In recent years, the perception has grown that conflicts of interest are having a detrimental effect on medical science as it influences health policy and clinical practice, leading medical journals to enforce self-declaration of potential biases in the attempt to counteract or compensate for the problem. Conflict of interest (CoI) declarations have traditionally been considered inappropriate in pure science since its evaluation systems themselves constitute a mechanism for eliminating the effect of individual biases. Pure science is primarily evaluated by 'peer usage', in which scientific information is 'replicated' by being incorporated in the work of other scientists, and tested by further observation of the natural world. Over the long-term, the process works because significant biases impair the quality of science, and bad science tends to be neglected or refuted. However, scientific evaluation operates slowly over years and decades, and only a small proportion of published work is ever actually evaluated. But most of modern medical science no longer conforms to the model of pure science, and may instead be conceptualized as a system of 'applied' science having different aims and evaluation processes. The aim of applied medical science is to solve pre-specified problems, and to provide scientific information ready for implementation immediately following publication. The primary evaluation process of applied science is peer review, not peer usage. Peer review is much more rapid (with a timescale of weeks or months) and cheaper than peer usage and (consequently) has a much wider application: peer review is a prospective validation while peer usage is retrospective. Since applied science consists of incremental advances on existing knowledge achieved using established techniques, its results can usually be reliably evaluated by peer review. However, despite its considerable convenience, peer review has significant limitations related to its reliance on opinion. One major limitation of peer review has proved to be its inability to deal with conflicts of interest, especially in a 'big science' context when prestigious scientists may have similar biases, and conflicts of interest are widely shared among peer reviewers. When applied medical science has been later checked against the slower but more valid processes of peer usage, it seems that reliance on peer review may allow damaging distortions to become 'locked-in' to clinical practice and health policy for considerable periods. Scientific progress is generally underpinned by increasing specialization. Medical journals should specialize in the communication of scientific information, and they have neither the resources nor the motivation to investigate and measure conflicts of interest. Effectively dealing with the problem of conflicts of interest in applied medical science firstly requires a more explicit demarcation between the communications media of pure medical science and applied medical science. Greater specialization of these activities would then allow distinctive aims and evaluation systems to evolve with the expectation of improved performance in both pure and applied systems. In future, applied medical science should operate with an assumption of bias, with the onus of proof on applied medical scientists to facilitate the 'data transparency' necessary to validate their research. Journals of applied medical science will probably require more rigorous processes of peer review than at present, since their publications are intended to be ready for implementation. But since peer review does not adequately filter-out conflicts of interest in applied medical science, there is a need for the evolution of specialist post-publication institutional mechanisms. The suggested solution is to encourage the establishment of independent 'CoI consultancy' services, whose role would be to evaluate conflicts of interest and other biases in published applied medical science prior to their implementation. Such services would be paid-for by the groups who intend to implement applied medical research.