Microsoft Tries to Patent Phylogenetics

| 16 Comments

According to an article in Science this week, Microsoft has basically tried to patent phylogenetics, with their application, Clustering Phylogenetics Variation Pattern. None of the broadly written claims in the patent application are novel, and most have been used by scientists for nearly two decades. I think Joe Felsenstein should walk over to Redmond and hit them with a cluestick or at least throw his book at them.

Many systematics blogs have weighed in on this application: Kevin Zelino, Dechronization, Myrmecos, and John Hawkes, to name a few.

16 Comments

Fun. maybe someone should try to patent a name for a new species or so, like Sophophora melanogaster.…..

I can’t walk far enough to hit them with my book, as the patent was filed by a Microsoft Research guy in the Bay Area.

Over on Dechronization (http://treethinkers.blogspot.com) you will find my comments, which are based on my understanding of Microsoft Research’s obsessive patenting policy, which suggests that they may not really have any intentions of claiming ownership of standard phylogeny methods. Note I said “may not.”

You’re a trusting soul, Joe. Microsoft would patent water if it thought it could get away with it.

RBH said:

You’re a trusting soul, Joe. Microsoft would patent water if it thought it could get away with it.

When I worked in industry, many of the companies I was familiar with bombarded the patent office with applications. They knew that the patent reviewers were overworked. They knew a few non-patentable ideas would slip through.

And if they were contested, the cost would break anyone who didn’t have deep pockets. The tactic was to tie up as many patents as possible, even if it meant buying whole companies and sitting on their patents.

I’ve seen patents granted for electronic circuits that have been commonly taught in textbooks for generations.

A friend of mine who worked at a pharmaceutical company saw a coworker of his successfully acquire a patent for a chemical process that is taught in nearly every advanced organic chemistry course.

Hurray for software patents!

Thanks for including my link! It is quite insane really. The thing I am more worried about is not whether the microsoft patent goes through, but will it (and other patent attempts) spur researchers to begin patenting software, metrics/measures, methods? Will universities encourage such behavior in order to acquire more revenue? This frightens me. Hopefully my fears are unfounded. Science appears to work more productively when open and freely accessible…

I agree Kevin, that prospect worries me a great deal as well, and as crazy as this patent application is, the possible after effects are even worse. I do not know how anything would get done if that started happening.

RBH said:

You’re a trusting soul, Joe. Microsoft would patent water if it thought it could get away with it.

… and maybe influenced by the fact that my current office, the first really good one I’ve had, is in a building constructed by Gates Foundation money.

But basically I am saying that, as Microsoft Research patents zillions of things, and as this one was probably mostly intended to patent the clustering of nodes by which sites had substitutions, we may not have to worry. There may be no big Microsoft interest in patenting standard phylogenetics. We flatter ourselves that what we do is important, but they may not see it as of much interest commercially.

@RBH

Hah! Microsoft Water. What a concept! I wonder what it would be like? Maybe you’d be filling up a glass when the “transparency bit” flips off unexpectedly and the water turns opaque. Then you might have to suck all the water out of the pipes and “reboot” with new water.

Microsoft Water. What a concept! I wonder what it would be like?

It’d be fine for a while, then start to slow waaaay down every time you used a new glass, then, suddenly, one day it would just stop working and turn blue.

Then you have to reinstall all your plumbing fixtures.

I was arguing that this is probably not a big Microsoft conspiracy to patent standard molecular phylogeny methods.

But let me add that, for probably-incidental reasons, that patent does state standard parsimony algorithms for counting state changes.

It would be helpful if systematics and molecular evolution societies (such as the Society of Systematic Biology, the Society of Molecular Biology and Evolution, the Systematics Association, and the Society for the Study of Evolution) tried to keep tabs on patents that include standard phylogeny methods and raise objections with the relevant patent offices. That way there would be less chance that some company would hold a patent on methods that are in fact “prior art”.

Weren’t all the claims on this one rejected?

But still, it’d probably help MS to not try and patent anything with enormous amounts of plainly available prior art in their patent binges. I always hear that this sort of thing is just a pre-emptive move to keep patent trolls at bay, but you’d think it would be easy for MS in cases like this one to just amass a collection of prior art examples rather than act patent trolls themselves.

Joe,

Since you are one of the respected leaders in quantitative aspects of phylogenetic reconstruction, wouldn’t it be possible for you to contact others who are as prominent as you are? Maybe such a group could compose some kind of general statement of principles to be used, when necessary, to read the riot act to Microsoft and other potentially offensive corporate patent seekers:

Joe Felsenstein said:

I was arguing that this is probably not a big Microsoft conspiracy to patent standard molecular phylogeny methods.

But let me add that, for probably-incidental reasons, that patent does state standard parsimony algorithms for counting state changes.

It would be helpful if systematics and molecular evolution societies (such as the Society of Systematic Biology, the Society of Molecular Biology and Evolution, the Systematics Association, and the Society for the Study of Evolution) tried to keep tabs on patents that include standard phylogeny methods and raise objections with the relevant patent offices. That way there would be less chance that some company would hold a patent on methods that are in fact “prior art”.

While I’ve not studied the Microsoft application and have no comment about it or Microsoft’s intent, I would like to briefly comment as a long-time patent attorney (biotech) concerning the apparent anti-patent stance among many of the posters on this site. Please don’t jump the gun and assume patents are a social ill because the patent system may not be perfect. Also, please consider making the effort to fully understand the economic principles underlying the patent system (if you have not already) before making such comments. Many would argue, in fact, in certain industries anyway, patents remain the lifeblood of innovation. With respect to dissemination and sharing, the irony is that public dissemination is exactly what the patent system was set up to accomplish. Full disclosure of inventions to the public in return for the possibility of a limited property right (should the invention be found useful, novel and nonobvious). Without patents, trade secrets would be the norm, at least in industry. Not much sharing there. As academics, I understand your point of view, but please don’t assume it is universal or that it is even workable in other sectors. By the way, I applaud and appreciate your efforts at educating the public about evolution. EKS

Eric, How does it benefit society when Microsoft patents a process already in use by society?

I don’t think anyone here is bashing patents per se, only this particular application for its non-novelty, obviousness, and attempt to lay claim to work performed by many other people.

I’ve not studied the Microsoft application. Don’t know if the claimed invention is novel and nonobvious or not. It may be that what they are actually claiming is not readily apparent from the wording.

I certainly agree that one should not be able to patent what is already in the public domain. But there are nuances there of course. As an easy example, the first entity to make insulin readily available to diabetics was entitled to patent protection even though insulin was already known.

In any event,I also agree that sometimes ill- advised patents slip through due to the lack of resources at the USPTO. Thanks for the clarification that you are not bashing per se :-)

We sometimes see influential individuals or watch-dog groups spreading misinformation to legislators and the press and wonder if they would be taking such alarmists positions if they really understood patent law.

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This page contains a single entry by Reed A. Cartwright published on August 17, 2009 6:05 PM.

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