Hi doma,
they put fluoride in water because they think it is helpful for teeth.
they put thiomersal in vaccines as a preservative, and this turns into ethyl mercury in the body. far as i know, it has no ill effects.
"The MMR vaccine controversy was a case of scientific misconduct which triggered a health scare. It followed the publication in 1998 of a paper in the medical journal The Lancet which presented apparent evidence that autism spectrum disorders could be caused by the MMR vaccine, an immunization against measles, mumps and rubella.[1]
Investigations by Sunday Times journalist Brian Deer revealed that the lead author of the article, Andrew Wakefield, had multiple undeclared conflicts of interest,[2][3] had manipulated evidence,[4] and had broken other ethical codes. The Lancet paper was partially retracted in 2004 and fully retracted in 2010, and Wakefield was found guilty by the General Medical Council of serious professional misconduct in May 2010 and was struck off the Medical Register, meaning he could no longer practice as a doctor.[5] The research was declared fraudulent in 2011 by the BMJ.[6] The scientific consensus is that no evidence links the vaccine to the development of autism and that the vaccine's benefits greatly outweigh its risks."
http://en.wikipedia.org/wiki/MMR_vaccine_controversy
but as i said, i am sure we do ingest, breathe and touch stuff which is harmful to us. a different explanation for this: until we have been somehow exposed, we don't necessarily know what we are doing wrong.
"Why do humans have 10 times more single gene mutations than primates..." - same answer as previously given: "our population is rather larger than that of other primates and we live in many different kinds of environment, so one would expect more challenges and more variations."
"why did evolution decide it would be good for the human immune system to no longer develop a response to cancer,malaria or AIDS....." - evolution is a process and the temporary state of a population is its result. what do you mean when you say "evolution decide[s]?"
nature is your example of a benevolent system? have you never heard of the caterpillar and the ichneumon wasp, or the carpenter ant and the ophiocordyceps unilateralis fungus? nature leads to lives which are nasty, brutish and short. whereas the average human leads a longer life than he did at any time in history.