Gosh, I'm afraid I can't answer all the topics raised in this thread, since it seems to be changing more into a rail about allopathic medicine than a focussed debate about vaccination. I have an ethical requirement to be as sure of any answers as I can possibly be, which means researching them which sadly I don't have as much time for as I'd need. I'll do my best with a few points though.
Firstly, Caithness your point on aluminium is a good one. Many of the newer vaccines (such as MMR II) don't use it, but there are still plenty that do. As for formaldehyde I'm afraid I'm woefully ignorant there, hands up to that one.
You're quite right to say that I'm educated by material produced by "scientists, doctors, professors and researchers in the pharma/industrial complex". When it comes to evidence-based medicine, they're the best sort of information. I think you have an idea that I've been handed a pack of glossies and taught to parrot the stuff though, and that's wrong. My degree course - and everything I've done since - was aimed at teaching me to find, gather and evaluate information, and make up my own mind.
Your mention of excitotoxins is a good case in point, since there's a staggering amount of disinformation on the web. The first things I ask when looking at any information is "Who's telling me this? Do they have the IQ of a garden fern? Do they have a vested interest, or an axe to grind? Are the trying to sell me anything?" Then there's the quality of their data. Where does it come from? Is it referenced? Only then do you even consider the information itself.
It's always worth chasing up the reference chain to the original data - sometimes it's misunderstood, misapplied, of poor quality, or just plain not there. One common trick is to publish a small trial - three groups of half a dozen volunteers, discarding data from any of the groups that doesn't support what you're trying to prove. That data won't stand up to even casual scrutiny, but all you need to do is get it published. Then you write an article elsewhere, referencing your original dodgy study. Thereafter you only ever reference the second article, and surprisingly quickly the thing gets quoted all over the place because people are too lazy to check up the references, and so don't realise you're actually quoting yourself. Another thing you often find is groups of websites quoting each other, with only one outside reference (such as a doctor selling a book). It looks like there's lots of information there; there isn't.
I'm not paid by pharmaceutical companies, but mainly by you the taxpayer. My salary isn't affected by "peddling" drugs, or not "peddling" them - I couldn't give a stuff about making sales or supplies. Sorry, but there you are. Number one thing I try to get prescribers not to give? Antibiotics. Number two? Sedatives. Number three? Anti-inflammatories. Not in all cases you understand, but they're often not necessary.
I also don't trust the pharmaceutical companies to do anything other than gun for profit. That's why we have systems to evaluate the data they produce that are as robust as we can make them (so far), such as the Cochrane Collaberation. There's a bit of fuss brewing in the industry at the moment because Cochrane has questioned the herd effectiveness of flu vaccination programmes, and the pharmaceutical companies are not pleased. No doubt that'll hit the media shortly. They won't understand it, will misreport it as questioning individual effectiveness, and public confidence in that vaccine will plummet.
The MMR vaccine is a good case in point. Harry is 3, so a year and a half ago I had to research the case for the vaccine myself. I came to the conclusion that there were risks inherent in the vaccine (temporary overload of the immune system being one of them), but they were smaller than the risks posed by the diseases themselves.
Antibodies to measles (an acute infection) are a good sign, because they indicate previous infection or vaccination, both conferring a degree of immunity (meaning you're unlikely to get it again). Antibodies to HIV (a lifelong infection) are a bad thing because there isn't a viable vaccine yet, so the antibodies indicate infection (meaning you've already got it).
I'm sorry I don't have time to address more of the many points you've both raised, but I must point something out.
Children do die of preventable diseases everyday in this country and your inference that we are being arrogant in questioning vaccines because you claim that children don't die of preventable of diseases here everyday is the prime example of why I don't trust those in your field.
I actually said;
this whole thread could only be possible in a society where children don't routinely die of these preventable diseases.
...and I stand by that sentiment absolutely. I don't think that my statement that "Everyone is of course entitled to their own opinions about vaccination" implies arrogance on your part at all - in conversations like this I often find myself walking a fine line between sounding pompous by being too technical, and sounding condescending by trying to simplify things too much. If you have any specific questions feel free to PM me and I'll chip in again.
I'm afraid I didn't understand your question about antigenic complexes though, sorry. In this context a complex is a group of two or more molecules loosely bound together, and if one is antigenic that simply means that it can stimulate an immune response, particularly the formation of antibodies. Hope that helps.