To add on to my above post, and to recontextualize it in the wake of Covenant – I obviously now no longer see the pathogen as the distilled form of the capital-A Alien, but rather, it is the raw material in its creation. I don't know if the Engineers created the pathogen, or if they found it thousands of years ago, but either way it is an ancient and mysterious biological matter and, in their time with the pathogen, the Engineers seem to have experimented and discovered properties that lead to the birth of the Deacon and other similar creatures, which are what the Engineers have depicted in the LV-223 installation's mural. The process through which the pathogen infects and changes lifeforms seems to be randomized, unless guided by an outside force, but with several dominant, consistent traits that can be harnessed and shaped to yield a desired result (acid blood, the elongated head, the gestation period inside a living host, etc). David, through his own experimentation with the pathogen, created his own perfect organism with a more rigidly defined lifecycle, the Alien that we know from the original films, and in a sense became a god/creator in a way that transcends what the Engineers before him had managed to achieve in their own experimentation with the pathogen.
