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Not only is bias introduced from accidental collection flaws, it’s also often tampered with intentionally cherry picking data, choosing interesting data or in some cases flat out falsifying data. In addition, evidence based reasoning often suffers from there being a lack of evidence to make a decision from. Or in some cases some critical aspect surrounding the decision is very niche to the case so the data may not take that into account unless it’s highly tailored data (evidence based reasoning tends to focus on breadth of applicability because gathering evidence is a long and often expensive process).
There’s still a lot of place for using theory and reasoning in conjunction with or in absence of data. Things like experience, professional opinion, etc. Medicine should be no different in that regard to any profession. The key is of course to always strive for sound empirical evidence/data where possible, but to use sound documented reasoning and theory in its absence if you want the best objective results.