From the objective standpoint of biochemistry, the three essential elements of life are proteins, DNA, and permeable membrane. From the standpoint of life itself, these are the three main tasks of procedure, memory and in-out boundary. We’ve already described procedure and memory (Left and Right, in Chapters 7 and 8). Now, we’ll look at the third essential – the in-out boundary. Before moving into the details of this task-structure, it’s worth taking a moment to appreciate its significance. From the perspective of life, the in-out boundary is the expression of awareness’ “inside” point-of-view and the way in which it distinguishes self from non-self. 1 From any point along the three-dimensional perimeter defined by this boundary, “forward” is “out / outside” and “backward” is “in / inside,” making the membrane the physical manifestation of the left-right forward orientation of awareness itself. Notice how this spatial point of reference parallels the temporal one, in which “forward” is the next “now” and backward is the past “now,” separated by a “temporal membrane” that is the present “now” moment. In this regard, the cell membrane is the forward- backward of time in physical form.
The connection between the membrane and awareness is revealed not only in form, but also in function. As awareness continually moves in and out from “now” to next “now” along an approximate straight 3D axis within the ideal sphere, it passes information gleaned in its probe of the environment to and from memory. Similarly, the permeable membrane allows for a physical flow of energy and selected matter parts into or out of the cell, establishing it as an open system operating in the context of its local environment. Awareness’ continual in-out probing of the environment expresses an essential energy linked to its own motion. This kinetic quality finds physical expression in the movement of energy and matter across the cell membrane – a continual flow, that as we’ll see, literally generates the power needed to drive the entire nested hierarchy of tasks that together comprise the living cell.
As with all other essential structures of the cell, the information required to evolve the membrane into the physical powerhouse of life co-evolved with the forward-directed spiraling genetic code. As life gradually learned to recognize and “grab“ the patterns of critical directional lines across countless generations of living time, their patterns were coded into memory. In this sense, both the permeable membrane and procedure “grew” into the directional size patterns embedded in the genetic code.
This understanding provides a new perspective for assessing questions concerning the origin of life, which otherwise lead to chicken-and egg dilemmas like the one we addressed in the previous chapter with respect to DNA and proteins. There, we showed how memory and procedure co-evolved with RNA acting as both a genetic and functional material. As we turn now to the in-out boundary, the same problem seems to re-surface in a different form. Here, the question turns on the functional work of the membrane task, which is to supply the energy needs of the cell. To establish and maintain the membrane structure requires energy that must be supplied by the membrane itself. How did life resolve the apparent conundrum? To find out, we need to look more closely at metabolism and the functional structure of the permeable cell membrane.
When we speak of metabolism, we’re essentially referring to the nested hierarchy of tasks, including the in-out boundary, that cooperatively supply the energy requirements of the cell and generate the task-based structures necessary to sustain life. The material components that form each of these self-assembling tasks rely on ready access to a handful of critical elements. Protein tasks primarily use hydrogen, oxygen, carbon and nitrogen to form the backbone of amino acids. The symbols of memory use the same four essentials plus phosphate to construct the backbone of nucleotides. The living task-structure of the permeable membrane requires a ready supply of lipids, with phosphate again playing a significant role – this time, in forming its physical structure. Together, amino acids, nucleotides, and phospholipids are the raw materials from which proteins, genetic material (DNA / RNA) and membranes are made and used by life to form its own physical body. 2
As we’ve said, the permeable membrane of all cells is comprised of lipids along with certain embedded proteins that assist in regulating the flow of molecules and ions into and out of the cell. Simple lipids like that shown in the stylized drawing of Figure 1 are made of a naturally-occurring sugar called glycerol plus fatty acids. 3 Fatty acids are chains of carbon atoms bonded to one another and to hydrogen atoms. These sugar and fatty acid components are also attached to a phosphate group, forming compounds called glycerophospholipids – the building blocks of all membranes in living organisms. Since phosphate is negatively charged, it’s polar and hydrophilic, while the glycerol ring and hydroxyl groups at the opposite end of the molecule are hydrophobic.
Unlike amino acids and nucleotides, the glycerol backbones of lipid “heads” don’t directly attach to one another. Instead, the molecules are linked indirectly through the interaction of their fatty acid “tails.” Because the tails are hydrophobic, lipid molecules can readily move sideways (laterally) within the fluid structure of the cell membrane. This ease of lateral motion facilitates the selective permeability of the membrane, allowing certain molecules or ions to pass through while blocking others.
Molecules like lipids, proteins, and nucleotides that display both hydrophobic and hydrophilic properties in different regions are referred to as amphipathic. In proteins, this dual response to water directly affects the way in which an amino acid chain folds into a finished protein. In nucleotides, the hydrophilic sugar-phosphate backbone coils around the outside of the hydrophobic bases in the center of RNA and DNA strands, resulting in their classic double-helical shape. Similarly, the amphipathic properties of lipids drive their orientation with respect to the in-out membrane as a whole. This orientation establishes the basis for membrane functionality as the all-important energy-generating task of living cells. Specifically, the opposing responses to water at opposite ends of the molecule cause lipid membranes to form a double layer, with their hydrophilic heads facing out and their hydrophobic tails pointing in toward one another in the interior region between the heads, as depicted in Figure 2. 4 Here, the darker color of the bottom layer indicates the one closest to the cell cytoplasm for easy reference in the depictions that follow; however, generally speaking, the structure of the two layers is identical.
Notice that this orientation is literally a bi-directional in-out-directed task-structure that allows the heads to interact with molecules in two different environments – one layer is in direct contact with the extracellular matrix while the other interacts with the intracellular fluid of the cytoplasm. As we might predict by applying the theory of transitional dimensionality, this two-layered structure begins with an individual lipid “point” that first aligns with a second point in the in-out head-to-tail / tail-to-head configuration shown in Figure 2. Any two of those lipid “points” forms a 1D line that then aligns laterally with another in-out-directed line formed by neighboring points to establish a bi-layered 2D plane. Because every point can form a line with any other point positioned within a 360° radius around it, any given two-point line ultimately intersects other lines in an infinity of 2D planes in every direction, forming a three-dimensional curved hollow sphere like that shown in Figure 3. To living awareness, this curving surface is the boundary – the perceptual limit that we “go around” to “see” and project the view from the other side. To the objective viewer, it appears as a three-dimensional sphere.
The parallels between this process and the multi-dimensional trajectory we’ve described for the other two building blocks of life are readily apparent. In every case, awareness continually interacts with the space-time dimensions of the physical world by relating them to its own left-right-forward orientation in the continual “now” moment in living time. In doing so, it constructs itself and the world around it by applying the concepts of transitional dimensionality to the tasks and sub-tasks of self-translation. First comes the “point” of an individual amino acid, nucleotide or lipid molecule that progresses to the “line” of a peptide chain, nucleotide strand or membrane filament, continues through 2D planes to end in the three-dimensional shape of a folded protein, the coiled double helix of a DNA chromosome or the curved 3D surface of the in-out membrane. Throughout all these dimensional transitions, the left-right-forward perspective of awareness finds self-expression in the interlocking compatibility of shapes and symbols constructed by means of a 360° spiral around the in-out direction that approximates a continual straight-forward line. 5
This shared origin in transitional dimensionality is not the only point of commonality between the raw materials of life. Like their counterparts, the lipid building blocks of the in-out boundary are chiral molecules. This is an important point that again underscores the left-right-forward orientation of awareness as it establishes the requisite conditions of life. Generally speaking, all three essential constituents of living organisms are made of enantiomerically-pure chiral molecules that reflect this same orientation in the construction of its own physical body. 6 In the case of membranes, the underlying homochirality (left or right) of the lipid bilayer affects certain of its critical functions like fluidity, permeability, topological packing, enzymatic activity and the ability to recognize and select molecular shapes of interest. 7 In turn, these functional properties derived from homochiral molecules drive the shape of the structure itself by causing the heads of the array to pack together at a specific angle. The resulting shape then feeds back on itself, influencing the very functions that drive its shape. 8, 9 This two-way feedback is the same self-balancing, mutually-defining interaction that we’ve seen repeatedly in our discussion of memory and procedure. In all three essential tasks, life self-selects, self-organizes, self-assembles, self-regulates, and most importantly, self-translates.
The chiral-based structure of the cell membrane aids in the chiral selectivity of the other building blocks of life as well. For example, the glycerophospholipids that form the cell membrane exhibit preferential behavior with respect to the chirality of amino acids, allowing left-handed molecules to pass through faster than their right-handed counterparts. 10 Their amphipathic properties with respect to water also contribute to the dynamics of intracellular tasks. Since both proteins and lipids are chiral and amphipathic, hydrophobic interactions between nonpolar residue (R) side chains of amino acids and lipid tails, as well as polar interactions between charged side chains and lipid heads, affect the rotation of the finished protein. 11 This membrane-linked influence has far-reaching effects on every aspect of cellular functioning – including the spiraling genetic code. Why? Because proteins are the task-based procedures that drive all of life – from the transcription, maintenance and feedback loops of memory to the nested hierarchies of cellular metabolism and energy generation to the maintenance and structure of the in-out boundary itself. The omnipresence of proteins in every aspect of life means that the tasks and sub-tasks of memory, procedure and boundary are and must be inherently intertwined; there is no one “starting point” simply because not one of these tasks and sub-tasks can arise independently of all the others.
The truth of this requires us to confront the inherent circularity of awareness and life. It’s everywhere in the story of living organisms. We find it built-in to the forward-reverse-projected flow of information in every “now” moment of living time, embedded in the symbols of the spiraling genetic code, expressed in the self-transcription and self-translation of proteins, and underlying the sub-tasks that drive the energetic powerhouses of the cell studded throughout the in-out membrane. With respect to the origin of life, this in-your-face circularity compels the conclusion that metabolism and protein synthesis surely co-evolved along with the codon-amino acid pairings of the genetic code. In other words, the functional structure-task of the in-out membrane – like that of the proteins embedded within it – must be encoded in the directional-size relationships of the genetic code. How is this so?
As outlined in our introductory remarks above, the theory of living awareness understands the cell membrane as the external energy manifestation of the self-generating in-out direction of the genetic code. Referring to our discussion of Size, Direction and Spiral in the last chapter, the reversal of base size and direction reflected in opposing triplets of the code maps the spiraling of awareness as it toggles between the three-dimensional world and its own two-dimensional representation of it stored in memory. In the permeable in-out boundary, a corresponding reversal in material form is reflected in the double layer of glycerophospholipids, wherein one layer points in and the other points out reminiscent of the opposing direction of codon-anticodon triplets embedded in the code. As the lipid bilayer curves to encapsulate the cell, the directional relationship between the layers reverses as depicted in Figure 4.
Notice how this transition mirrors the reversal of base size and direction within the genetic code. Referring again to the image of the spiraling middle-base table in the last chapter (copied at the bottom of Figure 4, as the codon in the top left corner of Quadrant 1 transitions to its directional size opposite in the anticodon at the bottom right corner of Quadrant 4, it embeds a left-right-forward spiral. In both the 2D code of memory and the 3D task-based structure of the cell membrane, the reversal of opposites maps the left-right-forward orientation of awareness represented by a spiral.
In thinking about this, notice that the physical molecules that comprise the codons and amino acids of each quadrant of the genetic code table individually spiral around their own respective axis. However, when considered in the context of their active functioning during translation, they orient relative to their shared virtual axis in an inverted “L” spiral of tRNA. When considered as an ongoing task-based structure in connection with others of its own kind, they orient relative to the axis of the shape adopted by the respective grouped whole. In the case of nucleotide triplets, it’s the virtual axis of a DNA double-helix; in the case of amino acids, it’s the virtual axis of a folded protein.
This same three-tiered axial relationship is present in the lipid membrane as well. As an individual “point,” the chiral lipid aligns from top-to-bottom along a 1D virtual axis that bisects the molecule from top-to-bottom / head-to-tail. As a functional pair, each set of opposite-directed lipids orients along a shared virtual axis that maps the up / down 2D “thickness” of the membrane at any given point along the envelope. This axis is represented by the dotted blue lines of Figure 2. As parts of the ongoing task-based structure of the permeable membrane as a whole, the orientation of an individual lipid is relative to the virtual axis of the membrane as a whole, represented by the green line in Figure 4. It is these nested axial relationships that allow lipids to form a 360° structure that is in fact two-dimensional at any given point along its surface.
We’ll turn to the question of how the in-out membrane may have evolved and take a more in-depth look at the metabolic process of cellular respiration on the next page.
1 For simplicity, we’ll sometimes refer to the in-out boundary as the “cell membrane.” However, like all the other “structures” that comprise the living cell, the in-out boundary is not a “thing” as such, but rather a nested hierarchy of functional tasks that continually operate on matter in the ongoing “now” moment of living time. In considering the information in this chapter, bear in mind that the cell membrane is not the cell. It is one of three overarching task-structures – DNA, proteins and permeable membrane – that function cooperatively in the task of metabolism.
2 In addition to these biological constituents, life also requires nitrogen and sulfur, as well as certain inorganic elements, including potassium, iron, calcium, magnesium, nitrogen, zinc and manganese. All of these have different shapes that life recognizes. We’ll discuss this in more detail later in the chapter.
The general formula for a fatty acid is CH3(CH2)nCOOH where "n" represents the number of carbon atoms in the hydrocarbon chain – usually an even number ranging from 2 to 28. CH3 is a methyl group at the end of the fatty acid chain, (CH2)n is the long hydrocarbon chain with "n" carbon atoms, and COOH is a carboxyl group that gives the molecule its acidic properties. Again, we’ll later address how these appear from the perspective of life.
4 An intrinsic tendency of a lipid bilayer is to adopt and retain a generally (but not entirely) flat shape. In a self-assembling lipid bilayer, the two monolayers will energetically tend to have the same lipid composition, as favored by the entropy of lipid distribution in the membrane. The resulting bilayer will be completely symmetric with respect to its mid plane, and, hence, there will be no preferential direction for its curving. See https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/membrane-curvature.
5 To envision how this works, imagine solving a 3D jigsaw puzzle. To connect any piece to the existing structure requires a 360° rotation in every dimension to check for a shape match relative to the contours of the empty space being tested. If left-right (two-dimensional) rotation of the piece turns up no matching shape, the piece is rotated forward or backward (in three dimensions) and then rotated left-right again to check for a match against the newly-revealed sides.
6 Although not all lipids are chiral, glycerophospholipids are invariably chiral. See https://www.sciencedirect.com/science/article/abs/pii/S0021967322004605.
The membranes of living cells contain a mixture of different types of glycerophospholipids, some with two saturated (straight) fatty acid tails and others with one saturated and one unsaturated (bent) tail like that shown in Figure 1. A saturated fatty acid in a lipid has no double bonds between carbon atoms in its chain, meaning it’s "saturated" with hydrogen atoms; an unsaturated fatty acid has one or more double bonds between carbon atoms, resulting in fewer hydrogen atoms attached and a less rigid structure. At room temperature, saturated fats are solid, while unsaturated fats are liquid. Unsaturated fats have at least one double bond, which creates a kink or bend in the chain, causing the tail to be less straight; this difference in structure impacts the fluidity and packing of lipid molecules in a membrane.
At cooler temperatures, the straight tails of saturated fatty acids can pack tightly together, making for a dense and fairly rigid membrane. Phospholipids with unsaturated fatty acid tails cannot pack together as tightly because of the bent shape of their tails. As a result, membranes containing unsaturated glycerophospholipids will stay fluid at lower temperatures than those made of their saturated counterparts. See https://www.khanacademy.org/science/ap-biology/cell-structure-and-function/plasma-membranes.
Despite these differences in their fatty acid chains, both types of lipids are chiral molecules, built around a directional center in their glycerol heads. See https://pmc.ncbi.nlm.nih.gov/articles/PMC4472042
7 See https://www.mdpi.com/2073-8994/12/9/1488 and https://www.nature.com/articles/s41467-024-47573-1
8 https://www.nature.com/articles/srep15652
9 Chiral lipid self-assembly is driven by the shorter fatty acid (or “alkyl”) chain, which exerts a stronger influence on the overall chirality of the assembly than its longer counterpart. As a result, the chirality of the membrane as a whole will generally mirror that of the shorter fatty acid chain. See https://pubs.rsc.org/en/content/articlelanding/2019/sc/c9sc00215d. We might also note that selectivity and shape, based on factors like size and charge, resemble amphipathic amino acid class distinctions.
10 A 2021 study looked at enantioselective permeation of alkyne-labelled amino acids (alanine, valine, phenylalanine and proline) and dipeptides through a chiral phospholipid bilayer using DIB transport measurements. The biological L (left) enantiomers permeated faster than the D (right) enantiomers. The differences ranged from a 1.2-fold variance in alanine to a 6-fold variance for proline. Enantioselective permeation poses a potentially unanticipated criterion for drug design and offers a kinetic mechanism for the abiotic emergence of homochirality via chiral transfer between sugars, amino acids and lipids. See https://www.nature.com/articles/s41557-021-00708-z.
11 https://pmc.ncbi.nlm.nih.gov/articles/PMC6801444
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