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The influence of funding sources on the scientific method.

Funding for scientific research in the USA has become harder to obtain, especially for discovery‐based science, requiring the analysis of large datasets to find patterns and correlations. It is through such analysis that new hypotheses are formulated and dogma refuted, particularly as it pertains to science in the ‘‐omics’ era. The battle for funding has led to a change in the types of experiment that are being proposed by scientists. Grant panels are most commonly interested in proposals that are focused on solving problems, such as novel targets to prevent pathogen infection, or are guaranteed to be successful in the short term. Although it is understandable that grant panels would want to ensure that the money spent on projects will yield immediate results, targeting of virulence factors and drug targets has led to a narrowed view of pathogens and pathogenesis. 
 
How does funding influence scientific ideas and hypotheses? It is common to design studies to examine genes already associated with virulence. Previous studies are the backbone of grant writing and help to solidify the logic of scientific studies. However, focusing on previously studied virulence traits and genes narrows our view of the biological processes that occur between host and pathogen. Experiments to find novel genes associated with virulence are often discouraged in grant writing, and such ‘fishing expeditions’ typically account for a very small proportion of proposed experiments. With the advent of novel algorithms for large‐scale in silico analysis of genes and genomes, it is possible to derive a great deal of information from RNAseq, genome sequencing and proteomics. Such large‐scale analyses go beyond ‘fishing expeditions’ and have shed light on biological functions that may or may not be involved in pathogenesis. Recent developments in bioinformatics have allowed scientists to test whether or not hypotheses derived from traditional experiments can be extrapolated to the whole genome. In addition, ‘‐omics’ studies can provide data that can be mined by an entire field for many years. Thus, large‐scale bioinformatics and ‘‐omics’ projects should be viewed as a ‘good investment’ during grant funding.