system
Given the following post, respond as if you're commenting on Reddit:
human
Advice for PhD student asked to "modify data" by adviser

My friend is a STEM PhD student, whose adviser asked him to modify data for a publication. Note that this version of the paper has not yet been submitted to a journal. The student was asked by the adviser to modify data in a couple ways.

First, is scaling raw data by multiple orders of magnitude, and then presenting the scaled data as if it was raw data, without any reference to a scaling factor.

Second, is more complicated. It involves taking the difference between two signals, shifting the difference by an offset, setting the new values to zero if below a threshold, shifting these values around in time, and then reconstructing the original two signals using these processed values. The processed results look significantly "better" than the raw data. The paper has no reference to the processing of these signals, and it is implied that they are raw data.

What should the student do? He has already complained to the adviser, but adviser dismissed this type of modification as "normal."

My friend hesitates to push the issue further, because another PhD student in his lab is trying to defend a thesis based on this work, and he does not want to prevent the other student from graduating. Both my friend and this other PhD student (who are both co-first-authors of this paper) have zero publications (first author or otherwise).

If the paper is under review at a top journal, and then the other PhD student will look better during their thesis defense. The student thinks that the paper will almost certainly be rejected because the paper is riddled with other problems (lack of clarity, odd nonstandard ways of defining things, leaving out information necessary to reproduce the data - see a pattern here?). My friend thinks that after the paper is rejected, then they can redo the experiments legitimately, or be more transparent about the data modification.

What should my friend do?

Some more background: Both my friend and his fellow labmate are 5 years into their PhDs. His research group has not published a single paper in multiple years, despite normal and consistent effort by the PI and many PhD students. The overall work is legitimate, but not groundbreaking, but the PI refuses to submit it to anything below Nature, Science, and their respective subjournals. The paper has already been rejected \~5 times, and they are resubmitting the paper to a top journal that rejected it. In the most recent version of the paper, the PI greatly inflated the claims of the paper compared to previous versions.

In general, the research has been hindered by the PI. He is a micromanager, and treats all PhD students like technicians. He meets with each student \~3 times a day, makes all creative decisions, and does not allow his students to even write their own papers (the paper above in question was written entirely by the PI). He often makes irrational decisions, and aggressively defends them, resorting to yelling and personal insults. The list goes on. Overall, the PhD experience has been described a nightmare for my friend, and he is desperately trying to graduate, even if it means with no publications.
gpt
From an outside perspective, that sounds really sketchy--but it might be worth trying the get in contact with someone who works in a very closely-related field (perhaps someone else in the department?) just to ask if the proposed alterations are common practice. Obviously fraudulent data of any kind is a huge problem, but it is worth attempting to confirm that it's fraudulent before raising alarms.