I am nearly to the end of my PhD and I am probability writing this post when it is too late. The studies I did during these years were faked by my supervisor: he wrote two papers and he added a fake graph on each on of them.
Now that I am at the end of this PhD, he said to me that I can write my thesis not necessarily based on the paper results, but I could just write my personal results as they are. I am doing a job like this, however there is my name (as first outhor!) on that two papers.

The question is: even if I do not fake anything in my thesis, is there any possibility that the commission would ask and blame me some "strange" results resulting in that papers?

Hmm, this doesn't sound good. Any reason you decided to publish papers with fake results?

This is an impossible situation really.

1. If you come clean and retract your papers, you probably won't get a PhD and will never work in Science again.

2. If you add these results to your thesis, it's likely no one will ever know that these results were fake and you can on as normal.

3. If you don't add the results to your thesis, people will definitely ask why eg in your viva, you could then say it was work that your supervisor did.

It's your decision to make. It's too easy to say do the right thing (option 1) in this case, because there's a lot at stake for you personally, and you were probably manipulated in one way or another by your supervisor, so it's not entirely your fault. On the other hand, the integrity of Science depends on the integrity of its researchers.

Whatever you choose to do, you need to distance yourself from this work and your supervisor as soon as you can.

I think I agree with ToL. Get away from that person and do not continue that terrible practice that he has taught you to do that utterly discredits science.

If you're not coming clean then I think ToL's 3rd suggestion might be best. You'd have to prepare the answer about it being your supervisor's work. They will ask why you are first author so you need to have some response (I guess you could say you did most of the writing - if you did?).

But can I ask why your supervisor has made this suggestion about not including those papers? I mean - why should he care if those papers are included in your thesis or not?

He knows that I can hardly discuss and defend a fake result like that ones he added on the two papers. For this reason he says to me that I do not necessary have to write down everything is reported on the papers.
He could add the first fake result on the first of the two papers as at that time I just trusted him but, after a discussion, I realized how he figure out that result...
Later on, he published a further paper, without asking me any authorization, I just realized I was author of a paper after it was already pubblished!
I will not mension the second paper at all on my thesis.

There is even more! He just published a third paper on my data, without let me know anything. And the name of the first outhor (which should be me!) is wrong! If someone ask me anything about that paper I will answer:
"I don't know anything about that and I am not the author of that paper as that is not my name!"

You can imagine the troubles he is giving me as I can hardly figure out a logically coherent test of about 100 pages...

I would seriously feel like exposing him and making him lose his career. But it isn't fair that you should suffer yourself (and it is likely that you would - eg by not getting your PhD and losing your own reputation). I think he knows this - which is how he has trapped you. Sort of like an abuse case - the abused person doesn't tell because they think they will be implicated somehow (and in this case - I think you would - because you made some mistakes eg by letting him publish in your name).

How about this...
- Can you exclude all the "fake" findings from your thesis
- Successfully defend your thesis and be clear to the examiners that the papers not included (if they ask about them) aren't actually your work - even though they are in your name
- Then once you have received your PhD on the basis of your work (none of which is made up) - just move away and start anew somewhere - never listing those papers as yours (and if anyone asks, say they were published in your name without your permission)

This may be what ToL has already suggested - just written in a different format.

I just know that he provided as final proof of the phenomena a graph that is totally invented!
Behind that graph there should be some further measurements and calculations, none ever did anything like that. And you can write down a small paper without engaging in details, but you can't write down a thesis on it!

Long story short, I will write my thesis based on my personal considerations, that comprend a quite large introduction, a review of similar papers, and dissertations about my measurements. I can add only one of the three papers already published (the first one!), except the last graph, that I would substitude with some qualitative considerations.

Other way I could include that graph, if someone ask me details about it, I can say that I wasn't the author of it (as he suggested me once long time ago)

I still don't know whether this is possible or not...

However, I am not that kind of person who fakes results and I alternate a kind of depression with intense writing and studies... That's what happen on a PhD like this

I would ensure that your thesis does not include anything faked. If there is any subsequent investigation into these papers then it's hard to make the case to take away your PhD if it's based on only the legitimate data.

On the papers, frankly, if what you report is 100% accurate then there's a good chance, it's not the first time your supervisor has engaged in research misconduct. It seems pretty blatant for a first offence. Does your discipline make use of PubPeer? https://pubpeer.com/ It might be worth checking to see whether queries have been raised about any of these three papers or any other articles by him. Serial cheats tend to get found out, and then you risk being dragged in. So I'd consider once you have your PhD being that whistle-blower yourself. With that possibility in mind, you might want to consider whether there are ways to correct the scientific record without full retraction e.g. through a correction. It depends how egregious the fraud is. Even if you decide not to, make sure now that any email evidence / early versions of the papers, anything you have that points to your innocence is stored somewhere off the university network, so you can always access it.

Final thought, if these papers have any potential to cause harm by not being retracted e.g. this is a Macchiarini type of issue http://www.bbc.co.uk/news/magazine-37311038 then I do think you have a moral duty to set the record straight.

Guaio1, how long have you known that these data are fake? Is it only recently or has it been for a while? If this matter came to light and it was being investigated or there was some form of review, you might be asked these questions. It is a serious ethical and practical dilemma you are in, and I agree with the others in that you do need to distance yourself from your supervisor and any false data and claims made. (Including ensuring your thesis does not rely on any of this data).

Is there any way you might be able to get some legal advice on this issue?

I really feel for you Gauio. You are in a very difficult position. you have a few options at this stage and all involve a bit of risk.

1) include forged data in thesis and hope know one ever notices

2) write your thesis without fake data, and be prepared to explain why you don't have the additional graphs and analysis that were in papers in your thesis

3) just walk away now and start a new Phd somewhere else.

so option 1; if you or your supervisor ever gets found out or investigated you will lose your Phd and your academic reputation. This could happen next year, 2 years time or 10 years time . you will never know and it is largely out of your control because it depends on careless and risky your supervisor decides to be in the future. You can move on and distance yourself from him, but if he proceeds with this line of conduct there is a chance he will get found out down the line.
google Deidrick Staple_ he is a social psychologist who forged most of his data, was eventually found out and 10 Phd students who had over the years completed Phd with him got their Phd award taken off them.

maybe he never gets found out; but there are a lot of ways he could. If he is too careless people will doubt his findings, if not now, maybe in the future (I think this is what happened to Staple)
if he puts other students in your position, they may be forced to 'out' him.

Option 2: this to me is a better option, less likely you will get your phd award taken away from you (if it is awarded). but here's the rub__ how do explain the difference between the papers and the thesis without arousing suspicion?? i don't know your field and maybe if your examiners haven't read your papers you could get away with it... but they could easily google you and find your papers when they are reading the thesis.
so how do you explain it??
and if your arouse their suspicion, you will then be accused of including forged data in a published paper... I'm not even fully sure of the consequences of this but I would imagine its the end to academic career and you may not get your phd.

Option 3: very drastic, but you start again and this time 4 years you have phd and nothing to worry about.

response continued in second message

continued from abve

How many years have you spent at this phd,now?

If it's two or less, personally I would walk away for sure. I know even two years, they have been blood, sweat and tears years, but in grand scheme of things I would chalk it down to bad luck and walk away.

If its more than two years the choice becomes difficult and you have a lot of soul searching to do.
everyone is different and everyone has different motivations and reasons for wanting an academic career.
personally I don't think any career is worth the kind of drama and turmoil this may bring.
If it were me and I'm in year 5, I would still walk and just go do a practical masters and move on with my life .
but factored into my decision is the fact that I don't love academia anymore, and wouldn't like all that stress of waiting to be found out, It would suck, but hopefully i could get a job to fund masters and maybe even talk to the university about allowing fee waiver for practical masters, given the circumstances.

The time spent on this PhD is already too much. I just kept going trying to figure out how to manage this issue and only now I've got the idea of writing this here.

Were those papers written right at the start of your PhD career/based on data from earlier on, eg from a masters? It is just that that could be a reason for not including them in your thesis. I know that there is a rule that says something like only work done for the PhD directly can be included in the thesis - eg not borrowing from your masters (or you would be getting double credit for it - which isn't allowed). Is this a loophole you could use?

Or - were other people substantively involved - eg. other authors? I think if they had substantial involvement - eg. analysed the data (which it seems like your supervisor did)... then you wouldn't include it in your thesis as it wouldn't be entirely your work. Could this be the reason you give if asked about why they are not in your thesis? You could say it was entirely joint work - ie. 50% each if there are only you two as authors - so you couldn't claim full credit for it by including it in your thesis?

The good thing is - if you don't include them in your thesis then if your supervisor's terrible behaviour ever comes to light and there is an investigation, then you would know your thesis is sound and you shouldn't lose your PhD.

I still think that if you can get away with not including them in the thesis and have a strong and solid reason WHY, then you'll be OK. Because your thesis will be "clean". As someone else has said, you could be the whistleblower yourself. I think that is something to decide once you have your PhD and are confident that the content of your thesis is completely sound. Personally I would just make a new start elsewhere but make sure I kept evidence of everything to prove my innocence the best I could later if needed. The most important thing is to decide now is surely about your thesis.

All the best

I second newlease36's advise. If possible, write your thesis excluding fake data. If asked, say that you only put in data if you contributed significant effort in generating it.

More consequences of fake data, read