Both prokaryotic and eukaryotic cells share the basic mechanisms of secretory protein synthesis. However, unlike prokaryotes, eukaryotic cells posses a system of compartments, the so-called endomembrane system, which are involved in the synthesis process. A comparison of the prokaryotic and eukaryotic protein synthesis processes and particularly the observation of the functional and structural similarity between the prokaryotic cell membrane (the interface to the cell exterior) and the membrane of the eukaryotic endoplasmic reticulum (one of the compartments within the endomembrane system) inspire a description that refers to either the eukaryotic endoplasmic reticulum or its membrane or the endomembrane system altogether as a representation of the extracellular medium. However, unless the terms in such a statement are carefully analysed and refined the description would be just a colloquial usage of the concept of “representation” rather than a biosemiotic statement. Another problem associated with employing the concept of “representation” in a biosemiotic context is due to the fact that it may evoke the impression of a conscious mind as the “owner” of the representation. In this paper theories about the emergence of the eukaryotic endomembrane system, as well as its functionality within secretory protein synthesis will be analysed in order to specify in what sense the concept of “representation” can be employed in this context without implying consciousness. Such a study is expected not only to provide an insight into the conditions and assumptions under which this concept can be used for lower level biological processes but also to shed some light on how representations emerge in general.