Ex parte Nehls

PRECEDENTIAL OPINION
Pursuant to the Board of Patent Appeals and Interferences Standard
Operating Procedure 2, the opinion below has been designated a
precedential opinion.
UNITED STATES PATENT AND TRADEMARK OFFICE
__________
BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________
Ex parte MICHAEL C. NEHLS, BRIAN ZAMBROWICZ, and
ARTHUR T. SANDS
__________
Appeal 2007-1823
Application 09/563,817
Technology Center 1600
__________
Decided: January 28, 2008
__________
Before MICHAEL R. FLEMING, Chief Administrative Patent Judge,
DONALD E. ADAMS, ERIC GRIMES, LORA M. GREEN,
NANCY J. LINCK, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.
Opinion for the Board filed by Administrative Patent Judge GRIMES.
Opinion Concurring filed by Administrative Patent Judge GREEN.
Opinion Concurring filed by Administrative Patent Judge ADAMS.
GRIMES, Administrative Patent Judge.

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DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
computer-based system for comparing nucleic acid sequences. The
Examiner has rejected the claims for lack of patentable utility and
obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.
STATEMENT OF THE CASE
The Specification discloses “nucleic acid sequences that partially
define the scope of human exons” (Spec. 1). These one thousand sequences,
referred to generically as “gene trapped sequences” or GTSs, are shown in
SEQ ID NOs 9 to 1008 (id. at 2: 28-32). The Specification states that the
GTSs were isolated using a technique (“gene trapping”) that was designed to
specifically isolate parts of exons (id. at 6-7, 105-113). Since exons are the
protein-encoding parts of genes, each of the disclosed sequences would be
expected to encode part of a protein that is expressed in human cells.
Claims 13 and 14 are the only claims pending and read as follows:
13. 	A computer-based system for identifying nucleic acid fragments of
the human genome of commercial importance comprising the following
elements:
a) 	a data storage means comprising the sense or antisense
sequence of at least 18 contiguous nucleotides of any one of SEQ ID
NOS:9-1,008;
b) 	search means for comparing a target sequence to each of the
sequences of the data storage means of step a) to identify homologous
sequence(s); and
c) 	retrieval means for obtaining said homologous sequence(s) of
step (b).
14. 	The system of claim 13, wherein said data storage means comprises a
combination of nucleic acid sequences comprising SEQ ID NOS:9-1,008.

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In response to a restriction requirement, Appellants elected the nucleic
acid sequence of SEQ ID NO: 9 for examination (response received May 10,
2001).
The Examiner has rejected claims 13 and 14 under 35 U.S.C. §§ 101
and 112, first paragraph, on the basis that the Specification does not disclose
a patentable utility for the claimed computer system comprising SEQ ID
NO: 9 in its data storage means. The Examiner has also rejected claims 13
and 14 under 35 U.S.C. § 103 as obvious in view of Altschul.1
Appellants have not argued the claims separately. We therefore focus
our analysis on claim 13. Claim 14 will stand or fall with claim 13. 37
C.F.R. § 41.37(c)(1)(vii).
UTILITY UNDER §§ 101 AND 112, FIRST PARAGRAPH
The Utility Issue
Claims 13 and 14 stand rejected under 35 U.S.C. §§ 101 and 112, first
paragraph, on the basis that the Specification does not disclose a patentable
utility for the claimed computer system comprising SEQ ID NO: 9 in its data
storage means. The Examiner’s position is:
While the specification asserts that the computer system is
useful 	in 	identifying 	exon 	splice 	junction 	and 	expressed
sequence in a given cell, this is not a substantial utility because
further research is clearly needed to determine any real world
utility of such an exon splice junction of the sequence, such as
any specific link with any diseases. . . .
Furthermore, the polynucleotide itself defined by the sequence
of SEQ ID NO:9 which is comprised in the computer system is
1 Altschul et al., “Basic local alignment search tool,” 215 J. Mol. Biol. 403-
410 (1990).

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not 	supported 	by 	a 	specific 	asserted 	utility 	because 	the
disclosed uses of the nucleic acid sequence in the specification
are not specific and are generally applicable to any nucleic acid.
(Answer 4.)
Appellants respond that “SEQ ID NOS:9-1,008 have a substantial
utility because they provide useful information regarding gene expression in
teratocarcinoma cells (which can be tracked using gene chips . . .), which
mimics gene expression during late stages of stem cell differentiation and
development” (Br. 7). Appellants also argue that the polynucleotides of
SEQ ID NOs 9-1008 are useful for “assessing gene expression patterns using
high-throughput DNA chips” (id. at 8) and that the claimed computer system
is useful for identifying introns and exons (id. at 11-12) and mapping human
chromosomes (id. at 12-13).
In view of these conflicting positions, we frame the utility issue as
follows: Does the Specification disclose a use for the claimed computer
system that satisfies the requirements of 35 U.S.C. § 101 and the how-to-use
prong of 35 U.S.C. § 112, first paragraph?
Findings of Fact Relating to Utility
1. The Specification discloses 1,000 nucleic acids (Spec. 1; Sequence
Listing filed May 3, 2000, SEQ ID NOs 9-1008).
2. The Specification states that the nucleic acids of SEQ ID NOs
9-1008 were derived from protein-encoding parts of human genes (Spec. 6-
7, 105-113).
3. The Specification does not disclose any specific human gene as the
source of any of the nucleic acids of SEQ ID NOs 9-1008.

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4. The Specification does not disclose the amino acid sequence
encoded by any of the nucleic acids of SEQ ID NOs 9-1008.
5. The Specification states that the disclosed nucleic acids “typically
contain only a portion of the mature RNA transcript . . . , and therefore such
clones may only encode a portion of the polypeptide of interest” (Spec.
13: 13-17)
6. SEQ ID NO: 9 is 210 nucleotides long (Sequence Listing filed
May 3, 2000).
7. The Specification discloses “methods of analyzing biopolymer . . .
sequence information comprising the steps of loading a first biopolymer
sequence into or onto an electronic data storage medium . . . and comparing
said first sequence to at least a portion of one of the polynucleotide
sequences . . . SEQ ID NOS:9-1,008” (Spec. 3: 7-16).
8. The Specification states that a computer system comprising SEQ
ID NOs 9-1008 in its data storage medium can be used to identify other
nucleic acids having sequences similar to those of the disclosed nucleic acids
(Spec. 100-105).
9. The Specification states that the disclosed nucleic acids
provide unique tools for diagnostic gene expression analysis,
for 	cross 	species 	hybridization 	analysis, 	for 	genetic
manipulations using a variety of techniques, like, for example,
antisense 	inhibition, 	gene 	targeting, 	the 	identification 	or
generation of full-length cDNA, mapping the human genome,
gene therapy, gene delivery, etc.
(Spec. 16: 8-24.)
10. The Specification does not disclose uses for any of the nucleic
acids of SEQ ID NOs 9-1008 that depend on the structure or physical or

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chemical properties of a particular nucleic acid or the peptide encoded
thereby.
Discussion of the Utility Issue
Based on our findings and those of the Examiner, we conclude that
the Specification does not disclose a utility for the claimed computer system
that satisfies 35 U.S.C. §§ 101 and 112, first paragraph.
The U.S. Court of Appeals for the Federal Circuit has held that § 101
requires a utility that is both substantial and specific. In re Fisher, 421 F.3d
1365, 1371 (Fed. Cir. 2005). The court held that a substantial utility requires
showing that “an invention is useful to the public as disclosed in its current
form, not that it may prove useful at some future date after further research.
Simply put, to satisfy the ‘substantial’ utility requirement, an asserted use
must show that that claimed invention has a significant and presently
available benefit to the public.” Id.
The court held that a specific utility is “a use which is not so vague as
to be meaningless.” Id. In other words, “in addition to providing a
‘substantial’ utility, an asserted use must also show that that claimed
invention can be used to provide a well-defined and particular benefit to the
public.” Id.
The court held that the uses asserted by Fisher were not substantial or
specific. The uses were not substantial because
the claimed ESTs act as no more than research intermediates
that may help scientists to isolate the particular underlying
protein-encoding genes and conduct further experimentation on
those genes. . . . Accordingly, the claimed ESTs are, in the
words of the Supreme Court, mere ‘object[s] of use-testing,’ to
wit, objects upon which scientific research could be performed

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with no assurance that anything useful will be discovered in the
end.
Id. at 1373 (alteration in original). The court concluded that “Fisher’s
asserted uses are insufficient to meet the standard for a ‘substantial’ utility
under § 101.” Id.
“Furthermore, Fisher’s seven asserted uses are plainly not ‘specific.’
Any EST transcribed from any gene in the maize genome has the potential to
perform any one of the alleged uses. . . . Nothing about Fisher’s seven
alleged uses set the five claimed ESTs apart from the more than 32,000
ESTs disclosed in the ‘643 application or indeed from any EST derived from
any organism. Accordingly, we conclude that Fisher has only disclosed
general uses for its claimed ESTs, not specific ones that satisfy § 101.” Id.
at 1374.
Here, the claimed computer system is disclosed to be useful for
identifying nucleic acids that are similar to SEQ ID NOs 9-1008 (Finding of
Fact (“FF”) 8). The utility of the claimed computer system therefore
depends on the utility of the nucleic acids of SEQ ID NOs 9-1008: if the
disclosed nucleic acids lack utility, so do nucleic acids similar to them and a
computer system for identifying such similar nucleic acids. 2
2 The preamble of claim 13 states that the computer system is for identifying
nucleic acids “of commercial importance.” This recitation does not impart
patentable utility on the claimed computer system, for two reasons. First,
the body of the claim only requires means for comparing a target sequence
to those of SEQ ID NOs 9-1008; the computer system defined by the claim
provides no means for distinguishing nucleic acids of “commercial
importance” from others. See IMS Technology, Inc. v. Haas Automation,
Inc., 206 F.3d 1422, 1434 (Fed. Cir. 2000) (“If the preamble adds no
limitations to those in the body of the claim, the preamble is not itself a

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The uses asserted in the Specification for the disclosed nucleic acids
(see FF 9) are not “substantial” or “specific,” as those terms were defined by
the Fisher court. They are not substantial because, like the ESTs claimed in
Fisher, the GTSs represented by SEQ ID NOs 9-1008 are “no more than
research intermediates that may help scientists to isolate the particular
underlying protein-encoding genes and conduct further experimentation on
those genes.” Fisher, 421 F.3d at 1373. Accordingly, the GTSs represented
by SEQ ID NOs 9-1008 are merely “objects upon which scientific research
could be performed with no assurance that anything useful will be
discovered in the end.” Id. The uses asserted for the GTSs represented by
SEQ ID NOs 9-1008 therefore do not meet the standard for a substantial
utility under § 101.
Nor are they specific utilities, because they could be asserted for any
partial cDNA transcribed from any gene in the human genome. Because
nothing about Appellants’ asserted utilities sets the nucleic acids of SEQ ID
NOs 9-1008 apart from any other human cDNA fragment, Appellants have
only disclosed general uses for the disclosed GTSs, not specific ones that
satisfy § 101. See id. at 1374.
claim limitation and is irrelevant to proper construction of the claim.”).
Second, the Specification does not describe the “commercial importance” of
the identified nucleic acids in a way that would allow those skilled in the art
to put them to a specific and substantial use. Cf. In re Kirk, 376 F.2d 936,
941 (CCPA 1967) (“[T]he nebulous expressions ‘biological activity’ or
‘biological properties’ appearing in the specification convey no more
explicit indication of the usefulness of the compounds and how to use them
than did the equally obscure expression ‘useful for technical and
pharmaceutical purposes’ unsuccessfully relied upon by the appellant in In
re Diedrich, 50 CCPA 1355, 318 F.2d 946, 138 USPQ 128.”).

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Appellants have provided no persuasive explanation why those skilled
in the art would find gene expression data from teratocarcinoma cells to be
useful, as that term was defined by the Fisher court. Nor have Appellants
rebutted the Examiner’s reasoning, and the reasoning we rely on above, by
showing that any of the uses asserted in the Specification or in the Appeal
Brief is both “substantial” and “specific.”
We therefore affirm the rejection of claims 13 and 14 under 35 U.S.C.
§§ 101 and 112, first paragraph, for lack of patentable utility.
Our concurring colleagues fault us for focusing on the specific SEQ
ID NOs recited in the claims when considering utility, but concluding (see
infra) that those same SEQ ID NOs do not patentably distinguish the
claimed computer system from the prior art. We see no impropriety in our
approach. The claims are directed to a computer system “for identifying
nucleic acid fragments of the human genome of commercial importance”
based on a comparison to SEQ ID NOs 9-1008. The claimed system
requires no functionality other than that required to compare a target
sequence to SEQ ID NOs 9-1008 and output the result. Therefore, it is
entirely proper to limit the utility analysis to the usefulness of the nucleic
acids represented by SEQ ID NOs 9-1008, even if the sequences themselves
do not distinguish the claimed computer system from the prior art.
OBVIOUSNESS UNDER § 103
The Obviousness Issue
The Examiner finds that Altschul discloses a computer system that
“differ[s] from the claimed invention only in the content of the nucleic acid

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comprised in the storage of the computer system” (Answer 6). The
Examiner reasons that
the sequence of a fragment of SEQ ID NO:9, or a combination
of the sequences of SEQ ID NOS: 9-1008, constitutes non-
functional 	descriptive 	material 	because 	the 	content 	of 	the
nucleic acid sequence database does not alter how the computer
system functions, i.e., the database of the claimed computer
system does not reconfigure the computer system to perform a
different function than the computer system of Altschul et al.
Therefore, no patentable weight is given to the content of the
database on the claimed computer system.
(Id. at 7.)
Appellants argue that “the difference between Altschul and the
present invention, specifically SEQ ID NO:9, is not ‘non-functional
descriptive material’” (Br. 18-19).
In view of these conflicting positions, we frame the § 103 issue as
follows: Does the claimed computer system differ from the prior art
computer system in a nonobvious way; i.e., in more than the content of
nonfunctional descriptive material?
Findings of Fact Relating to Obviousness
11. Altschul discloses a computer system that compares target nucleic
acid sequences to those in a database. (Altschul 403 (abstract): “The basic
algorithm . . . can be implemented in a number of ways . . . including
straightforward DNA and protein sequence database searches.”)
12. Altschul’s Table 2 shows the time required for “searching the PIR
database (Release 23•0) with a random query sequence of length 250 using a
SUN4-280” (Altschul 408).

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13. Appellants do not dispute that Altschul teaches a computer
system comprising a data storage means, “search means for comparing a
target sequence to each of the sequences of the data storage means . . . to
identify homologous sequence(s),” and “retrieval means for obtaining said
homologous sequence(s).”
14. Altschul does not disclose that the database used in the disclosed
computer system included at least eighteen contiguous nucleotides of SEQ
ID NOs 9-1008 of the instant application.
15. The computer system defined by claim 13 differs from Altschul
only in the content of the data storage means: claim 13 requires that the data
storage means comprises “the sense or antisense sequence of at least 18
contiguous nucleotides of any one of SEQ ID NOS:9-1,008,” which Altschul
does not disclose.
Discussion of the Obviousness Issue
Based on our findings and those of the Examiner, we conclude that
the particular sequence data recited in claim 13 is nonfunctional descriptive
material and does not distinguish the claimed computer-based system from
the prior art system that is the same except for its sequence data.
The distinction between functional and nonfunctional descriptive
material arose in the context of printed matter limitations. For example, in
In re Gulack, 703 F.2d 1381 (Fed. Cir. 1983), printed matter that was
functionally related to its substrate was held to distinguish the claimed
product from the prior art. In Gulack, the claims recited “three key
elements: (1) a band . . .; (2) a plurality of individual digits imprinted on the
band or ring at regularly spaced intervals; and (3) an algorithm by which the

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appropriate digits are developed.” Id. at 1382. With the digits generated by
the algorithm printed on it, the band could be used “to perform magic tricks
or to display various aspects of number theory.” Id. at 1383. The claims
had been rejected as obvious, based on prior art that differed only in what
was printed on the band. Id. at 1384.
The court stated that, although limitations reciting printed matter
cannot be ignored, “[w]here the printed matter is not functionally related to
the substrate, the printed matter will not distinguish the invention from the
prior art in terms of patentability. Although the printed matter must be
considered, in that situation it may not be entitled to patentable weight.” Id.
at 1385 (footnote omitted). The “critical question is whether there exists any
new and unobvious functional relationship between the printed matter and
the substrate.” Id. at 1386. The Gulack court held that such a relationship
had been shown: the looped structure of the substrate and the particular
digits printed on it interrelated to give the claimed product a property it
would not have had if either the structure or the digits were changed.
Therefore, the content of the printed matter was held to produce a
nonobvious difference between the claimed product and the prior art.
By contrast, in In re Ngai, 367 F.3d 1336 (Fed. Cir. 2004), a printed
matter limitation was held to be nonfunctional and therefore inadequate to
distinguish the claimed product from the prior art. Ngai claimed a kit that
contained at least one of several reagents (e.g., buffer) and instructions that
described a process of using the reagents to amplify RNA. Id. at 1337. The
claim had been rejected based on prior art that disclosed a kit containing
buffer and instructions that described a different process. Id.

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The Ngai court held that the printed instructions were not related to
the claimed kit in the way that Gulack’s numbers were related to his band.
See id. at 1339: “In Gulack, the printed matter would not achieve its
educational purposes without the band, and the band without the printed
matter would similarly be unable to produce the desired result. Here, the
printed matter in no way depends on the kit, and the kit does not depend on
the printed matter. All that the printed matter does is teach a new use for an
existing product.” The rejection was affirmed.
A similar distinction has been recognized in the context of computer-
related inventions. Compare In re Warmerdam, 33 F.3d 1354 (Fed. Cir.
1994), with In re Lowry, 32 F.3d 1579 (Fed. Cir. 1994). Both cases
involved so-called “data structures.” The court in Warmerdam concluded
that the claimed “data structure” was not a physical arrangement of hardware
but instead was “nothing more than another way of describing the
manipulation of ideas contained in” other claims and therefore not statutory
subject matter eligible for patenting. 33 F.3d at 1362. The Lowry court,
however, concluded that the claimed data structures were “physical entities
that provide increased efficiency in computer operation” and were not
analogous to printed matter. 32 F.3d at 1584. 3
3 Judge Adams notes that the Lowry court stated that the “printed matter
cases have no factual relevance where ‘the invention as defined by the
claims requires that the information be processed not by the mind but by a
machine, the computer’” (post at 43). That statement, however, must be
regarded as dictum, because the court went on to conclude that the data
structures at issue in Lowry were not analogous to printed matter. See 32
F.3d at 1584. Thus, the quoted statement was not essential to the Lowry
holding. The Lowry court did not consider whether, and under what

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Here, the descriptive material (SEQ ID NOs) recited in the claims is
not functional material like the data structures in Lowry. 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. 4 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. 5
Thus, the descriptive material in this case is properly considered to be
nonfunctional. The SEQ ID NOs recited in the claims are analogous to the
instructions in In re Ngai. The Ngai court held that, in contrast to Gulack,
the printed instructions were not functionally related to the claimed kit. See
Ngai, 367 F.3d at 1339: “In Gulack, the printed matter would not achieve its
circumstances, computer-readable information that is analogous to printed
matter can distinguish a claimed invention from the prior art.
4 Similarly, a claim to a computerized system for searching a phonebook
placed in a database would not be patentable, absent some novel and
nonobvious characteristic of the computer hardware or search tools.
5 Of course, the results of comparing a target sequence to a database may
change depending on which sequences are included in the database. That
possibility does not mean that the database sequences are functional: MP3
files encoding different songs will cause a computer’s speaker to output
different music, but music is a paradigmatic nonfunctional descriptive
material. Descriptive material is not functional merely because it results in
different outputs when acted on by a computer program.

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educational purposes without the band, and the band without the printed
matter would similarly be unable to produce the desired result. Here, the
printed matter in no way depends on the kit, and the kit does not depend on
the printed matter.” The same is true here. The recited sequences are not
functionally related to the computer system carrying out the comparison
because the computer compares a target sequence to a database the same
way regardless of whether the database includes any of SEQ ID NOs
9-1008: the SEQ ID NOs and the computer do not depend on each other for
their function.
Other panels of this Board have reached the same conclusion with
respect to computer-implemented methods. See Ex parte Curry, 84 USPQ2d
1272 (BPAI 2005), aff’d (Fed. Cir. Appeal No. 2006-1003, aff’d Rule 36
June 12, 2006) and Ex parte Mathias, 84 USPQ2d 1276 (BPAI 2005), aff’d
191 Fed.Appx. 959 (Fed. Cir. 2006). The Board in Curry held that a
computer-implemented method of providing “wellness-related services”
would have been obvious, even though the specific wellness-related data
were not taught or suggested by the cited prior art. According to the Board,
“the ‘wellness-related data in the databases . . . does not functionally change
either the data storage system or communication system used in the method
of claim 81. Nonfunctional descriptive material cannot render nonobvious
an invention that would have otherwise been obvious.” 84 USPQ2d at 1274.
Similarly, the Board in Mathias held unpatentable a claim to an “on-
screen icon for viewing the score of a broadcast sporting event,” even
though the cited prior art did not teach or suggest a sporting event in this
context. The Board noted that “our reviewing court has held that

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nonfunctional descriptive material,” such as the sporting event, “cannot lend
patentability to an invention that would have otherwise been anticipated by
the prior art.” 84 USPQ2d at 1278-79.
In both these cases, as here, a computer was used to facilitate
manipulating information that previously would have been manipulated by
less efficient means, for example, manually. In such cases, the nature of the
information being manipulated does not lend patentability to an otherwise
unpatentable computer-implemented product or process.
Our conclusion is also consistent with the USPTO’s examination
guidelines relating to subject matter eligible for patenting. See Interim
Guidelines for Examination of Patent Applications for Patent Subject Matter
Eligibility (“Guidelines”), 1300 Off. Gaz. Pat. Office 142 (November 22,
2005), especially pages 151-152. (The Manual of Patent Examining
Procedure includes substantively the same guidance. See MPEP, 8 th edition
(revised Aug. 2006), § 2106.01.)
The Guidelines state that “‘functional descriptive material’ consists of
data structures and computer programs which impart functionality when
employed as a computer component. . . . ‘Nonfunctional descriptive
material’ includes but is not limited to music, literary works and a
compilation or mere arrangement of data.” 1300 Off. Gaz. Pat. Office at
151. When claims comprise nonfunctional descriptive material recorded on
computer-readable media, the Guidelines direct the Examiner to
determine 	whether 	the 	claimed 	nonfunctional 	descriptive
material 	be 	given 	patentable 	weight. 	The 	USPTO 	must
consider all claim limitations when determining patentability of
an invention over the prior art. 	In re Gulack, 703 F.2d 1381,
1385, 217 USPQ 401, 403-04 (Fed. Cir. 1983). 	The USPTO

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may 	not 	disregard 	claim 	limitations 	comprised 	of 	printed
matter. 	See Gulack, 703 F.2d at 1384, 217 USPQ at 403; see
also Diehr, 450 U.S. at 191, 209 USPQ at 10. 	However, the
examiner need not give patentable weight to printed matter
absent a new and unobvious functional relationship between the
printed matter and the substrate. 	See In re Lowry, 32 F.3d
1579, 1583-84, 32 USPQ2d 1031, 1035 (Fed. Cir. 1994); In re
Ngai, 367 F.3d 1336, 70 USPQ2d 1862 (Fed. Cir. 2004).
(1300 Off. Gaz. Pat. Office at 151-152.)
Consistent with the Guidelines, the Examiner in this case considered
all of the limitations of the claims but declined to give patentable weight to
those limitations reciting nonfunctional descriptive material; specifically,
SEQ ID NOs 9-1008.
Appellants argue, however, that “the MPEP details that non-functional
descriptive material is not patentable (‘(t)he policy that precludes the
patenting of nonfunctional descriptive material would be easily frustrated if
the same descriptive material could be patented when claimed as an article
of manufacture’ (MPEP at 2100-14 (emphasis added)). As . . . nucleic acids
are patentable, this also supports the position that SEQ ID NO:9 is functional
descriptive material.” (Br. 19-20.)
This argument is unpersuasive. Nucleic acids are patentable, but SEQ
ID NO: 9 is not a nucleic acid – it is an abstract representation of the
structure of a nucleic acid. That is, nucleic acids are not made up of A’s,
T’s, G’s, and C’s, the way SEQ ID NO: 9 is; nucleic acids are chemical
entities made up of the bases adenine, thymine, guanine, and cytosine,
connected to sugar residues, which in turn are connected by phosphodiester
bonds. The compound represented by SEQ ID NO: 9 may be patent-eligible
subject matter, but SEQ ID NO: 9 itself is not. The potential patentability of

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the compound represented by SEQ ID NO: 9 does not support Appellants’
position that SEQ ID NO: 9 is functional descriptive material.
As further support for their position that the recited SEQ ID NOs
should be sufficient to distinguish the instant claims from the prior art,
Appellants point to issued patents that include a “comparison function” such
as patents involving the use of passwords to allow a user access to a
computer and computer virus scanning programs. Appellants reason that
“[i]n these and similar patents, the computer compares an input to authorized
passwords or known computer viruses, in the same way that the present
computer system compares an input sequence to a biologically verified
coding sequence (in this case, SEQ ID NO:9).” (Br. 20.)
This argument is also unpersuasive. It is undisputed that the instant
claims differ from the prior art only in the content (i.e., SEQ ID NO: 9) that
is being compared in the claimed computer system. Appellants have not
alleged that the patents cited in the Appeal Brief claim products or methods
that differ from the prior art only in the content (password or computer
virus) that is compared in the performance of the claimed security or virus-
scanning program. Since the inventions claimed in the cited patents
apparently differ from the prior art in more than the mere content of the data
being compared, the cited patents do not support the patentability of the
instant claims.
The concurrences believe that we have improperly disregarded the
SEQ ID NO limitation of claim 13 (post at 21, 45-46). The concurrences
misinterpret our reasoning and set up a false dichotomy between utility and
obviousness. We have not disregarded the SEQ ID NO claim limitation.

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The claimed computer system requires the recited SEQ ID NOs, but not
every claim limitation suffices to distinguish a claimed invention from the
prior art. In this case, we conclude that the particular SEQ ID NOs recited in
claim 13 do not patentably distinguish the claimed computer system from a
prior art system that is otherwise identical.
Our concurring colleagues would hold that the SEQ ID NOs recited in
claim 13 patentably distinguish the claimed computer system from the prior
art. The logical extension of that conclusion, however, is that putting any
new data into the storage medium of a computer creates a nonobvious
computer system. In our view, the case law does not support such a rule.
SUMMARY
We affirm the rejection of claims 13 and 14 under 35 U.S.C. §§ 101
and 112, first paragraph for lack of patentable utility. We also affirm the
rejection of claims 13 and 14 under 35 U.S.C. § 103.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv) (2006).
AFFIRMED

Appeal 2007-1823
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20
GREEN, Administrative Patent Judge, concurring in the result.
Claim 13, the only independent claim on appeal, reads as follows:
13. 	A computer-based system for identifying nucleic acid fragments of
the human genome of commercial importance comprising the following
elements:
a) 	a data storage means comprising the sense or antisense
sequence of at least 18 contiguous nucleotides of any one of SEQ ID
NOS:9-1,008;
b) 	search means for comparing a target sequence to each of the
sequences of the data storage means of step a) to identify homologous
sequence(s); and
c) 	retrieval means for obtaining said homologous sequence(s) of
step (b).
The only limitation focused on by the Majority is element a)—a data
storage means comprising the sense or antisense sequence of at least 18
contiguous nucleotides of any one of SEQ ID NOS:9-1008. In particular,
the Majority focuses on the limitation drawn to the sense or antisense
sequence of at least 18 contiguous nucleotides of any one of SEQ ID NOS:9-
1008, with SEQ ID NO:9 being drawn to the nucleic acid sequence elected
by Appellants for examination (response received May 10, 2001).
In affirming the Examiner’s rejection under 35 U.S.C. § 101, on the
basis that the Specification does not disclose a patentable utility for the
claimed computer system comprising SEQ ID NO:9 in its data storage
means, the Majority focuses on the lack of utility for a nucleic acid of SEQ
ID NOs 9-1008 (Majority Op. 3-9). Specifically, the Majority finds that the
utilities asserted in the Specification are not substantial “because, like the
ESTs claimed in Fisher, the GTSs represented by SEQ ID NOs 9-1008 are
‘no more than research intermediates that may help scientists to isolate the

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particular underlying protein-encoding genes and conduct further
experimentation on those genes.’” (Id. at 8, quoting In re Fisher, 421 F.3d
1365, 1373 (Fed. Cir. 2005).) The Majority also finds that the asserted
utilities are not specific “because they could be asserted for any partial
cDNA transcribed from any gene in the human genome.” (Majority Op. at
8.) In affirming the rejection of the claims under 35 U.S.C. § 103(a),
however, the Majority concludes that “the particular sequence data recited in
claim 13 is nonfunctional descriptive material and does not distinguish the
claimed computer-based system from the prior art system that is the same
except for its sequence data.” (Majority Op. 11.)
Thus, the Majority focuses primarily on the sequence limitations in
finding that the invention of claim 13 lacks patentable utility, and not on the
computer-based system for identifying nucleic acid fragments. In
addressing the rejection under 35 U.S.C. § 103(a), however, the Majority
refuses to consider the sequence limitations in determining the patentability
of the claim over the prior art rejection, concluding that the sequence
limitations are drawn solely to “nonfunctional descriptive material” that
“does not distinguish the claimed computer-based system from the prior art
system that is the same except for its sequence data.” (Majority Op. 10.)
The position of the Majority is inconsistent. It is unfair to Appellants
to rely primarily on the sequence data to find that the claims do not meet the
utility requirement of 35 U.S.C. § 101, and then state that the sequence data
are only nonfunctional descriptive material that does not contribute to the
patentability of the claim under 35 U.S.C. § 103(a). Which is it? See, e.g.,
In re Nuijten, 500 F.3d 1346, 1366 (Fed. Cir. 2007) (Linn, concurring-in-

Appeal 2007-1823
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part and dissenting-in-part) (noting that “[a]bsent Lowry, the PTO’s position
apparently would be that Nuijten’s claim 14 (the signal, standing alone) is
unpatentable subject matter under § 101, and that claim 15 (the storage
medium containing the signal) is unpatentably obvious under § 103 over
prior art storage media. The PTO’s position makes little sense. As a
doctrinal matter, the PTO should not look to § 101 sometimes and § 103 at
other times to accomplish the same end.” (footnote omitted).)
I agree with the Majority’s analysis under 35 U.S.C. § 101 that the
claimed SEQ ID NOs do not have patentable utility, and thus concur in the
result. I do not agree, however, that the SEQ IDs are nonfunctional,
descriptive subject matter, which should not be considered in the
obviousness analysis. I thus respectfully dissent as to the Majority’s opinion
as to the obviousness analysis.
“The Patent and Trademark Office . . . must consider all claim
limitations when determining patentability of an invention over the prior
art.” In re Lowry, 32 F.3d 1579, 1582 (Fed. Cir. 1994).
Differences between an invention and the prior art cited against
it cannot be ignored merely because those differences reside in
the content of the printed matter. Under section 103, the board
cannot dissect a claim, excise the printed matter from it, and
declare the remaining portion of the mutilated claim to be
unpatentable. The claim must be reads as a whole.
In re Gulack, 703 F.2d 1381, 1385 (Fed. Cir. 1983) (footnotes omitted).
According to the Gulack court, “[w]here the printed matter is not
functionally related to the substrate, the printed matter will not distinguish
the invention from the prior art in terms of patentability.” Id. Thus, the
issue is are SEQ ID NOs:9-1008 functionally related to the computer-based

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system for identifying nucleic acid fragments. See, e.g., Lowry, 32 F.3d at
1582. To determine when printed matter is “functionally related to the
substrate” as required by the Court of Appeals for the Federal Circuit
requires review of the case law relating to functional and nonfunctional
subject matter.
In In re Miller, 418 F.2d 1392 (CCPA 1969), the claims at issue were
drawn to measuring receptacles “adapted to ameliorate the mental strain on
cooks.” Id. at 1394. Claim 10 of the application was illustrative, and was
drawn to:
A measuring device comprising: a spoon for measuring
ingredient: and volume measuring indicia defined in normal
volumetric unit on said spoon of a selected ratio to but
indicating a volume different from the actual volume of
ingredients being added to and measured in said spoon by said
indicia, and a legend attached to said spoon specifying said
ratio.
Id at 1395.
The claimed measuring device contemplated not only measuring
multiple recipes, but also solved “the greater difficulty of measuring out
fractional recipes, such as 1/3 or 1/2.” Id. at 1393. The examiner rejected
the claims, noting that the claims were defined over any normal measuring
receptacle “only by the addition of unpatentable printed matter.” Id. at 1395.
The Court of Claims and Patent Appeals reversed, stating:
The fact that printed matter by itself is not patentable subject
matter, because non-statutory, is no reason for ignoring it when
the claim is directed to a combination. Here, there is a new and
unobvious functional relationship between a measuring
receptacle, volumetric indicia thereon indicating volume in a
certain ratio to actual volume, and a legend indicating the ratio,

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and in our judgment the appealed claims properly define this
relationship. No question as to novelty or unobviousness of the
invention as claimed is before us except with relation to an
‘ordinary measuring vessel.’ By implication, the examiner
admits that no such combination exists in or would be obvious
from an ordinary measuring vessel and we therefore deem
sections 102 and 103 to be satisfied.
Id. at 1396.
In re Gulack, 703 F.2d 1381 (Fed. Cir. 1983) involved claims to a
product having “three key elements: (1) a band, ring, or set of concentric
rings, (2) a plurality of individual digits imprinted on the band or ring at
regularly spaced intervals; and (3) an algorithm by which the appropriate
digits are developed.” Id. at 1382. Specific embodiments of the band set
forth in the specification included “a belt, hatband, headband, skullcap
border, necklace, ring, table edge, household device or utensil, jewelry, and
other artifacts.” Id. The objective of the claimed invention was “to create
the semblance of magic or to educate with respect to intriguing aspects of
number theory.” Id.
In rejecting the claims under § 103, the examiner stated that the
appealed claims differed from the prior art only in the specific digits printed
on the band, finding “no relationship between appellant’s digits and band
except that the band is the surface on which the digits are printed.” Id. at
1384. The board, in affirming the examiner’s rejection, “found no
meaningful relationship between the digits and the band of the type indicated
by the court in Miller.” Id. The board distinguished Miller, noting that the
digits printed on the claimed band did not convey any meaningful
information with regard to the band, did not require any size relationship of

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the substrate, and did not require any particular substrate to convey the
information. Id. Thus, as understood by the Gulack court, the board did not
give the printed matter, i.e., the digits, any patentable weight “because the
board felt that there is no functional relationship between the printed matter
and the substrate.” Id.
In finding that there was a functional relationship between the band
and the digits printed thereon, the Gulack court explained:
A functional relationship of the precise type found by the
CCPA in Miller—to size or to type of substrate, or conveying
information about substrate—is not required. What is required
is the existence of differences between the appealed claims and
the prior art sufficient to establish patentability. The bare
presence or absence of a specific functional relationship,
without further analysis, is not dispositive of obviousness.
Rather, the critical question is whether there exists any new and
unobvious functional relationship between the printed matter
and the substrate.
Id. at 1386.
Thus, according to the Gulack court, the digits were “related to the
band in two ways: (1) the band supports the digits; and (2) there is an
endless sequence of digits-each digit residing in a unique position with
respect to every other digit in an endless loop. Thus, the digits exploit the
endless nature of the band.” Id. at 1386-87.
In In re Ngai, 367 F.3d 1336 (Fed. Cir. 2004), the claim on appeal
was drawn to a kit comprising a 10X buffer and instructions on performing a
specific method of normalizing and amplifying an RNA population. Id. at
1337-38. Ngai did not dispute that the prior art taught a kit comprising
instructions and a 10X buffer, thus the only difference between the claim

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and the prior art was the content of the instructions. Id. at 1338. In
affirming the rejection of the claim, the Ngai Court stated:
This case, however, is dissimilar from Gulack. There the
printed matter and the circularity of the band were interrelated,
so as to produce a new product useful for “educational and
recreational mathematical” purposes. Here, addition of a new
set of instructions into a known kit does not interrelate with the
kit in the same way as the numbers interrelated with the band.
In Gulack, the printed matter would not achieve its educational
purposes without the band, and the band without the printed
matter would similarly be unable to produce the desired result.
Here, the printed matter in no way depends on the kit, and the
kit does not depend on the printed matter. All that the printed
matter does is teach a new use for an existing product. As the
Gulack court pointed out, “[w]here the printed matter is not
functionally related to the substrate, the printed matter will not
distinguish the invention from prior art in terms of
patentability.” . . . If we were to adopt Ngai’s position, anyone
could continue patenting a product indefinitely provided that
they add a new instruction sheet to the product. This was not
envisioned by Gulack.
Id. at 1339.
In my view, the claims at issue in the instant appeal are much more
similar to those in Miller and Gulack than the claim at issue in Ngai. In
Miller, the court found that there was a “new and unobvious functional
relationship between a measuring receptacle, volumetric indicia thereon
indicating volume in a certain ratio to actual volume, and a legend indicating
the ratio.” 418 F.2d at 1396. In Gulack, the digits were “related to the band
in two ways: (1) the band supports the digits; and (2) there is an endless
sequence of digits-each digit residing in a unique position with respect to
every other digit in an endless loop.” 703 F.2d at 1386-87.

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Claim 13 is drawn to a computer-based system for identifying nucleic
acid fragments comprising: (1) a data storage comprising the sense or
antisense sequence of at least 18 contiguous nucleotides of any one of SEQ
ID NOS:9-1,008; (2) a search means; and (c) retrieval means. The prior art,
Altshul, “differ[s] from the claimed invention only in the content of the
nucleic acid comprised in the storage of the computer system.” (Answer 6.)
The nucleic acid sequences of the claim are functionally related to the
computer system of the claim, because, as claimed, they can only be
accessed and searched through the use of the computer system. In addition,
the sequence of the nucleic acid stored is not a random collection of As, Gs,
Cs, and Ts. Rather, it is representative of a sequence of nucleic acid found
in nature which performs a specific function. Thus, the As, Gs, Cs, and Ts
have “unique positions” to one another based on the sequences of the
naturally occurring nucleic acids. The specific nucleic acid sequences are
integral to the invention being claimed. Thus, there exists any new and
unobvious functional relationship between the printed matter and the
substrate.
Therefore, the instant situation is not analogous to that in Ngai. The
rationale in Ngai was that the content of instructions, the only difference
between the claim at issue and the prior art, only taught “a new use for an
existing product.” 367 F.3d at 1339. To “adopt Ngai’s position, anyone
could continue patenting a product indefinitely provided that they add a new
instruction sheet to the product.”
Claim 13 is not an attempt to patent an old product by adding
instructions on using the old product in a different way. Rather, if we

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assume the nucleic acid sequences are new and non-obvious,6 one has a new
product. That new product is a computer system comprising a data storage
means having the new and non-obvious sequences, with which one can
compare a query sequence to those new and non-obvious sequences. Thus,
in the instant case, the computer system is more analogous to the measuring
vessel of Miller or the band of Gulack, rather than the instruction sheet of
Ngai, and the SEQ ID NOs are more analogous to the volumetric indicia of
Miller or the digits generated by the algorithm of Gulack than to the content
of the instruction sheet of Ngai.
The Court of Appeals for the Federal Circuit’s decisions in In re
Lowry, 32 F.3d 1579 (Fed. Cir. 1994) and In re Warmerdam, 33 F.3d 1354
(1994), do not dictate a different result. 7 The invention in Lowry “provides
an efficient, flexible method of organizing data in a computer memory.” Id.
at 1580. In affirming the obviousness rejection of the examiner, the board
found that the data structures required by the claims were printed matter, and
that they did not distinguish the claimed invention from the prior art. Id. at
1582. The Federal Circuit, however, found that the data structures were not
analogous to printed matter; rather they defined “functional characteristics of
the memory.” Id. at 1583. Thus, according the court, “[t]he printed matter
6 The Examiner did not apply any prior art against the nucleic acids of SEQ
ID NOS:9-1008.
7 I have considered the Majority’s arguments based on Ex parte Curry, 84
USPQ2d 1272 (BPAI 2005), aff’d (Fed. Cir. Appeal No. 2006-1003, aff’d
Rule 36 June 12, 2006) and Ex parte Mathias, 84 USPQ2d 1276 (BPAI
2005), aff’d 191 Fed.Appx. 959 (Fed. Cir. 2006). The fact patterns in those
cases are very different from those presented by the instant appeal, and thus
the outcomes in those cases have little bearing on the instant appeal.

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cases have no factual relevance here.” Id. The Lowry court went on to state
that even if the data objects and data structures are analogous to printed
matter, “the ADO’s perform a function. Gulack requires no more.” Id. at
1584.
The claims at issue in Warmerdam were drawn to a method of
generating a data structure that represents the shape of a physical object. 33
F.3d at 1357. The board sustained the rejection of the examiner under § 101,
finding that a “data structure” is not within one of the categories of
patentable subject matter. Id. at 1358. The Court of Appeals agreed, and
affirmed. Id. at 1361. Thus, the holding of Warmerdam “is a
straightforward application of the basic principle that mere laws of nature,
natural phenomena, and abstract ideas are not within the categories of
inventions or discoveries that may be patented under § 101.” AT&T Corp. v.
Excel Communications, 172 F.3d 1352, 1360 (Fed. Cir. 1999).
Thus, the Court of Appeals for the Federal Circuit’s decision in
Warmerdam has no bearing in the instant case, as neither the Examiner nor
the Majority argues that claim 13 “is a straightforward application of the
basic principle that mere laws of nature, natural phenomena, and abstract
ideas are not within the categories of inventions or discoveries that may be
patented under § 101.” Both the Examiner and the Majority appear to agree
that the computer system per se constitutes patentable subject matter under
section 101.
As to Lowry, as noted above, the data structures were not found to be
analogous to printed matter, thus the holding in that case has no applicability
to the issue of whether the nucleic acid sequences required by the computer

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system of appealed claim 13 are functional or nonfunctional descriptive
matter. Moreover, according to Lowry, all that is required by Gulack is that
the printed matter perform a function. 32 F.3d at 1584. Here, the nucleic
acids serve the function of allowing one to determine if a query sequence is
identical or homologous to any of the nucleic acids of the claimed SEQ ID
NOs. 8
The Majority finds that the SEQ ID NOs recited in the claims are not
functional, and thus not analogous to the data structures in Lowry, as 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.” (Majority Op. 14.)
Holding the descriptive material represented by the SEQ ID NOs to the level
of functionality found in Lowry, however, is not a proper application of the
law, as the Lowry court found that the data structures were not descriptive
material as they defined functional aspects of the memory. 32 F.3d at 1583.
What is required by the Court of Appeals of Federal Circuit is that the
printed matter be functionally related to the substrate, not that the printed
matter itself serve a function. If the SEQ ID NOs did “functionally affect the
process of comparing a target sequence to a database by changing the
8 I have also considered the Majority’s analysis based on the USPTO’s
examination guidelines relating to subject matter eligible for patenting. See
Interim Guidelines for Examination of Patent Applications for Patent
Subject Matter Eligibility (“Guidelines”), 1300 Off. Gaz. Pat. Office 142
(November 22, 2005), especially pages 151-152. (Majority Op. 15-16). The
Guidelines are essentially a restatement of the case law already discussed,
and I disagree with the Majority’s analysis based on the Guidelines for the
same reasons already stated with respect to the analysis of the case law.

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efficiency or accuracy or any other characteristic of the comparison,” we
would be back to the fact pattern in Lowry, and the printed matter cases
would have no applicability to the patentability of the instant claims on
appeal.
The Majority notes that the results may change based on which
sequences are included in the database (Majority Op, 14, n. 5). According to
the Majority, that “possibility does not mean that the database sequences are
functional: MP3 files encoding different songs will cause a computer’s
speaker to output different music, but music is a paradigmatic nonfunctional
descriptive material. Descriptive material is not functional merely because it
results in different outputs when acted on by a computer program.”
As noted by the Court of Appeals for the Federal Circuit, “[t]he very
constitutional provision that authorized Congress to create a patent system,
Article I, § 8, also limited the subject matter eligible for patent protection to
the ‘useful arts.’” In re Comiskey, 499 F.3d 1365, 1374 (Fed. Cir. 2007).
“The Constitution explicitly limited patentability to ‘the national purpose of
advancing the useful arts-the process today called technological
innovation.’” Id. (quoting Paulik v. Rizkalla, 760 F.2d 1270, 1276 (Fed. Cir.
1985) (en banc)). In my view, however, comparing sequences of nucleic
acids to music is comparing apples and oranges, as music is not one of the
“useful arts.” Using a computer based system, however, to determine if a
query sequence matches a nucleic acid sequence that serves as a cancer
marker, or a marker for other disease states, in my opinion, is a
technological innovation that would certainly fall within the “useful arts.”

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Thus, I agree with Judge Linn that “the outer limits of statutory
subject matter should not depend on metaphysical distinctions such as those
between hardware and software or matter and energy, but rather with the
requirements of the patent statute: is an invention a ‘process,’ ‘machine,’
manufacture,’ or ‘composition of matter,’ and is it ‘new’ and ‘useful’?”
Nuijten, 500 F.3d at 1367 (Linn, concurring-in-part and dissenting-in-part).
No one would argue that one would have to consider the sequence
limitations if one had a substrate, such as a glass slide, with a nucleic acid of
a specific SEQ ID NO immobilized thereon. In addition, an array made up
of said substrate would be newly patentable every time you added a nucleic
acid of a new and non-obvious SEQ ID NO. 9 Thus, an array of nucleic acids
comprising a substrate and nucleic acids immobilized thereon could be
covered by a thousand plus patents based on the SEQ ID NOs of the nucleic
acids immobilized thereon. The array could then be used to hybridize a test
nucleic acid sequence with nucleic acid sequences immobilized on the array
to determine which nucleic acids of specified SEQ ID NOs the test sequence
hybridizes to. In that way, one can determine the biological function of the
test sequence based on the sequences with which it hybridizes. For example,
one may be able to determine that the test sequence is a tumor marker, a
marker for Alzheimer’s disease, a marker for a congenital birth defect, etc.
Claim 13 is drawn to a computer-based system, a machine for
comparing query nucleic acid sequences to at least the sense or antisense
sequence of at least 18 contiguous nucleotides of any one of SEQ ID
9 Assuming, of course, that it met all the statutory requirements for
patentability.

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NOS:9-1,008. One can use the computer-based system and obtain the same
results as if those SEQ ID NOs were immobilized on the substrate of the
array discussed above. Thus, under the Majority’s analysis one product (the
array) is patentable because it can be used to perform the wet chemistry, but
the computer system, which can be used to obtain the same results as the
process using the wet chemistry, is not, because the SEQ ID NOs are merely
“abstract” representations of the structure of the nucleic acids.
I disagree that such a distinction is supported by the case law, and is
the result intended by the patent laws. Accordingly, I would reverse the
Examiner’s rejection of claims 13 and 14 under 35 U.S.C. § 103(a) as
obvious in view of Altschul.

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ADAMS, Administrative Patent Judge, concurring in the result:
The majority’s analysis of the record on appeal is internally
inconsistent. In evaluating the issue of utility under 35 U.S.C. § 101 the
majority gives the SEQ ID NOS patentable weight whereas the SEQ ID
NOS receive no patentable weight in their analysis of the claims under 35
U.S.C. § 103. In one breath the majority finds that “the utility of the claimed
computer system . . . depends on the utility of the nucleic acids of SEQ ID
NOs 9-1008” (Majority Op. 7), but in another the majority finds that “the
SEQ ID NOs and the computer do not depend on each other for their
function” (Majority Op. 15).
Along the way the majority engages in a metaphysical discussion of
the difference between nucleic acid molecules and SEQ ID NOS (Majority
Op. 17-18). Cutting through the chaff, there is no doubt that SEQ ID NOS
per se are data, and if Appellants had simply claimed SEQ ID NOS per se,
the claims would properly be rejected under 35 U.S.C. § 101 as directed to
patent ineligible subject matter. This is, however, not what Appellants have
claimed, and a rejection of the claims as drawn to patent ineligible subject
matter under 35 U.S.C. § 101 is not before this panel for review.
Nevertheless, the majority blends the concept of patent eligible
subject matter under 35 U.S.C. § 101 with the “printed matter” doctrine
under 35 U.S.C. § 103 to arrive at their conclusion that the claimed
invention is obvious over a prior art reference that does not teach the SEQ
ID NOS recited in Appellants’ claims.
Accordingly, I cannot join with the majority’s analysis of the record.

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Claim Interpretation:
Claim 13 is drawn to a computer-based system - a machine10. The
claim recites the intended function of the claimed machine; specifically it is
for identifying nucleic acid fragments of the human genome of commercial
importance. The claimed machine comprises three elements:
a) 	a data storage means;
b) 	a search means; and
c) 	a retrieval means.
Claim 13 requires that the “data storage means” 11 comprise the sense
or antisense sequence of at least 18 contiguous nucleotides of any one of
SEQ ID NOS: 9-1,008. In response to a telephonic Restriction Requirement
requiring, inter alia, Appellants to “elect a single nucleic acid sequence”,
10 According to Appellants’ Specification “[a]s used herein ‘a computer-
based system’ refers to the hardware means, software means, and data
storage means used to analyze the nucleotide sequence information of the
present invention” (Spec. 102: 21-24).
The Supreme Court has defined the term “machine” as “a
concrete thing, consisting of parts, or of certain devices and
combination of devices.” Burr v. Duryee, 68 U.S. (1 Wall.)
531, 570, 17 L.Ed. 650 (1863). This “includes every
mechanical device or combination of mechanical powers and
devices to perform some function and produce a certain effect
or result.” Corning v. Burden, 56 U.S. 252, 267, 15 How. 252,
14 L.Ed. 683 (1853).
In re Nuijten, 500 F.3d 1346, 1355 (Fed. Cir. 2007).
11 “As used herein ‘data storage means’ refers to memory which can store
nucleotide sequence information of the present invention, or a memory
access means which can access manufactures having recorded thereon the
nucleotide sequence information of the present invention” (Spec. 103: 1-5).

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Appellants elected SEQ ID NO: 9, which they affirmed in their May 21,
2002 Response (May 21, 2002 Response 3). Accordingly, the Examiner
finds “[t]he claims are drawn to a computer based system comprising . . .
sequence identification software and a database comprising a fragment of
SEQ ID NO:[ ]9 or a combination of the sequences of SEQ ID NOS: 9-
1008” (Ans. 4). Therefore, on this record, the “data storage means” is the
electronic equivalent of an array of nucleic acids on a substrate, e.g., a
microtiter plate (Cf. Green Concurrence 32; Spec. 54: 26 - 55: 6).
As to the “search means”, claim 13 requires that the search means is
“for comparing a target sequence to each of the sequences of the data storage
means of step a) to identify homologous sequence(s).” Appellants’ use of
the term “step” is misplaced. The “data storage means” of limitation “(a)” is
not a step, but instead is an element (e.g., a component or part) of the
claimed machine. Appellants’ Specification defines the term “search
means” to mean one or more programs which are implemented on the
computer-based system to compare a target sequence with the sequence
information stored within the data storage means” (Spec. 103: 6-9).
Accordingly, I interpret the term “search means” to refer to one or more
programs implemented by the machine to compare a target sequence to the
sequence information stored on the data storage means of element (a) in
order to identify homologous sequence(s). Therefore, on this record, the
“search means” is the electronic equivalent of the “wet chemistry”
methodology used to compare a target sequence to a sequence on an array
(see, e.g., Spec. 17: 9 - 18: 14).

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Claim 13 also requires that the “retrieval means” is “for obtaining said
homologous sequence(s) of step (b)” (Claim 13 (emphasis added)). The
“search means” of limitation “(b)” is not a step, but instead is an element
(e.g., a component or part) of the claimed machine. Appellants’
Specification does not specifically define the term “retrieval means”.
However, as I understand it, Appellants’ use of the term “retrieval means”
corresponds to an “output means”. 12 According to Appellants’
Specification, “[a] variety of structural formats for the inputs and output
means can be used to input an[d] output the information in the computer-
based systems of the present invention. A preferred format for an output
means ranks fragments of the homo sapiens genome possessing varying
degrees of homology to the target sequence” (Spec. ¶ 0266). Accordingly, I
interpret the term “retrieval means” of claim 13 to be one that obtains, or
reports, the identity of homologous sequences identified by the search
means. Therefore, on this record, the “retrieval means” is the electronic
equivalent of “wet chemistry” techniques well known to those of ordinary
skill in the art (see, e.g., Spec. 53: 5-8).
Notwithstanding the mischaracterization of elements (a) and (b) as
“steps”, claim 13 is drawn to a machine. Further, it should be clear that
claim 13 is not attempting to claim the content of each SEQ ID NO. or the
physical molecules that each represents. Claim 13 is also not drawn solely
to data on a storage means. Instead, when considered as a whole, the
12 This is consistent with the majority’s interpretation of the term. See
Majority Op. 9 (“[t]he claimed system requires no functionality other than
that required to compare a target sequence to SEQ ID NOs 9-1008 and
output the result.”).

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claimed computer system comprises a (a) data storage means, comprising
specific sequence information; (b) search means; and (c) retrieval means.
As such the subject matter claimed by Appellants falls within the statutory
category of a “machine”.
More particularly, the claimed machine is the electronic equivalent of
an array, hybridization method, and detection method utilized in “wet
chemistry to identify target nucleic acids that are homologous to nucleic
acids on an array. As my concurring colleague points out, no one would
argue that an array comprising a novel and unobvious nucleic acid on a
substrate (e.g., a microtiter plate) is a novel and nonobvious array (Green
Concurrence 32-33). Further, no one would argue that the use of such a
novel and unobvious array would be anticipated or obvious simply because
hybridization and detection methods are known in the art. Claim 13 is the
electronic equivalent of this “wet chemistry” array and methodology.
Accordingly, as the nucleic acids are functionally tied to a “wet chemistry”
array; the SEQ ID NOS are functionally tied to Appellants’ claimed
machine.
The only other claim before this panel, claim 14 is drawn to “[t]he
system of claim 13, wherein said data storage means comprises a
combination of nucleic acid sequences comprising SEQ ID NOS:9-1,008”
(Claim 14).
Patent Eligible Subject Matter:
“Whoever invents or discovers any new and useful process, machine,
manufacture, or composition of matter, or any new and useful improvement

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thereof, may obtain a patent therefor, subject to the conditions and
requirements of this title.” 35 U.S.C. § 101 (emphasis added). There are,
however, a number of judicial exceptions to these categories of statutory
invention. Therefore,
[d]etermining whether the claim falls within one of the four
enumerated categories of patentable subject matter recited in 35
U.S.C. § 101 (process, machine, manufacture or composition of
matter) does not end the analysis because claims directed to
nothing more than abstract ideas (such as mathematical
algorithms), natural phenomena, and laws of nature are not
eligible and therefore are excluded from patent protection.
Interim Guidelines for Examination of Patent Applications for Patent
Subject Matter Eligibility (“Guidelines”), 1300 Off. Gaz. Pat. Office 142,
145 (November 22, 2005) (emphasis added). In addition, descriptive
material (e.g., “printed matter”) standing alone and in the absence of a
functional relationship with the underlying substrate “does not constitute a
statutory process, machine, manufacture or composition of matter and
should be rejected under 35 U.S.C. § 101.” Id. at 152.
The law is clear, however, that there is a distinction between statutory
ineligible laws of nature, natural phenomena, abstract ideas, and descriptive
material per se and the practical application of each. See State Street Bank
& Trust Co. v. Signature Fin. Group, Inc., 149 F.3d 1368, 1373 (Fed. Cir.
1998) (“[W]e hold that the transformation of data . . . by a machine through
a series of mathematical calculations into a final share price, constitutes a
practical application of a mathematical algorithm, formula, or
calculation.”(emphases added)); In re Alappat, 33 F.3d 1526, 1544 (Fed.
Cir. 1994) (“This is not a disembodied mathematical concept which may be

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characterized as an ‘abstract idea,’ but rather a specific machine to produce a
useful, concrete, and tangible result.”); In re Cominsky, 499 F.3d 1365, 1379
(Fed. Cir. 2007) (“When an unpatentable mental process is combined with a
machine, the combination may produce patentable subject matter, as the
Supreme Court’s decision in Diehr and our own decisions in State Street
Bank and AT&T have confirmed.”); Guidelines at 152 (“Certain types of
descriptive material, such as music, literature, art, photographs and mere
arrangements or compilations of facts or data, without any functional
interrelationship is not a process, machine, manufacture or composition of
matter.” (emphasis added)); In re Gulack, 703 F.2d 1381, 1386 (Fed. Cir.
1983) (“the critical question is whether there exists any new and unobvious
functional relationship between the printed matter and the substrate.”
(footnote omitted)). 13
Simply stated, “[i]f the claim is directed to a practical application of
the § 101 judicial exception producing a result tied to the physical world that
does not preempt the judicial exception, then the claim meets the statutory
requirement of 35 U.S.C. § 101.” Guidelines at 146.
On this record, the majority correctly acknowledges that “[t]he utility
of the claimed computer system . . . depends on the utility of the nucleic
acids of SEQ ID NOs 9-1008” (Majority Op. 7). Stated differently,
13 As Justice Linn points out in his separate opinion in In re Nuijen, 500 F.3d
1346 (Fed. Cir. 2007),
[t]he “printed matter” rejection has been treated as a doctrine
under § 103 rather than § 101, but it seems potentially more
apposite as a consequence of the “useful” requirement of § 101.
Id. at 1365-66. Accordingly, there is a reasonable basis for addressing the
“printed matter” doctrine in the context of 35 U.S.C. § 101.

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Appellants’ claimed invention is not a disembodied listing of SEQ ID NO: 9
or SEQ ID NOS: 9-1,008 which may be characterized as an ‘abstract idea’
or ‘non-functional descriptive matter,’ but rather it is a specific machine that
“requires no functionality other than that required to compare a target
sequence to SEQ ID NOs 9-1008 and output the result” (Majority Op. 9).
The majority is also correct in finding that “the results of comparing a
target sequence to a database may change depending on which sequences are
included in the database” (Id. at 14 n. 5). As claimed, the machine and the
SEQ ID NOS are functionally interrelated as the SEQ ID NOS alone would
not be able to achieve the stated purpose of the claimed invention in the
absence of the machine, and the machine without the SEQ ID NOS would
similarly be unable to produce the desired result required by Appellants’
claimed invention. Cf. In re Ngai, 367 F.3d 1336, 1339 (Fed. Cir. 2004).
Therefore, Appellants’ claimed machine is not simply a compilation of
irrelevant SEQ ID NOS per se. Instead, Appellants’ claimed invention
defines a functional relationship between the SEQ ID NOS and the substrate.
Cf. Gulack, 703 F.2d at 1386 (“[I]n examining Gulack’s invention we find
that a functional relationship does exist between the printed matter and the
substrate.”).
For the foregoing reasons it is no surprise that there is no dispute on
this record that Appellants’ claimed invention is directed to statutory subject
matter.

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Utility:
The question of whether Appellants’ claimed invention comprising
SEQ ID NOS: 9-1,008 satisfies the utility requirement of 35 U.S.C. § 101 is
a different question. There is a valid issue, on this record, as to whether
Appellants’ claims have a utility that is both substantial and specific. In re
Fisher, 421 F.3d 1365, 1371 (Fed. Cir. 2005) (“[O]ur predecessor court, the
Court of Customs and Patent Appeals, and this court have required a claimed
invention to have a specific and substantial utility to satisfy § 101.”). As the
majority explains SEQ ID NOS: 9-1,008 do not have a “substantial” or
“specific” utility (see Majority Op. 7-8). Because “the utility of the claimed
computer system . . . depends on the utility of the nucleic acids of SEQ ID
NOS 9-1008”, the claimed computer system also lacks utility.
Accordingly, I concur with the majority’s decision to affirm the
rejection of claims 13 and 14 under 35 U.S.C. §§ 101 and 112, first
paragraph, for lack of patentable utility.
Obviousness:
The Examiner finds that the only difference between the computer
system of Altschul and Appellants’ claimed invention is “in the content of
the nucleic acid comprised in the storage of the computer system” (Ans. 6).
To make up for this difference the Examiner gives “no patentable weight . . .
to the content [(SEQ ID NOS: 9-1008)] of the database on the claimed
computer system” (Ans. 7). According to the Examiner, “sequences of SEQ
ID NOS: 9-1008, constitute[ ] non-functional descriptive material because
the content of the nucleic acid sequence database does not alter how the

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computer system functions, i.e., the database of the claimed computer
system does not reconfigure the computer system to perform a different
function than the computer system of Altschul” (id.).
For their part, the majority steps away from the findings they make in
their utility analysis regarding the interrelationship between the SEQ ID
NOS (see e.g., Majority Op. 7 (“[t]he utility of the claimed computer system
. . . depends on the utility of the nucleic acids of SEQ ID NOs 9-1008.””)
and 9 (“[t]he claimed system requires no functionality other than that
required to compare a target sequence to SEQ ID NOs 9-1008 and output the
result.”). Instead, contrary to their findings under 35 U.S.C. § 101, the
majority finds that under 35 U.S.C. § 103 the SEQ ID NOs have no
functional relationship with the computer system, and are thus analogous to
the instructions (e.g., the intended use limitation) in In re Ngai, 367 F.3d
1336, 1339 (Fed. Cir. 2004) (Majority Op. 13).
To support their position the majority provides a lengthy discussion of
a number of cases relating to printed matter (Majority Op. 11-15). It cannot,
however, be more clearly stated than our appellate reviewing court did in In
re Lowry, 32 F.3d 1579 (Fed. Cir. 1994), “[t]he printed matter cases have no
factual relevance where ‘the invention as defined by the claims requires that
the information be processed not by the mind but by a machine, the
computer.’” Id. at 1583 (Fed. Cir. 1994) (quoting In re Bernhart, 417 F.2d
1395, 1399 (CCPA 1969)).
Here, as in Lowry, the majority “erroneously extended a printed
matter rejection under section[ ] . . . 103 to a new field in this case, which
involves information stored in a memory.” Lowry, 32 F.3d at 1583. When

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the claimed invention is considered as a whole the SEQ ID NOS are not
merely data stored in a database with no relationship to the machine or its
function. Cf. Id. (“Nor are the data structures analogous to printed matter.
Lowry’s ADOs do not represent merely underlying data in a database.
ADOs contain both information used by the application programs and
information regarding their physical interrelationships with a memory.”).
The SEQ ID NOS contain information used by the claimed machine to
determine if a target sequence is homologous to the SEQ ID NOS. Stated
differently, the SEQ ID NOS are functionally related to the machine and are
required for the machine to perform its claimed function.
I recognize the majority’s attempt to contrast the “data structure in
Lowry” with Appellants SEQ ID NOS 9-1008 (Majority Op. 13). The
majority appears to be under the impression that in order for Appellants’
SEQ ID NOS to represent functional material the SEQ ID NOS must
perform the same function as Lowry’s data structure. Specifically, the
majority finds that
[t]he Lowry court . . . concluded that the claimed data structures
were “physical entities that provide increased efficiency in
computer operation” and were not analogous to printed matter. .
. . There is no evidence that [Appellants’] 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.
(Majority Opinion 13-14). Lowry does not stand for the proposition that in
order for a “data structure” to be considered “functional” descriptive
material it must somehow provide increased efficiency in computer

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operation. This idea of “increased efficiency” was one of the tangible
benefits of Lowry’s invention.
According to Lowry, the data structures provide tangible
benefits: data stored in accordance with the claimed data
structures are more easily accessed, stored, and erased. Lowry
further notes that, unlike prior art data structures, Lowry’s data
structures simultaneously represent complex data accurately
and enable powerful nested operations. In short, Lowry’s data
structures are physical entities that provide increased efficiency
in computer operation.
Lowry, 32 F.3d at 1584. The tangible benefit here is to identify whether a
target sequence is homologous to the sense or antisense sequence of at least
18 contiguous nucleotides of SEQ ID NO 9, or a combination of nucleic acid
sequences comprising SEQ ID NOS: 9-1,008 (Claims 13 and 14). Contrary
to the majority’s intimation, Appellant’s SEQ ID NOS are not non-
functional descriptive matter simply because they serve a different purpose
than Lowry’s data structures. On this record, the claimed machine would be
wholly incapable of comparing a target sequence to each of the sequences of
the data storage means comprising the sense or antisense sequence of at least
18 contiguous nucleotides of any one of SEQ ID NOS: 9-1,008 if SEQ ID
NOS: 9-1,008 were not present in the machine.
Even assuming, as the majority and Examiner would like us to
believe, that the data structures are analogous to printed matter; neither the
majority nor the Examiner have established that the SEQ ID NOS, within the
context of the entire claims, lack a new and nonobvious functional
relationship with the machine. Cf. Lowry, 32 F.3d at 1584. To the contrary,
as discussed above, the majority’s findings lead one to the conclusion that

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when the claims are considered as a whole the SEQ ID NOS are functionally
related to the substrate (see e.g., Majority Op. 7 and 9). Therefore, here as in
Lowry, the SEQ ID NOS “perform a function. Gulack requires no more.”
Lowry, 32 F.3d at 1584 (citation omitted).
“Under section 103, the board cannot dissect a claim, excise the
printed matter from it, and declare the remaining portion of the mutilated
claim to be unpatentable.” Gulack, 703 F.2d at 1385. As the Gulack court
explained, “[t]he claim must be read as a whole. If the board meant to
disregard that basic principle of claim interpretation, we must reverse the
rejection as a matter of law.” Gulack, 703 F.2d at 1385. This is, however,
precisely what the majority has done in this case. For the reasons stated
above, when the claims are read as a whole, the SEQ ID NOS recited in
Appellants’ claims are functionally related to the machine.
I recognize the majority’s discussion of the “data structure” in In re
Warmerdam, 33 F.3d 1354, 1362 (Fed. Cir. 1994) (Majority Op. 13).
According to the majority, “[t]he court in Warmerdam concluded that the
claimed ‘data structure’ was not a physical arrangement of hardware but
instead was ‘nothing more than another way of describing the manipulation
of ideas contained in’ other claims and therefore not statutory subject matter
eligible for patenting” (id.). The majority’s discussion of Warmerdam is off
base for a number of reasons.
First, the portion of Warmerdam relied upon by the majority is
addressing the issue of whether Warmerdam’s claimed “data structure” was
statutory subject matter within the meaning of 35 U.S.C. § 101, not whether
the “data structure” was obvious under 35 U.S.C. § 103, which is the issue

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upon which the majority relies on Warmerdam on this record. As discussed
above, there is no dispute on this record that Appellants’ claimed invention
is statutory subject matter.
Second, the claims before this panel are directed to a “machine”, not a
“data structure” per se. This is a significant distinction. Claim 5 before the
court in Warmerdam was directed to a machine. Warmerdam, 33 F.3d at
1358. The only rejection of this claim to a machine in Warmerdam was
under 35 U.S.C. § 112, second paragraph. Warmerdam, 33 F.3d at 1360. In
reversing the rejection under 35 U.S.C. § 112, second paragraph, the
Warmerdam court expressly stated that “[w]hether such a programmed
machine is new, useful, unobvious, or otherwise patentable is not at issue in
this appeal, and we express no opinion thereon.” Warmerdam 33 F.3d at
1361 (emphasis added). Thus, the majority’s reliance on Warmerdam serves
only to emphasize how they have dissected Appellants’ claimed invention to
reach their conclusion that “[t]he SEQ ID NOs recited in the claims are
analogous to the instructions in In re Ngai” (Majority Op. 14). As discussed
above, this analysis is contrary to the law the majority relies upon for
support. See Gulack, 703 F.2d at 1385.
Third, building upon the distinction between a machine and a “data
structure” per se, the Warmerdam court did not hold that all “data
structures” represent non-statutuory subject matter. Instead, finding that
Warmerdam’s specific “data structure” represented non-statutory subject
matter, the court went further to explain that in contrast “[t]he ‘data
structure’ at issue in [In re Bradley, 600 F.2d 807 (CCPA 1979)] . . . was a
physical, interconnected arrangement of hardware and thus embraced by the

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term ‘machine’.” Warmerdam, 33 F.3d at 1362 (emphasis added). 14 As my
concurring colleague points out the holding in Warmerdam
“is a straightforward application of the basic principle that
mere laws of nature, natural phenomena, and abstract ideas are
not within the categories of inventions or discoveries that may
be patented under § 101.” 	AT&T Corp. v. Excel
Communications, 172 F.3d 1352, 1360 (Fed. Cir. 1999).
(Green Concurrence 29).
In this regard, the Warmerdam court explained that “[t]he body of
claim 1 recites the steps of ‘locating’ a medial axis, and ‘creating’ a bubble
hierarchy. These steps describe nothing more than the manipulation of basic
mathematical constructs, the paradigmatic ‘abstract idea’. . . . As a whole,
the claim involves no more than the manipulation of abstract ideas.”
Warmerdam, 33 F.3d at 1360. Stated differently, Warmerdam’s claimed
data structure fell within one of the judicial exceptions of statutory subject
matter and when read as a whole the claimed data structure could not be
interpreted as a practical application of that judicial exception. Accordingly,
Warmerdam court affirmed the rejection of the data structure claims for lack
of statutory subject matter under 35 U.S.C. § 101. Warmerdam, 33 F.3d at
1362. As discussed above, this is not the issue before this panel.
For the foregoing reasons, I agree with Judge Green’s conclusion that
“Warmerdam has no bearing in the instant case” (id.).
14 See also In re Nuijten, 500 F.3d 1346 (Fed. Cir. 2007), wherein the court
noted that the Board “found that [a storage medium having stored thereon a
signal with embedded supplemental data] nominally puts the claim into the
statutory category of a ‘manufacture’ and thus reversed the Examiner’s
§ 101 rejection of that claim.” Id. 500 F.3d at 1351.

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I recognize the majority’s reliance on Ex parte Mathias, 84 USPQ2d
1276 (BPAI 2005), aff’d 191 Fed.Appx. 959 (Fed. Cir. 2006).
Notwithstanding the majority’s characterization of Mathias as a “computer-
implemented method” (Majority Op. 15), the panel in Mathias states that
Mathias’ “invention relates to an on-screen icon and method for producing
said icon.” Mathias, 84 USPQ2d at 1277. That is, however, the only
mention of a method in the opinion. The Mathias panel found that Mathias’
claim 1 was representative of the claimed invention. Id. Mathias’ claim 1
was directed to “[a]n on-screen icon for viewing the score of a broadcast
sporting event between contestants having color uniforms.” Id. The
Mathias panel found that the prior art “reference teaches everything recited
in claim 1 except the limitation ‘sporting’ as argued by Appellant.” Id. at
1278-79. Stated differently, the difference between the claimed “icon” and
the prior art was the intended use of the “icon for viewing the score of a
broadcast sporting event between contestants having color uniforms.”
Mathias, at 1277. Relying on Ngai and Gulack the panel correctly found
that “our reviewing court has held that nonfunctional descriptive material
cannot lend patentability to an invention that would have otherwise been
anticipated by the prior art.” Id. at 1279. Cf. Ngai, “[h]ere, the printed
matter in no way depends on the kit, and the kit does not depend on the
printed matter. All the printed matter does is teach a new use for an existing
product.” Id. at 1339.
Clearly, the facts in Mathias are analogous to those in Ngai, which for
the reasons set forth above are distinct from the facts in this case. Thus, the
majority’s reliance on Mathias fails to support their position on this record.

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The majority’s reliance on Ex parte Curry, 84 USPQ2d 1272 (BPAI
2005), aff’d (Fed. Cir. Appeal No. 2006-1003, aff’d Rule 36 June 12, 2006)
fairs no better in relationship to the facts on this record. The Curry panel
found claim 81 to be representative of the claimed invention. Id. at 1273.
For clarity, I reproduce Curry’s claim 81 below:
81. A method of providing wellness-related services, including
at least one of wellness, health, or fitness services through a
publicly accessible distributed network to authorized users
using authorized portals, comprising:
providing an online site that enables wellness-related databases
to be accessed from at least one of a sponsored and a non-
sponsored portal;
placing in communication at least one of a sponsored and non-
sponsored portal to the online site through the publicly
accessible distributed network wherein the publicly accessible
distributed network includes the Internet, wherein the
sponsored portal is at least in part sponsored by and located at,
a fitness center, and wherein at least one of the non-sponsored
portals accesses the on-line site through the Internet;
receiving a request at the online site requesting access to the
wellness-related databases;
processing the request at the online site to determine whether
the portal was sponsored and whether the request was received
from an authorized user; and
responding to the request based in part on whether the portal
was sponsored and whether the user is authorized.
Id. The Curry panel made two findings in the context of non-functional
descriptive material. First, as claimed, “the ‘wellness-related’ data in the
databases and communicated on the distributed network does not
functionally change either the data storage system or communication system
used in the method of claim 81.” Id. at 1274. Indeed, as claimed, Curry’s
method simply requires that wellness-related databases be accessed. The

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data on the databases is not functionally related to the method itself, the data
is simply stored in the database and accessed through an online site. Further,
Curry’s claimed method does not require that the data be manipulated in any
way. Therefore, as the Curry panel reasons, “if the prior art suggests storing
a song on a disk, merely choosing a particular song to store on the disk
would be presumed to be well within the level of ordinary skill in the art at
the time he invention was made. The difference between the prior art and
the claimed invention is simply a rearrangement of nonfunctional descriptive
material.” Id. at 1275.
The Curry panel’s second finding relates to the sponsorship status of
the portal limitation in claim 81. Curry, at 1275. As the Curry panel points
out, the prior art teaches that limitation. Id. (“We find that Baker clearly
teaches differing access rights based on location data including portal
addresses. We find that the further labeling of a portal as sponsored or
unsponsored does nothing to change the structure or functionality of the
portal. [In this regard,] [w]e concur with the Examiner that this is
nonfunctional descriptive material”). Stated differently, the particular
limitation was taught by the prior art. Simply using different terminology
(e.g. “label”) to describe the same limitation taught by the prior art does not
make the claimed invention nonobvious.
Clearly, the facts in Curry are not analogous to the facts on the record
before this panel. The SEQ ID NOS are not simply a compilation of data
that can be accessed by a computer as in Curry. Instead, as required by the
claim before this panel, the SEQ ID NOS are functionally related to each
element of the claimed machine and are required for the machine to perform

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its function of identifying homologous sequences and outputting the result.
Unlike the database in Curry that simply stores data for retrieval, like songs
on a disk, on this record the SEQ ID NOS are integrally related to the stated
purpose of the machine to identify target sequences that are homologous. As
the majority acknowledges, “the results of comparing a target sequence to a
database may change depending on which sequences are included in the
database” (Majority Op. 14 n. 5). Stated differently, the operation of the
machine to perform its stated purpose necessarily depends on the SEQ ID
NOS. Thus, the SEQ ID NOS are functionally related to the machine.
Further, unlike the facts in Curry there is no dispute that the prior art on this
record fails to teach SEQ ID NOS 9-1,008.
Accordingly, I agree with my concurring colleague that “[t]he fact
situations in [Mathias and Curry] . . . are very different from those presented
by the instant appeal, and thus the outcomes in those cases have little
bearing on the instant appeal” (Concurring Op. 28 n. 7).
Finally, I recognize the majority’s discussion of the Guidelines for
Examination of Patent Applications for Patent Subject Matter Eligibility
(“Guidelines”) (Majority Op. 15-16). The guidelines “are based on the
USPTO’s current understanding of the law and are believed to be fully
consistent with the binding precedent of the Supreme Court, the Federal
Circuit and the Federal Circuit’s predecessor courts” (Guidelines at 142).
Accordingly, for the reasons set forth above, the Guidelines fail to support
the majority’s position.
On reflection, I find that the SEQ ID NOS are not taught by the prior
art of record. In addition, I find that the SEQ ID NOS are functionally

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related to Appellants’ claimed computer-based system. Accordingly, claims
13 and 14 are not obvious in view of Altschul. Therefore, I dissent from the
majority’s decision to affirm the rejection of claims 13 and 14 under 35
U.S.C. § 103 (Majority Op. 19).
Ssc
LEXICON PHARMACEUTICALS, INC.
8800 TECHNOLOGY FOREST PLACE
THE WOODLANDS, TX 77381-1160