3) is interesting. In communication, there is a handshaking
  protocol, whether it is among humans or computers. Of course,
  handshaking protocols don't always (or usually) involve hands,
  so this should be familiar territory when dealing with aliens.
  There is a series of bootstrapping protocols that ensure a level
  of understanding is mutual. They might not have hands. Computers
  don't have hands either, so that's ok. But we didn't program the
  aliens with protocols. We're programmed with our protocols, like
  our computers are programmed with their protocols. Lacking
  knowledge of protocols for communication may make this task very
  difficult. Not impossible but difficult. There is no reason to
  assume good will nor is there any reason to assume hostile will.
  They may have access to emotions that we do not have on Earth.
  We might not have an equivalent to emotions that they have. They
  might not have an equivalent to emotions that we have. Emotions
  are first. Agreement needs to be established. Agreement on
  ANYTHING. That can be built upon from there. That is the
  beginnings of building a protocol. So, embedded in that act of
  attempting to establish a handshake process that allows for
  communication contains everything you need to know about human
  philosophy: the need to understand.