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Life, Biology discovery, Agency, Evolution

Biology

• Schroedinger, Delbruck - physical laws for biology
• Tauber 2012 population dynamics, vertex renormalization

Introns are possibly an example of Turing machine instructions whereby information is deleted (which introduces nonreversibility). I imagine the advantage of introns is that they allow multiple mutations (and reshufflings) to take place without having an effect. At some point, there will be an error that allows the inclusion and availing of the intron to see if it can catalyze proteins. In the rare case that it does, then this can result in a new gene. Thus introns allow evolution to occur by multiple steps without each step having to enhance viability. Introns are the equivalent of "scratch paper" on which calculations can be made.

• In this case, sex is important because it allows a preservation of the rich variety of these inactive junk-DNA libraries-nurseries for evolutionary blueprints. Thus the passage of time allows for an explosion of the hidden variety which means that when there is a change in the ecosystem, the species is ready with many possible variants, both yet to be expressed and already expressed.
• Thus viruses and bacteria are streamlined but tuned based on the past but aren't forward looking in this way. Storing and developing potential variants is a forward looking activity in time and expresses forward, global causality.
• Life as a necessary enabler of chemical reactions.

Nigel Goldenfield. Is there universality in physics?

• Nigel Goldenfield 2014 tree topology, balanced, unbalanced, phylogenetic.
• Nigel Goldenfield talks
• Antifragility
• Antifragile (book)

Consider the waste products that biological activity removes such as {$CO_2$} from animals and {$O_2$} from plants and how the waste products relate to inputs. Thus how different living beings or different organs are different parts of the cycle. Consider how these pieces may be put together as divisions of everything. How does that relate to language?

Carbon reacts with a single electron in a link, a one-step causality. Oxygen reacts with two electrons in a kink, two-step causality.

4+2 elements for organic molecules

• four structural chemical elements, hydrogen (H), carbon (C), Nitrogen (N), and oxygen (O) - note the latter have valences 4, 3, 2.
• two more functional elements of phosphorus (P), and sulfur (S) - these have valences 3 and 2 respectively

Alpha helix - amino acids relate to those which are three steps above in the chain, thus this gives the operation +3.

Think of life as an attractor. Express attractors in terms of Wondrous Wisdom.

The Story Behind "Silent Spring": How Rachel Carson's Countercultural Courage Catalyzed the Environmental Movement

• Professor Dave. Biochemistry.
• Andrey. Biochemistry.
• MIT Biological chemistry
• MIT Biological chemistry vaizdo įrašai

Oxygen, nitrogen, carbon are like the twosome, threesome, foursome of organic chemistry. It is not the atoms but their valences that matter. Thus they belong not to the world of matter but to the world of lack of matter, thus of flow.

David Corfield's video. Colin McLarty: semiotics as the language of biology - logic in a biological key - trying to categorify this?

The Physics of Evolution

Biochemistry

• Consider the octo-cycle form of sulfur (the eight-cycle) as a template for the arisal of life.
• Do the complements of the divisions of everything express the reverse Kreb cycle?
• Biochemijos paskaitos
• A cell has a boundary. If it is a single-celled organism, then its boundary can be thin. If it is multi-cellular, then there is no way to push out the protons, so that has to take place inside, into mitochondria, yielding inner boundaries. And this grounds self-awareness, bringing the outside inside of us.

Alan Turing, Cybernetics and the Secrets of Life

How do Dynkin diagrams relate to organic molecules such as sugars?

Open Learning Initiative. Biochemistry Course.

Yale. Freshman Organic Chemistry

• Atmosphere has mass of 5.15×10^{18} kg
• Person breathes 10 tons of oxygen = 10,000,000 grams of oxygen in their lifetime
• 16 grams of oxygen has 6*10^23 atoms of oxygen
• 1 gram of oxygen has 0,375*10^23 atoms of oxygen
• Reproduction - dialogue between man and woman, conscious and unconscious - dialogue for raising children

Body shape is not determined by the genome but by electromagnetic activity. The genome works locally.

Tet methylcytosine dioxygenase 1 Tet1 gene

Neurology: Arousal: Sympathetic (fight or flight) vs. parasympathetic (relaxed).