Peer reviewed scientific publishing is critical for communicating important findings, interpretations and theories in any branch of science. While the value of peer review is rarely doubted, much concern is being raised about the possible biases in the process. I argue here that most of the biases originate in the evolved innate tendency of every player to optimize one’s own cost benefits. Different players in the scientific publishing game have different cost-benefit optima. There are multiple conflicts between individual optima and collective goals. An analysis of the cost-benefit optima of every player in the scientific publishing game shows how and why biases originate. In the current system of publishing, by optimization considerations, the probability of publishing a ‘bad’ manuscript is relatively small but the probability of rejecting a ‘good’ manuscript is very high. By continuing with the current publishing structure, the global distribution of the scientific community would be increasingly clustered. Publication biases by gender, ethnicity, reputation, conformation and conformity will be increasingly common and revolutionary concepts increasingly difficult to publish. Ultimately, I explore the possibility of designing a peer review publishing system in which the conflicts between individual optimization and collective goal can be minimized. In such a system, if everyone behaves with maximum selfishness, biases would be minimized and the progress towards the collective goal would be faster and smoother. Changing towards such a system might prove difficult unless a critical mass of authors take an active role to revolutionize scientific publishing.
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