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I think the point of having a principal investigator, is that he is aware of what is going on.
If they are not in the loop of the research process, they is no point for them to be on the paper and they are just academic rent-seekers.
Granted, at some level, you have to trust in the non-maliciousness of your grad students. If a smart and highly capable PhD candidate decides to subtly massage their data, that could be difficult to impossible to catch by their supervisor. The way to avoid that is not to incentivize faking data (e.g. no "you need to find my pet signal to graduate"). The PhDs who would fake data because they are lazy are more easily caught, producing convincing fake data is not easy.
Of course, in this case, we are not talking about terabytes of binary data in very inconvenient formats, but about 170 patients. Personally, I find it highly unlikely that the graduate student found that data by happenstance, and his supervisor was willing to let them analyse it without caring for the pedigree of the data at all. I think the story that he provided the data in the first place, years after it was curated by another grad student whose work he did not check is more likely.
In my field, physics, I don't generally feel that is the case. For one thing, people tend to get their Nobels much later than their discoveries. From my reading of wikipedia, when Higgs (along with a few other groups) published his paper on the Higgs mechanism, he was about ~35 and had just had his PhD for a decade, and a job as a Lecturer (no idea if this implies full tenure) for four years. Not exactly the archetype of a highly decorated senior researcher whose gets carried by tons of grad students towards his Nobel.
In the traditional British system of academic titles, "lecturer" is the lowest of four grades of permanent academic staff (lecturer/senior lecturer/reader/professor) which loosely correspond to the tenure track in the American system. American-style tenure doesn't exist, because all UK employees benefit from protection against unfair dismissal after two years full-time work on a permanent contract. Taking 14 years to be promoted from lecturer to reader (per Wikipedia) was quite normal at the time for academics who were not seen as superstars by their colleagues.
So if we are going to draw a direct equivalent to the US system, Higgs was 4 years into his first tenure-track job when he published his Nobel paper, but the importance of the paper wasn't recognised for another decade+.
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