With an increasing number of studies evincing the effectiveness of simulation-based virtual laboratories (VLs), researchers have discussed replacing traditional laboratories. However, the approach of doing science endorsed by VLs has not been carefully examined. A survey of 233 online VLs revealed that hypothetico-deductive (HD) logic prevails in VL design. Most VLs convey an oversimplified view of scientific inquiry, which might handicap science education in terms of cultivating the ability to conduct authentic scientific inquiry and to solve everyday problems, or promoting students' scientific literacy. Ever since Duhem and Kuhn, philosophers of science have learned that the relationship between hypotheses and evidence is holistic rather than deductive; however the pedagogical value of this point has not received enough attention in science education. Many science educators and VL-designers still uncritically adhere to the HD method. This article comments on the HD method and how VLs can avoid embracing it.