How does the cell theory describe the levels of organization of living organisms

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It took over 200 years for the "cell theory" to be formalized and accepted. Hooke and Leeuwenhoek were early microscopist's but at the time the nature of matter, the belief in spontaneous generation, and the idea there were little worlds within little worlds ad infinitinum was popular. The discovery of the periodic table and establishment that atoms were real, the demolishing of spontaneous generation, all happened at the time that Schwann and Schleiden (and others) were working with better microscopes, better ideas about the material world, and better observations thus the cell theory.

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