What part of the scientific method would you have them invoke to start from the assertion that the natural world is very intelligent while crafting experiments?

What part of the scientific method would you have them invoke to start from the assertion that the natural world is very intelligent while crafting experiments? When I accidentally stepped on my dogs paw as a teen, the dog looked hurt and disappointed. The same dog barked at my sister when she tried to stick a pencil up his nose. Did the dog differentiate the scenarios based on intent or did it recognize my apologetic behaviour as non threatening? Or was it because my interactions with the dog were almost always positive while my sisters were not? Or simply because a pencil up the nose might have hurt a lot? Or because it was a hunting dog and we had hunted together multiple times? Was the dog actually disappointed in me or had they evolved to fake that by adjusting their eyebrows to this situation? Or did I project that emotion?