Spokes 1

Spokes 1: The Science of Existence  (Table of Contents) {Notes}

The Spokes series starts with the unfolding of the universe. After considering the cosmos, Spokes 1 settles on Earth, where its structure is explained.

Physics begets chemistry. Chemistry defines biology. Biology circumscribes life. Thus the path of Spokes 1: from physics to chemistry to cellular biology and genetics.

From the chapter on Physics:

Classical physics long accepted what the five senses facilely perceived: that there are only four dimensions: three spatial and a vector of time, in a universe self-contained within those four dimensions. As human perspective of the universe expanded, the scope of the universal laws shrank.

Inquiry into the nature of radiation ushered in modern physics: a post-Newtonian conception. Following along the lines of earlier work by others, Albert Einstein contemplated the speed of light and envisioned discrete quantities (quanta) of electromagnetic radiation, in papers published in 1905.

The onset of modern physics came from poking holes in classical descriptions, finding them lacking when considering the cosmic or infinitesimal. The irony of modern physics has been in creating new holes that brings physics knowledge to its limits; a demonstration of how little really is or can be known about the nature of reality.

From the chapter on Life Begins:

The parameters surrounding the origin of life on Earth are known. The geological conditions have been discerned, the requisite chemistry understood, the timing apprehended. Yet life’s onset retains mystery.

What is not yet known is exactly how and where the ingredients that spawned life came together with the spark that started life’s engine, though good guesses have been made. The enigma that lingers lays in life’s spontaneous generation: the force of coherence that led life to coalesce.

Life on Earth began as soon as environmental conditions permitted. The mathematical probability of elements randomly assembling into a metabolizing, self-replicating life is astronomically small. Yet it repeatedly happened, with nary a chance that it was happenstance.

From the section on The Evolution of Eukaryotes (in the chapter on Cells):

As the Earth and its atmosphere were transformed by cyanobacteria, viruses promoted prokaryotic evolution by providing genetic uploads.

2.5 billion years ago, eukaryotes arose. The first step to eukaryotic life was through unification: one prokaryote incorporated another. The host was an archaeon.

An intracellular bacterial parasite gave rise to the mitochondria found in all eukaryotic cells. At some point, the bacterium that beget mitochondria became benign, then mutualistic. The mitochondrial bacterium went from stealing ATP to providing it.

This sort of transition is not unusual. Viruses go from devastating to their hosts to being tolerable, as they learn to prolong their residency by not inflicting untold damage, and thereby benefit from host longevity.

From the chapter on Cells:

It is critical for cells, whether microbial or part of a larger organism, to adaptively configure their biochemical operations to current conditions. Cells do so through a host of measures, including altering protein production and self-manipulating their DNA. All cells intelligently manage their existence at the molecular level.

From the chapter on Genetics:

Genes are often described as if they are linear sequences, awaiting ready decoding as construction templates for useful products. Nothing could be further from the truth. The genetic coding schema defies easy characterization because it defies topological comprehension.

Individual chromosomes occupy distinct territories in the cell nucleus. Where they reside, and what other chromosomes are in the neighborhood, can strongly influence whether the genes in a chromosome are active, and how a cell functions.

The definition of gene is non-specific for good reason. A gene is conceptual, not an actual entity; a term for the information encoded within polynucleotides. Genes don’t exist in physical reality, only in the minds of geneticists.

The term gene is used as if the recipe and result were synonymous. They are not. Research into epigenetics has shown that genes as an adhered-to rulebook represents an inapt simplification.

Life begins in Spokes 1. Spokes 2 continues with an exploration of life on Earth.