Hi, I'm a patent examiner. I won't apologize for the agency, we have more than our share of problems, but I also think we get more than our share of criticism for bad patents.
The PTO simply has no ability to change patent law. We apply it as it's written by Congress and interpreted by the courts. A few points on the law without getting into criticism of the agency (you can get easily find that elsewhere):
1. The burden on patent applicants is too low. There's a presumption that a patent will issue as soon as it's filed. The patent examiner has to prove that whatever is claimed was obvious, didn't work, wouldn't work, etc. If the patent examiner can't meet that burden, the patent issues. The patent applicant doesn't have to tell us about the state of the art prior to the "invention", what the improvement is, or why it deserves a patent.
2. As discussed upthread, the obviousness standards are too low. If you can't find evidence that each and every aspect of a claim was in the prior art, you have to allow the patent. Even then, a patent attorney can attack the rejection if the different prior art documents wouldn't fit well together. As an examiner, you can't simply say that something would have been obvious, with no supporting evidence. If you try to make such a rejection, the patent attorney will appeal your rejection, you'll get reversed on appeal and the patent will issue anyway.
3. The process naturally skews towards patent applicants. Most (nearly all) patent applicants have an attorney who is fighting 100% for as broad a patent as possible. The examiner is supposed to be a neutral arbiter who applies the law in an evenhanded fashion. There's no party fighting for the public, pushing back hard against the patent attorney. It's like a courtroom where only one side of the story is presented.
You can find a lot commentary/criticsm of the patent examination process online BTW, but not generally on the tech sites - look more towards legal/academic literature.
I agree that the algorithm would have been published anyway, since it was part of Page's PhD work, I believe. But I disagree that the patent hasn't been used for "good."
Google has been a huge net positive in the development of the Internet in the last decade+. All of this development is the result of Google's dominance in search. The PageRank algorithm was where that began. Yes, things might have turned out the same without the patent. Or maybe Yahoo would have integrated the algorithm and cut Google off at its knees, and we'd all be stuck using hotmail with 2MB inboxes. I think it's unfair to simply dismiss the beneficial impact of the patent on the algorithm that started Google.
It explains the primary algorithm behind Google Search. I suppose it could have been kept as a trade secret all these years, if not for the patent system.
To be clear, patent "eligibility" usually refers to the requirements of 35 USC 101, i.e. any new and useful method or machine. Novelty and obviousness come later, hence OP's term "potentially patentable." The point is that pretty much any software process gets you past the initial hurdle.
And obviousness isn't as easy to show as you imply. Everything has to be based on prior art, which isn't always readily available.
Clarity is subjective, and even claims that seem clear can get twisted around once litigation starts. Attorneys are masters at this.
I'm just pointing out that it's not as easy as simply getting better examiners, although that would certainly help.
There is a prior user defense, see 35 USC 273. Unfortunately, in its current form it is essentially useless, as it only applies to method claims, and nearly all patents contain both product and method claims.
However, the House version of the reform bill expands the defense to cover all types of claims; thus if it survives reconciliation with the Senate bill it will likely become a viable defense.
It is still possible to protect an invention as a trade secret. Of course, if someone later independently invents and files, they get the patent. The earlier user is immune from infringement of the patent under the "prior user defense", though.
> He quotes Apple's legal papers in which they clearly state...
You mean he quotes Apple's attorney's quotation of a New York Times reporter? It's not quite so clear that this is Apple's statement, and reading the quote in context doesn't give the impression that Apple is claiming to have invented the concept.
> Saying that he fails to distinguish trademarks from patents is flat out wrong...
He seems to understand the difference but ignore it. He mostly argues that the concept of an app store pre-dated Apple's trademark filing. This is a patent-type argument in a trademark discussion, hence the confusion.
The only trademark law based argument he makes is that the term "app store" was generic. But without any evidence this conclusion is worthless.
The PTO simply has no ability to change patent law. We apply it as it's written by Congress and interpreted by the courts. A few points on the law without getting into criticism of the agency (you can get easily find that elsewhere):
1. The burden on patent applicants is too low. There's a presumption that a patent will issue as soon as it's filed. The patent examiner has to prove that whatever is claimed was obvious, didn't work, wouldn't work, etc. If the patent examiner can't meet that burden, the patent issues. The patent applicant doesn't have to tell us about the state of the art prior to the "invention", what the improvement is, or why it deserves a patent.
2. As discussed upthread, the obviousness standards are too low. If you can't find evidence that each and every aspect of a claim was in the prior art, you have to allow the patent. Even then, a patent attorney can attack the rejection if the different prior art documents wouldn't fit well together. As an examiner, you can't simply say that something would have been obvious, with no supporting evidence. If you try to make such a rejection, the patent attorney will appeal your rejection, you'll get reversed on appeal and the patent will issue anyway.
3. The process naturally skews towards patent applicants. Most (nearly all) patent applicants have an attorney who is fighting 100% for as broad a patent as possible. The examiner is supposed to be a neutral arbiter who applies the law in an evenhanded fashion. There's no party fighting for the public, pushing back hard against the patent attorney. It's like a courtroom where only one side of the story is presented.
You can find a lot commentary/criticsm of the patent examination process online BTW, but not generally on the tech sites - look more towards legal/academic literature.
(Speaking on my own behalf, not the agency's)