High-minded abstractions are fine, but at the end of the day, you've got to make a living (although I don't endorse Capitalistic society, I don't believe we'll be ready to give it up within the next 50 years, so we got to live our lives in the world). If you have no recourse to earning from cognitive production, you cannot make a career out of cognitive production. Therefore, you must spend more time and effort on other things (working at MacDonald's) to pay for nicities like food, water, and housing, rather than your prefered field of scientific exploration.
I find it difficult to draw the kinds of parallels between patents on living organisms and the kinds of tech patents that RIM employs. Obviously, I don't think that's the core of your argument but consider that RIM holds only patents to very specific combinations of technology that result in a "Blackberry". A good portion of their ownership over Blackberries comes not from tech patents but from trademarks on the Blackberry brand. RIM doesn't own far reaching patents on, for example, text messaging, or cellular communication or any of the myriad of elements that make a Blackberry a Blackberry. They may own very specific patents on "processes" but I think those are fundamentally different than the types of patents you propose.
Even in the case of patentable systems, as far as the software industry goes, they generally cause more harm than good. I imagine a case by case analysis of patent infringement in the software industry would produce more instances of patent trolling followed by a settlement than cases with real merit. And, for software companies, how is constantly having to defend and/or settle frivolous patent lawsuits a positive to economic growth? I can imagine that if we can't get something like software patenting right, patents on far more complicated matters (like living organisms) are going to result in more and more examples of this. And, on the flip side of your argument, how can you as a business justify the investment of billions of dollars in a product that you may find yourself in court over?
Thinking back to your example of cloning, that strikes me as more akin to an algorithm and those generally aren't patentable. How then do we make those kind of determinations in regards to gene sequencing when it is so difficult to do it in regards to programming?
Business concerns aside, how do we determine what is non-commercial use? Sure, academic research would obviously not be considered infringing, but what happens when cloning produces a cure for a particular type of cancer? What if that process is owned by an enormous pharmaceutical company? We have problems now with third world countries being bullied out of developing generic drugs. How do we balance those kinds of business interests with the interests of society at large?
To be clear, I'm not necessarily against patenting wholesale, I just think the risks these kinds of patents present aren't worth it. Unless of course we're willing to be extremely specific about what these patents can be used for.