No doubt true, and nothing in the article that Mitchel posted actually challenges HIV as the cause of AIDS. Researchers have been trying to pin down the detailed mechanisms of how the virus produces the disease, just as cancer researchers are still figuring out the exact mechanisms that cause cells to go awry, reproduce uncontrollably, and spread to other tissues. But no one questions that cancer does not exist or that it is not due to cell proliferation.
HIV is hard to pin down because it is a virus that specifically attacks the immune system. Mitchel posts these long articles but he would be hard put to either understand or defend the science behind these issues. So he simply posts longer and longer ones.
When he is ready to do what he agreed to, I shall be ready as well.
An alternative (and simpler) explanation is that the models are wrong because
ordinary differential equations do not capture the nature of HIV infection.
This could be due to a number of factors, not the least of which is the
'continuous' nature of the models, in contrast to the stochastic nature of
biological events. There could be missing (or wrong) parameters, missing (or
wrong) equations, etc. For example, the fact that HIV interacts with many
different cells in many different tissues is not accounted for by these
models. Many such objections could (and should) be raised against any
positive interpretation of the predictions of the models.