A global flood of metabolism

Michael Rynn
5 min readNov 2, 2022

Of course I put a mention of the global CO2 crisis into this article, as this industrial interference also pokes into every ongoing living metabolism on this planet. Also some appreciation of the science of biochemistry, the study of the processes which powers our lives and thoughts, some of which is surely worth knowing.

Model of Citric Acid

At every level of our virtual existence, this complex reality, is an emergence of mysteries from much lower levels of composition. I appreciate our biochemistry, and how so much of our living molecular components are constructed from repeated common steps of combining carbon dioxide and hydrogen. Progress has been made in finding out the steps of making all our important biomolecules. This has already been worked out by evolution but now many of them can be replicated in research laboratories. This chemistry of CO2 + H2 eventually produces complex multi-cellular life. The hydrogen comes from water molecules, in which all life metabolism is immersed. I haven’t forgotten nitrogen, phosphorus, and a host of other elements from our salty seas, its just that their isn’t room here.

My sketchy knowledge of this was recently updated by a you-tube video. ( “How the Krebs cycle powers life and death — with Nick Lane — thank you to The Royal Institute ). There is of course, his book “Transformer” as well.

Most of this article I have interpreted from this source. Control of this “Krebs” cycle, and its products is deeply connected to all metabolic processes in the biosphere, including some particular features of animals lives, including our obligatory aging and susceptibility to cancer.

This dance cycle of the atoms of CO2 and H is intimately associated with maintaining an electric charge across a nearby insulating membrane. In bacteria, and in the cellular mitochondria that are distantly related, the forward working of the countless numbers of this chemical generates a electric potential, an electric voltage gradient across the nearest membrane.

This biochemical cycle is so important it has been given at least 3 names so far. Citric acid cycle, Tricarboxylic acid cycle, Krebs cycle. Here I will abbreviate it as CC, short for “Central Cycle”. I just made that up to emphasize metabolic centrality. CC is also used for Carbon Copy, after the old means of making copies of handwriting on paper.

The CC ancient evolved cyclic reuse of a repeated sequence of variants of a six carbon chain backbone. Exactly how many steps is a few more than I like to count. There are several animations of the energy generation cycle version on You-tube.

Citric acid is a symmetric hydrocarbon that comes with carboxyl attachments. Each carboxyl is a double bound Oxygen and single bond Hydoxyl (OH). Glucose is also a 6 carbon molecule, but its carbon atoms are link closed in a loop. Citric acid is all opened up, ripe for processing, adding and subtracting.

As well as being used to regenerate energy carrying molecules, the CC is also an engine of biosynthesis. The CC can be made to run backwards, when the conditions and reactants are suitable, to make biochemical building block molecules while utilizing CO2 and energy.

In multicellular, specialised animal cells, both manipulations of the cycle are happening at the same time, only in different places. At one place, and one time, the CC is in operation in one direction only.

In the picture of the citric acid model above, Carbon is coloured gray, Oxygen red, and Hydrogen is white. This is a nice representation model, not quite to scale and flexibility of its typical working place that I cannot imagine.

The carboxyl arms are acidic, given to donating their hydrogen, and swapping other attachments for work in the chemical assembly line. These are chemical reactants just waiting for work.

CC works in a watery world of thermal crashing and bashing at molecular levels, with quantum forces and interactions at incredible small time and distance scales, invisible to our macro world. At molecular scales, bacteria and cells are giant living cities, with their dynamic construction managing incredible organization, consistent with thermodynamic purpose.

The speed of the cycle is accelerated by specialised protein machines, adapted by ages of evolution. The continuity and reproduction of life through 4 billion years of evolution has required continuity or reproduction of the energy or growth cycles of the CC.

At some point on the young earth, micro environments not now common, created the chemicals just right for some of this cycle to happen, catalysed by rocks and metals, rather than by proteins and genes. This started in an oxygen free environment. Ubiquity of oxygen today prevents a reboot.

The CC chemistry likely started spontaneously in nature, in deep-sea hydrothermal vents related to volcanism. Simple biosynthesis generated the building blocks of genes, and the beginnings of genetic inheritance emerged from its production of common amino acids and nucleosides.
In ancient bacteria, with relatives still around today, the CC worked backwards to react the simple gases of carbon dioxide and hydrogen to generate the universal precursors of life.

In us animals that are highly powered by aerobic oxygen using energy production, accumulation of oxygen damage to the metabolic and genetic machinery is unavoidable. It is the cost of high living and investment of energy in reproduction. The CC flux machines gets more sluggish with age, and this unmasks different age-related diseases in each of us. Lifestyle, food choice and exercise may modify the development of our propensities for diabetes and Alzheimers diseases that are linked to our failing cellular respiration through the CC.

Nick Lane also suggests that the CC flux of metabolism that generates electric potentials is also linked to our feelings of a stream of consciousness. Even in bacterium, that generate an electric membrane potential that varies moment by moment with metabolism and environment.

The recording of changes in electric potentials associated with our neural processing is due our neuronal depolarization signals, but from deep within the parallel inner plates (called cristae) of mitochondria generate their electric potential from the CC. Unrolled out, like many other fractal membranes and surfaces inside our bodies, they can cover amazingly large areas. Neurones are highly energetic and have lots of mitochondria. The feeling of being alive is always electric. May the force be with you.

Fossil Fuels are carbon and hydrogen that was buried and cooked over eons from the dead bodies of once living creatures, that spun their CC, in synthesis. We now release their oxidation products into the atmosphere at a huge rate of burning energy wastage. The resulting change in atmosphere composition and temperature, and ocean composition and acidity, now feeds back into the metabolism of every living plant and animal creature.

There is no possibility of not causing subtle and evolving changes in the functions of each and every living organism. Extra CO2 diffuses from water and air into every living metabolic reaction corner. Every plant leaf and fractal animal absorption surface, is passing additional CO2 flows into the living interiors of every animal cell and bacterium.

That last statement is meant to be scary and menacing, but without specificity, because that is what it is. The kingdoms of bacteria are the most likely to survive the onslaught.



Michael Rynn

Once was educated and worked in Medical Practice, then did software engineering. Now retired. Still doing music, reading and writing, and website tinkering