Gene,
I hadn't read about DNA coordination until you mentioned it, so I looked it up and it appears to me that yes, something more fundamental is occurring. If DNA replication and recombination is controlled, as you mentioned by neurotransmitters and hormones, then it must be a very complicated process. But in order to maintain genome stability and thus avoid mutation and disease it has to be extremely precise and accurate. Also, as you said memory is distributed which further complicates coordination. And more complicated usually means more chance for error, so there would have to be controls to monitor the process, and more controls to monitor the controls, etc. That sounds like a poorly run government, not a natural process.
Instead, what my model may be suggesting is that coordination among cells is a not something that is controlled from the outside of the cells themselves; it happens because every DNA molecule contains within it the exact (to the nth degree) same information so it already "knows" what every other cell in the body "knows". You said, "when the image is working correctly each cell knows where it is and what its function is" but I say, it does not require an image; it already knows because it already has the information. Communication among cells, on the other hand, is what you are referring to when you asked "whether the image in the brain is the response of cells that use this [wave] function." I wouldn't refer to an image, but rather to binary communication. For that, your model sounds good to me. I'll explain why.
You state that the equation (in Feynman #9.51 on pg 9-13) is "The wave function for any system that has an internal freedom that varies back and forth between two frequency (f) values". I am not sure that I would word it that way since I understand, from reading the chapter, that Feynman was describing the probability of an ammonia molecule being in one state or the other when subjected to a time-varying electric field, whose frequency is given by f (and f0 is the resonance frequency of ammonia molecule). So let me see if I understand how you have applied this to describe the eye's response to light. Are you saying that an image, projected onto the retina, contains various frequencies of light, which will stimulate the cells of the retina in such a way that is determined by the quantum state of the molecules within the cells? If so, that sounds reasonable to me.
Changing the state of molecules that have two possible states, such as is the case of ammonia, sounds like a great way to generate binary code. Rather than "focus the image," I would say the function of neurotransmitters is to transmit the binary code. So yes, I would agree that, in a sense, what we describe as "the image in the brain" is actually the response of the cells as opposed to an actual image (i.e. you couldn't see an image if you looked at the cell with a good microscope).
You said, "I think it is also correct to use equations where distance has been 'reduced in rank' to one distance as long as we do the same thing for time." I have no problem with that, except that it seems to imply some operation of "reducing" distance or time. I prefer to think of distance as fundamentally being a single unified dimension, like the radius of a circle. Thinking in terms of three dimensions is a good tool for analysis, and in my opinion, it seems natural because of the transformation process that I referred to in my essay: the same process that separates motion (unified) into our perception of movement through space and time (as if motion, space and time were three different concepts). It is a perpetual three-step process of [I] separation-recognition-return [/I] that is created by and creates apparent opposites. Let me explain this.
There are two ways of referring to opposites: 1) negative and 2) inverse. I can choose a distance in any direction. Specifying a negative of this direction creates a conceptual separation (the first part of the process). [I] Recognizing [/I] that the two opposite directions are both part of a single dimension is the second part of the process. We then identify a reference, which we call the origin x=0 (although it is an illusion since there is no such thing as zero space). Reuniting the positive and negative at the origin is the third part of the process. The entire process is thus [I] separation-recognition-return. [/I]
We repeat the process by separating the first (x) dimension into a second (y, using the inverse (y=1/x)), which is also assigned a positive and negative, then recognizing the same origin and reuniting the two dimensions, creating a plane. The inverse creates the illusion of dependent and independent variables, which is also an illusion because there is no y-axis, independent of the x-axis. We think there is because we can move North or South, for example, without changing our East-West coordinate (which are, of course made up for our information).
These two conceptual dimensions (pairs of opposites) are then used to create (or perceive of) the third dimension that is perpendicular to and thus independent of the other two. This third dimension is important because it provides elevation - a higher perspective that transcends both pairs of opposites. It allows us to look down on the opposites, to see the unity and re-cognize reality as a unified field.
My hypothesis needs a lot of work, but that is how I relate it to the expansion of awareness and DNA replication. Awareness grows as we gain information and we experience mini-revelations when the pieces come together. (Ah ha!) Even if we fail to recognize the unity, the process continues, creating more separations and increasing complexity until there is enough information to cause the reunion. DNA replication happens as a reunion but only after the strands separate and each base recognizes its "opposite" and reunites with it. Information only requires two binary bits, but since there are two types of opposites (negative and inverse) there are four bits available (just as there are four bases in the DNA molecule).