How can observable nature explain the atomic theory to describe matter

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The challenge with chemistry, the atomic theory has limited direct application in nature or how we define nature. Is there a good example to make this connection for a five year old?

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All of nature boils down to atoms, at some point. Trees use water to carry nutrients. Those nutrients dissolve due to intermolecular forces, that water climbs the tree due to intermolecular forces. The nutrients are divvied up and turned into cellular machinery made of complex atomic chains.

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