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I know that not all, but many papers (that are accepted and published) are based on ideas that can be patented as well. So, why is that there is no system in which a person can apply for a Publishing a Paper and also getting the Idea patented at the same time?

Is it possible that I publish a paper, do not get it patented (going to patent it at a later point of time - because of not having sufficient money to pay for the patent application or whatever) and during that time someone else patents my work in his name? Or Someone else picks up my theory, develops it further and gets a patent? How would the situation be then? What should I do under such a situation?

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not all, but many papers (that are accepted and published) are based on ideas that can be patented as well

This is a misconception. Even in engineering, only a small minority of papers contain ideas worth patenting. The further you get from engineering, the smaller this fraction gets.

So, why is that there is no system in which a person can apply for a publishing a paper and also getting the idea patented at the same time?

You can indeed do both things in parallel, but not via the same process. Publishing a paper is an academic process, whereas filing a patent application is a legal process, and the two things just don't overlap very much.

It's kind of like asking why you can't write your dissertation and apply for jobs via the same process. You can certainly work on both at the same time, and there is a relationship between them, but fundamentally they aren't the same thing.

Is it possible that I publish a paper, do not get it patented and during that time someone else patents my work in his name?

No, it's not possible. Well, technically someone could try, but they would be wasting their time, since your paper would serve as "prior art" that would invalidate the patent.

Or someone else picks up my theory, develops it further and gets a patent?

That could happen, whether or not you file for a patent. They would own the intellectual property rights to the extension of your work, but not to your work itself.

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    At least in the US, you have one year from the first date of publication to file for a patent. (Posting on the internet apparently counts as "publication".) And since when did prior art actually matter? – JeffE Jun 24 '12 at 6:13
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    The one-year grace period applies only to the inventor (the disclosure is prior art for anyone else). The stupid patent you link to is great, but it's got the opposite difficulty. The problem is that it's hard to find prior art, because there aren't many recorded descriptions of swinging techniques. That patent is pretty frivolous and would presumably be thrown out if it made it to court, on the grounds that it was obvious to anyone skilled in the art of swinging. :-) I imagine it got approved because it really didn't matter, and approving it was easier than trying to dig up prior art. – Anonymous Mathematician Jun 24 '12 at 17:26
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Patents are about owning and protecting an idea to make money from it in the future.

Papers are about advancing science. A paper lays claim to an idea, but anyone else is allowed to build on that idea without having to pay royalties.

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To add to Dave Clarke's answer: Even in the rare cases when a publishable result is also patentable, filing for a patent is a serious amount of work. Filing a patent application costs thousands of dollars; submitting a paper is free. Filling a successful patent requires very specific and formal language, which is not the same as the specific and formal language used to communicate with other researchers. Why should we spend all that extra effort for so little reward?

Or Someone else picks up my theory, develops it further and gets a patent? How would the situation be then? What should I do under such a situation?

You should cite the patent in your tenure case as iron-clad evidence that your research has real-world impact. Congratulations!

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