That's an interesting question, warhound. ( Welcome to the forum by the way.

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I'd not really given the moral implications any thought, mostly because I think as you point out they are absent from Shantaram(?). Well, as far as I can recall, there is no connection between the theory of complexity and any moral issues.
I'm no philosopher, so my best guess would be that the actions that promote complexity are inherently good morally? I.e War is divisive, drugs/prostitution is exploitative and isolating, hence they do not lead to greater complexity/harmony. That's sounds a bit flakey at best, but I'll give it some more thought.
It does appear though that the theory itself is the basis on which judgement is made, in effect the complexity is all that is good. That makes it quite difficult to analyse, because it is not a system of thought but a two point reference system. Not much wiggle room.
Now, as I said I'm no philosopher, so there could be other implications.
Perhaps other members might have an idea how the complexity theory relates to the moral issues in Shantaram?
Certainly there are some serious points that need consideration, as Khader himself was involved with War, and ultimately sanctioned murder to support his own means. How indeed are those actions explained within his own philosophical system? Interesting..
