This paper is actually the start of a very interesting academic brawl. I've reviewed that paper by Howarth and found it lacking in many ways. Howarth is included in a trio of academics from Cornell University that have become popular in the media for denouncing the increasing use of natural gas, and even suggest that coal is cleaner on a short time scale. Since this initial paper was published there has been a flurry of responses from another academic at Cornell, named Lawrence Cathles. Cathles is also the only geologist in the group, Howarth is a prof of ecology and Ingraffea is a structural engineer. This article sums up the history between Cathles and Howarth. [2]
So far Cathles has written at this point two or three papers in response to Howarth's original paper, and one of the later ones is a bit of a scientific smackdown.[1] It concludes that the estimates of fugitive gas emissions are very high and other assumptions are made that badly shift the conclusions against natural gas. The response papers by Cathles are very fun to read and I think they provide a great introduction to the current climate science on natural gas.
[1] http://www.geo.cornell.edu/eas/PeoplePlaces/Faculty/cathles/...
[2] http://energyindepth.org/national/cornell-response-to-cornel...