Apparently, he didn't directly open source it. He approved its inclusion in the Open Refine package. It's pretty obvious that he didn't understand the consequences of releasing his code in a project licensed by BSD. I can understand his frustration, probably because he was told that his conditions were covered under the BSD license. Given that he sells the same code as a commercial product, this was obviously not his intention.
However, he failed to grasp some basic IP concepts, especially wrt US law. Algorithms are not copyrightable, and most are not patentable (especially after Alice v CLS) under US law. However, there is solid precedent for similar systems being eligible for patent protection (soundex, other patents that cite his systems as source material, etc). It does not appear that he applied for this protection at this time.
Moreover, under the modification clause of the 3 clause BSD license he used in his source file, there is a significant amount of commentary suggesting such a rewrite would be permissible under the terms of that license. However, re-licensing it under MIT would on the surface not be permitted.
EDIT: he may have applied for a patent. This could preclude the project from including his system. However, I'm not a patent lawyer, so I don't know how well this would hold up in international implementations (github being a US entity makes this point relatively moot).
Unless he applies (has applied at this point) in a particular country, or has a Patent Cooperation Treaty application filed in some country and is pursuing it in a particular country, he is completely out of luck by publishing his algorithm. (And as another commentor mentioned, post-Alice, it's pretty unlikely that a patent applicant will succeed with software patent applications absent some pretty close coupling to something specific about the computer hardware.)
It's amazing to me that so many software developers have no basic grasp of IP--the thing they work so hard to produce. It's not like it's all that difficult: Copyrights protect the expression of an idea; patents protect inventions. This developer seems to think that copyrights protect ideas.
> However, he failed to grasp some basic IP concepts
Indeed. His patent was abandoned, according to the USPTO's PAIR website at [1], after being rejected for non-patentability. Aside from being apparently non-patentable subject matter, the examiner noted that Philips's application was similar to a previously rejected application no. 10/454,261, and rejected the former on the some of the same grounds as the latter.
The BSD license does not contain any patent grants, so he can still assert the right over the use of his patent in pretty much anything - the BSD licensed code can still only be used with his permission, since you need both the copyright license and patent license to use it.
When patents are involved, it makes more sense to us a license like the GPL3 or Apache2.0, which also grant licenses for any patents which are covered by the code.
Some interpret BSD to have an implied patent grant, but the law on the subject is sparse and mostly untested. The license do say that: "Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met", but if that will be enough is up the court, and to my knowledge they have not been asked yet.
However, he failed to grasp some basic IP concepts, especially wrt US law. Algorithms are not copyrightable, and most are not patentable (especially after Alice v CLS) under US law. However, there is solid precedent for similar systems being eligible for patent protection (soundex, other patents that cite his systems as source material, etc). It does not appear that he applied for this protection at this time.
Moreover, under the modification clause of the 3 clause BSD license he used in his source file, there is a significant amount of commentary suggesting such a rewrite would be permissible under the terms of that license. However, re-licensing it under MIT would on the surface not be permitted.
EDIT: he may have applied for a patent. This could preclude the project from including his system. However, I'm not a patent lawyer, so I don't know how well this would hold up in international implementations (github being a US entity makes this point relatively moot).
http://www.google.com/patents/US20090043584