How do you square the second law of thermodynamics and entropy with patterns and principles we see in nature?
I'm not saying living biological systems can't or don't swim against this tide,as clearly they do.
They are well squared. From the top hit of a google search:
"the spontaneous formation of millions of far more complex compounds than their elements is energetically favored by the second law. This is true whether the new molecule is more or less complicated than its starting materials because the second law is concerned only with energy. All other requirements or consequences are not within the purview of the law."
I'm not an expert on Thermodynamics, so I could be wrong. It was a random website. But it meshes with what I've read before. The second law is in regards to energy. I wonder why you think there would be a law of physics that runs contrary to the rest of scientific understanding? A whimsical oversight? A few intelligent men being dumb?
I don't see how a universal principle of simple to complex can be maintained in the light of this law of nature.
I've thought before that it's more of a bell curve. During the start of the universe, when the simplest of subatomic particles existed, is one of the lowest points on the bell curve. Complexity increases as time goes on. Gravity causes matter to coalesce, leading to stars and fusion, which creates more complex elements. The elements combine to form molecules, and molecules form more complex molecules. Water forms into snowflakes, other elements into crystals. Proteins into proto-life forms. The proto-life forms grow more complex, leading to life. Simple life to complex life. We're still on the upslope of the bell curve.
But in billions of years, our complex entropy-defying bubble will run out of energy to fuel complexity(the sun), and the downslope will be fast. Like climbing a cliff only to jump off. In the end, entropy will win, even if it is defied in local areas for long stretches of time due to local stars. The heat death cometh.
http://www.kortexplores.com/node/76