Transformer: The Deep Chemistry of Life and Death, Nick Lane, c. 2022.

High points:

• where is Nick Lane going with this book
• what is the transformer? The Krebs cycle
• reminder: animals came first; high CO2 environment
• reminder: plants came second: high oxygen environment
• plants -- autotrophs -- CO2 + H2 --> carbohydrates and everything else (?) --
• photosynthesis: energy (sunlight) -- built things from scratch
• animals:
• respiration (the other side of the photosynthesis coin)
• broke carbohydrates down
• starts with the Calvin cycle: why? I need to go back to this chapter
• BIG IDEA: the Krebs cycle was originally the "reverse Krebs cycle" and then flipped
• energy (the Krebs cycle -- or more accurately, the reverse Krebs cycle, drove DNA
• energy drove information
• BIG IDEA
• energy drove information
  
• BIG IDEA
• "classic," modern biology argues that information drives energy
• "classic," modern biology argues the chicken and egg problem, that information came first; then energy; DNA/RNA came first, and that put the Krebs cycle in motion;
• Nick Lane: energy came first (the Krebs cycle came first) and that drove the "evolution" of DNA/RNA

Rubisco:

• Rubisco: one job -- to fix CO2 --> carbohydrate and everything from that
  
• poor at its job
• struggles to tell difference between CO2 and O2
• is that a "plus" or a "minus" for the organism
• Nick Lane says rubisco first evolved "several billion years ago" during a period when CO2 concentration was very, very high

Rubisco:

• finally pages 95 - 96, we see where Rubisco "fits" and how it "fixes" either CO2 or O2 to a five-carbon sugar (ribulose bisphosphate) -- making a 6-carbon sugar which splits to two three-carbon acid, which with hydrogen from photosynthesis converts the acid to a three-carbon sugar.
• that three-carbon sugar then "fluxes" to that five-carbon ribulose bisphosphate again
• not sure where the two carbons come from to regenerate the five-carbon sugar to continue the cycle

But now, look at this.
in a low-CO2 environment, rubisco fixes O2 to the five-carbon sugar (ribulose bisphosphate) -- the oxygenase in rubisco fixes oxygen rather than CO2 -- O2 replaces CO2 

Now, abruptly shifts to the "Calvin cycle": p. 97
that CO2 fixation makes sugars is the central dogma of metabolism .. and it's wrong -- p. 98
Calvin cycle
UC Berkeley
discovered using newly discovered / identified C-14
so, is this what Nick Lane is saying? yes, the Calvin cycle is important, and it was a huge deal when discovered, but it is not the central dogma of metabolism and does not get us closer to the origin of life

Five years after Calvin's Nobel prize, a new development: Daniel Arnon, p. 98

Chapter 4: looking for origin of life

p. 121: admits that phylogenetics does not support the contention that the reverse Krebs cycle is ancestral to life, as would be the case if it arose at the origin of life. Besides the reverse Krebs cycle and the Calvin-Benson cycle, we now know of another four autotrophic pathways of CO2 fixation across the living world. 

Of these four, only one is found in both bacteria nd archaea, the two great prokaryotic domains of life, implying that this was the only pathway present in their common ancestor, the last universal common ancestor of all life (LUCA). Then read more ...

... all these factors indicate that the acetyl CoA pathway was the ancestral pathway of CO2 fixation. So, from this phylogenetic point of view the reverse Krebs cycle seems to be ancient but not ancestral. -- p. 122

But, back to Krebs .... starting at bottom of page 122 and going into top of page 123 --- key to the book ... 

The great, great story of the child prodigy, Harold Morowitz. -- page 124.

******************************
Now, The Notes From The Book

Transformer: The Deep Chemistry of Life and Death, Nick Lane, c. 2022.

Flow vs flux:

• flow: water flows; from "entry" to "exit," water does not change
• flux: "the object" flows but from "entry" to "exit," the "object" changes

Author uses city map, streets, and changing vehicles as the metaphor for "flux."

I think he could have also used branching assembly lines, allowing "objects" to move from one assembly line to another.

Ur-product at entry will look very different than finished object at exit. 

A robot or a person along the assembly line "changing" the "object" is the catalyst.

Nick Lane begins the book with the question: how is a "live" cell different than a "dead" cell one moment later?

The "live" cell has flux? 

From "live" to "dead" that flux stops immediately.

Perhaps later in the book but at the start, Nick Lane does not mention what will stop the flux:

• temperature (nothing moves in frozen water)
• pH (catalysts need a certain pH; protein's shape depends on pH)
• toxins can gum up an assembly line;
• mutated catalysts, proteins, can gum up thee assembly line;

Biology:

• information: DNA
• energy: Krebs cycle

Since 1950s, information / genes / DNA has been the center of biology; with result that energy was overlooked.

Nick Lane posits that energy is more important than information.

Most argue that information drove energy.

Nick Lane argues that energy drove information.

In the cell, the center of energy and matter is the Krebs cycle. 

Again, most high school students see the Krebs cycle as an energy cycle; in fact, its products include sugars, amino acids, fatty acids.

*****************************
The Calvin Cycle

From wiki:

The Calvin cycle, light-independent reactions, bio-synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into glucose. 

The Calvin cycle is present in all photosynthetic eukaryotes and also many photosynthetic bacteria. In plants, these reactions occur in the stroma, the fluid-filled region of a chloroplast outside the thylakoid membranes. 

These reactions take the products (ATP and NADPH) of light-dependent reactions and perform further chemical processes on them. 

The Calvin cycle uses the chemical energy of ATP and reducing power of NADPH from the light dependent reactions to produce sugars for the plant to use. 

These substrates are used in a series of reduction-oxidation reactions to produce sugars in a step-wise process; there is no direct reaction that converts several molecules of CO2 to a sugar. 

There are three phases to the light-independent reactions, collectively called the Calvin cycle: carboxylation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration (rubisco). 

Though it is called the "dark reaction", the Calvin cycle does not actually occur in the dark or during night time. This is because the process requires NADPH, which is short-lived and comes from the light-dependent reactions. 

In the dark, plants instead release sucrose into the phloem from their starch reserves to provide energy for the plant. 

The Calvin cycle thus happens when light is available independent of the kind of photosynthesis (C3 carbon fixation, C4 carbon fixation, and Crassulacean Acid Metabolism (CAM); CAM plants store malic acid in their vacuoles every night and release it by day to make this process work.

Chapter 2: The path of carbon.

Question:

• Reverse Krebs cycle: pre-dates photosynthesis; early in history of beginning of life when CO2 concentration was high
• Krebs cycle: flipped; much later in history of life; when O2 levels very, very high
  the Krebs cycle; at the root of ageing and diseases such as cancer where the balance between energy flow and growth is paramount?