Recently, I asked a question on a public Github repository about a formula that is used in the code that is hosted on that public repository. Basically, if you are familiar with Github, you can create an issue on any public repositories to ask question, report an error, request new features, etc. I use the similar formula, that is embedded in that repository, in my research and based on my literature review that formula is implemented incorrectly in that repository and I have the reference as well. So, I opened an issue and said I think the formula implemented in this code is wrong and I think based on the literature it should be implemented differently, and asked if there is any plan to change or fix it.
Someone, that is responsible for the code to merge the pull requests or close the issues, posted a comment on the issue that I created, and said that probably nobody is aware of the problem in that formula cause there are really small community that use that code at all and that code is not used for a while, so he would be happy if I create a pull request based on correct formula and give the literature reference as well for the future people.
Long story short, I just created that pull request and I put my reference to the correct formula as well and I'm waiting for the opinion of the admin of that repository if it's possible to merge it into the original repository or not. So, nothing really strange happened here, I think.
I'm informed that my PhD adviser found that issue + pull request that I created and he thinks I'm wrong and the existing formula in the code is correct. OK, I'm fine with that. I know there is no one solution for a given problem and different people have different approaches.
But, the problem is that he is saying that: I violated the academic integrity by creating that issue and submitting that pull request, which I'm surprised and can't understand what exactly I violated here. I'm just really angry and confused and can't understand what's wrong here. I can understand he is not OK with formula and I don't care at all and I'm 100% OK to use the wrong formula, but I can't understand why I should be prosecuted with violation of academic integrity because I don't have same opinion about that formula or created that issue or pull request? Also, I read the graduate manual in our university for the 10th time and there is no such thing in it as violation of academic integrity if you don't have same opinion as your PhD adviser or if you create an issue to ask question or create pull request to fix something. Any suggestion or recommendation is appreciated.
Responses to comments: You raised some questions that I think it might help if I clarify them. One of the comments was:
Is your advisor pursuing a violation of academic integrity with your department and/or the school, or is this just a personal dispute?
My answer: No, but this personal conversation was kinda a threat and he said if he likes he would use it against me and students are always loser in front of professor, which I think is true.
Is it possible that your supervisor used the formula before and, without realising, you implicitely suggested that some of his research is wrong? I could see some people reacting badly to that, especially if they find out from a a public Github repository instead of directly from you...
My answer: No, my supervisor is new in my PhD research field and he had no experience/paper in this field before I started my PhD, and as a result of that he has a really vague and wrong idea about literature in this field and what's accepted or what's wrong in this area.
"I'm 100% OK to use the wrong formula" that sounds like poor academic integrity to me
My answer: I'm just saying that I'm OK to listen to him and use even the wrong formula and get my PhD as soon as possible and stay away from academia forever despite the fact that I always loved the academic environment and wanted to become a professor some day. But now, I have a really routine job offer in a company that has nothing to do with PhD or research and I'm aching to just get my PhD degree and start that job and maybe I could be happier in my miserable life.
Two of your statements are conflicting. First: "...based on my literature review that formula is implemented incorrectly in that repository and I have the reference as well.", but later: "I know there is no one solution for a given problem and different people have different approaches.". Could you clarify whether the original implementation is incorrect, or just different from your own? That seems to be the crux of the matter, really.
My answer: The reality is that people use the wrong formula because it's easier to understand and based on my experience wrong formula is OK within a range of 5 to 10 percent error in comparison to correct formula. It's not like nobody uses the correct formula and there are tons of literature out there that use the correct one. So, my intention was: If we have lots of other uncertainties in our model, why we induce another one when we could use the correct formula to make sure at least we are not creating another source of uncertainties when we could eliminate it without a price. Even, performance wise, correct formula is the same as wrong one.
To expand; if there are alternative methods that are also valid, and you go around flagging them as 'errors' and then promote your own method, then this would certainly be perceived as academic dishonesty.
My answer: No, the alternative method which is this wrong formula is just a really good approximation of the correct formula. Obviously, it just gives a close number to what correct formula gives you, but the wrong formula does not satisfy other properties of wrong formula, like the orthogonality of the correct formula, which is crucial in our research. So, my intention was to just use the correct thing in its mathematical sense when it is available, it doesn't have any additional cost, and it is well documented in the literature.
"I'm just really angry". Don't be. Confused is ok, but why angry?
My answer: These days I see myself as useless and miserable person that just works more than 12 hours per day and the other 12 hours that I suppose to rest or sleep still I'm thinking about my research but I'm not happy, I don't have any friends, I'm depressed, I'm nervous, I'm stressful, etc. So, yeah I'm angry that people hates me if even I tell them the truth.
at most this is ignorance. Has nothing to do with honesty. And reality is that either the adviser is an idiot (wouldn't be the first time) or OP misinterpreted the situation.
yeah, why the academic world makes people angry... that's the question. Maybe because you are punished for being proactive?
My answer: My question is ignorance of who? Me? That I want to find what's right and what's wrong? Yeah, I'm an ignorant, idiot, useless person that just devoted my whole life to something that doesn't worth.
I think you're reading that wrong. I took "I'm 100% OK to use the wrong formula" to mean that OP does not dispute the supervisor's claim that the formula is wrong; they're "100% okay" to be told that they're using the wrong formula. The question is how on earth being wrong is somehow a "violation of academic integrity".
My answer: Thank you!
Based on Wolfgang's answer, yesterday, I had a meeting with my PhD adviser and I did my best to be calm as possible and be really polite. I just asked what is wrong in his opinion about opening an issue in a public Github repository and express a valid concern based on a peer-reviewed reference (this reference is not mine nor my adviser's for those who think I shared research results without permission and this reference is more than 7 years old with so many citations) and if the owner of that Github repository is happy to accept a pull request, why it should be considered a violation of academic integrity? Also, I asked in which part of the graduate manual, this rule of approval and permission to post anything in World Wide Web is stated for my more information? Furthermore, I asked even if I'm totally misunderstood here, the repository owner could just point me to their documentation or any other reference that justifies the usage of current formula and just close the issue, and that's it.
My PhD adviser response was the pretty much the same as his initial reaction. He thinks even a single comment in World Wide Web from me should be approved by him before posting and it doesn't need to be stated explicitly in the graduate manual and graduate school gave him such an authority where he sees fit to consider this commenting as a violation of academic integrity. By the way, he thinks I'm wrong, he doesn't care about the references that I showed to him to support my idea and says he is going to send an email to the repository owner and ask him to block me cause I'm wasting the time of repository owners, despite the fact that I feel just repository owner is a welcoming person and is open to answer the questions!
I'm just shocked...!
Response to some of comments and answers:
One of the main assumptions, that I saw in the answers and comments, is that my PhD adviser is unfamiliar with Github. No, he claims that he is indeed an expert in Github, open source software, programming, etc. So, he is indeed pretty familiar with the concept of open source and Github, but his main area of expertise during his PhD and his post-docs was something else and not related to my PhD research. He just picked this topic for my PhD research, because his latest post-doc adviser developed an open source software specifically within my PhD research area many years ago and he wanted to maybe use that software and continue his collaboration with his post-doc adviser.
I can understand this behavior of my PhD adviser, when I compare his interaction with other people not just myself. Cause, logically if he is so nice and welcoming to other people, so certainly something is wrong probably with me. But, based on things that I saw, I could say: generally, my PhD adviser only respects people that are above him in hierarchical ranking or he doesn't have any authority over them. Even, with other junior professors or post-docs (my PhD adviser is also a fairly new assistant professor without tenure), he acts in a way that a few collaborators that we had during past four years just left us and some of them even doesn't reply to our emails at all now. Even, 2 or 3 years ago, I was reading his comments on Github to his colleagues for many years ago, and I was able to imagine how snarky and bad is the tone of his comments that nobody bothered to reply after 10 years or so.
Also, thank you all for your supportive comments and answers as well as your lots of useful suggestions.