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The mathematics-only reality model would have one believe that the entire history of organic life—including the transformation of the early atmosphere to the current atmosphere, and the active ongoing maintenance of the current atmosphere in a state of disequilibrium—was accomplished in its entirety by common particles jostled about by random events.
Intelligent processes are too complicated to be explained by mathematical equations. Therefore, the mathematics-only reality model denies that there is any intelligence at the deepest level of the universe. By a process of elimination, the mathematics-only reality model has only common particles and random events with which to explain all the many innovations during the history of organic life.
 The oldest known organic life is bacteria. The fossil record shows that bacteria first appeared at least 3½ billion years ago. Since then, organic life has radically altered the atmosphere. For example, the removal of carbon dioxide from the atmosphere probably started with the first appearance of bacteria; and all the oxygen in the atmosphere originated from photosynthesis, an organic process.
The assertion that organic life actively maintains the atmosphere to suit its own needs, is known as the Gaia Hypothesis. The Gaia Hypothesis was developed by atmospherics scientist James Lovelock. While working as a NASA consultant during the 1960s, Lovelock noticed that Venus and Mars—the two nearest planets whose orbits bracket the Earth—both have atmospheres that are mostly carbon dioxide. As a means to explain the comparatively anomalous Earth atmosphere, he formulated the Gaia Hypothesis (Margulis, Lynn, and Gregory Hinkle. “The Biota and Gaia: 150 Years of Support for Environmental Sciences.” In Scientists on Gaia, Stephen Schneider and Penelope Boston, eds. MIT press, Cambridge, 1993).
The current atmosphere of the Earth is not self-sustaining. It is not an equilibrium atmosphere that would persist if organic life on the Earth disappeared. Instead, the atmosphere is mostly a product of life, and is actively maintained in its present condition by life. The composition of the atmosphere by volume is roughly 78% nitrogen, 21% oxygen, 1% argon, and 0.03% carbon dioxide. Other gases are present in smaller amounts. As Lovelock states in his book Gaia, if life on Earth were eliminated, the oxygen would slowly leave the atmosphere by such routes as reacting with the nitrogen. After a million years or so, the Earth would have its equilibrium atmosphere: The argon would remain, and there would be more carbon dioxide. But the oxygen would be gone, along with much of the nitrogen (Lovelock, James. Gaia. Oxford University Press, Oxford, 1982. pp. 44–46). However, instead of moving to this equilibrium state, the atmosphere is maintained in disequilibrium by the coordinated activities of the biosphere.
One of the more interesting examples of control over the atmosphere by organic life is the production of ammonia. The presence of ammonia in the atmosphere counteracts the acids produced by the oxidation of nitrogen and sulfur. Lovelock estimated that without ammonia production by the biosphere, rainwater would be as acid as vinegar (Ibid., pp. 68, 77). Instead, there is just enough ammonia produced to counteract the acids and keep the rainwater close to neutral. Besides ammonia production, there are many other Gaian processes (Shearer, Walter. “A Selection of Biogenic Influences Relevant to the Gaia Hypothesis.” In Scientists on Gaia, op. cit.).