Much of time spent in a PhD program is spent learning to conduct research. And, from what I can tell, learning to do research is something that half a decade in a research program cannot begin to touch if completion is the goal.
It is somewhat of a strange paradox. From one perspective, a graduate with a PhD is one of the most proficient and skilled researchers in the world. And yet, that same person with the very same training is merely a novice with so much to learn.
Not only are there more methods and statistical tools to learn than can be learned in five years of study, there are new methods being developed as we speak. In fact, there are people who make it their goal in life to develop research methods that take into account the complexities of real life.
To be a researcher, there are a few qualities that are necessary:
1. Persistence - few people just "get it" on the first go. Instead, learning to do research is something that requires going at it over and over again.
2. Courage - Research, by nature, is the intentional venture into places that few or no one has ever gone.
3. Commitment to learning - Research is learning on many levels. It is learning about the phenomena of interest, about the methods to get at the answers to the questions, about the works others have done in the same area...etc.
4. Humility - This one gets you coming and going. Initially, you must accept the reality that you do not know something in order to look for it. Secondly, when you do "know" something, you have to resist the temptation to equate that sense of knowlege with superiority. It is tempting to have pride in your work because of the effort placed in it. A sense of accomplishment may degrade into a sense of pride without detection.
"Knowledge puffs up, but love builds up."
Good researchers are certainly skilled, but beyond that they not interested in boosting their egos. Instead, they have a love that drives their passion.