Interfering with nature

In Lives of the Trees: An Uncommon History, next after almond is apple.  According to the book:

The Jewish religion forbade it, but the Christian church encouraged grafting because it symbolized attaching new members of the church onto the Tree of Christ.  Meddling with God's design by hybridization though was the subject of theological debate in Britain until almost the  nineteenth century....Johnny Appleseed...thought grafting "cruel" to the trees and collected leftover seeds from cider presses.

Now, the debate is over genetic engineering.  It seems to be an eternal question -- how much should we mess with nature?

Gardening is messing with nature  -- we encourage certain plants to grow, while uprooting others.  And if we weren't gardening, hunting and gathering also interferes with nature, by taking the life of animals, or taking parts of plants.

It seems every generation finds new ways to make life easier for humans, but at the same time, there are always people who object, saying nature should not be interfered with.  In time, the new ways become old ways.  We become accustomed to gardening, then to grafting.  We no longer object to those, but when someone comes up with a new way of interfering with nature, we are not comfortable with it.

How do we know what is right? How do we know where to draw the line?  It seems to me there isn't some moral law which for example says you can hybridize but not genetically engineer.  It seems to me that all life forms evolve toward preserving their species.  How do we preserve our species? By not only heaping the people alive today with wealth, but by preserving our health and habitat for generations to come.