Please be warned that at some stage in this I'm going to descend into alphabetic analysis, which should not be taken too seriously. It's a way to get at ideas more directly, but the ideas are the goal and the alphabet is just a rather odd means to get there.
Also, please note that it's late, and I'm really not thinking in English at the moment, so the following may be really incomprehensible at times, and is probably not of interest to anyone who doesn't do these things for fun. So be warned!
From the book: Zetter points out some analyses of the first sentence of Genesis, "Bereshit bara Elohim et hashamaim ve'et ha'aretz." (The usual translation of this is "in the beginning, God created the heavens and the earth," but the following is going to rely very heavily on precise translations) There are several things discussed. (1) Why does it begin with bet, the second letter of the alphabet, and not aleph? Consider the odd inversion of subject-verb order, "bara Elohim" instead of "Elohim bara." It would seem that Elohim is the object rather than the subject here. Elohim, however, is the name of God used to refer either to the Sephira of Binah, or to the Sephirot in general. The subject of this verb is thus the implicit subject, referring to the absolute and unwriteable name of God, which is representable by the letter aleph, and the sentence can be parsed, "(aleph) in the beginning created Elohim, the heavens and the earth." (2) The word "bereshit" can be parsed in a few ways as well, since "rosh" means "head" [and thus beginning, as in the head of a river] and so it may also be parsed as "by means of wisdom" or "by means of chochma" (3) The syntactic particle "et" (in Hebrew denoting a direct object when the word has the definite article "ha") isn't just a syntactic particle. It is spelled aleph taf, the first and last letters of the alphabet, and thus stands for everything in between. Thus "(aleph) in the beginning created Elohim, the alphabet of the heavens and the alphabet of the earth," or alternately "(aleph; keter) by means of (wisdom; chochma) created Elohim (binah), the alphabet of the heavens, and the alphabet of the earth."
Now, some generally related thoughts which follow. First of all, the word "water" appears very frequently in the first few lines. In the second line, "Ve ha'aretz haita tohu vavohu vekhoshech al-pne'i tehom veruach elohim merakhephet al-pne'i hama'im" (ending with "and the spirit of god was passing over the waters"), then the second day specifying the separation of the waters into the sky and the sea, and the third day separating the waters from one another. The waters are, in a sense, the primordial matter of creation. They flow and are divided, are separated, and form the contents of the universe. The "waters" are thus the emanations which enter into the lower Sephirot; the "aretz" (land) is the cup (the shells) into which it can flow.
How does this relate to the first line of Genesis? Consider the word "shama'im," used for "heavens." This is a compound word, "sham + ma'im" - "there water." (The word has immediate kin in other very early Semitic languages as well. Compare the word for sun, "shemesh" = "sham + esh" - "there fire." Literal-minded, no? And don't forget, so long as we're talking on a very literal level, that sky and sea don't even get differentiated until the second day. If you've ever watched a sunset over the Mediterranean, it should be clear why the boundary is a bit iffy) So the heavens are the place of the initial waters; that is, it is the initial cup full of the light of the ein soph or before it is poured into each of the emanations. Thus "(aleph) by means of (chochma) created (binah), the waters of the ein soph or, and the containers which would hold them."
So far, pretty standard. However, I'm noticing something which appears to be missing. In "shemesh," no letters are lost; but in contracting "sham ma'im," an extra mem (m) vanishes. What does this mem mean? I'm not actually certain. I suspect at least one meaning refers simply to "secret;" the shape of the letter is the shape of a closed mouth; but there is probably something much more to the point which is concealed within or extracted from the initial waters. I do have a suspicion about where it comes out at the end - in the word "emet," truth. This word is spelled "aleph mem taf." That is, it contains the entire alphabet (aleph taf) but in the center it has something more than that, perhaps the discriminant capacity which tells truth from falsehood, or otherwise partitions reality?
(Edit: OK, I was obviously half-asleep while writing this. "Shemesh" drops an aleph in the middle; I'll have to think about the significance of that later.)
Another hint on this might be the unusual frequency of the word "col" (all) in the sixth day, specifically after the creation of adam. (Every herb, every creature, etc) This word is spelled "caph lamed," and these two letters are the precise middle of the alphabet. (If you were to write out the alphabet, it would balance on the point between these two letters) So these two, in a sense, also stand for the entire alphabet, but differently. Caph implicitly stands for all the ten letters before it - aleph through yod, which represent the ten sephirot, and thus the process of creation up to this point. Lamed implicitly stands for all the ten letters after it - mem through taph, which therefore stands for all the actions which will be done in the universe from the moment of creation up to the ending. The word "col" therefore is the bridge between these two, meaning "All things which have been created and all the things which they shall do;" it is the bridge between creation and the institution of action into the world.
The letter mem, therefore, is the first letter after "col," and thus the first independent action within the world. What is this action? We are told that it is when adam eats the fruit of the tree of knowledge, thus completing the transition of adam out of the garden and into the world, moving out of yesod (the house of the sixth day, and the last sephira of the conceptual world) into malkhut (the house of the seventh day and beyond, the sephira of Assiyah, the physical world). This first action is the acquisition of the facility of discernment, and thus the letter mem symbolizes that. The word "emet" can thus be read as follows: The set of all things, separated by the discerning faculty which is the signal of conscious entry into the world.
So I would interpret the missing letter in "shama'im" as follows: The heavens (the light of the lower emanations) are created, but (aleph) conceals a part of them, which is the "ignition;" the impetus to action, which is the conscious, discerning facility. The world is created through all of the sephirot but it remains in stasis; we have the aleph-taf but the mem remains hidden until afterwards, when (by eating from the tree of knowledge) the world is brought into action, and the second part of "col" can commence.
(Edit #2: And "mem" is also the shape of a mouth about to open or to speak.)
