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I would like to see a study that compare the commercial incentive vs the deincentives cause by the chilling effects from patents. It should be a standard cost-benefit analyzes with no emotional/political bias that could give a final scientific answer if patents are beneficial for software or not.

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There are tons of studies around patents and the economics thereof, but you will not find such a convenient answer to your question. The reason is that it's very hard to measure the costs and benefits to quantify these incentives and dis-incentives. Furthermore the benefits and costs of patent systems are often orthogonal. If you want to get an idea of the depth of the field, look at all the studies cited by this paper, and look at all the various methods, metrics and datasets that have been considered so far: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2139260

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