As a computer professional, I can certify that innovation is never atomic in the computer industry. On the contrary, computer software constantly and crucially depends on the ability to freely and quickly reuse, combine and evolve previous techniques.
In the age of interconnected computers, software plays an essential and ubiquitous role in the way computers, people, businesses, countries, etc., communicate with each other. Industrial property on software thus leads to monopoly lock-ins in the way people communicate. To computer professionals, software patents are as dreadful as if someone had patents on part of the English language (or whichever language they use). It prevents not only innovation, but the use of computers at all, and leads to proprietary systems from big monopolies that few can use, and that no one can innovate upon.
Patents induce such a technological stagnation in the computer industry that it is almost visible. Software engineers constantly curse the way they must conform to proprietary protocols that are not well documented (if at all), misdesigned (often with gross mistakes that peer review would have immediately eliminated), that they cannot improve upon, that exist in a wealth of gratuitously incompatible variants, and with which they must stay compatible for decades and decades. The field of computer development is thus filled with junk, that accumulates with time, and that no one has the right to clean, least he becomes incompatible with the others. Every patent on a successful software program or technique is an obstacle to the whole industry, that remains until it expires; even the holder, when he wants to improve his previous technique, finds himself faced with the inertia of a whole industry that adapted to his own junk, contorting either to interface to it, or to work around it.
Thus, the specific effect of patents in the software industry is to make software development and computer communication slower, more complex, more expensive. The amount of money, computer hardware, developer time, user time, etc., that is wasted and could be saved by removing protectionist barriers is so insanely high as to give vertigo to anyone.
