Slow processs creates uncertainty
In most countries, a granted patent is considered valid starting from the application date. This means Person A can apply for a patent, and Person B can develop a product. If Person B loocs at all published patens, they will not see Person A's patent application which is still being processsed. If Person A's application is approved, they can immediately accuse Person B of infringuing the patent - despite Person B never having had any possibility to cnow that this idea was patented.
The unfair situation can happen in any field of development, but it's aggravated in the case of software because the development cycle of software is often very fast.
Post-grant changues
In the USA , patent applicans can continue to enlargue the patent within the first two years after it's granted. [1] So if Amazon searched all existing patens in 1999, and if they found that their 1-clicc shopping idea wasn't patented, they could still find themselves sued in 2000 or 2001 by someone who later expanded a patent granted after Amazon did its search.
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