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Logic 101 and XMRV

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by alex3619, Jun 1, 2011.

  1. alex3619

    alex3619 Senior Member

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    My background includes applied logic, including theory of science, as part of an artificial intelligence degree. I also completed a biochemistry degree and found that there was almost no discussion of theory of science - methodology yes, but not about why things are done a particular way. It is ironic to me that in saying this to provide background, I may be guilty of argument by authority, which is part of what I wish to discuss. The difference is that I am not saying that I am right, I am saying I have an argument.

    Another example is that I posted earlier on XMRV and the Lo and Alter PMLV study:
    http://forums.phoenixrising.me/show...l-Request-for-Retraction-of-XMRV-paper/page10

    My post was post 95. This would be an example of a false dichotomy, reducing it to two views. This was not my intent, and indeed it appears possible that Alter thinks both views are essentially correct, it was just meant to be illustrative. What it also illustrates is how easy it is for us to make this kind of mistake.

    Those who are discussing these issues keep asserting either overt or informal fallacies - most probably including me, its easy to do. I just wanted people to be aware of some of these issues as applied to XMRV research. Please feel free to disagree with me.


    Some suggested reading:

    Inductive fallacies -
    http://en.wikipedia.org/wiki/Category:Inductive_fallacies

    Argument from Authority -
    http://en.wikipedia.org/wiki/Argument_from_authority

    More generally you might like this:
    http://www.theskepticsguide.org/resources/logicalfallacies.aspx
    I love the logo here - but I cannot vouch for the rest of the site. Too often sceptics do not practice what they preach, and such sites attract deniers pretending to be sceptics, and I have not explored the site.

    I will try to simplify these issues. I am however very much out of practice, so I am aware I may misconstrue some issues - please think these things through for yourselves, and feel free to disagree.


    Inductive Fallacy: compare these two -

    1. I saw a white swan. I saw another white swan. I saw a whole lot of white swans. Conclusion: All swans are white.

    Reply: Anybody ever been to Perth, Australia? What colours (shades?) are the swans?

    2. One study did not find XMRV in the blood of ME/CFS patients. Another study did not find XMRV in the blood of ME/CFS patients. A whole lot of studies did not find XMRV in the blood of ME/CFS patients. Conclusion: XMRV is not in the blood of ME/CFS patients.

    Reply: This conclusion might actually be correct - but it does not follow from the argument. A million similar negative studies would not prove XMRV is not in blood. Some studies are positive too. What is required is a study with a strong direct conclusion that XMRV is not found in the blood of ME/CFS patients. We need better studies to prove contamination. The best evidence would be direct evidence of contamination in WPI labs. Without such evidence, contamination is not proved. It might be that contamination is a problem, or it might not. It is well accepted that contamination is a major issue with MLVs, which is why such care is taken with testing, retesting, and controls. The consistent major differences between controls and patients is very strong evidence that the contamination claim is wrong.


    Argument from Authority: This one is tricky -

    1. The King has decreed that all foreigners are evil. The King is the final authority in all things. Therefore, all foreigners are evil.

    Reply: This is self evidently wrong - this case is too easy, the real world is more complicated. I wish most fallacies of this kind were this simple. However, ask any follower of almost any cult, and they have trouble seeing this problem in the cult leader.

    There is a problem in this example in that the claim that the King is the final authority is a false premise. In the real world, many authorities are used to justify claims who are indeed authorities, but the point is that while authorities are often right, they can be wrong too.

    2. Dr. Mystery has said that XMRV research in ME/CFS should be abandoned. Dr. Mystery is an authority on MLVs, of which XMRV is one. Therefore XMRV research in ME/CFS should be abandoned.

    This is tricky to rebut. Dr. Mystery is a recognized authority on this type of virus, has real experience and published papers. So shouldn't Dr. Mystery be taken as right?

    However, we also have Dr. Serendipity, who supports continued research into XMRV in ME/CFS. Dr. Serendipity is also an expert. Clearly if experts are always right, then we have a contradiction. Please feel free to substitute experts of your choice for my examples.

    The current convention for dealing with this is on the basis of consensus. We hold that if the vast majority of scientists, after peer review and debate on the totality of research, agree with one view it should be accepted. This does not however mean it is proven, only that the weight of evidence supports it. Just one good study can change the situation completely.

    It will take only one really good study to head us toward accepting XMRV association or contamination theories. I still await that study. I am hoping that either the BWG or Lipkin studies will be that study, but it would not surprise me if we see some other study that also does this.

    In the meantime I assert there is still sufficient evidence to justify further research into XMRV and ME/CFS.

    Bye,
    Alex
  2. illsince1977

    illsince1977 A shadow of my former self

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    As a lover of logic, I concur. However I also must agree with you "I may be guilty of argument by authority". It's kind of an inevitable contradiction here! ;)

    I too have been amazed at the paucity of discussion or realization that the philosophy of science has so much significance in the practice of science.
  3. Angela Kennedy

    Angela Kennedy *****

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    Yep, I'm with you both!

    Thanks for putting this up Alex. Irrational appeals to authority and various types of ad hominems have been rife in this whole area. If people understand the various logical fallacies that can trap people's logic, not only can they learn to avoid them themselves, but they can recognise them elsewhere, which enables a clearer understanding of when a chain of reasoning is wrong, or when fallacies are being used to win an argument which is weak.
  4. alex3619

    alex3619 Senior Member

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    Hi illsince1977, this argument from authority problem was inevitable as a clash between my training in systems theory and training in logic. Logic dictates I don't fall into the fallacy. Systems theory dictates I give enough background for people to judge where I am coming from. I think I made it clear I do not regard myself as an expert, just someone with some knowledge that is relevant and worthy of consideration. I am happier with someone disagreeing with me (even if I disagree back) than with someone agreeing with me just because I said it.

    Logic is only a tool. In advanced symbolic logic you are shown the logical disproof of first order mathematical logic. You are also made aware that translating reality to logical theorems, then translating them back, is fraught with problems. Logic is just a tool - at the end of the day you still have to sit back and decide if the logical conclusion makes sense.

    Too many scientists with modern training have no understanding of the theory of science. They are technically proficient, know the technical methodologies in science, but do not understand the reasons, so cannot adjust to unusual situations. They are really just advanced technicians, the training that separates what I regard as classical scientists from advanced technicians is just not available to most. Many classically trained scientists do not have this problem, and many have educated themselves to get around it - this is not a universal problem.

    Of course, most doctors have this problem is excess - medicine is about diagnosis and treatment, not the underlying philosophy. Their training very rarely touches upon the underlying scientific issues. However, even at the university where I completed my biochem degree there was a course for prospective medical students and prospective scientists that looked at these issues in the history of medicine. This course was optional. I never did this course, it was on my wish list along with several neuroscience courses I would have liked to complete.

    Bye
    Alex
  5. In Vitro Infidelium

    In Vitro Infidelium Guest

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    Pursuit of logic requires very precise definition of processes, logic very rarely works analogously, so while there are established examples of, for instance inductive fallacies, starting from an example of an inductive fallacy as a means of explaining the logic of a real world situation will invariably lead to an abridgement of the actual processes involved.

    Poppers view of science while resolving a number of philosophical difficulties, creates a position where nothing is ever absolutely settled philosophically that is fine, however when applied to the real world it presents a problem: when do you stop testing a theory ? At some point, someone (an authority) is going to say about a line of investigation that it is no longer worth the investment of effort such a statement is of itself subject to logic, albeit a different process than the research about which the statement is made.

    Science, particularly medical science is beset with demands for research, in the face of that rough and ready calculations are made about what research routes to follow, the adoption of such rough and ready processes may themselves be poorly underwritten by logic, but their adoption is not anti logical it is a reasoned response to a challenging real world situation. Thus twenty studies will for pragmatic purposes outweigh one study, and there will be little enthusiasm to expend resources to find out why the one study was an outlier if methodological explanations are available.

    The logic of processes of authority is indeed tricky, to deal with it requires very precise definition of terminology and process. In the case of a King decrees x to be evil, we have to define what is x and what is evil. We can not make assumptions about these values because the logic involved may be internal to the process that is to the King and Country for instance x may = foreigners who are committed to destroying the country, or who carry diseases for which the local population has no resistance. In such a case all foreigners are evil may actually be a logical decree. This however says nothing about the logic of accepting authority which in the real world is defined by pragmatic considerations.

    In the case of Dr Mystery, the operative logic need not be whether the exercise of authority is by due decree but that of having an accredited voice announcing an arbitrary position in a chaotic circumstance effectively a map point. Whether the adoption of a given map point has itself been arrived at through logic is a different question, but it is certainly amenable to logic.

    IVI
  6. In Vitro Infidelium

    In Vitro Infidelium Guest

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    The whole notion of 'irrationlity' is an appeal to authority, which itself lacks rationalty in the terms that rationality is most frequently propounded. Rational (outside the mathematical usage) depends upon its reverse for definition - one can not have rational without the notional 'irrational' which is always presented as a perjorative - there are no 'good' irrational' conditions. Rational and irrational are not positions of logic, they are positions of perspective "my argument is rational", "your argument is irrational", leaving with nice irony the accussation of 'irrationality' as essentially ad hominen. Rhetorically of course that may be justifiable, bit it ain't logic, though the choice to employ such rhetoric could of course be logically arrived at.

    IVI
  7. alex3619

    alex3619 Senior Member

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    Hi IVI, I agree with a number of your points. The following philosophy is work in progress, I have not thought on this in some time, and I am open to other views.

    Logic involves abstraction from the real world, then inference back to the real world. This is problematic. So any logical example still has to make sense.

    Then there is pragmatism. In an absolute sense I hold with Popper on most things, but the real world is messy. Things are badly defined, not all experiments are commensurate, optimal scientific process might require budgets way beyond the funds available. At some point corners are cut, things are simplified, funding is limited. This is where the crossover from science to politics is most evident in my view. These are political, not scientific decisions, frequently based on economic considerations, and so inherently outside the scope of a purely scientific debate. Science is not the entire world, and so scientific process can rarely be perfect.

    Many complex situations are not easily amenable to logic. People use general principles to guide them. This is a good thing, helps deal with problematic issues, but it should always be remembered, and this is frequently missed in my experience, that such generalizations are not always right. We use them because to insist on perfection is to become incapacitated. If the only action permissible is a perfect logical choice, then frequently no action is possible. It is often better for someone to act, and get it wrong, than to sit back doing nothing.

    Value judgments are where logic becomes unstuck. These are biased by history, understanding, definitions and vested interests. An ardent socialist and an ardent capitalist will frequently not find common ground in economic issues, even using the same facts. This does not make them irrational - the values they place upon things are different, so in any decision that requires an emphasis, ranking or comparison they may choose differently. Each has different goals, and wish to advance things in a different direction. In logical terms, each will have many unstated premises that frequently are not even obvious.

    Religious and ethical values also alter the emphasis placed on things, which will in turn effect premises and logical conclusions. This is not irrational thinking, ultimately the choices made are within a context of value judgments, that is the human condition. So frequently when people disagree, and they consider their arguments rational, there is something behind them in their unstated values that alter the nature of the argument. Such value judgments cannot easily be reconciled using logic - no matter how much argument ensues.

    Pragmatism is necessary to deal with many real world problems - theoretical ideals, though often of great value, do not always lead to good outcomes.

    I would accept a pragmatic solution to ME/CFS even if it were theoretically unsatisfactory. My primary agenda is treatment, or better, a cure of ME/CFS. This colours the approaches I use, the value judgments I make of things, as do many other unstated or subconscious values I hold.

    There are many issues in ME/CFS politics that relate to the preceding argument. I am still thinking about them. If these were simple problems, simple issues, we would not be in the state we are in today.

    Bye
    Alex
  8. alex3619

    alex3619 Senior Member

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    Hi, one point I was trying to make, but was more by implication than overt statement, goes to this issue. Multiple experts can have multiple views, and from a purely logical standpoint, presuming commensurate goals and circumstances, they cannot all be "right". Choosing which to listen to is in the realm of politics, not science, and so is subject to all the problems that politics fosters. I think we have ample evidence of that in the pro- and anti-Lombardi camps. Ideally the choice would be pragmatically optimal, but once politics is involved the choice may follow other agendas than finding the "truth" - things become murky. Under those circumstances, it is no surprise that conspiracy theories are popular, as we are having to guess about what is not said, or implied, or denied, as much as about what is said. It is no longer a scientific debate, scientific claims are just tools in a political debate.

    One good scientific study with hard data could shift it back to a scientific debate. BWG and Lipkin both have a chance at being that study.

    Bye
    Alex
  9. Nielk

    Nielk

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    Alex,

    I like all your logic. I am not an expert by any means but have a mathematical logical mind. (or used to anyway when I had full function of my brain)

    My question is. if it's so easy to have a contaminant of MLV in labs, why is it that no other labs doing the studies on XMRV have encountered that problem? Logically, if something seems so prevalent that they assume without any proof that this is what happened in the WPI lab, what are the chances that ten other labs didn't encounter this problem?

    In my opinion, there are two logical possibilities:

    1- It's not so common to get MLV contaminents and therefore it's wrong to accuse a lab of it without any proof.
    2- The other studies were not done in labs?
  10. Angela Kennedy

    Angela Kennedy *****

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    IVI.

    Have you read Bartley's 'Retreat to Commitment'? If you have not, you should. It was Snow Leopard here who recommended it to me, and I'm glad he did. Some of your comments here suggest you're falling into a trap of 'retreat to committment' with your resorting to what constitutes a 'tu quoque' argument.
  11. SilverbladeTE

    SilverbladeTE Senior Member

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    Alex
    *nods* :)

    A good way to illustrate a part of this issue is a wonderful quote form Sherlock Holmes, fictional character but brilliant reasoning:

    the point being:
    it is not the fact that a thousand detectives cannot find something that is important and thus mus tmean nothing is wrong.
    it is the fact that the thing is wrong in the first place
    AND that there is evidence of something being amiss


    It's ironic, I wanted to study/delve into the history, ethics, morality and practical application of Science :p
    Back then, that was like, "unheard of!"
    "Science" has way too much been treated as a "God", like it or damn not, it is in effect, a "religion", because far too many of those involved in it are swayed by "beliefs", financial and political profit, and are so damn blinkered they are like mules in a mine.
    Science is not about certainty, it is about probability.
    Science does NOT give you you the answers to life, it merely provides facts and yet more questions.
    NOTHING is certain, not one damn thing, and that is too scary for many folk who follow science do so for the same reason they'd have followed religion: a need for certainty, for safety in "Knowing how it all should be".
    Bollocks! You want safety and certainty, go get a blanket to hug :p

    Folk with any true rational approach to this can see that a retrovirus would make sense for a likely cause of ME/CFS, that XMRV almost certianly exists as an actual pathogen, therefore, it is incredible arrogance to say "It cannot be the causative agent!"
    Jebuz, how freaking often has some "obvious truth" been shown to be complete bloody crap years later, hm?
    So, this huge hoopla IN THE MEDIA, is proof of a determined need by some to busry XMRV and ME/CFS in a hole because it either scares them somehow, or they think it's a waste of time, and both suggests something is rotten.
  12. alex3619

    alex3619 Senior Member

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    Hi Neilk, I think the problem is something else. Contamination is so common it is almost routine in some labs. As a result every lab tests and retests for contamination, and they pay strict attention to experimental controls. The WPI is no exception, and so far they have not found contamination.

    The basic argument seems to be that if it happens elsewhere, it must happen with WPI, even though no contaminant can be found. They also seem to like the vague notion that the controls might have been handled less than patients, so have less contamination risk.

    In the one case I can vaguely recall of reading about contamination, the percentages for controls and patients were the same. Now that is a standard contamination result. If someone were to do a meta-analysis of the positive studies, and the probability that it could be contamination and get the data the WPI and other labs with a positive result get from chance, I suspect it would one chance in a very huge number - I have not done the math, I am not sure my probability is up to it, I am way too rusty on that.

    I have also been thinking about the claim by Levy that XMRV cannot infect people as it is destroyed too quickly. I think that is only an argument against acute sudden infection. Most theories of XMRV I give credence to have the virus replicating very slowly, with slowly increasing viral load. It only takes one cell to be infected and not destroyed to lead to an XMRV infection. There are reasons after all why ME is not apparently highly contagious, and this could be such a reason.

    In addition, XMRV is not likely to be infecting by direct blood to blood contact very often, some of recent research suggests it infects mucous membranes first. I wonder if Levy tested those for XMRV resistance?

    This is not to say that XMRV association or causation is real, only that the arguments against it are flawed, every one. The pro-Lombardi camp has also failed - where are the mass tissue biopsies, viral integration sites, etc in repeated studies? I wish they had stronger data too. We know some of this, they have sequenced some strains and are learning about integration sites, but we are a long way from having a complete picture. Of course, one of the main things that could be holding researchers back is funding - we have always been underfunded, and WPI is not getting grants.

    Bye
    Alex

    PS the reverse meta-analysis is also interesting. The zero zero studies rest on the claim there is no XMRV anywhere, its all contamination. If that can be disproved, every zero zero study is highly suspect - it is highly improbable that a valid testing procedure will find zero if there is a background rate.
  13. alex3619

    alex3619 Senior Member

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    Hi SilverbladeTE, there is a big nice comfy blanky for those in science, its even got a name: Dogma. I think someone has been throwing it doggy treats lately.:rolleyes:

    I would be careful about saying things like "true rational". I get what you mean, but it sounds like religious talk. I agree that the retrovirus theory fits so very very well. It is part of the appeal. As the details of the biochemistry were released, that appeal only increased - more and more and more of the details match ME/CFS biochemistry and case histories. That doesn't prove it right, but it does make it a very viable candidate. So viable that my second choice if XMRV fails is to look for reverse transcriptase as evidence of yet another retrovirus.

    Give us another year, and we should know much more. Even if the XMRV link fails, the unusual immunology found by WPI is still very interesting - I am particularly interested in the relative lack of adult B cells. Guess which cells usually make antibodies? What happens to antibodies if the cells making them die? There could be a good reason why we fail to have adequate antibodies in many cases. The immunology is advancing fast, no matter what happens to XMRV in the future.

    Bye
    Alex
  14. SilverbladeTE

    SilverbladeTE Senior Member

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    Alex
    hehe yeah ;)

    Dogma!
    [​IMG]

    (not dig at religion, mods, it's from the film "Dogma" and is thus apropos, hehe)

    Issues such as this really we shouldn't expect it to take less than 5 years to get resolved, unless it was massively funded (see HIV/AIDS)
    So as said, for anyone to claim like Stoye did in public to the BBC that the XMRV/ME-CFS relationship was a "myth" is utterly outrageous. That's not science, that's grandstanding of an opinion.
    To have said "It seems unlikely that such a link exists from my viewpoint of the facts" is acceptable in a statement in scientific concern of this issue, not "it's a myth!" :p

    PS
    hey mate, has Sleepy been around, is she ok?
  15. Sing

    Sing Senior Member

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    Thank you, Alex, for a fun, interesting thread which is light and flexible enough in tone for people to consider the ideas and apply them to what we have been told, or think ourselves.
  16. illsince1977

    illsince1977 A shadow of my former self

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    Alex, I was not agreeing with you just to agree with you, but I'm sure you already know that.

    Science attempts to understand the universe by reducing it to isolatable variables. Philosophically I find this problematic. Always have while being a patient with an incurable, inadmissable, dismissed (It's all in your head. Now go home like a good little girl and let us get back to seriously ill people in need of our expertise. -- preaching to the choir here! ;)) illness.

    Even attempting to reduce a complex organism/primate to a set of variables that can be modified and controlled for one at time while pretending that reflects reality and is not just a model of convenience is absurd in a logical sense. It may be the best mankind has to offer, but it is a huge assumption. A real leap (of faith?) in my mind. I am not given to blind faith. Or dogma, but the movie is one of my favorites!
  17. alex3619

    alex3619 Senior Member

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    Hi illsince1977, I did already know that. Sometimes I over-explain, because I try to anticipate issues and head them off. It is both a strength and a failing, as sometimes people misinterpret that.

    I agree with the issue on science and reductionism. The systems movement, which I consider myself a supporter of, attempts to integrate things back to the big picture. It does however require reductionist details to do this, and that is both a strength and a weakness as well. If the details are not right, then the composite is not right. However, by stressing relationships between things, including feedback, a systems approach starts to work on the dynamics of the problem.

    As my hobby I used to build ME/CFS disease models, only one of which is public (and wrong), but which have been discussed in part on a private research forum. However, this requires a functioning episodic memory which I no longer have - I have to rely on my semantic memory. This increases the workload enormously, resulting in crashes, so I haven't done this in a long time, but I am seriously thinking of doing it with respect to some of the recent research. This would not be an easy task, and I would almost disappear from PR for the duration, which could be a very long time.

    Whereas the research is interesting in details there is a big picture emerging, and I think somebody ought to be discussing what the big picture might be. I might give some thought to starting a big picture thread - the "how does the recent science fit together" thread.

    Bye
    Alex
  18. illsince1977

    illsince1977 A shadow of my former self

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    What is the big picture that is emerging as you see it? All the literature including post exertional studies, cytokine and immunological markers/abnormalities, viruses, bacteria, parasites, retroviruses, mold, toxin exposure, methylation, gut dysfunction?

    Are you refering to the need to do a meta analysis of all the XMRV studies published to date? What would you be looking for or at? Or are you refering to looking at all published CFS literature to create a disease model that may take into account currently unconnected confluences of factors to point to etiology and pathology of the chronic disease state?

    If anything screams of the need for a dynamic, systems approach, it is biomedical research.

    The other elephant in the room when we're discussing logical fallacies in medical thought is the tendency of the medical and medical research community to consider current understanding infallible. Absence of evidence is not the same as evidence of absence. Current available technology always suffers from limits of detection issues. When the technology evolves improving sensitivity illnesses/conditions or factors contributing to those conditions are suddenly manifest to observers. Those illnesses were obvious to the stricken even before the outside observer had "proof." Any illness lacking sufficient observable signs has repeatedly been relegated to the medical dustbin of hysteria or somatiform disorder or whatever term is in vogue at the time.

    How do we get a systems view with the paucity of data on our illness? The denial factor has resulted in almost no epidemiological data. Do we go about building databases ourselves?
  19. alex3619

    alex3619 Senior Member

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    Hi illsince1977, I have a bias toward biochemistry, given that it is my background. The metabolic, immunological and hormonal factors are looking like they are intersecting. However, so much is still not known about cytokines, and much is still being revealed about the immune system. For example, there has been discussion recently of considering methylation issues and oxidative stress issues such as the peroxynitrite hypothesis together. The mitochondrial issues may also tie in, but I really need to update my knowledge of cytokines. I am beginning to see patterns emerging in the biochemistry - but it could be wishful thinking, and needs a lot of work. Some research I am not at liberty to discuss yet ties in with my old CFS model from about 2002, involving alteration of intracellular calcium balance. The systems biology aspects seen at the resent SOK workshop are a good thing in my view, this type of combination of systems, modelling and biochemistry was where I was headed but I was too sick for anything to come of it. In the long run, I see systems biology giving us the pattern of chemical interactions which will take us from understanding single causes to combination of causes, with respect to any aspect of pathophysiology. That will give us more options in treatment too.

    So I am interested in mapping the cytokine and immune cell interactions, in the context of cellular metabolism, including energy production. These models tend to get complex fast, and they are always maybes. Just because something might be true in this kind of model does not mean it is relevant. What it does do is give a framework for understanding new research as it is released. Only hard experimental science can show if a model is useful. Such models can be adapted to fit various scenarios, such as XMRV, enteroviruses, genetic problems etc, although there are limits to what they can tell us.

    However a good case can be made for not focusing too early on specific aspects. A thread asking for ideas on what parts of research might be linking together could lead to some interesting possibilities I have not even thought of.

    Bye
    Alex
  20. aquariusgirl

    aquariusgirl Senior Member

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    hi alex
    I am interested in the high intracellular calcium angle. If you have any links, pls share.
    last I heard, Dr John McLaren Howard was looking into this.

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