I don't want to sound discouraging, but as your supervisor has clearly given you some really bad advice thus far, be very careful about his claims to be able to sort everything out behind the scenes. At both the university where I did my PhD and where I work now, this would quite simply be impossible. The examiners' reports would have been written and signed off by the dean, and to get the PhD you have to do what they say. The only route would be a formal appeal. Now your university might have different procedures, but I'd genuinely be surprised. Given the growing litigiousness of students when they don't get the result they want, most universities have really become much more careful to have set procedures and to follow them to the letter.
Reading between the lines, it sounds like you've done some great research but possibly not followed the expectations of what a PhD thesis should contain. It sounds like your supervisor's odd advice about not mentioning other methods had left you open to the criticism that you weren't aware of the wider literature, which is actually a serious flaw in a PhD thesis. Where I work there are criteria for passing a PhD (available to students) and each examiner has to independently submit a written report on the thesis prior to the viva rating the thesis against those criteria. If both examiners had decided there was a serious flaw in the thesis prior to the viva (and the reports agreed on what the problem was), then to some extent, the decision was already made however well you defended. Good luck, but I'd check everything your supervisor tells you from here on in against the regulations to protect yourself.

I won't put it as bluntly as the previous poster but as far as I can see it, you have two options.
1) Look up the appeals process and follow it to the letter. I'd imagine you'd have to claim bias / unfair examination. Based on your account, your supervisor has been monumentally incompetent in choosing an entirely irrelevant external examiner. You will have to make this clear in your appeal, so you probably will burn some bridges, but if the viva was as unfair from the outset as you say, then this is the only way to get a new set of examiners and the viva rerun. Your big problems will be a) your internal examiner has agreed that these changes need making for you to pass, so you will have to find a way of deeming them as biased as well, and b) your supervisor might be moved to defend his choice of examiner. Before you do this, really try to look at things dispassionately - how much of this is really unfair and how much injured pride talking? Only you can really tell.If you are going to appeal there's probably a time limit in which you need to do it. Seek advice from your students' union - they tend to be clued up on appeals.
2) Swallow your principles and make the changes required, walk away with the PhD and chalk it up to experience. If you want an academic career, you will have to learn to live with unfair reviewers, people who fail to see how brilliant your grant application is, and those pesky students who complain about everything, so it's unlikely to be the last time you have to do this.
Actually you do have a third option, which is to walk away with your principles intact but minus a PhD, however, I rather doubt that this is really what you want to do.

Majar - what hazyjane said is spot on. This is always a busy time of year for academics and this year is exponentially worse because of the pressure of the REF preparations. Have you tried looking for a training course you could go on or whether there are any online training resources in this technique? If your suspicion is correct (although I honestly suspect this is a case of overwork), that this is a hint to start being a bit more independent, then doing things like that would allow you to go back to her with an update on things you've tried.

Ask your supervisor for advice. You need someone who understands the etiquette of your particular discipline to advise you whether this is viewed as unprofessional behaviour that would damage you. In my own field any student behaving like that would acquire a terrible reputation very fast, and we don't even count conference proceedings on the rare occasion they exist as real publications.

Your tuition fee is for supervision (and obviously access to the university's facilities). That suggests to me that your supervisor has a duty to try to ensure that you are progressing satisfactorily and meeting the milestones expected by the university/graduate school (because if you don't, you'll fail any progress review). I think supervision, like Eska says, is always more directional in the first year / 18 months because this is when PhDs can go really wrong. Gradually as time goes on, I think you get more ownership of the project, as you mature as a researcher.
I realise English isn't your first language so I might be misunderstanding your post - is it that your supervisor wants you to do something that you don't want to do, or is it (like your post seems to suggest) that you wish him/her to act as your employee? If it's the latter, forget it. Your tuition fee is not paying his/her salary - you are just one of a variety of tasks funded in a multitude of different ways that s/he is expected to perform as part of the job. If you left, it's not as if s/he would lose his/her job.
If it's the former, reflect long and hard before you refuse. It's not just because it tends to be wise to maintain good working relationships and to pick your battles carefully, but also because they may be trying to stop you heading down blind alleys and wasting a lot of time, simply because in the early stages, they tend to have a better sense of what is required for a PhD than you will have.

Without knowing what subject it's a bit difficult to advise, but if you were a social scientist I'd suggest concentrating on giving a short background (why the topic matters) then spell out the research question and say something about what theoretical and/or methodological approach you intend to take. The lit review would be the bit I would skate over.

Hi journey,

I think scientists are now having to deal with the same kind of academic job market that those of us in other disciplines have had for well over a decade i.e. one where the majority of PhDs will not get academic jobs of any sort, even postdocs. This is a nasty thing to come to terms with, particularly if you are in an area that traditionally has been well-funded. I wondered from your last post about friends' successes whether this reflects the environment there was a few years ago, rather than that of today? If so, you do need to accept that the goalposts have ben moved, unfair though it is. It's not personal, it's structural.
This might be an off the wall suggestion but would you consider going abroad? Investigate the Marie Curie postdoc scheme for example. I'm not in a science field but in my discipline there seem to be quite a few postdoc jobs in Germany and the Nordic countries, just as there always was i.e. the funding doesn't seem to have dried up as much as in the UK. I also agree with pjlu that developing a plan b is a good idea. There's some good material on the vitae site for scientists, about doing exactly that.

I've no experience myself but I wanted to suggest something. Would it be possible to change to part-time status so that you could maximise your time with your mother, but still feel that you were doing something? A friend of mine lost her husband to cancer during her PhD and the AHRC allowed her to do that. It was a financial struggle but for her that was the best solution.

I think both the relevant research councils (assuming MRC and EPSRC?) award funding for doctoral students directly to universities, who then decide who gets the money, so this may be what you've already been considered for. I think the quickest way of finding out what possibilities there are would be to ask the department, what other students have done in this situation. One thing that does occur to me is whether you might be able to get an industrial sponsor through a collaborative studentship for something like that. Sadly, getting a PhD place is a lot easier that getting funding. On another note, if the supervisor is semi-retired, is s/he necessarily going to be the best person to supervise you? I'm just thinking that someone winding down their research career may not be interested in publishing more articles etc with you.

I think the book you remember is the Directory of Grant Making Trusts.
The Leverhulme Trust won't fund PhD projects directly, what it will fund is projects proposed by academic staff at universities, which can include in the costs payment for research assistants, who can be PhD students. But what the OP is looking for, I think, is funding for their own project not to work on a larger project designed by the supervisor.

To the best of my knowledge the Leverhulme Trust does not fund PhD study. For the social sciences the main funder is the Economic and Social Research Council if you meet their eligibility criteria, but I think the deadlines will have passed for this year by now. There's also basically no funding for MSc programmes for social sciences - the only option if there's no university scholarships, is part-time or a career development loan (not advised if you intend to go onto a PhD as the repayments start at the end of the MSc). Is ethnobotany definitely a social science though? It might be worth checking whether it falls under biology - the funding picture might be less bleak.

Hi Kojo,

It's very much subject dependent. In some of the sciences, it is still possible to go from a Bachelors to a PhD, but it is very unusual in the social sciences and humanities. 1+3 integrated programmes are now very common though, as more of the UK research councils adopt this model. Similarly, there's more science funding available than there is for other subjects so having a first matters more for a subject like English than it does say for Chemistry when it comes to funding decisions. Funding is more difficult too if you are not a UK resident or EU citizen, as some major funding sources are only available to those people.
In terms of English tests, what flexibility there is depends on whether you are a non-EU citizen or not. If you are, the rules are set by the UK border agency, and if they say you need IELTS or equivalent to get a visa, regardless of whether you've been educated in English, then you have to jump through that hoop. They define which countries count as 'majority English speaking country' and which don't. There really is no wriggle room if UKBA are involved!

You are going to have to communicate with these people if you get corrections, which your post seems to suggest you're expecting, attend graduation, want publications out of this or references, so I'd think of this as an opportunity to break the ice rather than anything else. You won't be turning up out of the blue, your supervisory team will know the date and time of your viva, so I think whether you do it in person or email or even a thank-you card, it would be a bit odd not to inform them of the outcome. In fact, you might want to prepare yourself for their possible presence around the beginning / end of the viva. They are the people who appointed the examiners, so avoiding and not thanking them for examining you would be a professional faux pas for the supervisors. My supervisors took my examiners out for lunch after the viva as a thank-you for example.
You said the angry reaction to your mistake came from the lead supervisor - could you possibly send a short formal email ahead of the viva to the second supervisor asking if s/he had any advice for your viva to open communications and make it less awkward on the actual day?