Life as we know it would not be possible without the universal genetic code. With few exceptions, this code is common to all known life forms – from the simplest single-cell organisms to the human genome. Traditional biological dogma defines this code as the set of rules living cells use to translate genetic information into proteins. As such, it is understood to be a one-way flow of information from the genome into the protein-based structures of life. But as we’ve repeatedly shown, life is not a one-way biological process. The Chiral Theory of Life posits the living organism as a two-way integrated hierarchy of tasks predicated on left-right chirality in which information is continually fed both forward into the next “now” moment and backward into memory in living time. From this perspective, the genetic code is the Code of Transitional Dimensionality – a universal language by which awareness communicates with the world in which it lives. Transitional dimensionality describes a self-referential, circular flow of information orchestrated by awareness that progresses from directional lines in the world to shapes formed by the intersection of directional lines to DNA symbols that code for those shapes to the protein shapes represented by the symbols to the directional lines used to shape-fit those proteins to matter in the world. In the process of shape-fitting, a new “snapshot” of information about the directional lines in the world is captured and the cycle is continually repeated.
In this chapter, we will examine transitional dimensionality in more detail, specifically considering how shapes become symbols and symbols become shapes. The four bases of DNA – guanine, cytosine, adenine and thymine (uracil in RNA) – are the symbols of transitional dimensionality. However, as we saw in Chapter 7, these symbols are not directly translated to amino acid shapes. Rather, the “letters” of DNA are transcribed into RNA codon “words” that are then translated to amino acids “words” that fold (by transitioning from one dimension to three dimensions) into protein “sentences.” The codon, then, is the link between the symbols of memory and the directional shape of an amino acid. Like the amino acids they represent, the RNA codon has a directional shape that derives from the order of bases in the underlying DNA code. To understand this, we need to look more closely at the RNA codon.
Codons are three RNA nucleotides that are strung together in one direction to form a single strand. There are 64 possible three-base permutations of the four DNA nucleotide bases. The combination that constitutes a specific codon is derived from the bases read on only one of the two strands of the DNA double helix. 1 As described in the last chapter, these strands are homochiral and opposite-directed, or anti-parallel; one strand is oriented with the C5’ atom up (referred to as the 5’-3’ strand) and the other is oriented with the C3’ atom up (referred to as the 3’-5’ strand). The anti-parallel double-strand is an example of directional shape; the bases are symbols. The codon combines the two, stringing three base symbols in a specific sequence that produces a directional shape. We’ll discuss the way in which RNA codons are transcribed from DNA later in this chapter. As we’ll see in that discussion, the means and the end of transcription and translation tasks is directional shape. In a very real sense, living awareness pulls symbols out of shapes by way of shared direction in the lines that comprise the three languages of transitional dimensionality.
The “nested wheel” shown in the image above provides a convenient way of visualizing the key concepts associated with the time-linked tasks of memory and procedure in a living organism. Beginning at the center, the first three “rows” of the wheel (shaded in yellow, aqua, green and pink) represent the RNA nucleotide bases that come together in triplets to form a codon. We’ll refer to these rows collectively as the “codon wheel.” The outer row (shaded in tan and white) represent either specific amino acids or functionality related to translation (namely, “stop”). 2 We’ll refer to this outer row as the “amino acid wheel.” Together, the codon and amino acid wheels describe how the symbols of RNA codons translate to amino acids that form the shapes of proteins. Reading out from the center to the perimeter, we have all possible three-base combinations of the RNA nucleotides that form a codon: uracil (U), adenine (A), cytosine (C) and guanine (G). For example, in the top right quadrant, we have uracil (in green) as the first base in this particular set of codon triplets. If cytosine is the second base (in yellow) and adenine (in pink) is the third, we have the UCA codon, which translates to the amino acid serine (symbolized as “Ser” or “S”). Notice that the direction of the codon is indicated in the wheel by the 5’ notation at the center and 3’ at the outside edge of the codon quadrants. Reading from the center out reflects the 5’-3’ sequence from top (front) to bottom (rear) of the strand. Reading from the periphery in reflects the 3’-5’ sequence, from bottom to top.
The sequences of amino acids outlined in purple and shaded in tan represent protein “sentences” that are formed when these amino acid “words” are linked in any combination. The start and stop codes (indicated by the black arrow and black circles, respectively) distinguish the beginning and end of a specific gene during translation and, together with other factors, during transcription.
In addition to the nucleotides and amino acids shown in the figure, sixteen vectors (in gray) radiate from the center into the area beyond the outer perimeter of the wheel. There are an infinite number of these passing through all points of the perimeter, of course, but these few are sufficient to represent the directional lines of the physical, or external, world. Life uses these directional lines to build and recognize the shapes stored as symbols in DNA memory. These symbols that are later re-constituted by ribosomes into the protein shapes that comprise both the functional structures of the living organism itself as well as the means by which it interacts with shapes of interest in the external world. In describing this self-referential relationship, we might say that using directional lines, the shapes of tasks remembered as DNA symbols build and recognize the shapes of other tasks and of matter in the world.
Each of the sixteen vectors crosses a point on the perimeter of the nested codon and amino acid wheels. At each of those points, the line of the vector bisects any of an infinite number of lines that lie at a tangent to the curving arc of the circle, forming the edges of a plane. To envision this, we can imagine standing at the center of the wheel, looking out along the vector in green that borders the lower edge of the GAU codon and Asp amino acid (in the upper left quadrant). From that viewpoint, any two of the tangential lines intersecting at the periphery of the codon and amino acid wheels (shown as red dots) would form a two-dimensional plane like the one shown here in blue. Our line of sight would approximate a left-or-right angular view along the vector itself, with the same relational perspective to the 2D plane that we described in our discussion of the ideal sphere. Here, the third axis of awareness represented by the green vector is projected to the focal point on the other side of the plane (shown as a yellow dot) – a virtual vantage point from which we can imagine the view of the vector from the other side.
Notice that this “both-sided” view of awareness (one seen from the center looking out and the other projected as the view from the outside looking in) is mirrored in the position of the protein as it connects the nucleotides of memory with the dimensional lines of the external world. On “this side” (that is, the side nearest the center), the protein has direct access to memory and a previously stored view of the 2D plane. On the other side, it has direct access to the external lines of currently passing matter. Together, in spiraling left-right approximation along the third axis, the patterns of memory are matched to those of the external world and the patterns of the external world are transmitted back as shapes to be stored in memory by combinations of the four nucleotide symbols.
Succession (that is, pure time without differentiation) is also reflected in the wheel. As previously described, the homochiral curvature of self-translation in living time turns left-right into clockwise-counterclockwise spiraling around an imaginary central axis. This spiraling curvature is the shape of succession in the living organism; in the figure, it is indicated by the red left / counterclockwise and blue right / clockwise arrows shown in the upper right quadrant. We can imagine the amino acid wheel spinning counterclockwise in the direction of the red arrow, while the codon wheel spins clockwise in the direction of the blue arrow. To incorporate time into this spinning motion, imagine that both wheels are also moving outward toward the back side of the 2D page in a spiral. This outward flow away from the front side of the page (facing us as viewers) represents the flow of succession in living time. With each angular rotation of the two wheels clockwise or counterclockwise, living time flows off the surface of the page and into the past as the new ”now” moment appears on “this” side of the page. The ever-changing content of “now” is briefly captured on the surface and then instantly disappears to the rear side of the page in the eternal flux of living time.
As we envision this, it becomes clear that translation is not just a connector linking the physical patterns of memory to those of the external world; it is also a connector of past and future. Self-translation of symbols (genes) to shapes (proteins) by way of shapes (proteins) in a forward direction is the basis of awareness. The codon and amino acid wheels are a depiction of the symbol-to-shape code that underlies translation. The origin of the code is the origin of living awareness and living time. We’ll explore this origin later in this chapter.
By integrating both spatial and temporal aspects of awareness, a protein is a physical representation of the living coordinate at any given instant of living time. Spatially, it expresses left-right forward chiral direction that allows it to match a self-assembled shape (DNA) with a specific external shape. Temporally, it expresses “now” – the instant in which past memory (gene) transitions to future (task-based procedure). It is this physical expression of “now” embodied in the protein that explains why translation – and not DNA or the nucleolus – is the basis of living time as pure succession. (However, as we saw in the last chapter, the nucleolus does establish the rate (or pace) of succession – that is, the spacing between one instance of succession and the next.)
We can also visualize the succession of amino acid assembly in the context of this imagined spinning of the wheel. The task begins at the start codon (AUG – designated with the black arrow), which we’ll take to be the site of amino acid translation for our purposes here. As the outer amino acid wheel turns counterclockwise and the codon wheel turns clockwise, new amino acids are translated and added one at a time at the position of the start codon arrow. The specific sequence they follow is dictated by the underlying DNA sequence that has been transcribed as messenger RNA codons. For example, if the 5’-3’ RNA sequence is AUGUACGAGAACCGA, the amino acid sequence is methionine (start), tyrosine, glutamate, asparagine and arginine. Translation ends when a stop codon is reached. In both the growth of proteins and the transcription of DNA to RNA, the first building block (amino acid or nucleotide) in the chain is the oldest and is continually in motion outward toward the back side of the 2D page as new building blocks are added to the rear (or newest end) on “this” side of the page. The timing (rate of repeat) for both transcription and translation is established by the nucleolus.
Now, let’s consider how the overall elements of the nested wheel approximate the nested hierarchy of tasks that comprise the living organism. In the following description, the wheel-based corollary of the functionality described will be briefly identified in italics. As we’ve said in previous chapters, the vantage point of the living coordinate is the center of the ideal sphere (wheel center). From there, awareness occupies the intersection of left-right chirality and forward direction, sensing the two-dimensional shape of objects in the external world through the in-out boundary (outer perimeter of the wheel). By integrating a series of left-right angular views that approximate the third axis (green vector), it projects the “other side” of those objects (blue-shaded plane at ten o’clock). In doing so, it relies on both the compatible chirality of the world in which it lives (i.e., that the two halves of a 2D plane are mutually defined chiral-fitting opposites that correspond to left-right spiraling approximation), and on the mutuality of in-out directional motion (i.e., that in-and-out changes on the third axis are also mutually opposite). Based on these self-compatible features of matter, awareness overlays the directional lines of the third dimension (all vectors) onto the projected two-dimensional shapes in the field-of-view (blue-shaded plane) to generate a compatible shape – one in which left-right / in-out on “this” side aligns with right-left / out-in on the “other” side. This “other side” matching, like the handshake analogy described in Chapter 4, produces a pattern that is stored in memory. When it is needed, awareness rebuilds the pattern from pure succession (spinning wheels) in living time, passing through the three chiral dimensions (symbols, lines and shapes) to turn the remembered surfaces of objects around as tasks.
With this overview in mind, let’s briefly consider succession as it applies in the context of the external world in which the organism lives. Succession of both left-handed amino acids and codons derived from right-handed nucleotides meet in self-translation. The cyclic frequency (or rate) of transcription and translation is controlled by the nucleolus in tandem with the availability of useful patterns in the world. As we saw in the previous chapter, this availability is linked to the circadian cycle. In a world of days and nights, matter changes with light-dark succession, but the change is without meaning or direction in and of itself. In the context of the nested wheel, we might say that if there were only one wheel that turned either clockwise or counterclockwise, direction would be meaningless. Similarly, lacking any self-referential means of differentiating the light-dark cycles of the world, the distinction would be meaningless from the perspective of life. However, life applies meaning and direction to the light-dark distinction by establishing a self-referential corollary in which one (light or dark) is associated with right / clockwise rRNA transcription in the nucleolus and the other is associated with left / counterclockwise translation in the cytoplasm of the cell. 3
Understood in this context, the circadian rhythm linked in the nucleolus to the cyclic repeat of precursor accumulation and ribosome assembly / export is the coordination of light-dark with the awareness-in-matter cycle of life. 4 In this respect, the dynamic equilibrium of homeostasis (literally “same steady”) might be better described as homeorhesis – the means by which living organisms maintain a preferential state of flux. 5 Since the codon-ordered symbolic information in memory must be in place before amino acid-ordered functional shapes can be assembled and folded, unidirectional order in the presence of change is inherent in the flow of living time. Unidirectional chiral transcription of genetic information and codon-by-codon translation of amino acids spatialize succession. By controlling the respective beginning and ending points of these processes through the functionality of the nucleolus, life establishes a sequential directional order in time. The built-in sequences of self-translation continually propel life into the next “now” moment – into a future that does not exist until it arrives as “now” and instantly passes as past “now”.
Before moving on, it will be helpful for our future discussion to briefly consider the flexibility built into the process of amino acid translation. We touched on this in Chapter 7, where we noted that the 61 RNA words (codons) in the language of memory translate to only twenty amino acid words in the language of proteins. The meaning of each codon depends on assembly speed as well as contextual position within the amino acid sentence. Just as in the translation of one human language to another, the significance or meaning of sentences hinges on interpretation. Beyond the sense of individual words, meaning is captured in their integration into whole sentences contextualized by paragraphs.
The value of this way of organizing the “sense” content of language is readily apparent. The ability to apply a different meaning to a given word based on context and the complementary ability to apply the same meaning to that word in a similar (but not identical) context is fundamental to the operation of any language. Imagine for a moment that the English language required a unique word for every instantiation of every object or action. Such a “language” would be entirely non-functional, since memory (and hence, communication) would be rendered useless. Unlike a literal word-for-word translation, interpretation affords flexibility that both limits meaning to parts and expands meaning to wholes. 6 For example, take the sentence, “Bear left for the bear enclosure, where the mother bear will bear her cubs.” Here, the meaning of the word ”bear” is limited in that it can only refer to 1) the action of directional going (intransitive verb), 2) a type of enclosure (adjective), 3) an animal (noun), or 4) the action of giving birth (transitive verb). At the same time, the meaning of the word is also expanded in that all of these are possible interpretations of a single word when considered in the context of an entire sentence.
Of course all languages rely either on words or characters as the fundamental unit of meaning. In the language of memory, words are codons; in the language of proteins, words are amino acids. And, as we’ve already noted, there isn’t a one-to-one correspondence between the two. Sixty-four codons translate to only twenty amino acids – a fact that allows for interpretative flexibility like we just described. The number of unique codons in the language of memory is linked to the total number of nucleotide bases (four) and the number of bases needed to form one codon word (three). Looking at the wheel, there are four bases at the center, four in the second row and four in the third: 4 x 4 x 4 = 64. Sixty-one of these code for an amino acid, including one (methionine) that codes for “start”; the remaining three code for “stop.”
If codons consisted of only two bases, then the total possible number of unique configurations would be sixteen, equal to the number of cells in the second row of the codon wheel. This is substantially less than the number needed to code for twenty unique amino acids plus stop codons. To get 64 unique sequences with only two bases per codon, we’d need eight unique nucleotides in the first row and eight in the second (8 x 8 = 64). Obviously one base can't code for one amino acid, since that would leave sixteen amino acids without a corresponding RNA codon and no stop codes. Clearly, three bases per codon translating to one amino acid is the only efficient combination to code for twenty amino acids plus stop codes. 7
This raises a few questions. Why are there only twenty amino acids? How do the codons reflected in the wheel match to a specific amino acid? 8 In other words, what is the operational code? The answers to these questions as well as to the origin of life in chirality itself will be explored in the following pages beginning with a closer look at mRNA and tRNA.
1 Although the nucleotides combine as codes on a single strand by linkage of the sugar-phosphate backbone, they also combine as a double stranded shape by linkage to a complementary base. For continuity of shape, cytosine and guanine combine as base pairs, as do adenine and thymine. Adenine and thymine form a loose bond, while cytosine and guanine are tightly bound. As described in the last chapter, adenine and guanine are larger than cytosine and thymine (or uracil). Therefore, to avoid steric clash, there are no cytosine-adenine pairs. The opposite is also true: to avoid distances too weak for hydrogen bonding to occur within the DNA helix, there are no guanine-thymine (or uracil) base pairs. However, these limitations don’t apply to codons, since they are single strands and hence, don’t have the same size-related constraints as the paired molecule. For example, there is a CAC and a GUG codon.
2 In unusual cases, there may be 22 amino acids and two unused codons.
3 In a world of directional lines, the distinction between light and darkness per se is no more meaningful than it is to someone who is blind. However, rhythmic pulsations of coolness and warmth are another way to gauge the 24-hour circadian cycle. Heat is inherent in the angular change associated with directional lines in that change is motion that may be objectively measured as energy and subjectively sensed as heat by an organism operating within the left-right-forward orientation of life. We’ll explore this relationship later in this chapter.
4 Even single-cell organisms exhibit circadian-like cycles that dictate a “wake” and a “sleep” state (see https://www.popsci.com/blog-network/our-modern-plagues/do-microbes-sleep/).
5 https://www.genengnews.com/cell-biology/book-review-i-think-therefore-i-evolve/
6 The fundamental question is how these regularities of the standard code came into being, considering that there are more than 1084 possible alternative code tables if each of the 20 amino acids and the start / stop signals are to be assigned to at least one codon. If we consider all possibilities for mapping the 64 codons into twenty amino acids and one stop codon, there are more than 1.51×1084 possible genetic codes (see https://www.researchgate.net/figure/Amino-acids-properties-15_tbl1_273519201).
7 Two of the stops have turned out to be placeholders for two newly discovered amino acids, leaving UAA as the one stop code. In the past two decades, researchers have discovered two additional amino acids that are incorporated into natural genetic codes – selenocysteine (Sec) and pyrolysine (Pyl). These amino acids are encoded by UGA and UAG codons, respectively, which normally serve as stop signals. Nevertheless, even with these two additional amino acids, there are still 64 codons – 63 that code for amino acids (including the one start codon – methionine) plus one stop codon (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/).
8 There are a few hypothetical correlations between amino acid properties and the codon table. The third row of the wheel is where duplicates are found (for example AGC and UCC both translate the amino acid, serine. Uracil in the second position of the codon tends to correlate with hydrophobic amino acids. Other observed correlations include the following:
• The second codon correlates with one class of aaRS (aminoacyl-tRNA synthetase) proteins
• The number of synonymous codons for an amino acid correlates with the frequency at which the amino acid appears in proteins, the apparent minimization of the likelihood of mistranslation and point mutations, and the near optimality for allowing additional information within protein coding sequences.
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