Wednesday, April 08, 2009

Patenting biodiversity tools

The e-Biosphere online forum has a topic entitled Why open source code? Why not patented softwares?. This thread was started by Mauri Åhlberg, who notes that the EOL codebase is open source, and asks "why not patent software." Åhlberg has patented NatureGate (US Patent 7400295), which claims:
In the method of the invention objects can be identified on the basis of location and one or more characteristics in an improved way. The method is performed by means of a user device and a service product offering a service with which objects can be identified. In the method of the invention, the object to be identified is positioned and the position of the object is informed to the service to which the user device has connected. The user of the user device selects one or more characteristics presented by the service for an object to be identified. A message containing the position of the object to be identified and selected characteristic(s) is then sent from the user device to the service product. The service fetches information on the basis of the position of the object and the selected characteristic(s) from a database. The fetched information is presented for the user device in the form of alternative objects to be identified. The system of the invention is characterized by a...
The description seems very general, and I can't see anything that qualifies as novel, but on a quick read suggests that anybody writing, say, an iPhone application to identify an organism based on where you are and what it looks like will be in trouble.

There are other patent applications in this area, such as Managing taxonomic information by the developers of uBio, which claims:
In a management of taxonomic information, a name that specifies an organism is identified. Based on the name and a database of organism names or classifications, another name that specifies the organism and that represents a link between pieces of biological identification information in the database, or a classification for the organism, is determined. Based on the other name or the classification, information associated with the organism is identified.

Now, I'm clearly no expert on software patents, and this is a contentious area, but this strikes me as a little worrying (worst case scenario, biodiversity informatics becomes a victim of patent trolls). One could argue that patents can be used defensively (i.e., to ensure that a technology is not claimed by another, say commercial, party who then limits access based on cost), but I'd like to see a little more discussion of these issues by the biodiversity community.


Roger Hyam said...

Oh know they are going to take all our money way! Phew, it's OK I just looked and we don't have any money. But hold on the RSPB are loaded and they are already breaking the patent

Mauri Åhlberg said...

Dear Roderic,

Thanks for your message. I appreciate your expertise on your own field:

However, I think that you have written false claims about these patents we are discussing. I am happy to have a dialogue with you, and all interested partners, searching for thruth and common good, concerning biodiversity informatics and biodiversity informatics education.

Firstly, I want to emphasize that I do not own the patents. But, I have tested from the beginning of 2006 all web sites that I have found, where I have found a claim about an interactive key or keys for identifying species. I have not found anything like the method Eija and Jouko Lehmuskallio were able to patent. I will answer to your claims in the way you structured your message on the Online Forum of e-biosphere 2009 Conference.

Roderic wrote:

”I have read the patent
( )
and am horrified that such a trivial idea
(identifying objects based in part on
knowing where you are) warrants a patent.
The patent is almost devoid of intellectual content,
in the sense that it is an obvious thing to do.”

My comments for answer:

(_1) The claim that ”a trivial idea” would have been patented:
The point is that it is not the ”idea” that is patented, but the METHOD AND SYSTEM, the way the identification is done, that the patent was given.
Please, check again:
And you'll receive: Results of searching in PCT for:
The invention is based on a method and a system, wherein objects can be identified on the basis of location and one or more characteristics by means of a user device and a service product. …
In the method of the invention objects can be identified on the basis of location and one or more characteristics in an improved way. ...

(_2_) The claim concerning that
”The patent is almost devoid of intellectual content,
in the sense that it is an obvious thing to do.”
For sure it is trivial that you can create matrices in which organisms are on the rows and characteristics are on the columns.

However, as far as I know, no taxonomists have done even this kind of work over hundreds of different species and families. Taxonomist mostly use dichotomous keys, even when they claim that these keys are interactive. Taxonomists mainly concentrate rightfullly only the groups they are actively making research on. Even from this kind of matrix, it is a long way to apply the idea to online service as done in the patent application. (Even after that it is very hard to create a fast, reliable service in practice. NatureGate® Online Service has achieved this by applying the patents of Eija and Jouko Lehmuskallio.)

As lifelong educators of biodiversity, Eija and Jouko Lehmuskallio have the same interest that all in my NatureGate® Research Group have: promoting identification of as many species as possible, promoting lifelong learning of biodiversity and sustainable use of biodiversity, about habitats, ecosystems and ecosystem services.

(_3_) Answering your question:
”I'd be curious as to why you think patenting
this idea benefits biodiversity research?”

Firstly, WHY patents, what are patents and intellectual property, and how these are safeguarded:
Starting from the basics:
”The World Intellectual Property Organization (WIPO)
is a specialized agency of the United Nations.
It is dedicated to developing a balanced and
accessible international intellectual property (IP) system,
which rewards creativity, stimulates innovation and
contributes to economic development
while safeguarding the public interest.”

As a background, I want again to emphasize that I do not own the patents. University Professors and other university experts typically do not patent results of their work. We have our monthly salaries, and accordingly scientific results are mostly open and free for everybody to test and use.

But inventors and enterpreneurs create their own intellectual property and according to international laws some of these inventions can be patented. Regardless how self-evident these patents may seem to be, after the patented method and system have been revealed. The point is that nobody did that invention before those people who created and who applied and received patent for their work. Eija and Jouko Lehmuskallio have devoted their whole life to this method and its applications and it really works. They are enterpreneurs who with partners like the University of Helsinki created a NatureGate® Ltd, a company for public good. The NatureGate® Ltd creates and maintains, continually enlarges and improves its Online Services of Biodiversity (Informatics) Education.

Above is necessary background to be able properly to answer your question:
”… why you think patenting this idea
benefits biodiversity research?”

a) Intellectual property, patents and trademarks are necessary to have a real business organisation, to create wealth for salaries for people involved and for creation and maintenance of free, open acess online services for identification. We would not have funding for NatureGate® Online Service without the patented and registered intellectual property. We are inviting all interested experts and organisations to discuss with us, how we could promote biodiversity research and education together.

b) We are paying for services of some of the taxonomists. This way we are supporting biodiversity researchers and research.

c) Some taxonomists are collaborating for free, e.g. in order to have this free service to the organisms groups that they have special interest.

d) Some experts are collaborating with us for beeing accepted as partners in future NatureGate® sister company in their own country or region.

e) When more of the patented METHOD and SYSTEM is implemented, then people are able to link their observations to the core identification service and upload their own photos with GPS to the separate servers of NatureGate® user community. The end result is free data for all biodiversity researchers, biodiversity and biogeographic research. If the amateurs cannot identify some of the species, then s/he may upload the photo and attached decription to a specific file and our collaborating experts will try to identify at least a taxon, e.g. family or genus of the organism. This data may also become valuable for biodiversity research who are willing to have a look an use of this kind of data that amateurs have provided.

(_4_) Concerning you last and funny fake example:
”Perhaps it might be worth discussing the issue more generally,
as there are other patents that impact biodiversity research,
such as "Managing taxonomic information"”
Now I learnt that Google can be cheated to represent anything you want, if you have motives and competence to do so.
But, please check this funny fake ”patent” by using the service of the United Nations’ IPR Organisation: You cannot find that your ”strawman” patent.

(_5_) We are ready to discuss with all honest and serious researchers and developers in Biodiversity Informatics and Biodiversity Informatics Education, who are seeking truth and common benefit for conservation of biodiversity and sustainable use of biodiversity.

Please, check: IUCN:

With best wishes,

Dr. Mauri Ahlberg FLS
Professor of Biology and Sustainability Education
University of Helsinki, FINLAND

Roderic Page said...


1. I'm sorry but I find the idea straightforward. This is one problem with software patents, given that ideas are cheap and the same idea can occur independently to many people, one can come up with an idea only to discover that it is patented (and therefore there may be severe limits to what they can do). I think this limits progress.

2. Where in the patent are the algorithms or methods used to identify organisms? I've read other software patents (e.g., System and method for browsing node-link structures based on an estimated degree of interest) where the intellectual content is clear (albeit it wrapped up in hideous "patent-speak").

3. Patenting is not the only way to create fundable tools, and software patents are a contentious area (and idea was rejected by the EU Parliament). Why do you think restricting the freedom of others is a good idea? I don't see why this is essential to making the kind of tools and services you propose. Open source companies that make their code freely available still get funded. Funding and openness are not mutually exclusive.

4. I don't know why you suggest that the patent application "Managing taxonomic information" is fake. It's real (although it's not clear to me if it's been granted, which is why it might not show up in the WIPO search engine).

I take your implication that I have the skills to "cheat" Google into showing anything I want as a compliment, although I think I deserve extra credit for managing to insert the patent application into and FreePatentsOnline.

5. I think there is an interesting discussion to be had about intellectual property, open source, and access to data in our field. I'll declare my own bias at the outset, namely that I don't see that software patents help us, quite the opposite.

Mauro Cavalcanti said...

This is a return to the Dark Ages, the complete negation of all the Free Software movement has been hardly building during his history, fighting greedy megacorps as M$... Too bad if there are people who are talking seriously about this, especially in a moment in history in which the entire world economy is facing the results of the unregulated capitalist greed...