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The Fringe symbols are used, before each commercial break point, and before the end of the show to spell out a 5-8 letter word in each episode. Here is the key to that cypher. Thanks to Ars Technica for the solution, from the first 14 episodes.

Decoder
A	B	C	D	E	F
					speculated
G	H	I	J	K	L
			speculated
M	N	O	P	Q	R
				speculated
S	T		U	V
W		X	Y		Z
		speculated			speculated

[edit] Cyphered words in each episode

[edit] Season 1

[edit] E01 Pilot: "OBSERVER"

[edit] E02 The Same Old Story: "CHILD"

[edit] E03 The Ghost Network: "AEGER"

[edit] E04 The Arrival: "ROGUE"

[edit] E05 Power Hungry: "SURGE"

[edit] E06 The Cure: "CELLS"

[edit] E07 In Which We Meet Mr. Jones: "CODES"

[edit] E08 The Equation: "TAKEN"

[edit] E08 The Dreamscape: "VOICE"

[edit] E10 Safe: "TRADE"

[edit] E11 Bound: "SAVED"

[edit] E12 The No-Brainer: "BISHOP"

[edit] E13 The Transformation: "AVIAN"

[edit] E14 Ability: "OLIVIA"

[edit] E15 Inner Child: "WALTER"

[edit] E16 Unleashed: "PETER"

[edit] E17 Bad Dreams: "BELLY"

[edit] E18 Midnight: "EIGHT"

[edit] E19 The Road Not Taken: "VISION"

[edit] E20 There's More Than One of Everything: "GRAVE"

[edit] Season 2

[edit] E01 A New Day In The Old Town: "TOWER"

[edit] E02 Night Of Desirable Objects: "MIRROR"

[edit] E03 Fracture: "BURIAL"

[edit] E04 Momentum Deferred: "MEMORY"

[edit] E05 Dream Logic: "BETRAY"

[edit] E06 Earthling: "DEJAVU"

[edit] E07 Of Human Action: "ARRIVE"

[edit] E08 August: "BLIGHT"

[edit] E09 Snakehead: "HIDDEN"

[edit] E10 Grey Matters: "PORTAL"

[edit] Images

[edit] A

[edit] B

[edit] C

[edit] D

[edit] E

[edit] F

As yet unseen!

A guess about what it might be.

[edit] G

[edit] H

[edit] I

[edit] J

Has not appeared yet.

A guess about what it might be.

[edit] K

[edit] L

[edit] M

[edit] N

[edit] O

[edit] P

[edit] Q

Wonder how we'll get this rarest of letters.

A guess about what it might be.

[edit] R

[edit] S

[edit] T

[edit] U

[edit] V

[edit] W

[edit] X

They haven't used this one yet.

A guess about what it might be.

[edit] Y

[edit] Z

We'll get Z eventually, I am sure.

A guess about what it might be.