Software progress happens without patents
History shows that software innovation and research clearly do not need patents.
Microsoft Windows 95
Microsoft DOS and Windows 95 are two examples. In 1995, Microsoft had only 77 patents.
After Microsoft attained a dominant market position, they started saying patents were necessary for software development, but they actually wrote their software before they started getting patents.
Free software such as the GNU/Linux and FreeBSD operating systems were developed without software patents.
91% of the top 500 super computers run GNU/Linux. 
The WWW and email
The World Wide Web is another example, and email is another.
Is Apple an example?
Apple spent many years developing the base of their system (kernel, libraries, system tools) only to throw it all away and use the equivalent components from FreeBSD. Some research would be needed to find evidence to support this, but it's likely that they patented their base system during development, so it's noteworthy that they discarded their patent-fuelled software for software whose development was fuelled not by patents but by copyright alone.
According to the 2008 Berkeley Patent Survey:
Among software companies, the results are even more striking, with them reporting that patents provide less than a "slight" incentive.
Why didn't you patent this yourself, if you developed it first?" My reply was "It only took me an hour to build; if I went down to the patent office after every hour of programming, I wouldn't get very much done.
- More than innovation - software patents harm innovation, but the problems are also much bigger than just innovation
- Innovation Can Be, And Has Been, Achieved In The Absence Of Software Patents - from the Bilski v. Kappos amicus by End Software Patents
- Internet Software Patents, by Philip Greenspun
- The Most Important Software Innovations, by David A. Wheeler
- Why Must Patent Supporters Rewrite History In Attempt To Have The Feds Subsidize Patents, 1 Oct 2010, Techdirt