This is a bit long ? sorry in advance and congrats if you read it through!
It?s quite right that anecdotal evidence often drives hypotheses. However, anecdotal evidence cannot determine whether the hypothesis has been proved or not. That?s why you need scientific evidence.
So, anecdote or if you prefer ?stories? or if you don?t like stories (wonder if I?ll get told to ?fuck off? for that ?offensive? comment) then personal accounts.... My child/friend?s child/cousin/someone on mumsnet?s child (delete or add as appropriate) regressed/developed autism (put in your issue of choice) following MMR (many such examples in UK following our ?vaccine scare? but surprisingly not in the Netherlands, for example). Another example: I know of a nurse who developed MS after multiple jabs of Hep B vaccine (many such anecdotes in France during their ?vaccine scare? but surprisingly not in the UK). It?s interesting that the anecdotal evidence tends to surface in those countries where there is a scare flamed by the media.
It?s not new either ? it was pertussis and the dangers of the DTP vaccine in the 1970s (we all know what happened to Japan when they actually acted on the anecdotal evidence with no scientific basis ? wonder who cares about their pertussis damaged or dead children ? are they collateral damage of the anti-vax movement???) You can see that most of what one is told by Team Anti-vax ?shows? that vaccines have caused harm to children comes down to anecdotes or stories, if you prefer.
One essential quality of the stories that come from the anti-vaxers, and those that read, consume, repeat and spread them, is that any story that tells something framed as ?vaccine damaged child? is automatically regarded as believable and accurate and cannot be challenged. The person telling the stories anecdotes could not possibly have misremembered, conflated, exaggerated, or ?shock horror? made it up (following in the footsteps of Saint Andy wakefield). Even inadvertently.
Indeed, the stories are regarded as so true, and so convincing, that the science that fails to find evidence for theses stories must (in the slightly warped Anti-Vax world) be wrong. I think I was even called evil for daring to challenge this presumption. 
This is actually a stock line of denialist movements.
It doesn?t mean we should ignore anecdotes. We don?t. Scientific enquiry based on this anecdotal evidence subsequently found no evidence of a link between autism or any development disorder and MMR (or any other vaccine) or of a link between Hep B vaccine and MS.
What?s an amusing feature of the denialist anti-vax movement is that they pick and choose which scientific evidence they use. When it doesn?t agree with the anecdotal evidence that they present then it?s flawed or corrupted or ghostwritten or impossible to completely 100% prove or whatever ? anything but correct! But when the occasional paper does semi-agree with them or is even suggestive of agreement (which can happen by the law of probabilities), whatever its flaws, then it?s wheeled out as an example of scientific evidence!! These ?replications of wakefield?s study? say nothing about his evidence free hypothesis that the vaccine triggered a gut infection that contributed to autism, as well as "autistic entercolitis?, but are used in a sad attempt to establish the credentials of a discredited researcher.
Anyway, however great a researcher Wakefield may have once been, if it has been demonstrated that you have falsified data then you lose all credibility. And the studies posted by saintlyjimjams in the other post that silverfrog is so concerned about did not implicate vaccines anywhere ? in fact, explicitly said so! So what was the big hoo-haa? That the immune system is involved somehow in the aetiology of autism. Well, that could equally mean that being exposed to all the lovely preventable diseases is a trigger for autism.
The funniest one is ?right? quoting from the Marsden paper where they explain the justification for their study of half a million children. Yes, that?s the point of such a huge study ? in order to have sufficient power to pick up what are tiny effects. If the effects were large, then power wouldn?t be an issue. But the effects, if they exist, are so tiny that a study of half a million children can?t find anything (which according to ?right? means that they accidentally on purpose must have left something out). That?s all that they are saying. Epidemiologic studies do indeed have their flaws: sometimes there isn?t sufficient power, unobserved heterogeneity can be a problem, interactions between confounding variables can be complex ? but when study after study after study says the same thing then the evidence becomes much more compelling.
Another ?right? classic was her assertion that an error, multiplied by thousands or millions, becomes correct! Umm, an error multiplied by a million becomes a million errors.
Our understanding of the immune system indeed has some holes. For example, we don?t understand quite why administering multiple vaccines in one shot leads to an improved immune response. Another interesting thing we do know is that one of the suspected causes of autism is if the mother has rubella. So, really, by not vaccinating against rubella, we?re contributing to the next generation?s burden of autism.
We do know however that multiple infections in children are harmful to their growth and development. We also know that being ill with measles, mumps, whooping cough, diphtheria, polio, or meningitis is really not conducive to child development even if it doesn?t kill the child or leave them permanently damaged. Our immune systems are exposed to multiple bacteria and viruses all the time. They?re more than capable of handling multiple vaccines which are viruses or bacteria which simply don?t reproduce but stimulate an immune response. What is less good for children?s bodies is when the viruses or bacteria DO have time to reproduce ie make them ill, and that DOES overload the immune system and leaves children susceptible to secondary infections. With the increase in antiobiotic resistance, it may become much much harder to treat those illnesses. In any case, an extended hospitalisation, even without long term complications, it?s not pleasant for any child and exposes them to much more chance of side effects from medicine as well as potential infection in hospital.
Wakefield has been found to be dishonest and unethical. Read this and this in the internationally respected British Medical Journal]] He has been struck off. He pulled his libel suit as he couldn?t prove his innocence (nothing to do with not having money, the man is raking it in in Texas by acting as a beacon to the anti-vax movement, no need to worry about his finances).
Supporting Wakefield is a calling card of the anti-vax denialist movement as it?s all about conspiracy and paranoia (even the term ?collateral damage? is used for emotional effect). The GMC is corrupted, the editors of the BMJ and Lancet as well as Brian Deer (boo! Slimey journalist, yuk, don?t believe him) are ALL LIARS ? only Wakefield (who is so lovely you just have to kiss and believe him) cares about us and our poor neglected children, only wakefield believes us (wonder why that is!), only Wakefield is telling the truth. I guess everyone needs to decide who they believe. Respected professionals in the GMC committee, in the BMJ and in the Lancet or Wakefield and his gang of anti-vax nutter denialists who he has gathered around himself. I know where I stand on this one.
Of course my PhD counts for nothing in the eyes of the anti-vaxers. It would be the same if it was an MD, MBBS, MPH or any other relevant scientific qualification that you care to add as long as you disagree with them. It threatens them and their pseudoscience conducted at the university of google so they have to pretend that it doesn?t matter, that it doesn?t count. (although they love scientific credentials if you do happen to agree). Because they know best and only they know the truth. The rest of us have not yet been enlightened and have not seen the terrible conspiracy against the poor dr wakefield (can he even use dr as a title once he?s been struck off?) and in favour of vaccines with BIG PHARMA dictating the shots (which doesn?t explain why the chicken pox vaccine wasn?t taken up the NHS).
I guess it is hard for anti-vaxers to accept that there are people who know much more than them and that the vast majority of these people simply don?t agree with them (and many find the claims of the anti-vax movement absolutely ridiculous). That said though, I have never made any argument from authority (I only mentioned my phd in defence to some provocative comments ? I shouldn?t have stooped down to the same level, my mistake) and I certainly don?t expect anyone to accept anything I say because of my expertise in epidemiology. I discuss logic and evidence and my analysis stands on its own merits.
Vaccines are not a holy cow. They are treated in exactly the same way as other medications. There is zero evidence that they are treated any differently to other medications. If there was evidence that they are unsafe, they would be withdrawn, in exactly the same process that applies to all medications. Sometimes these effects are so small that they are not picked up in the clinical trials (eg the first rotavirus vaccine which caused an intestinal blockage in one in 10,000 children ? you?d really need a large sample to pick up an effect of this magnitude but picked up it was when it was rolled out and vaccine was withdrawn with no screams of conspiracy).
In the past 15 years or so the anti-vaccine movement was absolutely certain that MMR caused autism. When that hypothesis did not pan out, then they shifted focus to thimerosal. That hypothesis is now dead, so they are moving on to the other ingredients in vaccines. It?s endless, and clearly all they care about is blaming vaccines. The claim is also demonstrably not true. Vaccine safety is closely monitored, and there are many published studies of vaccine safety ? not just for MMR or thimerosal. Here is a list of such studies from cdc Even if some are flawed, just look at the huge amount of evidence that has been generated. Just wanted to flag up this one as it?s under methodology not safety and is very interesting:
Glanz JM, McClure DL, Xu S, Hambidge SJ, Lee M, Kolczak MS, Kleinman K, Mullooly JP, France EK. Four different study designs to evaluate vaccine safety were equally validated with contrasting limitations. Journal of Clinical Epidemiology 2006;59:808?818.
I also really like a policy brief by ?Sense? which is a charity to provide support to deaf-blind people ? many of whom have been disabled by preventable disease (the collateral damage of not vaccinating). Here you go www.senseaboutscience.org.uk/pdf/MMRPolicyBriefing.pdf
However, all the overwhelming evidence about vaccine safety is sometimes forgotten when some elder stateswomen of mumsnet ? with no authority whatsoever ? declare that vaccines are responsible for causing some awful condition in their child. The fact that entry into a child?s system is made to administer a vaccine (love Leonie?s emotive descriptions of administering a vaccine injection), can override a parent?s common sense, set off alarms, and bring about panic that the government is imposing a vaccine progamme on the population that is not necessary and that may be harmful. Every parent will defend a child; withholding legitimate, effective, medication is not the way to do it? That is self-deception, resulting in well-meant but often fatal and tragic results.
That said, in purely selfish self interest for my children, those who choose not to vax are doing my children and other vaxed children a nice favour. My children are highly unlikely to develop one of the preventable diseases since they are immunised against them. Yet all the unvaxed children, who are exposed to the dz, and transmit it in the community once herd immunity decreases sufficiently, are giving my children natural boosters all the time and keeping their immunity up. So thanks for that guys. Shame it?s also putting at risk your own children and children who the evidence does say shouldn?t be vaxed.