Given the existence of prior art, patent applications that lay claim to widely used methods should be shot down during their application process, but that hasn't stopped even big companies from trying, or the Patent Office for granting them. Microsoft's seen both sides of this problem recently, as it was granted one patent for storing formatting information in XML files, and faced a damaging injunction for violating someone else's patent on the same general thing.

In a bit of awkward timing, it was recently discovered that, two years ago, Microsoft filed a patent for clustering phylogenetics methods, which have existed for years, and are currently in use by just about anyone who does evolutionary biology. The filing has been compared to attempting to patent multiplication tables, and has the phylogenetics community on edge.

Clustering algorithms allows researchers to take a collection of related sequences—the amino acids in proteins, the bases in DNA—and figure out the likely evolutionary relationships among them. The sequences that have the fewest changes among them cluster together, suggesting that they were most recently derived from a common ancestor.

The patent, filed by Microsoft researcher Steve Ozer in July 2007 and recently discovered by a graduate student at the University of Texas in Austin, claims ownership of several common phylogenetic methods. At its most basic, however, it seems to patent identifying any evolutionary relationship from sequences: "receiving a plurality of sequences across a plurality of species [and] mapping at least a portion of the plurality of sequences to an evolutionary tree."

This may seem like it falls well outside the range of Microsoft's typical interests, but the company appears to be taking an interest in bioinformatics. In June, Microsoft bought assets of Rosetta Biosoftware from Merck. Microsoft intended to integrate Rosetta's software with its own Amalga Life Sciences platform, which is used for research at drug companies and universities.

Hopefully, a patent with this much prior art will not be approved by the US Patent and Trademark Office because the methods it details are so common—and, in fact, a reader noted that it has received a "nonfinal rejection" from the USPTO. That still allows the patent to be resubmitted in a modified form, however, so the biomedical community may want to follow it carefully.

There is some precedent for patent applications that put entire fields at risk: according to Science, in the mid-1990s, a molecular biologist in Canada tried to patent the use of a particular type of mitochondrial DNA. A senior researcher at the Natural History Museum, backed by the UK government, challenged the application, and it was withdrawn.

A similar point of patent contention has been the use of DNA for bar-coding organisms, such as plants, by using a short piece of their own DNA sequence to help identify their species quickly. The Consortium for the Barcode of Life is a international initiative that advocates for the open standards in this field, but the same Science article indicates that the project has been threatened by patents three times, the most recent happening last month.

In any case, these events make clear that technology isn't the only field where patents with extensive prior art puts common practices at risk; they also make it clear that gene patents aren't the only things that threaten progress in biomedicine.