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Biotechnology increasingly relies on the algorithmic manipulation of information to discover new products. It is now possible to screen huge amounts of archived data for useful chemical structures. But one must first know what to look for. What scientists look for are common structural sequences that predict important biological or immunological functions, such as a particular enzymatic activity, the ability to attach to another molecule or cell, or the ability to be recognized by the immune system. Similar structure predicts similar function, and the similarities among two or more molecules are used to define a “motif.” Motifs can be identified in large databases of chemical structures, allowing us to find the needles in the haystack. Since the algorithms that identify and manipulate these motifs have “real world value,” they should be patentable. CAUSE FOR UNCERTAINTY In State Street, the U.S. Court of Appeals for the Federal Circuit determined that a mathematical algorithm that produces a useful result is statutory subject matter even if that result is expressed in numbers. The State Streetdecision reasserts the fundamental purpose of 35 U.S.C. � 101 — to limit patent protection to inventions with real world value. State Streetis in fact consistent with the stance that the Federal Circuit’s predecessor, the Court of Customs and Patent Appeals, took in earlier decisions, such as In re Benson, 169 U.S.P.Q. 548 (C.C.P.A., 1971). Nevertheless, for much of the past three decades, the PTO discouraged claims containing mathematical algorithms. This policy was due in part to logistic and fiscal strains from the influx of software-related inventions. The point for us is that — regardless of how the State Streetdecision should apply to “bioalgorithmic” processes — because of the historical dissonance between court opinions and agency policies, it is unclear how the State Streetdecision will affect the PTO’s biotechnology and chemical examination policies. No guidelines affecting bioalgorithmic or bioinformatic claim language have been published. Processes that involve computerized information processing of biological information may be patentable under the PTO Guidelines for Computer-Related Inventions, MPEP � 2106. These guidelines are applicable to bioalgorithmic processes performed on a computer system or limited to a specific machine. In fact, several patents directed to computer-implemented methods of analyzing biological information have issued ( see, e.g. U.S. Patent Nos. 5,856,928; 5,930,154; 5,933,859; and 5,953,727). Process claims using algorithms may also be statutory subject matter if they fall within a “safe harbor.” Safe harbors entail adding significant pre- or post-solution activity to a claim, such as information-gathering for input into the algorithmic process, or testing or producing a product based on the output of the algorithm. A process reciting an algorithm that falls within a safe harbor results in some type of physical transformation in the real world. Patentability is based on this physical transformation, not the mere solution of the algorithm. Despite the existence of a few bioalgorithmic patents and safe harbors, however, the future is uncertain. One problem is that if the PTO does not interpret a biological process claim using an algorithm as a computer-related invention, it will not apply its examination guidelines for computer-related inventions. Another concern is that chemical and biotech examiners may interpret State Streetdifferently from the way examiners in the computer arts do. The law should not, however, turn on which examining group examines the invention or on whether a process manipulates biological information or other types of information, such as the mutual fund share prices at issue in State Street. WET OR DRY? Should patentability depend on whether a biotechnology process uses “wet steps” carried out in a test tube or only “dry steps” performed using an algorithm? For instance, screening a genomic library to identify a biologically useful sequence can be done wet by contacting an actual DNA probe with DNA molecules expressed in a genomic library. Or, it can be done on a computer using an algorithm to screen a database containing genomic DNA sequence information. The former — a process for using a hybridization probe to identify a clone consisting of a DNA sequence from a genomic library that encodes for a useful antigen — is clearly statutory and patentable. Under the PTO Guidelines, the latter — a computer-implemented process for screening a genomic DNA database (corresponding to the wet genomic library) using a short DNA sequence motif (corresponding to the hybridization probe) to identify the same sequence — should also be patentable. Both the wet and dry methods identify the same useful DNA sequence. Unfortunately, it is not yet clear whether the PTO computer-implemented guidelines will be consistently applied to biotechnological inventions, or whether similar “dry” non-computer implemented processes will be deemed statutory. State Streetsuggests that what really matters is that a process produce a useful result. Therefore, a bioalgorithmic process that screens chemical structures should be patentable, because it produces a useful result. The biotechnology industry uses computers to do what can be done in the lab. If the lab work deserves a patent, so should the computer work. Thomas Cunningham practices in the chemical department of Arlington, Va.’s Oblon, Spivak, McClelland, Maier & Neustadt. He holds a Ph.D. in microbiology and immunology and is a former biotechnology patent examiner. He may be reached at [email protected]

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