entirely in the human mind are the types of methods
that embody the “basic tools of scientific and technological
work” that are free to all men and reserved exclusively to none

(quoting Gottschalk v. Benson, 409 U.S. 63, 67 (1972)).
Appellant’s Specification discloses no express definition of the claim
term “transcoder.” However, the transcoder is described as being
“configured to both encode and decode an input human readable symbol
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sequence, [and] it should be understood that the associated encoding and
decoding logic may be separated and/or distributed among multiple systems,
devices, and/or computer networks.” Spec. ¶ 75; see also id. at ¶ 120,
describing:
[A]n exemplary transcoder 200 configured to encode an input
symbol sequence into a codon sequence such that the codon
sequence has substantially no biological impact on a host
organism if introduced into the organism as a synthetic nucleic
acid sequence (e.g., as free DNA). The transcoder 200 may also
be configured to decode an input sequence of codons and thereby
yield the originally input symbol sequence. Thus, the exemplary
transcoder 200 depicted in Figure 2 may be used to both encode
a human readable symbol sequence into a codon sequence, and
to decode a codon sequence into a human readable symbol
sequence.

In other words, the transcoder functions to “read” the symbol/codon map
either forward (i.e., readable symbol sequence to codon sequence) or
backwards (i.e., codon sequence to readable symbol sequence). Moreover,
Appellant’s Specification discloses that the transcoder can be distributed
within the processor unit. See Spec. ¶ 123:
In some embodiments, the I/O modules 216 may consist of one
or more device drivers adapted to interface a set of hardware
devices with an operating system associated with the transcoder
200. Note that the I/O modules 216 may be implemented as any
combination of software, firmware, or hardware according to
embodiments described herein.

Because this relatively simple function could also be performed
mentally, or with paper and pencil, we similarly find that this step (step 3
supra) is also directed to an abstract idea. See Cybersource, 654 F.3d at
1373.
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Because we find that these steps are directed to an abstract idea, we
then proceed to the next step of the analysis, which is to determine whether
the limitations of the claim reciting the judicial exception are integrated into
a practical application. 2019 Guidance 54 (Step 2A, Prong 2). The 2019
Guidance provides additional context for this analysis, stating 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.” Id. at 53.
We conclude that the claims are integrated into a practical application.
Although, as we have explained, the claims are directed to an abstract idea
(i.e., a mental function), the preamble of claim 1 recites: “A method of
generating a sequence of codon identifiers corresponding to a sequence of
human readable symbols, and assigned according to a coding scheme to
convey a non-genetic message in a human reference language.”
Furthermore, the final limitation of claim 1 recites: “synthesizing a nucleic
acid with the sequence of step (iii).”
Generally, a preamble limits the invention if it recites essential
structure or steps, or if it is “necessary to give life, meaning, and vitality” to
the claim. See Catalina Marketing Int’l, Inc. v. Coolsavings.com, Inc., 289
F.3d 801, 808 (Fed. Cir. 2002) (citing Pitney Bowes, Inc. v. Hewlett–
Packard Co., 182 F.3d 1298, 1305 (Fed. Cir. 1999)). Conversely, a
preamble is not limiting “where a patentee defines a structurally complete
invention in the claim body and uses the preamble only to state a purpose or
intended use for the invention.” Catalina, 289 F.3d at 808 (quoting Rowe v.
Dror, 112 F.3d 473, 478 (Fed. Cir. 1997)). In this instance, we conclude
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that the preamble is limiting upon the claim, because it is necessary to give
life, meaning, and vitality to the claim. Although these words are inexact in
their precise meaning, we understand them to apply in this case because the
language of the preamble describes the essence of the invention, that is, to
generate a sequence of codon identifiers corresponding to a sequence of
human readable symbols and creating a coding scheme to convey a non-
genetic message in a human reference language. As the Specification
discloses, Appellant’s invention is
directed to generating an encoding scheme configured to
translate human readable symbols into codon identifiers (i.e.,
discrete sequences of preferably three elements, where each
element contains one of four selected nucleotide bases). In this
manner, sequences of human readable symbols can be used to
convey non-genetic messages (for example, text messages,
trademarks, copyright notices, unique identifying information,
etc.) by encoding the message into sequences of codon
identifiers. These sequences of codon identifiers may then be
used to generate synthetic nucleic acid sequences that are
introduced into a living cell or organism as free DNA or
incorporated into other various types of cellular nucleic acid
materials…. The resulting set of codons or codon identifiers
effectively serves as a memory source for the encoded sequences
of human readable symbols.

Spec. ¶ 17. In other words, the abstract mental steps recited in claim 1 are
integrated into an application for inserting into a living cell a sequence of
free nucleic acid that is not metabolically active, but can represent a message
that is readable by observers. We find that this is not an attempt to capture
the entire abstract idea of substituting human readable symbols for
nucleotide based-codons in a table, but rather as a means of generating a
nucleic acid-based message in a cell.
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This conclusion is further reinforced by using the abstract idea of
encoding symbols as nucleotide based-codons to synthesize a corresponding
nucleic acid, as recited in the final limitation. As the Specification discloses,
such synthesized DNA can subsequently be inserted into a cell or biological
system as a persistent message or identifier. See Spec. ¶ 17.
Because we find that the claimed method “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,” (see 2019 Guidance 53), we
conclude that the claims are integrated into a practical application under step
2A, prong 2. Consequently, our analysis ends there. We therefore reverse
the Examiner’s rejection of the claims upon this ground.

C. Rejection of the claims under 35 U.S.C. § 103
Issue
Appellant contends that the Examiner erred in concluding that the
symbol map and data structure recited in the claims are descriptive data that
do not perform a function within the computer, and do not have a functional
relationship with the process performed and are therefore not limiting on the
claims. App. Br. 12.

Analysis
The Examiner finds that Wong teaches “a method of storing data in a
living organism,” comprising receiving specific data to be stored in DNA,
and “encoding DNA to represent [the] specific data by selecting at least 2 of
the four DNA nucleotide bases to represent specific text and arranging the
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nucleotide bases in a manner to represent the data.” Final Act. 10 (quoting
Wong ¶ 21). The Examiner finds that Wong teaches that the data can be
encoded by using a look-up table in which codons are used to represent
numbers, letters and punctuation marks. Id. (citing Wong Table 1). The
Examiner reasons that this teaches the limitation of claim 1 reciting “the
human readable symbol map is configured to determine a codon identifier
that maps to each human readable symbol within the sequence.” Id. The
Examiner finds that Wong further teaches outputting the DNA sequence that
encodes the data, and synthesizing the DNA sequence. Id. (citing Wong ¶
36).
The Examiner acknowledges that Wong does not teach that in the
look-up table
[T]he human readable symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is
less than one percent within a reference language to a start codon,
and wherein the symbol map is further configured to map a
human readable symbol with a frequency of occurrence that is
greater than five percent within the reference language to a stop
codon and no symbol is coded for by ATG.

Final Act. 10. However, the Examiner finds that the “human readable
symbol map” is descriptive material that does not have a functional
relationship with the memory module into which it is loaded, but is, rather,
nonfunctional descriptive material. Id. at 10–11. The Examiner maintains
that differences in nonfunctional descriptive material are not sufficient to
patentably distinguish an invention from the prior art, and that a claimed
computer-implemented method must be distinguished from the prior art by
the functional steps that are performed, not by the non-functional data on
which the method operates. Id. at 11 (citing Ex Porte Nehls, 88 USPQ2d
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1883, 1889 (BPAI 2008); King Pharmas., Inc. v. Eon Labs, Inc., 616 F.3d
1267, 1280 (Fed. Cir. 2010)). The Examiner therefore reasons that this
difference between the teachings of Wong and the claimed invention is not
sufficient to patentably distinguish the invention from Wong. Id.
The Examiner also acknowledges that Wong does not teach the
limitation of claim 1 reciting “a memory module” in which the specific data
and the symbol map are loaded, or implementing the method as “an
apparatus ... comprising a processor ... and a storage module,” as recited in
claim 15. Final Act. 11. However, the Examiner finds that Ludwig teaches
a suite of software for working with sequence data, in which “the sequence
data can be visualized and modified with a powerful editor” that allows
sequences to be created or edited as desired. Id. (citing Ludwig 1365 §
“Sequence editors”). The Examiner finds that Ludwig teaches that this
software runs on computers with processors and memory. Id. (citing
Ludwig 1370 § “Systems, hardware and processing time requirements”).
The Examiner concludes that it would have been obvious to a person
of ordinary skill in the art to implement the data encoding procedure of
Wong using software, as taught by Ludwig, resulting in a software system in
which the specific data being encoded as DNA, and the look-up table for
translating symbols in the data as nucleic acid codons, are both loaded into
memory. Final Act. 11. The Examiner further concludes that such an
implementation would also result in a computer apparatus comprising a
processor and “a storage module,” comprising the look-up table (i.e., “a data
structure for mapping codon identifiers”). Id.
On appeal, Appellant argues that the Examiner’s reasoning is legally
incorrect, and that the facts of the present case are similar to those of In re
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Lowry, 32 F.3d 1579 (Fed. Cir. 1994). App. Br. 12. Appellant contends that
Lowry involved a claim reciting a stored memory data structure, which both
the examiner and the Board found were analogous to printed matter that,
lacking a functional printed matter-substrate relationship, was therefore
deserving of no patentable weight. Id. (citing Lowry, 32 F.3d at 1580).
Appellant points out that the Federal Circuit reversed, stating that the
Board must consider all claim limitations when determining the patentability
of an invention over the prior art, and that claim limitations comprised of
printed matter may not be disregarded. App. Br. 12 (citing Lowry, 32 F.3d
at 1582). Appellant notes that the Federal Circuit cited their decision in In
re Gulack, 703 F.2d 1381 (Fed. Cir. 1983), cautioning against a liberal use
of “printed matter rejections” under 35 U.S.C. §103. Id. at 12–13 (citing
Lowry, 32 F.3d at 1583 (quoting Gulack, 703 F.2d at 1385 n.8)).
Appellant argues that the Examiner’s rejection of the claims on appeal
is based on a misinterpretation of Lowry. App. Br. 13 (citing Final Act. 12–
13). However, argues Appellant, the language of Lowry makes it clear that,
similar to the disputed limitations, the data structures of Lowry are not
analogous to printed matter. Id. (quoting Lowry, 32 F.3d at 1583).
Appellant argues further that Wong neither teaches nor suggests
mapping a symbol with a frequency of occurrence of greater than 5% to a
stop codon, as recited in the claims. App. Br. 14. According to Appellant,
Wong teaches to map the ATG start codon (which is excluded by the claims
on appeal) to the letter “E”, which in English (or French, German, and
Spanish) has a frequency of occurrence much higher than the “less than one
percent,” recited in the claims. Id. (citing Montague Decl. ¶ 5). Appellant
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contends that Wong therefore teaches away from the claimed invention by
teaching a symbol coded for by ATG. Id.
Appellant argues further that Wong fails to teach or suggest that a stop
codon should be mapped to a symbol with a frequency of occurrence of
greater than five percent. App. Br. 14. Appellant argues that Ludwig does
not provide any teachings or suggestions that cure these alleged deficiencies
of Wong. Id.
The Examiner responds that the “human readable symbol map” and
“data structure for mapping codon identifiers into human readable symbols”
of the instant claims are not analogous to the data structures of Lowry. Ans.
14. The Examiner finds that the attribute data objects (“ADOs”) of Lowry
are functional data structures because they “do not represent merely
underlying data in a database. ADOs contain both information used by
application programs and information regarding their physical
interrelationships within a memory.” Id. (quoting Lowry, 32 F.3d at 1583).
The Examiner finds that the limitations of the claims reciting “human
readable symbol map” and “data structure for mapping codon identifiers into
human readable symbols” contain no “information regarding[ ] physical
interrelationships within a memory.” Ans. 15. Instead, finds the Examiner,
the “human readable symbol map” and “data structure for mapping codon
identifiers into human readable symbols” are, as illustrated and described in
Appellant’s Specification, nothing more than a data table. Id. (citing Spec.
Fig. 3, ¶ 114).
The Examiner further finds that the Specification further describes “a
transcoder module for translating a sequence of symbols into a sequence of
codon identifiers and/or for translating a sequence of codon identifiers into a
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sequence of symbols .... The transcoder module may utilize one or more
symbol maps as an input argument, value, or parameter.” Ans. 15 (citing
Spec. ¶ 132). In other words, the Examiner reasons, the “symbol map” and
“data structure for mapping codon identifiers into human readable symbols”
are the input data used by the transcoder module to encode the input
sequence of human readable symbols as the output sequence of nucleotides.
Id.
The Examiner finds that the claims recite that the actual function of
mapping human readable symbols to a nucleotide sequence is performed by
the “transcoder,” which implements a “mapping function.” Ans. 15 (citing
Spec. ¶¶ 93–94) that utilizes the “one or more symbol maps.” Therefore, the
Examiner reasons, whereas the “transcoder module” would be implemented
as programming or computer executable code, the “symbol map” and “data
structure for mapping codon identifiers into human readable symbols” are
not programming or computer executable code. Id. Rather, the Examiner
finds, they are descriptive data that do not perform a function within the
computer, and do not have a functional relationship with the process
performed by the computer or the machine readable media that contains
them. Id. The Examiner notes that, where “the computer-readable medium
merely serves as a support for information or data, no functional relationship
exists.” Id. (citing MPEP § 2111.05(III)).
The Examiner finds that, in view of these disclosures of the
Specification, the instant “human readable symbol map” and “data structure
for mapping codon identifiers into human readable symbols” are unlike the
ADOs of Lowry, and are instead analogous to the nucleic acid sequences in
the system at issue in Nehls. Ans. 15. The Examiner notes that, in Nehls,
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the claimed invention was directed to a computer system that differed from
the prior art “only in the content of the data storage means.” Id. (quoting
Nehls, 88 USPQ2d at 1887). The Examiner points out that the Board
reasoned that:
There is no evidence that SEQ ID NOs 9-1008 functionally affect
the process of comparing a target sequence to a database by
changing the efficiency or accuracy or any other characteristic of
the comparison. Rather, the SEQ ID NOs are merely information
being manipulated by a computer; the SEQ ID NOs are inputs
used by a computer program that calculates the degree of
similarity between a target sequence and each of the sequences
in a database. The specific SEQ ID NOs recited in the claims do
not affect how the method of the prior art is performed – the
method is carried out the same way regardless of which specific
sequences are included in the database .... Thus, the descriptive
material in this case is properly considered to be nonfunctional.

Id. at 15–16 (quoting Nehls, 88 USPQ2d at 1888).
The Examiner explains that, like the SEQ IDs in Nehls, the “human
readable symbol map” of the instant claims “do not affect how the method of
the prior art is performed – the method is carried out the same way
regardless of which specific [symbol mappings] are included in the
database.” Ans. 16. The Examiner emphasizes that the Specification
expressly discloses that it is the transcoder, and not the “human readable
symbol map,” that is the functional element that “encode[s] an input symbol
sequence into a codon sequence.” Id. (quoting Spec. ¶ 120). The Examine
further finds that Appellant’s Specification discloses that “the non-volatile
memory may include one or more symbol maps which may be used to
construct synthetic nucleic acid sequences,” and that the system, specifically
the transcoder, operates in the same manner regardless of which symbol map
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is actually being used. Id. (quoting Spec. ¶ 128). The Examiner finds that
the symbol maps do nothing more than describe the correspondence between
human-readable symbols and the codon identifiers, which the transcoder
uses to perform its function of mapping a sequence of human-readable
symbols to a sequence of codon identifiers. Id. The mapping itself, explains
the Examiner, is a nonfunctional descriptive data table, and the instant
symbol map is therefore insufficient to patentably distinguish the invention
from the teachings of Wong, which also teaches a data table that maps
human-readable symbols to codon identifiers. Id.
We are not persuaded by the Examiner’s reasoning. Specifically, the
Examiner finds that the “human readable symbol map” and “data structure
for mapping codon identifiers into human readable symbols” are analogous
to printed matter because it is not, as in Nehls, functional material. See
Nehls, 88 USPQ2d at 1891. The Examiner contends that it is the transcoder,
which “map[s] a sequence of codon identifiers corresponding to each human
readable symbol within the sequence according to the human readable
symbol map and output[s] the sequence,” operates in the same manner
regardless of which symbol map is actually being used, and that the symbol
map and data structure are merely inputs. See Ans. 16.
We disagree. Claim 1 recites, in relevant part:
Receiving the sequence of human readable symbols at a memory
module [and] loading a human readable symbol map within the
memory module, wherein the human readable symbol map is
configured to determine a codon identifier that maps to each
human readable symbol within the sequence, wherein the human
readable symbol map is further configured to map a human
readable symbol with a frequency of occurrence that is less than
one percent within the reference language to a start codon, and
wherein the symbol map is further configured to map a human
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readable symbol with a frequency of occurrence that is greater
than five percent within the reference language to a stop codon
and no symbol is coded for by ATG….

In other words, the memory module receives a set of human-readable
symbols and configures the symbols into a map in which a given symbol
corresponds to a given codon. The map is not simply loaded into the
memory module as a map, rather, the symbol/codon map itself is configured,
or structured by the module itself, and the map forms a functional unit
related to the substrate (i.e., the non-volatile memory) of the module.
Furthermore, the limitations require the memory module and,
specifically, the “data structure for mapping codon identifiers into human
readable symbols” to impose certain rules upon the manner by which the
data is structured. Specifically, the claims require that:
[T]he human readable symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is
less than one percent within the reference language to a start
codon, and wherein the symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is
greater than five percent within the reference language to a stop
codon and no symbol is coded for by ATG.

These rules, imposed by the functioning of the memory module, are critical
to the functioning of Appellant’s claimed invention, because, as the
Specification explains:
[E]mbodiments described herein utilize an encoding scheme
with a remarkably low probability of biological impact. That is
to say, a low probability exists that a synthetic nucleic acid
sequence created using invention methods and schemes win be
transcribed or translated by a cell’s internal biological processes.
As a result, the non-genetic message created using invention
methods and schemes may be innocuously carried and replicated
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by cells comprising the message, but may be decoded to provide
the human readable symbols, i.e., the message carried therein.

Spec. ¶ 18.
We agree with the Examiner that the transcoder serves the function of
“map[ping] a sequence of codon identifiers corresponding to each human
readable symbol within the sequence according to the human readable
symbol map and outputting the sequence,” but we find that that function is
in response to the input sequence (i.e., the intended encoded message) and
does not form the map itself. The formation of the map, incorporating the
rules recited in the preceding limitation, and pairing collective readable
symbols with the collective codons, according to a set of given rules, is the
function of the memory module and the “data structure for mapping codon
identifiers into human readable symbols.”
We therefore find that the disputed limitations are analogous to the
data structures of Lowry, in which our reviewing court found that:
[The] data structures, while including data resident in a
database, depend only functionally on information content.
While the information content affects the exact sequence of bits
stored in accordance with Lowry’s data structures, the claims
require specific electronic structural elements which impart a
physical organization on the information stored in memory.
Lowry’s invention manages information.

Lowry, 32 F.3d at 1583.
Furthermore, and contra the Examiner’s findings, we can distinguish
the claims on appeal from those in Nehls, in which our reviewing court
found that there was:
[N]o evidence that SEQ ID NOs 9-1008 functionally affect the
process of comparing a target sequence to a database by changing
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the efficiency or accuracy or any other characteristic of the
comparison. Rather, the SEQ ID NOs are merely information
being manipulated by a computer; the SEQ ID NOs are inputs
used by a computer program that calculates the degree of
similarity between a target sequence and each of the sequences
in a database.

Nehls, 88 USPQ2d at 1591. In the claims before us, the symbol/codon table
is not merely descriptive matter input to the memory module, rather, it is
constructed by the memory module, according to the rules of the data
structure, and the way the table is constructed is critical to the function of the
transcoder and the invention itself.
Our reviewing court has warned us that:
A “printed matter rejection” under § 103 stands on questionable
legal and logical footing. Standing alone, the description of an
element of the invention as printed matter tells nothing about the
differences between the invention and the prior art or about
whether that invention was suggested by the prior art.... [The
Court of Customs and Patent Appeals], notably weary of
reiterating this point, clearly stated that printed matter may well
constitute structural limitations upon which patentability can be
predicated.

Lowry, 32 F.3d at 1583 (quoting Gulack, 703 F.2d at 1385 n.8). We
consequently conclude that there is a functional relationship between the
table constructed by the memory module and its substrate.
The Examiner acknowledges that neither Wong nor Ludwig teaches
or suggests the limitation of claim 1 reciting:
[T]he human readable symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is
less than one percent within the reference language to a start
codon, and wherein the symbol map is further configured to map
a human readable symbol with a frequency of occurrence that is
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greater than five percent within the reference language to a stop
codon and no symbol is coded for by ATG.

However, because we conclude that this limitation is, for the reasons
we have explained, limiting upon the claim, and because neither reference
relied upon by the Examiner teaches or suggests this limitation, we reverse
the Examiner’s rejection of the claims upon this ground.

CONCLUSION
The Examiners rejection of claims 1, 3–5, and 15–17 under 35 U.S.C.
§ 112(b) is affirmed.
The Examiners rejection of claims 1, 3–5, and 15–17 under 35 U.S.C.
§ 101 is reversed.
The Examiners rejection of claims 1, 3–5, and 15–17 under 35 U.S.C.
§ 103 is reversed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED

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DECISION SUMMARY
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 3–5, 15–
17
112(b) Indefiniteness 1, 3–5, 15–
17

1, 3–5, 15–
17
101 Subject matter 1, 3–5, 15–
17
1, 3–5, 15–
17
103 Wong, Ludwig 1, 3–5, 15–
17
Overall
Outcome
1, 3–5, 15–
17