I will explain our mission Log by showing it in Level 2, the ugly labs I posted screenshots from. When you enter the level, your previous log is cleaned (achievements and learnt skills prevail that) and you are presented with the Log and the general mission goals:
Note the char descriptions. On the left side, you have the self-description from Pete playing the PI as cautious tinker and investigator, on the right page you read Pete describing himself as tough soldier.
Below you have the general mission goal for the level. Left (blue) it`s all about gathering information and background reseach, right (red) it`s about getting biosamples from creatures that won`t donate voluntary.
If you play on and examine certain objects and areas, the mission log gets updated. A message appears on the screen.
This message is semitransparent and disappears quickly, so you won`t be prevented from fighting your foes. However, here the Log Update would most likely be "Got killed today."
You collect hints for Adventure style gameplay on the left side in blue, hints for the soldier in you on the right in red. You can follow both pathes quite some time, then your log looks like that:
However, at some point during each of the levels you will have to take FINAL decisions. Decisions like with whom of the rivaling parties in this secret war you tumbled into you will ally up and whom you will fight (however, this is coming much later in the game). Decisions like "Will I try to flood the whole area to swim to the roof or will I take the elevator downstairs?"
And so on. After that final decision your log looks like that:
For me it`s also important to note that the game gives you only hints what you could do and what would come in handy, but it`s never telling you exactely what to do. You shall think on your own!