In the wake of breakthroughs in biotechnology and prosperous development in the biotechnology industry, the field of biomedical upstream research has experienced a large increase in the number of patents granted. This Article concerns mainly the threat that the proliferation of upstream patents pose to biomedical research and commercialization, especially the danger posed by research tool patents. The propagation of research tool patents may impede access to those research routes that are most promising to scientists. These patents also create substantial burdens, including research delays and financial costs, for independent researchers seeking authorization for the use of research tools. There are two contending camps—the prospect theorists and the anticommons theorists—arguing over the influence of patents on biomedical upstream research. Although the anticommons theory is more sensible and coherent, the reality of biomedical science does not unfold as predicted by this theory. Empirical studies suggest that the reason for this disparity lies in the nature of biomedical research, as well as in the informal research exception that the scientific community has developed. However, even such empirical findings cannot convincingly negate all of the problems created by upstream patents, including blockages in downstream development and increasing delays and costs for follow-on research on the patented upstream inventions. In this article, I review proposals now put forward by scholars for eradicating these problems. Finding fault with most of the resolutions proffered thus far, I argue for a compulsory license system that charges reach-through royalties, which are measured by the contribution that patented research inputs make to the individual research. This is a method that can calibrate royalties to the actual value of these research inputs. With this proposal, I hope to bridge the gap between patentees and independent researchers so as to alleviate the problems that biomedical science suffers now.