Data quality is only one of many uncertainties involved in our attempt to understand, model and predict complex nonlinear systems and to identify the properties emerging from them. Perhaps not surprisingly, less than half of published scientific studies can be successfully reproduced, with the earth sciences occupying an intermediate position among the major disciplines. The uncertainty of data quality is only one factor that contributes to the relatively poor reproducibility of research studies and the resulting hypotheses. Potentially more important factors include unsuitably low thresholds for assessing statistical relevance, inappropriate data manipulation, inadequate research design, and outright fraud. Data quality for earth science data can be communicated via measurement errors (e.g., instrument accuracy, technician practices) and addressed by employing measurement quality codes, whereas the other aforementioned factors can be identified or controlled through rigor, methods selection and research competency. A more difficult source of uncertainty includes biases, assumptions, and environmental or social influences that affect the judgment and perceptions of scientists themselves. The difficulty is that many of these factors operate beyond one’s awareness or control, residing within automatic processes of the human brain. From continually seeking, interpreting and projecting patterns (spatial and temporal) to confabulating answers and relying on heuristics, we are largely at the mercy of what the brain has evolved to do, which is not necessarily to accurately perceive the natural world. Peer reviews, precision instruments, mathematical abstractions and digital computers certainly assist us in probing nature; nevertheless, we ultimately perceive the world as we are, rather than as it is. Consequently, a scientifically “objective” view of nature is being questioned in research ranging from quantum mechanics to human consciousness. To what extent are the peculiarities of human brain responsible for the uncertainty and nuances that we believe exist in nature? Are scientists fooled by a brain that constructs, rather than simply observes, the world around us? If so, do we have the tools to deal with this kind of uncertainty?