2nd Law of Thermodynamics Doesn't Prohibit a Decrease of Entropy

This article starts from a completely wrong premise: a beneficial mutation is not a decrease of entropy in a closed system. There's no closed system involved.

Organisms are not thermodynamically closed, because they take in both material and some sort of free energy (whether together in the form of food, or separately as in water, air, sunlight, etc), and also emit both waste heat and waste material. Organisms don't even have any (nontrivial) closed subsystems.

Most of the interesting things organisms do -- grow, reproduce, evolve progressively, maintain their states -- run counter to the general thermodynamic tendency for systems to approach equilibrium. This does not violate the second law of thermodynamics because organisms' inputs have lower entropy (and higher free energy) than their outputs. As long as there's more entropy leaving than coming in, internal entropy decrease is allowed by the second law (up to the difference between influx and efflux).

(Actually, I'm cheating a little bit here. Entropy is a property of things, not a thing itself, so talking about it entering or leaving isn't really right. But it acts like a thing, and entropy flux is (usually) well-defined and acts as you'd expect flow of a physical thing to work.)

(BTW, there's a bit of inconsistent terminology here. Physicists call systems that don't exchange either energy or matter with their surroundings "closed". Chemists call those systems "isolated", and use "closed" for systems that exchange energy but not matter. Which physicists call "open". Yeesh. Anyway, this version of the second law applies to physicist-closed/chemist-isloated systems. Organisms exchange both energy and matter, so they're "open" in either terminology.)