Can the history of life on earth be proven to be the result of any natural process?

I did. The physical differences between humans and chimps is due to the mutations that have accumulated in each lineage since we shared common ancestry.

Whether bipedality is an advantage or not is a much larger question. No difference between species is automatically assumed to be advantageous. As to bipedality, it does appear to be quite advantageous for modern humans who live in a savanna-like environment. The pelvis and lower girdle that we have is very good for moving about land, and pretty efficient at jobbing pace. For an ape species moving from an arboreal environment into a savanna environment, it is easy to see why a human-like pelvic girdle would be advantageous. Comparatively, chimps walk around on their two leggs like bow-legged cowboys. They aren’t good walkers or joggers, but their pelvic girdle is well suited for living amongst trees.

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Mammals didn’t evolve from fish. We evolved from reptile-like amniotes. Modern reptiles already have adaptations for separating the the oxygen rich and oxygen poor blood in the form of a three chambered heart with a restriction between the ventricles that prevents complete mixing. Amphibians don’t need a separation between the ventricles because they get about 30% of their oxygen by absorption across their wet skin, much like fish extract oxygen across gills. Some amphibians have no lungs at all and depend entirely on their skin for respiration.

You can also read here on the current research on the molecular basis of heart evolution:

Also, the tissues that make up the atria of the heart can be traced to tissues found in lungfish:

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