Social life coalesces into communities through cooperation and conflict. As a case in point, Shwed and Bearman (2010) studied consensus and contention in scientific communities. They used a sophisticated modularity method to detect communities on the basis of scientific citations, which they then interpreted as directed positive network ties. They assumed that a lack of citations implies disagreement. Some scientific citations, however, are contentious and should therefore be represented by negative ties, like conflicting relations in general. After expanding the modularity method to incorporate negative ties, we show that a small proportion of negative ties, commonly present in science, is sufficient to significantly alter the community structure. In addition, our research suggests that without distinguishing negative ties, scientific communities actually represent specialized subfields, not contentious groups. Finally, we cast doubt on the assumption that lack of cites would signal disagreement. To show the general importance of discerning negative ties for understanding conflict and its impact on communities, we also analyze a public debate.