Smith and Morowitz, The Origin and Nature Of Life on Earth

[casualphysicsenjoyer]

I'm trying to pick through this pretty dense textbook from Smith and Morowitz about their theory of the fourth geosphere.
Main problem to me is that the amount of pre-requisites it requires is pretty huge. I do not know much geochemistry or biology, and even the physics section in chapter 7 on statistical physics is hard. Friends who also are trying to read this book say it's hard.

Trying to find people for a reading group on this stuff, reply here if interested. I found an email reading group that might work.
Also more thoughts - wondering if there should be a formalisation effort underway here since there are a lot of claims.

[casualphysicsenjoyer]

Chapter 1
Main idea - life was a cascade of phase transitions

• as opposed to what though?
  • feels so vague but i guess more in chapter 7
• what exactly was transitioning?
  • was it something like a dyson's theory of life thing where there was some jump from a dead state to an alive state with low probability?
  • pre 1975 phase transitions were pretty much only a physics thing
    • i wrote this for casual physics enjoyer - notes to follow here
• he argues that a cascade of transitions has precedent in equilibrium systems, and that these equilibrium systems move in a path to complex order — and that this cascade is the basis for a current hierarchical theory of matter
  • not clear to me what this exactly looks like - later references in chapter 7

Chapter 2

• right now I have very little intuition about biochemistry at all — like what the main mechanisms are that people use to reason about living things.
  • one reasonable thing to dig into is just how enzymes work, since I know they speed up reactions — so I'm going to try to ask some dumb and basic questions about enzymes.
  • in another direction, I'd like to figure out what chemical reactions are actually important — like, what does a living thing actually do?
  • one reasonable thing is to look at the most basic lifeforms and start to figure out what inputs they take, what outputs they produce, what energy this requires, and how it all works.
• I'm actually more convinced now that learning these things would have broad applicability, even if I don't end up working on an origin-of-life problem. For example, if I understood photosynthesis better, it would be an interesting exercise to figure out how one could improve the physics of it.
  • So in a sense its a fairly good pick to try and work on this.
• p. 36 — I don't understand this at all: "a theory of biogenesis must ultimately account for why so many forms exist and why there are so many qualitatively diverse, and what role each plays in the function/maintenance of the biosphere"
• the main source of energy for life on earth
  • Chemistry is confusing, but Smith argues that life is a chemical process. This isn't obvious to me — for one, it draws a line between what counts as chemical versus physical, quantum, and so on. And if chemistry is really just about electrons hopping between different molecules, then that actually constrains quite a lot about what life can be.
    • What does this actually mean by a chemical process? Well, he says that chemistry is the dynamics of an electron being transferred across molecules — and this is a fairly reasonable way to describe chemistry in my opinion.
    • reduction is when an electron is added to the system, think 'the charge number reduces by -1'
      • when does this happen in a general reaction?
        • is it when
      • oxidation is when an electron is removed form the system
        • an example of an oxidation reaction is Zn → Zn²⁺ + 2e⁻, where the zinc atom loses two electrons and its charge rises from 0 to +2. Biologically, NADH → NAD⁺ + H⁺ + 2e⁻ dumps electrons into the respiratory chain.
      • what is an example of a reduction reaction?
        • a simple one is Cu²⁺ + 2e⁻ → Cu, where the copper ion gains two electrons and its charge drops from +2 to 0. The biologically important one is NAD⁺ + H⁺ + 2e⁻ → NADH, where NAD⁺ picks up electrons to become the cell's main electron carrier.
        • any ways to do this easily?
  • what elements do we actually care about in biochemistry? Smith puts a useful categorization here, in section 2.5.1, the 'scales of biochemistry' subsection.
    • These are the categories
      • carbon, hydrogen, and oxygen — for structure
      • nitrogen — for catalysis and information, i don't know what 'information' in this context means
      • phosphorus and sulfur — for energetic bonds, again i don't know what this means
      • transition metals — for electron transfer
        • this feels important and I need to get back to it later
  • then the interesting question is
    • what conditions can CO2 and H2O convert into biomass?
      • how much energy is required for this reaction to happen
        • when did the first reaction happen...
          • what geothermal conditions would lead to the first type of reaction happening?
            • on p. 53, Smith and Morowitz talk about hydrothermal vents.
              • the black smoker from the mid-Atlantic ridge — temperatures around 350 °C and an acidic pH of 3.
              • the white smoker from the Lost City hydrothermal field on the Atlantis Massif, near the mid-Atlantic ridge — temperatures of 50–90 °C and an alkaline pH of 9–11.
              • there's more here about serpentization, but I don't understand it.
      • what is the basic reaction that converts CO2 and H2O into something
        • methanogens grow from 4H2 + CO2 -> CH4 + 2H2O
        • what kinda enzymes are involved in this
          • rubisco?
            • apparently this is the most abundant enzyme there is on Earth
            • what are the current research problems in this?
            • how big is rubisco in size
            • how fast does rubisco
          • how does rubisco work
            • what is Calvin–Benson–Bassham cycle
              • seems to be the first part
            • why are there three steps?

(attached image 1 below)

• Why has rubisco not evolved to be a better catalyst?
  • When did rubisco appear? 4 billion years ago?
  • Is there a question around why rubsico is slow?
    • How many molecules are there per second that are

• what does rubisco catalyse
  • what is the shape
    • its made out of large subunits and small units
      • 8 large and 8 small
        • the large subunit is around 400 amino acids
        • small subunits is around 200 amino acis
    • we know the amino chain from gene sequencing

• what is the amino acid sequence for plant rubisco? (attached image 2 below)

• Everrett shock has done some work in hot springs that some reactions can convert CO2 to biomass
  • need to understand this more
  • the minimal example is the conversion to the carbohydrate
    • 4H2 + 2CO2 -> 2 C H2O + 2H2O?
• how much energy does this reaction need?

• an example of this would be aquificales
• what are fermenters?
• serpentisation
  • i see this word in other origins of life texts but I'm not sure what it means, for example Nick Lane mentions it here: https://www.cell.com/action/showPdf?pii ... %2901438-9
  • apprently this occurs in hydrothermal vents but I haven't grokked the significance of this
  • how acidic are they
  • what is this serpentisation thing everyone seems to talk about

Stuff I don't understand

• what is this RNA world business

Other cool origins of life stuff

• discovered nick lane's work

https://www.chemistryworld.com/features ... 88.article