Monday, April 18, 2016

Synchronicity and transcription in development

I awoke for the final time at 0839 Monday April 18, 2016 with the remnants of a vivid dream still in my consciousness:

I was seated in a waiting room with many connected chairs. It apparently was a large hospital waiting room. A man was seated next to me. He was approximately of Cheri's [Cheri is my late wife] older brother D___'s body proportions and I had the impression he was wearing black plastic glasses. I had the thought later that this could have been her second husband, the father of her two daughters, although I had never met that individual. I think I asked where Cheri was and the D___ person told me that she was in "proline" (I seemed to hear it pronounced proe-lee-in with the accent on the first syllable, but this may have been a waking interpretation of the characters that appeared clearly in the dream in my mind). He added that "only loved ones were permitted into that area to see her." This annoyed me and I dismissed it as an absurdly inappropriate qualifying comment, since I was undoubtedly one of her loved ones, if not her primary loved one. I got up and went into adjoining large rooms, pale yellow institutional cinder block construction with linoleum floors, white or light, I think. There were many people seated or moving about everywhere. I think I asked a woman dressed in 1950's era nursing uniform (starched white hat and skirt) where was the "proline area, i.e., where was Cheri. I saw Cheri in my mind's eye around this time in the dream. She was young as when I first met her in 1972, lithe, with blond hair and energetic lovely eyes. The nurse told me that Cheri had already been moved to the area for the procedure. It came to my mind that the procedure was some kind of mental surgical operation. The concept was somewhat confused, but it didn't seem abnormal to me, nor was there an atmosphere of extreme concern surrounding these events.

As I finished writing a brief note in my medical journal regarding the dream, the words of John 3:6 – 8 came into my mind, " must be born again." I smiled to myself, considering the Phoenix Fire Mystery, i.e., the reincarnation hypothesis. I went about my morning and got online later to search for the word "proliene," (since I thought I had heard "proe—lee—in" when I felt the word in the dream earlier) but saw nothing interesting in the Google SERP (search engine results page). Google responded with "did you mean proline" and gave me a link to some site doing lien-related legal work and the like. I dropped the subject and continued with my day. I wondered later if I should email Cheri's daughter, C___, and assure everything was ok with her and her family, but decided that this would be intruding without reasonable benefit for her (I like hearing about how she is doing, but realize I am not very relevant now).

Later I returned to the computer and resumed work I was doing on a proposed article explaining how it is that a spider "knows" how to spin a web innately from the DNA of its genome. I digressed into the detail of DNA transcription and was reviewing the DNA codons, the base pair codes for amino acids that constitute the genetic code. Suddenly the codon "CCC" and its product "proline" stood out on the page. My heart skipped a beat and my eyes widened. "CCC" mRNA codes for an amino acid called "proline." I immediately realized that the actual DNA template coding for CCC in mRNA would be "GGG," the DNA base sequence being complementary (and antiparallel, but that is irrelevant when the codon is three identical codes). Cheri-Cheri-Cheri associated with Gary-Gary-Gary (Cheri had always addressed me by Gary, my first name) it seems, cued by the dream word "proline."

After that discovery, I looked at the amino acid proline. It was curious that proline is the only amino acid that stains yellow rather than blue in chromatography (via ninhydrin), recalling the prominent yellow color of the walls in the dream. Of deeper significance, I discovered (following the dream suggestion) that proline is considered to be a phosphorylation marker, normally found immediately prior to the amino acids serine and threonine (in a polypeptide chain) to mark them as phosphorylation targets in cellular signal transduction, for example, to activate a responder which then binds to DNA to modify the expression of of a gene. Why was that of particular significance to me?

My research (for the article) the last few weeks had been concerned with development, in particular the development of the neural substrates required for the demonstration of innate behavior sequences. The DNA constituting the genome of the developing organism cannot "know" where a particular embryonic cell will be at a particular place and time, but the interaction of the DNA of each cell with the information that is generated dynamically as the embryo develops (the nonlinear evolving external and internal environment of the cell, which is in large part other cells and the mechanical and chemical influences they generate) results in a fairly consistent resulting organism (and behavioral repertoire), i.e., the phenotypic expression of genotype.

I use the term "bioworldline" to signify the trajectory a cell or other biological entity follows in the phase space consisting of all possible states of the entity. For example, with axes for time, position (three dimensionally spatially in the developing embryo) and relevant biochemical parameters (like phosphorylation target status modulating transcription status of local DNA), following the bioworldline of a cell in the multidimensional phase space so defined would be equivalent to a detailed fate mapping of the cell through the process of development. It was therefore of interest to me that my dream pointed me to another entry point in the analysis of development.

These kinds of synchronicities (odd coincidences) are for me rather like a portion of Carl Sagan's plot in his novel, Contact, where the character Ellie looks at a computer computation of the digits of pi on the suggestion of an extraterrestrial who tells her that even more advanced beings than himself have left messages embedded in transcendental numbers like pi. Out at 10e20 decimal places (10 followed by 20 zeros, a very large number of decimal places), the value of pi becomes a string of 1's and 0's which cause a circle to be drawn on a computer screen (when arranged as a suitable array of pixels, the process of which I won't describe further). That, of course, implied that intelligence had been embedded in the very fabric of reality---as does synchronicity.