home .Featured Patenting obvious methods in Microbiology of the Built Environment?

Patenting obvious methods in Microbiology of the Built Environment?

(edited 7:15pm 3-7-16, to make it clear this was a patent application not a patent)

So I got an e-mail from Jonathan Eisen this morning asking me if I had seen this tweet about a patent application regarding surveying the microbiome of the built environment:



And my first thought was, that’s crazy!  Reading the bits of text in that picture is (as Ameet pointed out) just like reading the Materials and Methods section of the vast majority of microbiome papers… built environment or otherwise.  So I skimmed through the entire application (“Monitoring and managing a facility microbiome”) and indeed that’s what it appears to be.  The authors of this patent application are proposing that their “method” would involve collecting building metadata (“facility operation parameters”), and then examining the microbiome over time.  In the end, they would then propose changing building parameters in order to facilitate a healthier microbiome of the building.   In their words “altering the changeable facility condition by altering the facility microbiome to effectuate the desired change in the facility performance indicator.”

There are two parts of this I don’t get at all.  The first, and less important, is that from what I understand of the field we’re a long way from being able to propose changes that results in a healthier building microbiome so it’s hard to see where this can accomplish that goal.   But that is where a lot of this research would like to lead so maybe this is just visionary.   The second, and most critical, is that I don’t understand how this is patentable.   I’m no patent expert or lawyer but we’re talking here about techniques that are used by many people in the field on a regular basis.   I both don’t see how this is defensible, and I wonder about the effects on research if a patent such as this were granted.  Would that mean that many of the other studies on the built environment microbiome would have to close up shop or pay royalties?  Where does this end?

And then this gets even more complicated because this patent application was filed by Phylagen.  A company co-founded by a colleague I respect, staffed by another colleague who I also greatly respect… and my boss is one of their scientific advisers.

So I challenge any of those folks (or anyone else) to please explain to me how such a patent application as this is defensible, and how it wouldn’t be used in the future to stifle research.


David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter

11 thoughts on “Patenting obvious methods in Microbiology of the Built Environment?

    1. Thanks David, I edited the post to make it clear that this was a patent application.

      At a casual glance the patent application you linked to is just as crazy as this one! “Industrial activities” is pretty broad and it looks like they are saying “we will use QIIME to study this stuff”.

    2. There are a whole series of these, and even a series from Seres … I don’t understand the landscape at all and find the breadth of some of these applications vexing (including this one). But as I said, I don’t understand the landscape at all.

      For the record here are some Tweets of mine about other microbiome patents that I did not grok.

  1. One thing to know when looking at a patent (or patent application) is that the only part that really matters are the Claims (usually at the end). The Claims dictate the scope of what is protected by the patent. Since the claims matter so much, the standard technique when submitting a patent application is to have a huge set of claims that start off as broad as possible (see Claim 1), and then get more and more specific. The patent examiner will likely fight back on many (or all) of the claims and then it is a back and forth between the applicant and patent examiner. For a claim to be valid it has satisfy three criteria:
    1) Be novel (new)
    2) Useful
    3) Non obvious (tricky to explain, but works fairly well in practice)
    Patent examiners frequently cite academic literature to show that a claim or set of claims do not satisfy 1 or 3 (2 is easy to satisfy as one rarely tries to patent something that is not useful!)
    By this system, applications always look very scary and most of the time the actual patent will be pretty narrow.
    There is a research exemption / safe harbor for patents (as far as I know) so the worry isn’t usually in stifling academic research but may affect other companies (start-up or not).
    Hope that helps!

    1. Thanks! That is very helpful. Sounds like it’s a bit of a game then… toss it all in and hope the patent examiner lets some good stuff through. I’m beginning to see why the process takes so long.

  2. A little late to this party, but still wanted to participate. This patent application just came to my attention and while I agree with the comments above about how the patent process works, I still have pretty serious concerns about this.

    1. Although patents generally don’t impact academic research they certainly can. One way is that a patent application is used to bolster a trademark application and then a litigious trademark holder can threaten academics who don’t use a trademark in academic publishing.

    2. Methods can be part of patents. Academics who use those methods can face either higher costs and/or attention (AKA bullying) from a litigious/zealous patent holder.

    3. Although patent application != patent, there are lots of really troublesome things that do make it into patents. An example, heating of buildings as part of moisture remediation is patented. If you heat a building for remediation purposes, you will face a lawsuit (as an aside, in this particular case, membership in a professional organization includes the use of this patent – I will avoid commentary about parallels to organized crime protection).

    4. IP from patents is routinely traded, included in business agreements, and otherwise such that it is easy for the original inventors to lose control of the enforcement/non-enforcement.

    5. It is easy to say that a patent is obvious and/or non-novel and quite another thing to actually have to defend this position in the face of a legal threat. For many academics, the idea of actually doing this is unappealing especially because we have so much else to do. Different universities will provide different levels of support as well.

    There is one big take home message from this: people in our community should not participate in applications like this and when they do, they should be called out for doing so. If nothing else, it is contrary to the interests of the community.

    And to show that I am not just a humourless curmudgeon on this issue, here is a patent from my great uncle: http://www.google.ca/patents/US2556893. It basically consists of taking pressurized DDT and rapidly expanding it (and, of course, venting it to the atmosphere) to cool a single can/bottle of a beverage. It thankfully never went into production because of the vast amount of environmental damage that results from its use.

  3. All of these comments are silly because at the end of the day nearly all microbiome papers AND start ups (that rely on correlating the 16S/ITS to some metadata based on the relative abundance of those 16S markers) infringe on this patent:


    It is shocking that people are focused on some lame Knight patent or some lame Phylagen patent. Those are totally irrelevant, probably don’t even work (most of these places don’t even culture microbes!), and ultimately not enforceable. Microbiology is NOT a data science problem. It is biology problem.

    Good luck to everyone to not getting sued by DuPont (who acquired that company Taxon and now owns that IP family/portfolio)!

Leave a Reply to David Mills Cancel reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: