In learning chemistry at the entry level, many learners labor under misconceptions about the subject matter that are so fundamental that they are typically never addressed. A fundamental misconception in chemistry appears to arise from an adding of existing phenomenal concepts to newly-acquired chemical concepts, so that beginning learners think of chemical entities as themselves having the very same ‘macro’ properties that we observe through the senses. Those who teach or practice chemistry never acquire these misconceptions because they were able (...) to naturally pick up the nature of the subject to begin with. But as a result, they remain unaware of the foundational assumptions and understanding that they operate with and that many beginning learners persistently lack. Thus, a systematic picture of the workings of chemical theory as they relate to observable phenomena needs to be elucidated so that the attention of chemical educators is drawn to the fundamental understanding of the subject that they already possess and that beginning learners of chemistry lack, so that beginning learners can be given the opportunity to gain an understanding of how chemical explanations are in general related to observable phenomena. The ‘layered’ way in which chemical and physical entities are related to each other within chemical theory can also be clarified in this way. To afford this picture, the philosophical concepts of supervenience and emergence are explained and applied to chemistry, as philosophers of chemistry have already done. The result provides a model for teaching chemistry that, if consistently applied, has the potential to greatly enhance fundamental understanding of the subject matter. (shrink)