First Implementation of Bump Life

I implemented my program in java and called it Bump Life. My initial idea is pretty boring. It does make dimers, but then not much else happens.

Initial Idea: a simple one-shape/three-state system that seems capable of self-replication:
1) O bumps O --> PP
2) O bumps PP --> PQP
3) O bumps PQP --> PQQP
4) QQ is set to break apart --> PP  +  PP

I should test all 64 rules with the 3-state system to see if any of them do something interesting.

Rule Systems (true or false for each):
Bond:  0-0, 0-1, 1-1
Break: 1-1, 1-2, 2-2

For the first implementation, I think I'll just make an array for bond and array for break and then test all possible values.

I also inadvertently invented Glitch Life that comes to life when I allow three connections--a glitch in Box2d causes the balls to start moving on their own, often erratically. Maybe I'll take a movie of that one because it's interesting to look at even though it's not very useful for artificial life studies.

Simulating Self-Replicating Molecules

My web site Fourier Life explains how I developed a system to detect self-replicating patterns by searching many different rule sets in particular cellular automata systems. These patterns are a collection of cells that turn into either two or four copies of themselves. None of the patterns were engineered--they were all discovered as naturally occurring phenomena within the particular set of rules in the cellular automata.

The rules determine how the patterns evolve and the patterns determine if it will self-replicate when the rules are applied. I don't see any reason why this system couldn't be extended to atoms and molecules to explain the origin of life. But I'd like to demonstrate this idea.

I want to make a system where:

• shapes such as circles represent molecules
• the shapes will randomly bump into other shapes and connect
• certain combinations of shapes will break some connections

Here's a brief comparison of the two systems:

	Fourier Life	Bump Life
System	Cellular Automata	2D Brownian Motion
Rule Codes	Set in world	Set in shapes
Beginning State	Random cells	Random vectors

In Fourier Life, I didn't see self-replicating patterns until I got to a certain complexity that seemed to be correlated with the number of possible rules. In cellular automata, the rules determine if a cell lives, dies or is born. For Bump Life, I think the rules should determine if a bond is made, broken or remains. The shape could have different regions that have a different color or state. The shape should also contain the rules for what happens when it bumps into other shapes. Every time step in a cellular automata should correspond to a bump in Bump Life.

When the shape bumps into another shape, each shape should read it's code and current state (what other connections exist) and then:
a) connect to new shape
b) break an existing connection
c) do nothing (just bounce apart)

To get interesting interactions between the shapes, the shape should have at least three areas it could connect to. The maximum number of areas would be six. Each of the three areas could have four states: not connected (0) or connected to another shape in one of the three areas (1, 2 or 3). So each shape has a total of 3^4 states, or 81 states. This seems like too many states.

A simple two-shape system seems capable of self-replication:
1) O bumps O --> PP
2) O bumps PP --> PQP
3) O bumps PQP --> PQQP
4) QQ is set to break apart --> PP  +  PP

This uses 3 states (O = no connections, P = 1 connection, Q = 2 connections).

Need only 3 rules for bumps (Q cannot bump):
OO connect, OP connect, PP bounce

Need only 3 rules for breaks (O is not connected):
PP stick, PQ stick, QQ break

This system only has 2^6 = 64 possible rules. This seems like a simple system to begin with and study.

A shape with three connections would have four states (O, P, Q, R), need 6 rules for bumps, need 6 rules for breaks, and have 2^12 = 4096 possible rules.

By extension, I believe a shape with four connections would have five states, need 10 rules for bumps, need 10 rules for breaks, and have 2^20 = 1,048,576 possible rules.

A shape with five connections would also be possible, have 15 rules for bumps & breaks, and have 2^30 = 1,073,741,824 possible rules.

These systems seem reasonable to program, but can I use the Fourier Transform to detect self-replicating creatures? I suppose I could test it with the very simple two-connection system above.

Leslie Orgel's Reality Check

Leslie Orgel is a pioneer in Origin of Life research. In 2008, a colleague published a manuscript by Leslie entitled, "The Implausibility of Metabolic Cycles on the Prebiotic Earth". It is a useful reality check on Kaufmann's autocatalytic sets idea.

In summary, Leslie is not a fan. He sums up his paper with this:

[S]olutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.

The bottom line for any theoretical system involving autocatalytic cycles is that they can't have chemically unrealistic assumptions. The paper also has a good discussion on actual autocatalytic cycles in biology such as the reverse citric acid cycle and the formose reaction.

Overall, an important paper for me to keep in mind.

Nomenclature of Sets

I want to understand what's already been done on autocatalytic sets in relation to the Origin of Life. Wim Hordijk and Mike Steel seem to be the leaders in this area so I want to read their 2004 paper on the subject.

Unfortunately, they use Set Theory Nomenclature heavily in the paper (see example at right) and so I need to learn that first. Fortunately, I found this nice primer from Clemson University.

Symbol summary:

• members of a set are put in curly brackets: S = {1,2,3,4}
• x ∈ S means x is a member of set S (∉ means x is not in S)
• ∅ is the empty set
• |S| means the number of elements in the set
• S ⊂ T means S is a subset of T
• S ∩ T means the intersection of sets S and T
• S ∪ T means the union of sets S and T 
• S \ T means the elements in S that are not also in T (difference operator)
• If a reference set is defined as all possible elements, U, then S' is the complement of S and means all elements in U but not in S

Lipid World

This Lipid World paper is must reading for me. From 2001, the authors lay out the case for lipids being involved in the origin of life. The title is in contrast to RNA World which is the common theory that life started with RNA molecules that were autocatalytic.

Summary & Review

Section 1: Introduction: Did Life Processes Necessarily Begin with Biopolymers?

• Biopolymers means RNA, DNA and proteins
• One advantage of RNA World is that it seems to have the evolution and information storage problem solved already
• On the other hand, RNA World is quite complex and so the chances of life starting from it become increasingly small

Section 2: Lipid-like Amphiphiles Are Highly Diverse

• Current lipids are highly diverse and have multiple functions rather than simply being a barrier between inside and outside
• This would be expected if lipid evolution was involved in the origin of life (but it could have also evolved later, so it's a chicken and egg argument)

Section 3: Amphiphiles Undergo Self-Assembly

• This is one of the most compelling arguments for Lipid World--the cells form by themselves once concentrations of lipid are high enough
• The problem is reduced to finding building blocks and reactions that can form lipids
• The lipids also don't have to be the same type in order to form; however, some combinations will be more stable than others and this would create a selective pressure enabling the early proto-cells to evolve

Section 4: Lipid-Like Amphiphilic Molecules Predated the Origin of Life on the Earth

• Both prebiotic reactions and source from space (meteors, comets, space dust) could have created lipids
• Here the paper diverges from my hypothesis which is that the first life forms found a way to efficiently synthesize lipid molecules and only the basic building blocks needed to be available

Section 5: Prebiotic Synthesis and Assembly of Membranes

• Quote: "One aspect of early cellular life that is often disregarded is that primordial membranes would need to continuously add amphiphilic components in order to accommodate the growth and replication of the encapsulated macromolecular system or of the lipid aggregate itself." Exactly!
• Studies done in 1977-78 discovered the lipid properties for self-assembly of micelles. They formed with a minimum of 10 carbons. A variety of polar groups were used such as carboxylic acids, alcohols, amines, alkyl phosphates, and alkyl sulfates (some of these may have required more than 10 carbons). They also studied mixtures and found some were more stable than the single components.
• Experiments have shown that PAH (polyaromatic hydrocarbons, e.g. phenanthrene) can photochemically react with CO2 to form aliphatic acids. These hydrocarbons could float on top of the water and be exposed to UV light from the sun.
• "There are two challenges for future research in this area. The first is to find a plausible synthetic pathway for hydrocarbons with 10 or more carbons in their chains. [...] Second, reactions must be established by which both polar and ionic character can be added to the hydrocarbon chains." Yes, these are what I need to find with an autocatalytic set of molecules.
• Alternatively, a polar building block could be extended to a long chain hydrocarbon which is how lipids are formed in our current cells (this makes much more sense)

Section 6: Lipozymes: Non-covalent Amphiphilic Aggregates with Catalytic Properties

• Many reactions are catalyzed by the presence of micelles (apparently by the concentration of greasy reagents into the hydrophobic portions, or by changes in reactivity similar to solvent effects)
• One useful reaction is the hydrolysis of esters with n-heptyl-SH
• Keep in mind: Catalysis can take place in the aqueous cytosol and in the lipid bilayer
• They introduce the term "lipozyme" to describe lipid aggregates that enhance the rate of a chemical reaction (this is a lousy term because an enzyme refers to a specific molecule but lipozyme refers to an aggregate state of molecules)

Section 7: Autocatalytic Lipozymes May Self-reproduce

• Here they get to the idea of autocatalytic sets!
• Criticism of this idea: "But they have been argued not to embody some of the properties essential for initiating an evolutionary process, since they lack information carriers such as nucleic acids or peptides." I need to come up with a mechanism to add information carriers.
• "autocatalytic lipozymes would belong to the class of phenotypic replicators, because of their functional rather than digital inheritance." Good to know the term for what I'm proposing.

Section 8: Statistical Properties of Lipozyme Catalysis: the Importance of Diversity

• They introduce their Graded Autocatalysis Replication Domain (GARD) model which is essentially a model of molecular reactions where the molecules have a range of catalytic abilities to not only replicate themselves but also other members in the set

Section 9: Mutually Catalytic Networks Within Complex Lipozymes

• This section outlines the same series of steps I proposed for the origin of life in this post
• Here they explain why they started with simulations instead of wet chemistry experiments: "Future experiments could be initiated with a mixture resembling a possible prebiotic amphiphile repertoire, and while keeping the system far from equilibrium, the composition of individual assemblies would be monitored. Such experiments are still very challenging and could be characterized by utterly slow rate constants of months and years. For this reason we have resorted to a mathematical modeling approach, based on computer simulations of the kinetics of self-assembly in complex molecular mixtures." I agree.
• They also make the very interesting point that catalysis could happen in the membrane. I like this idea because the membrane concentrates molecules (easier for them to meet) and also provides another dielectric constant for reactions which will increase the speed of certain processes (e.g. hydrolysis by aliphatic thiols)

Section 10: Compositional Information in Lipozymes

• Discusses how these Lipid World protocells would legitimately evolve with collections of molecules being passed on to daughter cells
• They make the important point that our modern day cells to the same thing with structures of membranes and the collection of molecules in the cell, including RNA and proteins
• Questions I have: What parts of the cell aren't encoded by DNA? Are any molecules in modern day cells replicated by an autocatalytic network not driven by DNA and proteins?

Section 11: Evolution of Autocatalytic Lipozymes

• More details of their simulations which supports Lipid World
• Reference The Major Evolutionary Transitions which discusses a nucleic acid takeover leading to the modern genetic code. I'll read this next

Section 12: Summary

• RNA world has problems. Nucleotides are complex and not present in prebiotic soup experiments. They also don't have a way to carry out metabolism.
• They offer an interesting theory on the evolution of protein and nucleotide biopolymer. Amino acids and nucleotides could have formed some head groups on lipids. Then, being in the 2-dimensional lipid layer would aid their oligomerization. These could then be detached and wind up in the cytosol as further catalysts.
• "An important goal for future research will be to provide an additional experimental basis for the Lipid World scenario." I agree.  I'll get on it.

I believe this will end up being one of the seminal papers on the origin of life.

Late to the Party

I was just reading this paper called "The early evolution of lipid membranes and the three domains of life" from 2012 in Nature Reviews. It talks about the dominant research areas on the origin of life:

Despite the crucial role of membranes in allowing the genetic and metabolic systems to interact and evolve together, most studies on the origin and early evolution of life have focused on the emergence of either the genetic system or energy and carbon metabolism

 But they go on to say that a focus on membranes as an early key component is changing:

This avenue of research is progressing quickly, to the point that the traditional focus on self-maintenance (metabolism) as a major property of life, together with self-replication (a genetic system), is shifting towards a focus on self-assembly (membranes) in contemporary origin-of-life thinking.

And they give references that I'll have to look up:

• Mansy, S. S. et al. Template-directed synthesis of a genetic polymer in a model protocell. Nature 454, 122–125 (2008).
• Segre, D., Ben-Eli, D., Deamer, D. W. & Lancet, D. The lipid world. Orig. Life Evol. Biosph. 31, 119–145 (2001).
• Mansy, S. S. & Szostak, J. W. Reconstructing the emergence of cellular life through the synthesis of model protocells. Cold Spring Harb. Symp. Quant. Biol. 74, 47–54 (2009).

It looks like I'm late to the party with my idea about focusing on membranes. However, the article doesn't mention autocatalytic sets. I'll have to see if any of the references mention them.

Hanczyc's Oil Drop Life

I found a Nature News article discussing Hanczyc's oil drop life which was also the subject of the TED talk I saw. My opinion is that this is a system that has life-like behavior but is not relevant to the origin of life. They are nitrobenzene droplets in basic aqueous solution (with a pH indicator to make the motion more interesting) and a greasy anhydride as "fuel". Differing gradients of pH allow the drops to skim across the surface and move like cells.

I've noticed something similar while watching crystallization of an organic compound. The first crystals formed on top of the solution and as the crystals grew, they scooted across the surface, either from the impact of molecules being added to the crystal or from the temperature of the solution heating up (or cooling) on the side that was growing. (At a molecular level, are these two explanations really different?)

So while Hanczyc's oil droplets are fascinating to watch, they are a physical phenomenon and not a useful step in the direction of autocatalytic sets which could explain the origin of life. However, the article mentioned research by Jack Szostak at Harvard who is doing research on protocells focusing on the lipid portion so I'll look in to that next.