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Cleaning up after XMRV

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by Ecoclimber, May 18, 2012.

  1. currer

    currer Senior Member

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    I've just read the paper (I havent much time these days and am trying to follow these threads without doing any actual work on them!) and it does seem that of the sequences they found, only one was 100% identical to mouse and they concluded that was probably contamination. The sequences they found are described as related to polytropic MLV-like sequences.

    So how can they be contamination? And if they do not exist in the known mouse genome, where have they come from?
    Are these fragments accurately amplified?
     
    SOC likes this.
  2. George

    George waitin' fer rabbits

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    It's a good question about the sequences and where they come from. The most definitive answers I've found so far come from the researcher Christine Kozac and her team. One of the first papers Common Inbred Strains of the Laboratory Mouse That Are Susceptible to Infection by Mouse Xenotropic Gammaretroviruses and the Human-Derived Retrovirus XMRV, traced the origin of the receptor xpr1 back to the cross breeding of Asian and European mice on the west coast between 1830 and 1870. This was the first time this receptor could have been established in mouse lines. The team also showed an interesting Polytropic- MLV cross in wild mice in the mid California area that is still there today.


    Next the team goes on to look at specifics of the XPR1 receptor breaking them down into very specific branches in the paper Evolution of Functional and Sequence Variants of the Mammalian XPR1 Receptor for Mouse Xenotropic Gammaretroviruses and the Human-Derived Retrovirus XMRV. This paper looks at the possibility's for actual creation of XMRV as it was known at the time from the data base sequences that had been uploaded both by Lombardi and Lo. It concluded that it was perfectly feasible for this virus to be wild and capable of infecting humans. Most of what is in this paper was a direct rebut both to the Paprokta paper as well as the Towers paper that were published later that year. However, it was ignored completely.

    I remember at the time the Kozac papers where featured on the main page here at PR and were a powerful argument against the really loud wailing of people from the top like Dr. Coffin. Personally I'll take Christine Kozac's careful work over the sloppy papers that were presented during the winter 2011 retro-viral conference.

    Finally Kozac et al produced a paper that while maintaining that XP-MLV's did have the necessary receptors to infect humans and to replicate, that current research supported a benign role for XP-MLV infections. Oral presentation Mouse "xenotropic" gammaretroviruses, XMRV and their XPR1 receptor. I was mildly disappointed at the conclusion since not enough research had been done at the time to say if any of the XP-MLV's were pathogenic or not.Which is why the impression of "coverup" and "agenda" have left such a strong impression during these last few years.

    All in all there are a still a lot of dangling threads to be claiming clean up just yet. Even buying that XMRV has come to be equated solely with the VP62 clone and that particular clone is a exactly as claimed a recombinant event that could never happen ever again. Ever. Assuming that it is only this which is being "cleaned up" there is still far to many open doors and windows that look into the possible answer for many illnesses to just start nailing boards over them.

    I find it quite likely that the retraction of papers regarding XMRV were probably necessary in order to attack the problem from another angle. Removing the argument surrounding XMRV from the equation will hopefully provide an opportunity for the researchers involved in the current studies to go back and put together an iron clad argument for XP-MLV infections in patients verses controls.






     
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  3. Mark

    Mark Acting CEO

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    I'll start my reply here, because I'm of course very pleased to see you recognising and understanding this background of the political situation around ME in the UK. I'm especially pleased to see you recognise the problem of the UK researchers and their associated industry interests.

    I'm very glad I asked you that question about them, and gave you the opportunity to say publicly what you said in the quote above, because my reason for doing so was to suggest to you that you might be more able to make the points you want to make if you were to acknowledge these factors more often. That would be a much more diplomatic approach, and you might find a much more receptive audience if you were to say as much about these problems as you say about the approach of patients elsewhere. I think you would represent the interests of your research contacts more effectively if you take these points on board, which is why I suggested that to you.

    A large part of what I was trying to say to you in my post above was that this background, this social and political context for ME research and policy in the UK - and also elsewhere in the world - is a reality that many patients have been living with, and campaigning against, for more than 20 years. I was trying to point out what I think should be obvious: it is this policy, and this history, which is responsible for the attitude of distrust of researchers amongst many patients. That is clearly the origin of this problem, so I think that would be a sensible point to acknowledge frequently if you do want to communicate effectively with the group of patients whose behaviour you are concerned about. It also seems to me that if you, and your research contacts, are upset about the treatment you have received, then you would do well to recognise that ultimately the source of all these problems lies with those researchers.

    Of course that does not excuse any aggressive behaviour directed at researchers who have nothing to do with all this, and of course it is not fair and it is not right that other researchers, such as your friends and contacts, who presumably have no connection with this shameful history and don't condone it, should suffer the consequences of the cynicism and distrust of researchers that has built up over decades in the UK - just as it isn't fair that all ME/CFS patients worldwide should suffer negative consequences as a result of the actions of a particular group of activists. And of course I do not for one second condone any attacks on Professor Lipkin or other researchers, or aggressive emails that may have been sent to them. Of course I don't know what Professor Lipkin has received, but I don't see that he has done anything to deserve to be attacked - quite the reverse. Of course it's wrong and unfair that he should be the victim of anything like that. I actually think you will find very, very few members here, if any, who support or condone any such attacks.

    Other forums have different rules, so it's not surprising that we have members who post in a different way elsewhere. We don't have any control over what our members may post on other forums; when they post on our forums they are required to abide by our rules.

    Your views on how a moderator should behave are noted. My post was really aimed at suggesting to you some more diplomatic options you could take, and highlighting why the approach you are taking is divisive and counter-productive. My reason for posting was because you made some inflammatory comments, and as a moderator I was concerned about the direction this thread was heading. I have seen more than enough arguments on these forums when you've attacked the behaviour of patients and provoked an angry response, and my concern is that this has frequently been very divisive and unpleasant for this community.

    I do take offence to the attempt to emphasise that I am from the UK and have 'embedded myself in the forum', as if to suggest that this represents some kind of invasion. This forum is not, and was never intended to be a US-only forum, it has members from the US, the UK, Australia, Canada, and many other countries around the world; the moderators are from Canada, the Netherlands, the US and Australia. There is absolutely no reason why members from any country should not be here, and the founder of the organisation, the rest of the board, and the constitutional arrangements for US non-profit organisations, have all apparently had no problems whatsoever with me "embedding" myself here - I have been made to feel very welcome. My nationality should be of no relevance whatsoever - but if you introduce the subject of nationality into the discussion, by making generalisations about UK patients and drawing attention to members' nationalities, then it should come as no surprise that I take exception to that.

    As other members have pointed out on this thread, your emphasis on the nationality issue is not really borne out by the evidence: there are US members who have concerns and scepticism about the research in this area, and there are UK members who broadly agree with your general view of the science. The points of view do not divide neatly along national borderlines as you seem to imply.
     
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  4. Mark

    Mark Acting CEO

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    Fine.



    Then pursue them if you wish. I do not think you will find any defamatory content on this forum, but if there is any that we have missed we will of course take it down; we don't support or defend the posting of defamatory content and we take it down when we are alerted to it. If you believe you have a case, then pursue it, that is your right. If you believe there is anything defamatory on these forums, report it and we'll remove it.


    I am not aware of any disparaging of prostate cancer researchers on these forums. We frequently critique papers, and where their conclusions over-reach their results that is certainly criticised, and rightly so, but I'm not aware of the disparaging comments you're referring to. I don't understand why you keep criticising our forums for the behaviour of other forums. If there is behaviour here that you or others don't like, it would make more sense to criticise it as and when it happens, so that we have some idea of what you're talking about.


    Yes, quite, I have emphasised that above: it is just hearsay, and if the communications are private and can't be disclosed then perhaps you shouldn't be making these general comments if you can't explain with evidence what exactly you are talking about. As I pointed out above, you criticise others for posting without providing evidence. Respected journalists quoting unnamed sources is one thing; anonymous posters making contentious claims that can't be verified on discussion forums is a rather different scenario.



    I've made it clear that we don't condone or support defamatory statements here. I don't recall there ever being any attacks of that nature on Lipkin or Racaniello here - I criticised a specific comment in Racaniello's blog recently myself, but also emphasised that I think his blog is a very refreshing and welcome type of public communication about science, and I think he has generally been very open-minded and fair about this research.

    If members of other forums are posting defamatory comments on other forums, then you should take that issue up on those forums and take any legal action you see fit on those other forums. Why drag us into it? It doesn't seem fair to us to drag us into arguments you have with members on other forums. If some of our members are involved on these forums too, then I think when you're here you should respond to what they are saying here rather than bringing up separate arguments from elsewhere.


    I'm not sure how you understand what my authority to be and how you feel I've exceeded it. I don't see where anything that I've posted above represents biased commentary or prejudice. Being a moderator does not mean I may not express my opinions, and I mainly expressed the opinion that posting here to criticise the behaviour of patients elsewhere, in a generalised way, is inflammatory and divisive. It's part of my job as moderator to try to deal with such problems and that's what I was doing. As far as the moderation of this thread is concerned, I asked other moderators to take care of that and check the thread for any rule breaches, because I am posting myself, and if anything I've said breaks any rules, I've encouraged them to treat it objectively.


    If the problem you want to correct, and the issue you want to discuss, is comments that have been made on other forums, then it's a good thing that you should take those issues up elsewhere, where they belong. If you want to post here about discussions that are happening here, rather than elsewhere, that's fine.

    You frequently seem to provoke a contentious reaction here by criticising the behaviour of patients in a general way, without being able to produce evidence, and you seem to post about that subject out of context on a forum whose members have nothing to do with what you're describing. All I can suggest is that if you see or hear about behaviour you are not happy about, you should take those issues up in the proper context, when and where those incidents occur, rather than taking it out on us.

    I'm sorry that you don't seem to have taken on board the points I have tried to get across. I was trying to suggest ways that you might engage with patients, here and elsewhere, more effectively. If you feel the approach you are taking is appropriate and effective, and you're helping to reduce tension and effectively tackle the problems that concern you, then I guess you'll continue with that approach. I was just trying to suggest that if you ever feel like you're banging your head against a brick wall, maybe you might like to consider another approach.
     
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  5. currer

    currer Senior Member

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    Hey George, glad you are back here!

    http://forums.phoenixrising.me/inde...en-hanson-david-bell.17574/page-3#post-268615
    O'Keefe yesterday said that her BPH virus had an env that was related to one in wild mice.
    This makes the Kozac paper interesting and relevant. Thanks for reminding us.

    "it is interesting that everyone, us included, seems to have much more trouble amplifying the env and LTR regions - if gag amplification was merely due to mouse contamination, why don't these regions amplify as well? Keeping in mind that tests for mouse DNA are coming up negative...this might suggest that there is more divergence from known MLV-type sequences in these regions - we managed to sequence the variable region of env from one patient -- the sequence was most similar to env from an MLV virus known to cause disease in mice in the wild -- which is pretty interesting if you think about it... "
     
  6. Esther12

    Esther12 Senior Member

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    Quick note: this thread is going way to quickly for me to keep up with, so I may have missed bits I should respond too.. sorry.

    Maybe we're talking slightly at cross purposes here. I'm not saying that there is no legitimate work to be done arround XMRV/HGRV/etc.

    I think that work will need to be much more limited in scope than you seemed to...

    I think that we are unlikely to ever be able to fully explain the results of many of the experiments around XMRV/HGRV. Just like we will be unable to fully explain all manner of other results from other studies in the past - there are so many variables that exploring these things becomes prohibitively expensive, and beyond our capabilities.

    It's possible that I misunderstood you, or you misunderstood me. I'm not too sure.
     
  7. SOC

    SOC Senior Member

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    That's a surprisingly pragmatic position coming from someone who has been vehemently opposed to pragmatism in other threads.

    Whether science is capable at this moment of knowing everything about these studies is not the point. The nature of science is to seek a full explanation, not to give up and claim mysterious unknowable conditions are at play.

    Just because we don't have the ability to explore certain things today (and I don't agree with you that we're in that position with regard to HGRVs), it isn't a logical conclusion that efforts to know the currently unknowable should stop. In fact, all scientific breakthroughs are made because science is willing to explore things currently beyond our capabilities. What is (or seems to be) beyond our capabilities today, could be well understood a year from now.
     
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  8. Esther12

    Esther12 Senior Member

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    There's a difficulty with the use of the term 'pragmatism', as it can refer to different things. My understanding is something like this:

    There's 'practical pragmatism' which is pretty much always a good thing - recognising the limits of what we can do, and making decisions based upon on honest discussion about what are priorities should be within those limits.

    Then there's 'philosophical pragmatism' or 'pragmatic conceptions of truth' or 'pragmatic management of cognitions' - this is much more problematic. This sort of pragmatism could be used to justify encouraging people to hold particular beliefs about reality not because there is good evidence that these beliefs are likely to be true, but because it's thought that these beliefs will lead to improved outcomes. (eg: "If CFS patients believe that deconditioning is the problem, then this leads to a greater sense of control, responsibility etc, and it doesn't really matter whether it's really true or not"). I think that this form of pragmatism is intellectually and morally cowardly, undermines much of what is valuable about life, and will almost always lead to the manipulation and abuse of those in positions of weakness.

    So I'm not arguing that we should not commit ourselves to discovering all the sources of positive results because such an understanding and cognitions could harm outcomes (pragmatic conception of truth), but because such an endeavour is likely to demand such a massive amount of limited resources which I think could be better spent in other areas (practical pragmatism).
     
  9. SOC

    SOC Senior Member

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    Agreed. I'm inclined to practical pragmatism.

    Agreed these two are different. I also think the phrase 'pragmatic conceptions of truth' is a deliberate misuse of the world 'pragmatic' and I therefore refuse to use it in that context. I'm not one of those people who can conceive that truth is not truth because it's inconvenient, so 'pragmatic conceptions of truth' sound completely illogical to me.

    I see your point. My point is simply that such information is not unknowable and we are likely to understand it at some point. Certainly resources should be spent to further the science, not for the sole purpose of answering someone's criticism. However, furthering the science with the criticism in mind is likely to provide answers at some point.
     
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  10. Esther12

    Esther12 Senior Member

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    Right - I think that a lot of people see 'pragmatism' as just meaning 'being sensible'. But pragmatism as a philosophy means much more than that, and is quite important within psychiatry.

    When Chalder or someone says that their treatments are "pragmatic evidence-based approaches" then a lot of people interpret that as meaning "sensible approaches based upon proven claims"... when it often means almost the opposite! When most people have pragmatic philosophy explained to them, they're unimpressed by it (although Americans seem keener on it than most. Theologians too), but often it slips under the radar. Pragmatism as a philosophy tends to favour those in positions of power and authority, which could explain why it continues to have such influence.

    I thought I'd post this Bertrand Russell quote on pragmatism:

     
  11. Mark

    Mark Acting CEO

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    Thanks for the continuing insights on the philosophy of pragmatism Esther. I never looked into pragmatism before, and your posts on this subject have been most illuminating; I think you're right that it's an important issue to focus on. I've found the associated ways of thinking objectionable for a very long time, but never had the right label to describe this kind of thinking before, so it's really helpful to me to get the technical name for this. There are shades of 1984 in this idea that truth can be defined as whatever it is most convenient to believe - as Russell says, the proponents may often be unaware that the political context automatically makes this philosophy merely a tool of oppression, but I agree with him that such a corruption of the concept of truth inevitably has those kinds of dark consequences.
     
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  12. SOC

    SOC Senior Member

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    Oh really? And on exactly what do you base that?

    I've had enough of this conversation.
     
  13. Mark

    Mark Acting CEO

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    This is all off-topic so yes, it's probably best we return to the calm and uncontroversial subject of XMRV...;)

    I'm sure Esther didn't intend any offence SOC, but generalisations based on nationality seem to come out quite easily between US and UK - on both sides - and there have been a few other examples in the past where unwitting generalisations about what Americans or Brits have caused offence. I definitely think it's best to steer away from making such generalisations.

    My perspective on this is that many of our impressions about each other are formed by the media, and by the cultural exports that we encounter - and this leads many of us to completely unrealistic assessments of each other. The 'pragmatic philosophy' as I understand it: culturally I've perceived that way of thinking as an American import; it has been US influences in the past that have been the conduit for those ideas coming into the UK. And I just looked it up to check my vague recollection, and it's correct that pragmatist philosophy is mainly associated with the American philosophers William James and John Dewey - the books I read many years ago did say that's where it came from, I think.

    But what I think we often miss in the UK is that when things like this get imported, they aren't representative of America as a whole, but of one part of America - and there is a strong counter-culture to those influences that doesn't get represented over here. From experience, I think it's the same the other way round, with UK cultural exports like the royal family, tradition, plummy accents etc...those things aren't at all representative of all of us here, either.

    So I'm sure no offence was intended, but it's always wise to be cautious when generalising about the behaviour of nationalities, especially on an international forum like this.
     
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  14. SOC

    SOC Senior Member

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    The 'pragmatic philosophy' that you perceive as an American import is the gross misrepresentation made by your political/social system of a philosophical theory the originated in the US. But sure, blame us for your ills. It's not the first time and it probably won't be the last.

     
  15. Mark

    Mark Acting CEO

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    I really hope you weren't reading me as 'blaming you for our ills', or even as saying that philosophical pragmatism as it's understood here is the same thing as James and Dewey's philosophy. Quite the opposite really, in the portion you quoted all I was trying to say was that, if you're living over here, ideas like those are examples of ideas that are presented here as if they were the same as the original American ideas, and so the perception here will tend to be that they are. I actually agree with you that the way these things work out is probably getting completely lost in translation and turned into the opposite of what was intended once they reach our society - it probably works that way the other way around too. I think it works that way with all cultural exports really...Italian restaurants here are really serving a British idea of Italian food, 'English Pubs' abroad always seem to blend the local culture with an idealised version of what an 'English Pub' is, and so on and on. Actually, I was trying to make basically the same point you just made, and say that when ideas get imported we falsely assume that they are truly representative of the culture they were imported from - but I guess that got lost in translation as well...:rolleyes:...two nations divided by a common language, and all that...
     
  16. Bob

    Bob

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    Wow!
    Are we arguing over the origins of a philosophical school of thought?
    Or are we arguing over the origins of a way of thinking, that has been given a name?
    It's a bit over my head at the mo! :confused: ;)

    But I'm impressed that some of us have managed to have a heated discussion about an obscure school of philosophy that I've never heard of before!
    And added to that, we are veering towards becoming tribal regarding who to blame for a rotten philosophical theory!
    It could only happen on Phoenix Rising, amongst all my PR friends! :thumbsup: :)


    I just want to agree with something Barb said earlier in the thread...
    The XMRV threads often get heated and polarised... :mad:
    But I think it's worth remembering that we are all on the same side here... o_O...
    I've been having discussions with all of you on PR for years... And I'm on very friendly terms with 99.9% of you... :hug:
    We all come here to share out thoughts with each other about the subject, because the outcomes are very important for us all.
    The only difference between us, is our opinions about the potential significance and the importance of the MLV research.
    And that's something that even many of our 'best' scientific minds don't even agree on.

    I just wanted to say this, because I'm often guilty of ranting on the XMRV threads, and forgetting to be as friendly as I could be. And sometimes it's nice to take a step back, and remember that we are with our friends here. :cautious: ;)

    OK, apologies for my brief interlude... I should be in bed, so I've probably just talked a load of nonsense...so please carry on! ... ...
     
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  17. barbc56

    barbc56 Senior Member

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    Thanks Bob. I think that we all need to step back and and think about this. It doesn't mean we on the forum will always agree. But we can disagree without put downs and wearing our blinders. Hard to do when we are talking about our illness as it's such a personal issue We have all been guilty of this. Well accept me, of course!!:rofl:

    Not!!

    I think the several day respite really helped.

    MY COMPUTER IS FIXED!!!!!!!!!!!

    I am keeping my finger's crossed that this fix will be what is needed.

    Barb C.:>)
     
  18. Bob

    Bob

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    Glad you had a nice mini-break from the thread barb.
    Well done for fixing your computer.

    You might be pleased to know that your debate with Mark wasn't totally unproductive, even if it felt like it...
    I actually learnt some very interesting things from the discussion.

    The one positive thing about arguing on these xmrv threads, however frustrated we get, is that we stretch ourselves to do further research, and we share what we discover.
    I always find it incredibly interesting, even if we can get immensely frustrated with each other at times.
     
  19. barbc56

    barbc56 Senior Member

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    Well it turns out I owe Mark an apology. I thought the responses of the Singh study were the ones in the Blood working group webinar and the presentation that answered FAQ about the study. Facepalm!!! :thumbdown:

    I will post these later.

    Barb C.:>)

    http://www.research1st.com/2011/10/14/xmrv-updates/

    About a third of the page down.
     
  20. Esther12

    Esther12 Senior Member

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    Sorry SOC - that really wasn't meant as any sort of nationalist dig. I have just found that when speaking to people, Americans are more likely to see pragmatism as obviously right than other groups. Mark also pointed out that pragmatism had its origins and has had more influence in American intellectual life. Of course I never meant to stereotype all Americans, or say that those Americans more supportive of pragmatism were also unperturbed by the worst aspects of it. It was a slightly casual aside, and I didn't even think about whether it could seem offensive to anyone. The pragmatic biopsychosocial approach CFS has been at its worst in the UK, and I think that this is a result of aspects of our culture, but I don't see that as insulting to UK patients.

    Often people's responses to these sorts of foundational issues do seem to be heavily influenced by culture (eg: 'pragmatic conception of truth' seeming like an abuse of language to you), so if some people were reading this discussion and thinking 'pragmatism is clearly great... what are these people upset about', I wanted to point out that this could be because they started with different cultural assumptions or were educated as part of a different intellectual group. I could have done so better!

    PS: Thanks for pulling out a link from wikipedia to this article: http://hpq.sagepub.com/content/14/6/800.abstract?rss=1 It looks potentially interesting.

    That's pretty much exactly what I thought when I started reading more about it: "I thought this was just a repulsive embrace of intellectual and moral cowardice that people do instinctively and need to be taught to abandon... not a 'philosophy' anyone could ever choose to promote".

    I studied some philosophy at uni, but never pragmatism, even though Blair, Clinton and W Bush were all so influenced by it (especially Blair), and they were in power as I was studying. I get the impression that it's seen as a bit of a joke by most academics, so it gets ignored despite its importance and influence. Reading mid-90s biopsychosocial papers/lectures/etc people like Chalder were promoting ways of treating patients which sounded pretty immoral, but they seemed to think it was justified by pragmatism... so that led to me digging in to William James (who suffered from neurasthenia, was an important figure in psychiatry, and whose ideas are particularly influential on the biopsychosocial approach). He also promotes an pretty vile approach to life which did seem to serve as a foundation for most of the ideas and beliefs I thought it was important to fight against... yet for much of my illness I was oblivious to the fact that these ideas were guiding the way in which I was being viewed and treated!
     

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