Note
This method doesn't work in EEv6+ as the recipes were all removed.
End note
After 45 mins of tracing recipes, I settled on a roughly 23 step conversion process that can convert cobble into wood.
Basically it goes like this (I won't have access to the computer with the details again until later):
1) Cobble
2) Dirt
3) Sand
4) Glass
5) Ice
6) Lapis
7) *lots of changing dyes*
8) Cactus green
9) Saplings
10) Wood
From experimenting with that it seems that you should be able to navigate from cobble to any other item on the EE crafting tree by using dyes as a go-between. =)
edit
After further perusing recipes, here's the shortest version so far:
1) Cobble
2) Dirt
3) Sand
4) Glass
5) Ice
6) Lapis
7) *lots of changing dyes*
8) Cocoa beans
9) Wood
"Equivalent Exchange"
in the question title I started looking for a fullmetal-alchemist tag.