At any rate, let's keep the discussion about "a patent seeker" rather than about me specifically.
While this is an admirable goal - it will be hard, especially considering you seem to be the only one arguing FOR the application of patents in this particular field of interest on the forums. As such, the best "example" to use when required will be yourself.
I would say it would be correct that they would be patented, in order that Newton would get the money to pay for the years he spent researching the ideas.
Without trying to be offensive, this iw where you ignorance of how & why patents are granted shows through. It is not "legally" possible to patent mathematical concepts in & of themselves. They (along with abstract ideas and laws of nature) are exempt from patentability. When regarding the "nature" of software - this becomes another (much more fundamental) problem to be addressed. I will talk about this later.
I'm not saying we should give everyone who has a patented idea millions, just that they should get some compensation to cover their costs. The terms of granted patents and therefore how much money one can expect from them are independent of the notion of patents at all.
Again, this shows some ignorance about the concept of patents and how they are applied. Patents are, basically, a government approved monopoly on an "invention" (or, more recently, an "innovation"). As such, "how much money one can expect" is very much an integral part of the "notion of patents". Whether someone is WILLING to pay you the amount you ask is independant, but teh simple fact that one has a monopoly on the innovation in question means that anyone desiring/requiring access to it will NEED to pay you what you ask or wait twenty years for the patent to expire.
That's true, but I don't think the fact that there are other ways to make money argues against patents specifically.
Agreed. However, your initial question (as I understood it) was not whether or not money argues against patents, but what one should do to commercialize their research. Patents are only one such way of doing this. So flipping it around, because patents are available does not argue against making money in some other way.
I guess my real question is this: given that the patent system does exist, for better or for worse, if you spend years developing a truly original and beneficial and non-trivial contribution without any pay, would you, as the inventor, feel guilty in filing for a patent in order to seek some compensation for that idea?
This would depend on the idea and how I came about it. Standing on the shoulders of giants is somewhat difficult when said giants demand a fee for the boost.
So far I think most of the arguments have been against patents in general, against the idea of owning an invention. But as a reality, should one feel guilty in using this imperfect mechanism to seek compensation? If so, what are the reasons?
Actually, what most people are expressing on these boards (and pretty much world-wide from my reading & experience) is that they are not against patents "in general" but the use/abuse of "software patents" in particular.
For example, it is not possible to patent Newton's laws of dynamics. However, were they discovered today, they could be patented so long as the calculations in question were performed on a computer. This is important. Patents in other areas apply because no matter how they are used - they are a "legal patent". If I patent the use of "inverse electro-magnetic fields to bend light around arbitrary objects" (i.e. some sci-fi invisibility field). It doesn't matter if I do it with static magnets, electro magnets, positrons, or silly string - so long as the inverse electro-magnetic fields are used to bend light, the patent holds. However, with "sofware patents" the patent only holds if the "computer" is used to implement the invention. I could come up with a novel way of inverting matrices that is orders of magnitude faster than anything you have ever seen. However, that by itself is not patentable. Stick it into a computer however and it is. Given the amount of math in physics engines and the innovations surrounding them - this is a hot topic, and one that should not be brushed over to argue about "general patents"
One should also remember that software patents are only valid in the US, Australia, & Japan (unfortunately, the only countries I have worked for/in). And in the last case before the Supreme Court of the US, it was remarked that the Supreme Court has yet to rule on sofware patentability. In other words, it is still possible that software patents as a whole will be deemed unconstitutional (though this is by far to complex an issue for me to make predictions on it).
I'm looking for arguments of the second kind: what makes the action of filing a patent so wrong in and of itself? Or is it just a case of maximizing global happiness with no regard to whether it's right or wrong?
The action of file "a" patent is not wrong. The action of filing "specific types of patents" is another question. I think part of the problem we have in communicating on this issue is the fact you want to argue generalities when it is the specifics that are at fault.
One thing you need to remember about copyright is that one can only sue for infringement if there is a provable case that the infringing IP is a "derivative" of the original. That is, you need to prove that I used the original in some "significant" fashion to create my copyrightable work. If I come up with an almost identical copyrightable work without knowing or or referring to your copyrighted work - there is no infringement. This is not so with patents. It matter not that I came up with the innovation the patent covers without ever referring to yours. The fact that you patented the innovation before I did means I am liable, regardless of how I came about the innovation.