You can add me to the list of folks that was disappointed to see that smart thermostat startup Nest wound up paying licensing fees to patent troll Intellectual Ventures (IV). GigaOM’s Jeff John Roberts continues to cover this issue very well, noting “The deal may improve Nest’s position in the ongoing litigation with Honeywell, and could lead to a truce, or some sort of licensing deal between the two companies.” No word on whether IV threatened Nest into paying it licensing fees.

Honeywell’s response to Nest’s innovation has been to sue the company while attempting catchup in the market with its own smart thermostat. Although interestingly the company has been careful not to describe the thermostat as a “learning thermostat.” It makes me wonder if Nest has its own patents surrounding its algorithms and analytics technologies. And Honeywell is aware that it could be vulnerable to becoming the defendant, should it try to rip off some of Nest’s better learning capabilities.

The net effect of all this is less innovation, slowed down competition, and Intellectual Ventures taking in more patent licensing cash. All is not lost. Apparently the Obama Administration has hired a Santa Clara Law Professor who is critical of patent trolling to advise its Office of Science and Technology Policy unit.