Sunday, June 05, 2016

Cells are computers, organisms are fractals

     Cells are computers, organisms are fractals

Some notes towards a concept. I’ve long thought that the notion that a neuron as an on-off switch was too simplistic. These notes represent an attempt to produce a better notion. 2016-06-03 & 05. WEK.

The metaphor of DNA as blueprint is misleading. Better: DNA is a program guiding the assembly of proteins. Better yet: It’s the operating system, since it’s RNA that produces the proteins. But if DNA is a program, then the question is, How does it execute? The answer: like any program, at any given time some part is running, the other parts are silent. A program can also trigger other programs. The operating system controls how multiple programs run, it allocates memory and CPU time, access to video and audio subsystems etc. A “call” from one program will stop or start some part of another program. An “interrupt” will cause (re-)allocation of memory, access to subsystems, etc. DNA starts and stops protein synthesis, turns genes on and off, analogous to OS controlling program execution. So the cell is a computer

Recent research shows that inputs to the cell “turn genes on and off”, analogous to calls and interrupts controlling how a program runs. The genes control the functioning of the cell. Exactly how is complicated, but the general pattern is chemical feedback loops. A substance increases, which triggers or stops gene expression, which results in a series of reactions, which cause that substance to decrease, which stops or triggers gene expression, and the cycle repeats.

A neuron responds to the chemical environment outside it by adjusting its internal processes. These processes control gene expression. The feedback loops within the neuron determine the types and quantity of neurotransmitters emitted at the synapse with the next neuron in the circuit. Since both type and quantity of neurotransmitter vary depending on the inputs to the neuron, the neuron is computing the output. The concept of a neuron as simple on-off switch is inadequate.

But a cell is an odd kind of computer. The relation between input and output depends on the internal feedback loops. A given substance may be implicated in two or more feedback loops, which means that the neuron is topologically a net. The computation of the output depends on the topology of the net of chemical reactions, which happen both simultaneously and in sequence. That makes the cell a parallel computer.

More precisely, the cell is a net whose topology varies over time as the chemical feedback loops cycle between limiting states and intersect with each other. Thus, the cell cycles through a series of topologies. It’s a self-modifying net.

The concept of a self-modifying net applies to assemblies of cells (tissues), to organs, and to the organism as whole. The organism too is a complex system of feedback loops. Mathematically it’s a chaotic system: it tends to maintain itself within an envelope of states (the attractors). Illness and disease move the system outside the envelope, and recuperation is a return of the system to the dynamically stable cycles within the envelope.

Conclusion: An organism is a multi-dimensional net of feedback loops. Its topology varies over time at many scales, which implies it’s a fractal system.

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