Scientist discovers new thermodynamic theory for origin of life.

[eppur_se_muova]

3. What can you possibly mean by "contradiction" ?? There is none there, even if you choose to see one.

The whole explanation is in this line in the OP:

Although entropy must increase over time in an isolated or “closed” system, an “open” system can keep its entropy low — that is, divide energy unevenly among its atoms — by greatly increasing the entropy of its surroundings.

This provides pretty much the basic definition of life -- living systems are those that systematically function as entropy "refrigators", pumping entropy out of their own systems into their environment. Nothings forbids such a system in principle, so why shouldn't it happen ? Once such a system gets going, it's in its very nature to continue/propagate.

Anyone who thinks life is in contradiction with thermodynamics doesn't understand even basic thermodynamics. You have to read the entirety of the Third Law -- it applies to closed systems, and places no direct restrictions on open systems. Living organisms -- and the whole planet -- are open systems, so do not contradict the Third Law. No contradiction, no big mystery. Yes, life is amazing, but not magical.