Chapter 40 is essentially a long, drawn-out series of scenes continuously depicting Jones throughout the ages, getting progressively longer and longer, without actually explaining what Jones is, culminating with Jones being present at the formation of the planet. At the end, Jones finally tells Annie that she doesn't even know what she is, with Tom's comment being, well....
What Could Have Been: According to Tom's Formspring, Zimmy (a.k.a. Zeta) and Gamma were originally to star in a comic idea known as Alphabet Soup (hence their names). It was also mentioned that Zimmy was around before even that and used to look quite different. Also, Tom considered naming Annie Imogen before his idea for Gunnerkrigg Court consolidated in his mind.
He's mentioned later on that he might still want to do the comic about Zimmy and Gamma as a spin-off prequel of Gunnerkrigg Court, some day.
Word of God: Tom Siddell frequently posts on the forum or Shout Box to clear up confusion or give background info. There's an article in the GC Wiki for an index of such information. He also has a Formspring account where he answers questions about the story, and a Twitter account. Somebody built a handy search engine of the 3000+ questions he answered, which can be found here.