Invalid patents remain unchallenged
For various reasons, when software patents are considered to be invalid, they're often not proposed for re-examination.
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Case #1: Defense is economically bad value
One is example is the Divine e-commerce patents. The patent holder asked each "violator" to pay less than a challenge would cost.
This problem is also explained by patent attorney Dan Ravicher:
"...the remedies, what happen when you infringe a patent, are critical to think about when you talk about these issues of patent policy. So, most software technologists think the penalty for infringing a software patent is too high. And even if they're not found guilty, the risk of being found guilty one day causes them to either chill their behaviour now or divert funds to build a "rainy day" fund to protect themselves, etc. There are also the litigation abuses, primarily from these non-producing entities. The cost of litigation is so high that patent trolls know, if they offer you a licence for $200,000, you're going to take that every single time, just like Chris said. The cost of defending yourself in a litigation is so much more than what they're offering you a licence at, that even if you think the patent is worthless, it's still economically wise to pay them a licence fee rather than take it to court."[1]
Case #2: There are just too many
- Sun Microsystems inc.#Paying IBM for nothing
- MPEG video formats - with over 1,000 patents covering these formats, who would bother invalidating one?