Resources/methods to teach how to perform research logically Can you point me to resources (e.g. book, articles, etc.) or methods on teaching students how to think more logically/systematically about doing research?

I've seen a number of intelligent graduate students who do great in performing experiments, but struggle to make logical arguments about their research and conclusions. For instance I see students making statements without providing evidence/arguments for such statements (e.g. "increasing the temperature will cause the experiment to proceed better" but no evidence/reasoning is provided). I see writing from students that is an organized mess with no clear path or direction. I often see short confusing descriptions in written drafts when thorough explanations should be given. I see students put together graphs that are incomprehensible. On and on...

It seems that many students don't "get" how to think scientifically or research-oriented. I know this comes with time and experience, but perhaps there is a way to teach students the underlying principles and approach to doing research?
Of course there's a way to teach them: have them enroll in a research oriented PhD program and practice for five years! An effective approach to research is a skill that takes a long time to develop and will have prerequisites that also take a long time to develop (e.g. how to read scientifically, how to formulate scientific questions, how to verbally express a scientific thought clearly).

That being said, engineering degrees are largely aimed at formalizing the skills that would take a decade or more to acquire through practice. If you can describe a procedure formally in enough detail, maybe, students can just follow the procedure exactly and get acceptable results. I don't know whether this would work or be a good idea for research (BS in Research Engineering anyone?) but it's moot because science programs tend to emphasize content rather than process.