Flow control

From hunters and gatherers to farmers and citizens, we are conditioned to be consumers of continuous physical flows. Water and air, food and warmth, these are just some of the things we need to receive regularly to sustain our existence. Our bodies can adapt to changes in flow to some extent, like a thermostat, but too much or too little of a good thing can still kill us.

Always ready to invent a simple model to explain complex realities, in the past we have explained the workings of the body as a balanced reservoir of essential fluids, or taken to extreme the idea that anything physical can be either poisonous or beneficial, depending on dosage. Although we retain some reservoirs inside, our bodies are primarily not bottles, to be filled or emptied. We are processes, and we must continue to consume as long as we live.

Modern man has learned to store materials outside of his own body. When hunting was unfavourable, and weather destroyed plant life, caches of food would help ensure survival for the tribe. As gatherers collected foods that seem to preserve best, some of these caches of foods will have started growing, all on their own. Curious beasts that we are, we discovered what seeds are, by trial and error.

More and more we relied on stored food, and gradually became obsessed with the logistics of it: How much water is in that waterskin? How much grain can we store in that cave? Can you make those clay pots bigger? Is there a way we could extract just the most nutritious parts of the plant, so we can store more of it in the same volume? And also make it last longer without spoiling? And so on, until most of us forgot that we used to hunt our food in the wilderness.

Resource anxiety, the worry that we might at any time run out of something that we need, has never left us, even though we live in the midst of historical abundance. The precursors of such ideas as ownership, budgets, and trading, might have existed in some form in the tribal era, but it was our transformation to farmers and citizens that made them real.

Economy is all about controlling the flow of goods and consumables. But to properly understand the flow of materials around the world, we need to represent them in a more handy form: currency. Even though we constantly compare incomparables, like apples and oranges at the market, we think we can compare against something that stays fixed and solid: the value of money. But of course there is nothing that is infinitely solid and fixed, all assets can be liquidized, given time.

There is one physical resource that we need to live, that cannot be stored or traded. Even the richest man in the world only has a finite time to live, and the clock ticks for everyone alive. Even though we do not know exactly how much time we have left, we know we cannot live forever.

But flow control is not just about quantitative logistics. By controlling flow as it solidifies, forms and patterns can be stored: Ink flows onto paper and dries, storing words and pictures in solid 2-D form. With some more work, we can cause clay, wax, resin, and various polymers to solidify in a desired shape (with 3-D printers, if nothing else).

Life forms are processes that consume and produce resource flows with intricate, and often efficient patterns. Evolution makes individuals compete on resources, so that natural selection can improve resource usage among the survivors. In the broadest sense, anything that is limited, acts between individuals, groups of individuals, or between them and the non-living environment, can become a contested resource for the purposes of evolution.

A page completely covered in ink is as void of information as one left blank

For example, space for storing patterns can become a contested resource, but how to measure it? It is not possible to optimize for quantity and quality at the same time: a page completely covered in ink is as void of information as one left blank. Shapes cannot be stored from just one resource, at least two are needed, like paper and ink, or wax and empty space.

Life stores its patterns efficiently, in molecules so small we cannot see them with the naked eye. To control its flowing patterns, life as we know it fluctuates somewhere between liquid and solid. DNA is a one-dimensional strand, folded for storage into big 3-D bundles, called chromosomes. The machinery of the cell will unwind these strings regularly for copying, or for protein synthesis.

Grossly simplified, the copying or expressing of DNA is a process of controlled solidification. The surrounding liquid floats abundantly with assorted building blocks, free amino acids or nucleotides. The machinery of the nucleus guides them to connect one after the other in the order determined by the strand being copied, to grow into a long 1-dimensional floating crystal chain, a transcript or copy of the original. After synthesis, proteins twist and fold into space-filling 3-D knotty shapes, to be able to perform their tasks inside or outside the cell.

The inner machinery of the cell is contained inside the cellular membrane, which is a flexible 2-D liquid crystal forming the walls of the cell. Unlike the folding-unfolding 1-D strings inside it, the cellular membrane is not a copy of anything, it is one half of the original membrane that broke in two as the parent cell divided. Like a soap bubble that keeps growing and dividing forever, the cellular membranes inside our bodies are all pieces of a cell that lived and died billions of years ago.

What does change about the walls of different cells is the intricate system of gates and filters straddling it, bundles of 3-D-folded 1-D macromolecules that the cell manufactures. These gates decide what material can flow in or out of the cell. For example, distant parts of a complex multicellular organism can communicate by sending or receiving messenger chemicals via the bloodstream. The immune system can also order cells to stop molecules it considers harmful from entering, by programming the gates in the membrane.

With our mechanistic intuition, we think of gates as solid mechanical objects and flow as matter in a liquid state. These are the kind of machines we build: silicon crystals printed with intricate systems of billions of tiny gates controlling the flow of electricity. Such machines can be very precise and efficient, but they are not very adaptive. We probably expected to find such a mechanistic system inside the cell as well, engineered to precision. That is one of the reasons why molecular biology has baffled our expectations so many times during its short existence.

For example, unlike simpler life forms, most of the DNA in a human cell is not genomic, or blueprints for proteins. Instead we have discovered in the ‘junk‘ parts a complex RNA-based regulation system for deciding what genes the cell should be expressing, and when.

We have also discovered what can only be described as life fragment parasites, lonely strands of macromolecules that travel from host cell to host cell, hijacking their replication systems to produce copies of themselves. Although these parasites usually only harm their host when in the process of jumping from one species to another, we somehow decided to call them viruses, meaning poison. (But as noted earlier, the difference between poison and medicine is dosage, not chemical composition)

Most of the cells in our bodies are not even human cells at all: the colonies of billions of single-cell organisms that live in our gut.

Proteins can apparently also be more dynamic than previously thought. Instead of folding into a deterministic 3-D shape, some proteins that our genes express do not have a native shape, but are said to be intrinsically unstructured.

Misfolded and tangled proteins get produced by our cells all the time, mistakenly or on some not-yet-understood purpose. As these proteins cannot be consumed as signals at their destinations, they accumulate as plaque in our central nervous system, which can be very harmful. But it seems that evolution has already created a mechanism, the recently discovered glymphatic system, that cleans our brains when we are not using them, during the deeper phases of sleep.

All in all, the programming language of life seems more like lisp than Fortran, in that separation between what parts are programs and what parts are data is not clean. Also, a lot of hidden garbage collection seems to be required, to recycle finite resources and thus hide the quantitative flow regulation from the reproducing parts of the organism.

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