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John, I like what you wrote about the "messiness" of how science is done. I have two comments (one minor; one more interesting)
1) You wrote "If none of your original hypotheses are consistent with the data, you need to think up one or more new hypotheses ...". There may be times when you have NO good hypothesis that fits the data. That shouldn't necessarily stop the publication of the results.
2) Scientists may be partly to blame for the perceived "linear process" of science because that is how the reports are written and presented to the scientific community and to the public. While the process is indeed the looping process you describe, the report is almost always linear:
* here is our project
* here are the papers that relate to the final hypothesis
* here is the experiment we performed and the results
* here is the analysis
* here is our conclusion
Yes, that makes for a much more readable report. But it can be dangerous too, making even other scientists think the process was more linear than it was. And perhaps more dangerous (or at least less efficient) is the fact that "blind alleys" are rarely mentioned. Medical research comes to mind, where all the ineffective treatments (or even harmful treatments) can be left unreported. Or marginally effective treatments could be repeated (many times perhaps) until the p < 0.05 level is achieved.
Reporting null results is important too, and is rarely done.
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