War is a big differ and a similarity is how we act as a result.
Within the span of a hundred years, in the seventeenth and early eighteenth centuries, a tide of emigration -one of the great folk wanderings of history-swept from Europe to America. This movement, impelled by powerful and diverse motivations, built a nation out of a wilderness and, by its nature, shaped the character and destiny of an uncharted continent.
The basic difference is that a confederation is basically an agreement among States. Whereas a federation is a union of the states under one central government. A confederation is pretty much a single house congress lead by a congressional president. There is no Executive or Legislative Branch. A federation involves setting up a complete single government with a complete Legislature, Judiciary and Executive separate from the individual States' governments.
It's most associated with John Locke, a 17th century English philosopher.
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The positive effects were that they were allowed to easily assimilate and become a part of the American society according to American traditions. They were given all rights that all other citizens of the United States had which meant that they could vote or purchase property or anything similar.
The negative effects are that in assimilating them they would often abandon their own culture in order to adapt so they were not included as so much as assimilated. The idea was not to make the two cultures co-exist, but rather have the Native Americans become like the everyday US citizens.