I'll do my best..

1. A hatchery fish is any fish that has spent any part of it's life in a hatchery. In other words any fish that is not the result of two fish coming back and spawning in the wild on their own.
Including straight hatchery fish, hatchbox or captivly reared.

"" The reason I ask is because to me, hatchery-raised fish are those that are raised to something larger that fry-size, i.e., pen-fed fish in rearing ponds. I don't regard hatching eggs and planting fry as hatchery-raised. To me all that constitutes is giving the brood stock a better chance at reproducing. Does that weaken a fish? How does it damage anything to plant fry in the water systems? It would seem to me that if the dispersal of fry is well planned and spread out, and that if hatchery-borne diseases are closely monitored, that the numbers of wild fish could be greatly and quickly increased, and at a much lower cost. I have heard and read about egg -hatching protective cages buried in selected spots designed to do the same thing. How are these working out?"""

Several issues here: The reason hatcheries went to releasing fish as smolts is because of the extremely poor survival of fry releases. Hatchbox type programs as you are eluding to have been widely used and mostly abandoned because of their ineffectiveness. On tributarys of the Alsea hatchboxes failed to increase the number of returning adults and in most cases streams returned fewer than streams that were unplanted. Thoes streams that were planted showed great declines in the natural productivity of the exsisting wild run. In the North fork lewis net pen raised salmon and steelhead have added to the sport fisher but do nothing for the health of the wild stocks in the system and draw attention away from protecting and restoring important habitat.

""Here's a compromised-gene-pool question. Have there been studies done to determine which
genes are dominate and which are recessive (or is it regressive?) in fish? I don't know the
answer to this, but it seems to me that the dominate genes would be the ones associated with all of the necessary survival characteristics, and will nearly always predominate in a mix of "hatchery and wild" fish. Like a blue-eye, brown-eye cross nearly always produces a brown
eye.""

Excellent question.. I am not aware of such research but that doesn't mean anything. I am not a genetisist or even a biologist only somoene who is read up on the issue. It's not that hatchery fish have different genes it's that they have different amounts of certain genetic traits. As an example when spawned and raised in a hatchery Deschutes river wild steelhead survived very poorly in the hatchery enviroment, they lacked the genetic charecteristics to survive in a concrete holding tank, while even first generation hatchery fish showed the same poor survival when in the natural enviroment.. In short fish that are gentically more adapted to concrete holding ponds do poorly once released because they lack the diversity in their genes for such survival. If i was a scientist i am sure i could explain this better but maybe this analogy will work. Say we go to a football game together and it's snowing we are both wearing jeans shirts boots and jackets. Your jacket and boots are heavily insulated and mine are not. You are comfortable through the game and I am freezing. I am not freezing because i don't have boots and a jacket but because they are not proper for the situation.
The problem here grows exponentially with additional generations in the hatchery system. Each generation the fish that survive become more and more homogonized and genetic diversity ( ability to survive in diverse situations) is lost as a result because the fish don't need thoes genetic chareceristics to survive in the wild. The ones that do have some wild survival genetics die off because they do not have the genetic make up to survive in a concrete tank..


""Is there documented evidence of damage to wild fish populations by hatchery-raised fish? I
have heard an awful lot of selective and subjective theology (whatever happened to science
objectivity? ""

YES ther is a ton of science and study on the effects of wild fish on natural populations:
and here it is in bite sized pieces
http://home.teleport.com/~salmo/docs/Biblio/bib.htm


""I am not impressed with the uprooted spawn theory or the too many fish in a
river theory, as there are numerous rivers in Alaska that have so many fish in them every year
that the eddys are filled with uprooted spawn.""
I agree 100%

"" I'm guessing that if the fish-demand for food exceeds the river's capability to
provide, then some of the fry die off and provide food for the remaining fry?""
I dunno..

The DNA thing can no longer be argued as well, since both wild and hatchery fish can not be shown to be genetically different. (Who the Hell is responsible for lending credibility to that creative science?

Untrue. Biologists can and do tell the difference between wild and hatchery fish. Not only that but they can tell how much genetic interaction there has been. For example through genetic testing they know that planting chambers creek for XX? years in north puget sound has done very little if anything to the genetic integrity of wild steelhead in thoes streams but in the south sound area such is not the case , chambers creek hatchery steelhead have greatly influenced the genetics of wild steelhead in the south sound and hood canal streams.
The same tests conducted on the Oly Penn rivers shows that though there was some introgression when plants were first started the genetic's of the chambers creek fish have not increased in naturally spawning populations. On the Washougal ( a lower columbia tributary) The genetics of fish in the lower river has greatly been influenced by chambers creek steelhead plants but winter steelhead in the uppper reaches show very little influence of the chambers creek fish. So you see the Bio's can and do tell the difference between wild and hatchery steelhead. if they can tell one from the other through genetic testing then that means that they are genetically different.

""To all of the problems exposed in the answers of the above questions, how difficult would they be to mitigate?""

I don't know. It's never been attempted... WDFW is content to continue the mass planting of chambers creek winter runs andSkamania summer runs throughout the state with little regard for the consequences. ( note) This is not a problem with local biologists it's a problem of the agency's management priorities and managment personel.
I would imagine some of these problems could be dealt with through better managment of the hatcheries. but i don't know enough about it to say what would be good to do..

""It is my hope that with the answers to these questions, that I become more knowledgeable, so please don't try to snow me with half-truths.""

I personally have no political agenda. My only desire is for there to be lots of wild steelhead in all of our rivers so we all can go fish for them. Consequently I want what is good for wild fish. I simply take what the bio's tell us in their studies and apply it to my goals of having more wild fish and form my opinions about what we should do. I am not out to decieve anyone because that would be anti productive towards my goals.. Hmm maybe that meand i do have an agenda. Oh well.. believe me if the scientists were saying hatcheries were the way to have healthy runs of wild fish I'd be all for them. Unfortunatly the problems we are facing are too complex for such a simple answer..
The truth is we need first to protect wild fish habitat ans secondly to not harvest wild fish..