Alex, an entomologist at the fabulous Myrmecos blog, was also infuriated by the news piece by Pennisi (subscription required) in the latest issue of Science. His take was slightly different than my take on it a couple days ago. Alex is most upset about the pending Microsoft patent claim on, according to the language of the patent,
“BACKGROUND
[0001]Biomolecules are composed of monomers in which one or more monomers may share a relationship with another monomer. For example, a protein molecule or polypeptide may be composed of any number or type of amino acid residues linked in a polypeptide chain in a particular sequence. Some of the amino acid residues in the molecule may be related to other amino acid residues either in the same molecule or in another molecule with which it interacts.
[0002]Similarly, other biomolecules, such as nucleic acid molecules also contain different monomers–in this case consisting of nucleotides–of which some may be related to others. The relationship of such monomers in a biomolecule may include, for example, a structural relationship or a functional relationship.
[0003]Efficient and accurate identification of related groups of monomers of biomolecular sequences is important in achieving biotechnological advances in research and development. However, there is currently no efficient method for determining groupings of monomers in a biomolecular sequence, or among related interacting sequences. “
Aside from the Bio 101 lesson, the last line (bolded) was pointed out by commenter Robert Keller, who blogs at Archetype. This patent has only been on the table for 2 years, so either someone at Microsoft hasn’t done their homework or is outright lying.
In his comment on Alex’s post, Keller also brought to my attention that this is nothing new in systematics. In 1990, two individuals tried to patent the basis pf phylogenetics as we know it. In fact, the title of the patent reads like it could have been a revolutionary paper in the field, or an important early review paper at the least:
TEST TO DETERMINE AN ORGANISM’S SPECIES AND/OR POPULATION IDENTITY BY DIRECT NUCLEOTIDE SEQUENCE ANALYSIS OF DEFINED SEGMENTS OF ITS GENOME
It almost sounds like a precursor to the DNA barcoding approach, using a defined genetic nucleotide sequence to identify a species or a population within a species.
“Many government agencies require a means of identifying the species origin of meat or other biological specimens. For example, law enforcement agencies need to know if a blood stain comes from a human or an animal. Food inspectors check meat for accurate labelling for economic (e.g. selling cheaper meats, e.g. horse for beef) and religious (e.g. pork for beef) reasons. Wildlife officers must be able to identify the species type of meat to detect animals that have been obtained illegally (i.e. hunted without a permit, out of season, or the quota exceeded). In addition, customs officers require methods for identifying restricted, endangered species or products derived from them. There is therefore, a need for a rapid, accurate and reliable method for determining the species origin of a biological sample.”
Oh my God!! It is DNA barcoding. Though the NCBI was created in 1988 as a national database for storing molecular information, I am not clear on how populated and useful, or in use, that database was by the time of the patent application in 1990. Additionally, the Consortium for the Barcoding of Life was not in place until about 2003, coinciding with what the group considers it’s “founding publications” by Dr. Paul Hebert at the University of Guelph. The “Folmer” primers of the mitochondrial COI region, that was the benchmark of DNA barcoding was not published until 1994.
It is curious how this patent didn’t make it through. Perhaps because they never made the analogy to barcoding the patent clerks, who studied the claim and knew the field, thought the methods involved were indeed nothing new. Maybe 20 years ago there were other phylogeneticists, systemacists, and molecular biologists who stood up in opposition to such obvious overstatement of novelty. A careful examination though really reveals that what they were trying to accomplish was devising a system of identifying animals based on a portion of the cytochrome oxidase b gene by utilizing methods already in existence and developed by other labs, though widely used by biologists. For instance, they state,
“The advantageous effect of this invention, relies on the ability to isolate DNA from the sample in question; the amplification of a defined segment of the DNA; the determination of the DNA sequence of the amplified segment; the comparison of this DNA sequence with a data base of sequences from known species; and a cladistic analysis of these sequence data.”
In other words, the “advantageous effect of this invention” relies several independent methods already widely in use, used in concert. This sort of rhetoric is what researchers need to be wary of and keep a watchful eye on. It adds nothing new, only reviews the literature up to the point and applies it to identifying freshly frozen, ground up, smoked, pickled, canned, salted, and partially cooked animal flesh. This is part of the current applications of DNA barcoding. It makes me wonder, not being in that community per se, what the contribution of this patent or the contributions of the authors of the patent had in the development of DNA barcoding as a useful and now widespread enterprise?
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