The episode of Fringe “Nothing As It Seems” explores the consequence of having Peter and Olivia with memories from their timeline now poised to deal with cases which parallel ones that, for them, had already happened. While the differences between the timelines result in not all details being the same, the similarities allow for them to address the cases with an element of what could be considered precognition. It also gives them, and us as viewers, the opportunity to see a little deeper into what is going on, and what those behind it (including David Robert Jones) are trying to accomplish.
The aim is one that was summed up in another episode this season as making “a better human being” and which in this episode is described as “the guided evolution of man.” What they are guiding evolution towards seems like it is monstrous – who in their right mind wishes to become a flying porcupine? Then again, if the options were become what seem to us monsters or become extinct, we might well choose the former, and it may be that David Robert Jones and his followers view those as their only two options.
Religious references abound in the episode. The porcupine is mentioned as evidence that God has a sense of humor. The mention of cuneiform and Sumerian leads to discussion of new generations of gods overthrowing the previous in that culture’s mythology, as well as to a serpent god in Mayan mythology.
The woman in a couple that is part of the cult trying to improve their humanity through viruses that alter their genes and thereby their nature talks about them being “special…like Adam and Eve.”
There is also reference to human beings having a “God complex” and to the alternatives that either human dominance is an accident or it is an indication of some sort of divine plan.