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The fact that there are exceptions to the rule means it cannot be proven by science. We cannot prove that the copper used at the recommend levels will kill all strains of CI. We cannot prove that a 72 day fallow period will eliminate all CI strains. We use the available science as the basis for these recommendations. Hence, decisions based on science but not proven by science. This is the key. We cannot prove the bacteria we add to our system or are in their food are the strains the fish need to boost their immune system. There is a scientific basis for trying to add these bacteria in an effort to boost the fish's immune system. So again, based on science, not proven by science. It doesn't matter if it is @atoll or @Paul B using live food and ocean muck to keep fish parasite resistant or myself or @4FordFamily using copper to treat fish prior to adding them to our systems. Any success or failures we have are completely anecdotal. There is science to support both methods. Neither method can be proven to work via science. There are too many variables each way.
Of course what you say above about 'proof' is true. Likewise, when people use the term 'scientific proof' they (as I was) usually are suggesting that the preponderance of evidence favors one method or another to explain an observation. In this case, I would humbly suggest that one side relies on a mixture of anecdotal stories to explain their success and the other side relies on established scientific protocols used by zoos and major national and international aquariums. Thats not to say that a person cant have success using either or even components of both methods.
To make it perfectly clear - I think its entirely possible for Paul, Atoll and others to run their aquariums and be successful. It is my opinion that feeding random live bacteria or constantly exposing their fish to parasites is not as important, as compared to providing good water conditions (stable at least) and excellent food is far more important. Unless the food contains a bacteria specific to the location from which the fish is from - and has been shown to be specifically beneficial to that fish. Additionally, the studies that show benefits to probiotics are using this as a supplement in specific numbers with specific bacteria. Thus, the use of Reef Frenzy, for example with probiotics (which I use) does seem to make good sense.
Interestingly, many of the studies on probiotics in fish suggest, as I did above that they are most effective if they are host-specific probiotic additions. Also - studies suggest that it is antagonism between bacterial species and even antibiotic properties of certain bacterial toxins that provides the benefit though some also show general increase in immune function.