Science is in crisis: a crisis of trust, and a crisis of values. Yet, this is an opportune moment for scientists to examine the issues that underly science to discover how they may be of use, beyond their laboratory or field experience, to improve the research and publishing landscapes to create an environment that suits their needs more. Traditionally, the science publishing landscape had been controlled by the science, technology and medicine publishers, who have always taunted their peer review systems as being fail-safe. Yet, considerable moss has been gathered by the post-publication peer review (PPPR) movement over the past few years, indicating that the voice of the average scientist now carries more weight, and more value, than ever before. Despite this, most scientists are unaware of their potential power of opinion. Especially when it comes to commenting on, and correcting, the already published literature. Commenting by name, or anonymously, is the new PPPR publishing reality. There needs to also be a concomitant movement away from artificial metrics, such as the impact factor, which serve only as ego-boosting parameters, and which distract the wider readership from the weaknesses of the traditional peer review system currently in place. Increasing cases of the abuse of peer review, such as the creation of fake identities, affiliations or e-mail addresses further highlights the need for scientists to be vigilant, without necessairly being vigilantes. The discovery, within a matter of years, that the literature is more corrupted than was previously thought, in some cases caused by clear cases of editorial cronyism, or abuse, has resulted in a need for scientists to exceed their functions as mere scientists to evolve into whistle-blowers. Some ethical guidelines are in place, such as those by COPE, yet what is being increasingly witnessed, is a discrepancy between preached values by select COPE member journals, and the literature that they have published. Authorship issues continue to be plagued by inconsistencies in the application and verification of the ICMJE’s definitions. In a bid to expand their publishing options, open access has also reached a crisis with wave upon wave of predatory journals, leaving scientists in a quagmire. This paper serves two purposes: to raise red flags and to call for greater awareness and discussion of these issues.