The Living Chain

Draft for the author's reading and rewriting.

Irreducibility of Quantum Systems

As we begin exploring the science which serves as the foundation for our living being, we ask once again, what sort of being are we, what sort of universe do we exist in, and why are we here in the first place?

Although the science reveals an almost indescribable physiological and anatomical complexity, a moving picture which becomes increasingly complex the more we examine it, we are going to freeze the moving frames sufficiently to understand the beauty of the details.

Today this takes us quickly into the field of biophysics, which leads us into the discovery that both our physical and psychological processes are tightly wired into the quantum universe.

This is foundational to understanding why the carpet is moving under us, as we seek to understand why neither our own physiological selves or the universe of which we are inextricably interconnected will hold still so we might accurately measure it.

The echo which boomerangs back to us is an uncomfortable recognition

Telegraphing the message that both ourselves and this universe are emergent in character.

Forms and functions not frozen into an inflexible state of easily measured stuff, but a constantly changing, constantly evolving and emerging set of conditions .

While this relays the end of a Newtonian existence, built of tiny particles which combine into a set, inflexible framework of a mechanical system, it relays the beginning of another and more interesting system.

A system in which every freeze framed illustration must be set back into motion once we have understood the form and function of the paused process.

This Quantum Paradigm demonstrates a flexible process, a continuously emerging and changing system, which never holds still for examination of measurement.

Every time we freeze the frame and seek to examine and measure the substance and to reduce the process to an abstracted object, we lose so much information it becomes useless.

This concept of irreducibility is critical as we proceed, understanding the built in limitations of our human perception and methods of investigation.

I concur, at least partially, with Denis Noble, demonstrated in the following video, as he speaks of the end of the Newtonian paradigm and of the inception of the Quantum Paradigm: The End of Central Dogma

The standard telling of protein synthesis is a pipeline of words: DNA is transcribed into mRNA, mRNA is translated into protein. Three nouns, two verbs, all of them borrowed from printing. The picture is of text being copied, carried, and read out — a flat hand-off from one document to the next. In the living cell nothing of the kind happens. What actually moves down the chain is shape: a helix opens, a single strand folds itself as it is made, a two-part machine the size of a small virus grips that strand and ratchets along it, and a chain of amino acids folds — often while it is still being built — into an object that works. At every step the information is carried by geometry, charge, and motion, in three dimensions, in water, in a crowd [6].

The messenger is a shape too

The mRNA that leaves the gene is not a flat courier. It folds as it emerges, forming loops, hairpins, and helices that change with temperature, salt, and stress; it is carried to particular addresses in the cell; some transcripts anchor the cell's architecture without ever being translated at all. The essay mRNA as Dynamic Ensemble follows this in detail: the code is not the object, the trajectory through the folding landscape is. What reaches the ribosome is already a three-dimensional structure whose shape helps decide how, where, and how fast it will be read.

The ribosome: a machine that is mostly RNA

The ribosome is the largest and oldest of the cell's machines — in a human cell, a two-part assembly of some eighty proteins wrapped around four long RNA chains, roughly three million daltons in all. Its heart is not protein at all: the catalytic centre, where amino acids are joined, is RNA [2]. Proteins decorate the outside; the engine inside is made of the same stuff as the message it reads. The deep ancestry of that fact — RNA as machine before it was message — is one of the standing hints about how the living chain began.

And it is a machine in the strict mechanical sense. As translation proceeds, the two subunits rotate against each other; transfer RNAs swing through the assembly in a choreographed sequence of hybrid states; the whole structure flexes, ratchets, and steps forward one codon at a time, driven by thermal motion rectified into directed movement — a genuine Brownian motor [1, 3]. A frozen crystal structure of a ribosome is a stopped frame of a thing that is, in operation, visibly walking. Between ten and twenty times a second it takes a step, grips the messenger, and adds one more link to the growing chain.

Folding while being built

The protein does not wait to be finished before it begins to fold. The new chain emerges link by link from a narrow tunnel through the large subunit, and as each segment appears it starts exploring shapes — helices zipping up inside the tunnel mouth, domains collapsing as they clear the exit [4]. Folding is cotranslational: the order in which the parts arrive is part of how the structure forms. A chain synthesised all at once, if such a thing were possible, would not be guaranteed the same destination as the same chain grown link by link in time.

Nor does the chain fold alone. The cell is crowded — a third or more of its interior is occupied by other molecules, so there is barely room for the wrong shapes to exist [6]. Chaperones stand by at the tunnel exit and further downstream, holding open routes the chain cannot find by itself, catching intermediates that would clump, giving misfolds another attempt [4, 5]. Protein quality control is a standing institution of the cell, not an emergency service: surveying, refolding, and dismantling are continuous processes, run at continuous energetic cost, for as long as the cell lives. The folded protein of the textbook figure is the survivor of a guided, crowded, kinetic journey — a trajectory, not a pose.

Tissue: the origami that holds the chain

And the cell itself is not a bag floating in emptiness. In living tissue every cell sits inside, and is held by, the extracellular matrix — a woven scaffolding of collagen, elastin, and linked sugars that the cells themselves build and continually rebuild [7]. The matrix is not packaging. It is tense, structured, and specific: its stiffness tells a stem cell what to become; its fibres carry mechanical force from one end of a tissue to the other; cells grip it at focal adhesions and read the pull through their own internal architecture. Cut the scaffolding and the tissue loses not just its shape but its instructions. Living, in vivo tissue is unique precisely here: it is origami that folds itself, holds itself, and reads its own folds — scaffolding and inhabitant at once.

The membranes, the slipstream, and the relations

This is where the book's two pictures meet. Earlier chapters spoke of the dual electromagnetised membrane — the standing voltage across a five-nanometre bilayer — set in the fluid slipstream of the universal substrate. That picture is true, and it is not enough. Suspended on those membranes, threaded between them, and crowded into the water they enclose is the whole intricate anatomy this chapter has walked: the helix and its reader, the folding messenger, the walking ribosome, the chaperones, the matrix outside the cell holding cell to cell. The physics gives the fields and the forces; the biochemistry and anatomy give the relations those fields are actually organising. Lose either side and the picture flattens — into membranes without life, or life without the field it stands in.

What the pipeline drops

Transcribe, translate, fold: three flat words for three storms of geometry. What the pipeline drops is everything this chapter has described — the messenger's own folding, the machine's walk, the chain folding in time inside a crowd, the scaffolding that makes a collection of cells a tissue. Each stage is a relay of three-dimensional relations, carried out in water, at the speed of thermal motion, under fields the earlier chapters measured. The code passes down the chain, yes — but it passes as shape meets shape, and what is living in the result is the meeting.

Living fluid process of beingness

When viewed from this perspective the biological being becomes a process, and not a simplified container, the contents of which may be reduced to a static thing,

From this view , we are not a thing at all, but a process which takes on a temporary shape and form as a human being.

We can begin to perceive that as a process we are more like a standing wave, coming into being, growing, changing, evolving and eventually transforming back into the universal slipstream from which we emerged.

Thus, our beingness, unfolds to reveal a chain of being.

Our existence, a process in which we consciously perceive a personal identity over time, and through which, we experience the universe itself.

From this perspective we may consider that we are, in a manner of speaking, the universe's way of experiencing itself,

Beings of Light, Electromagnetism, and Frequency/Resonance

Before life can exist as biological beings. it exists as an electromagnetic voltage pattern .

From the quantum perspective to say we are electromagnetic beings is not an exaggeration.

As biological beings we are quite literally composed of light, resonance/frequency and electromagnetism.

In many respects our physical form reveals deeper patterns of light, resonance/frequency and patterns of electromagnetism

Hold in mind the concept of patterns of light energy, patterns of resonance/frequency, and patterns of electromagnetic energy as we merge into the next section

Back to the book's contents