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This is the basic Darwinian answer to the chicken and egg problem of the development of living cells:

1. In the Beginning, nucleic acids managed to spring into existence in pre-organic seas. RNA - a simpler form of DNA was created.  

2. Mutation resulted in variety of RNA molecules.

3. RNA - which contains code for creating other molecules - managed to create protein-based enzymes.

4. Some of these enzymes facilitated the formation of the RNA by which they are defined.

5. These RNA and enzymes combinations gained competitive advantage over other molecules in the pre-organic sea.

6. The RNA and enzyme combinations managed  to become encased in cells.

7. Once established as "living" entities, these cells competed with one another and evolved to fill available niches.

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Howard Morowitz, a biochemist associated with the Sante Fe Institute, argues that life is an inevitable result of the laws of chemistry that were established when the universe was formed.  He calls this principle the Universal Metabolic Chart (comparable to Mendelev's periodic chart). His answer to the chicken and egg issue is this: Neither nucleic acids nor amino acids came first - it was the cell itself. The story goes like this.

1. In the Beginning, pre-organic seas contained fatty molecules called lipids. These molecules didn't mix with water and joined naturally into sheets. Conserving energy, the sheets folded into vesicles - the precursors of cells.  

2. Semipermeable vesicle membranes blocked some molecules and allowed others to pass. Unique chemical combinations formed inside the vesicles.

3. Some vesicles absorbed basic chromophores - molecules capable of storing solar energy. Using this energy, vesicles "pumped" other, more unlikely molecules across the membrane barrier, into the cell.  

4. Bumping into one another like oil drops in standing water, vesicles combined - growing in size and developing even more varied internal chemistries.

5. Vesicles beyond a certain size become thermodynamically unstable. They split, creating multiple instances of the same contained chemistries.  That was a form of cell division.

6. Some vesicles developed the ability to create their own membranes, chromophores, etc. These vesicles, with their self-sustaining metabolisms, were better able to compete with other vesicles for free-floating molecules (e.g., "food").

7. Some of these self-sustaining vesicles developed simple amino acids which catalyzed the development of even more unlikely chemical combinations.

8. Finally, the end of this particular stage occurred when one of these unlikely combinations contained, as a string of nucleic acid molecules, instructions for creating itself.  This was a true, living cell.

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This is a basic Darwinian answer to why prokaryotes were incorporated in eukarytotes and why eukaryotes combined into multicellular organisms.

1. Sometime after the Beginning, in times of famine and extreme competition, smaller, food-burning prokaryotes found their way inside larger prokaryotes. They attempted to use the latter's internal waste as food.

2. Most of these combinations didn't work. Both parties died. However, some provided survival advantages.  Some prokaryotes became oraganelles called mitochondria. In plants, some became chloroplasts - the organelles that convert sunlight into energy.

3. Random mutation produced various specialized eukaryotes - some good at detecting light, some good at locomotion, etc. .

4. Occasionally, these specialized eukaryotes would "stick" together.

5. As before, most combinations didn't work and the cells died. However, also as before, some combinations provided survival advantages. They prospered and according to the standard myths eventually became us.

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This is an elaboration on the basic Darwinian explanation for the development of hierarchies. It is based on the notion of sacrifice.

Individuals sacrifice themselves to a larger whole, and in the process create new individuals who sometimes sacrifice themselves for an even larger whole.

Richard Dawkins in his 1976 book, Selfish Genes, says that organisms, such as humans, are really vehicles for genetic survival.  What appears to be sacrifice at the multicellular level is the work of genes - shared by the entire organism - promoting their own self-interest.

Leo Buss, in his 1987 book, The Evolution of Individuality, develops the idea of "kin selection" to explain why smaller individuals sacrifice themselves to create larger individuals - and how this results in hierarchies.

Here is the origin myth based on kin selection:

1. In the Beginning, the pre-organic sea contained various molecules that used enzymes to help reproduce themselves.

2. Some self-replicating modules combined into metabolisms (e.g., new, larger individuals) that could make their own enzymes. The metabolisms gained competitive advantage over other, simpler molecular combinations.

3. These single-metabolism entities evolved to fill in all the niches allowed by their chemistry (which struck a balance between change at the component level and self-destruction at the entity level).  

4. Eventually there was a shortage of "food" at the entity level.

5. Evolving in the only direction available, some single-metabolism entities combined into entities comprised  of multi-metabolisms.  They could "eat" other simpler metabolisms plus they could explore heretofore untapped food sources. Again, the individual sacrificed for the good of the whole.

6. Prokaryotes happened when these multi-metabolisms "discovered" that they could do better when contained within protective cells.

7. As before, entities (prokaryotes) evolved into all niches available to their chemistries  - until there were no more niches to fill.

8. Responding to another famine, evolution once again proceeded in the only direction available - toward increasing complexity. Prokaryotes combined with other prokaryotes to become eukaryotes.

9. A similar process caused eukayotes to combine into multicellular entities and, as niches at various ecological levels filled, for multicellular entities to combine into other entities.

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Stephen Jay Gould is the famous evolutionists who asked what would happen if the geologic clock were rewound and then run again.  Would the same species be present? Would there be a hierarchy of creatures from simple to complex?  Would we (or some other thinking creature) arise?  Unlike the structuralists, whose myths are described on the other side of this page, Gould thought not.  He said that what we see now is the result of random events and is so accidental that it would not likely to appear again.

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Doyne Farmer, Stuart Kauffman, Norman Packard and others wondered if autocatalytic systems (e.g., prokaryotic cells) would happen regardless of the particular elements (such as carbon) available at the time.  They wondered if such development is inherent in the laws of complexity.  

To investigate this idea, they developed a computer simulation called "Artificial Chemistry".  Reducing chemistry to a few basic rules, the model would show whether complex systems could automatically arise from a mix of simpler constituents.

Here is how it works:

1. Define the Beginning as a time with a mix of things (real or "artificial" chemicals) that can combine to create new, more complex things.  Assume that some of the combinations can be catalytic - promoting other combinations. Also assume that combinations can undergo random mutation.

2. Initially,  combinations are simple.  (A combines with B; B combines with C.)

3. Later, more complex catalytic combinations occur.  (AA promotes the formation of CC).

4. When catalysts promote catalysts that promote themselves ((AA promotes BB which promotes AA), an autocatalytic (self-catalyzing) system occurs.

5. Given the presence of things (enough A's, B's and C's) to sustain the process, simple metabolisms happen.

6. Such metabolisms contain one or more "seeding sets" - subsets of the network of things that make up the metabolism.  Put a seeding set in a pool of things and a new instance of metabolism will be generated. The seeding set can be viewed as a genome of the metabolism.

7. Mutations in the genome result in more complex metabolisms - some of which survive.

8. When encased (in cells for instance) the metabolism becomes a self-sustaining, separate thing.  

This is not evolution in the Darwinian sense - at least not until separate cells start to compete for available resources. It is development - a series of steps leading toward a known end.

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Algorithmic Chemistry is another computer simulation showing how hierarchies happen. It was developed  by Walter Fontana, Leo Buss and others. In Fontana's words, "Biology ... lacks a theory of organization." He and his colleagues intended to demonstrate one possible organization.

The simulation was created using "the lambda calculus".  Its functions specify how...

... three shapes (circles, squares and triangles) representing molecules ...

... can combine into strings...

... which are new functions that, because they are both information and rules...

... are objects...

... which represent enzymes.  

Following is a summary of how it works:

1. In the Beginning, God (Walter Fontana) created a universe. This universe consisted of 2,000 to 3,000 strings (enzymes).

2. God selected two strings at random (Adam and Eve strings) and let them bump into one another.

3. Following rules laid down before the Beginning, the strings combined, one string becoming input to another string. The result was a new string (e.g., a new  enzyme object).

4. The new string became input to another string producing a different string which became input to still another string.

5. Pretty soon the universe was filled with string interactions.

6. Responding to a mistake in an earlier iteration of His universe, God included one restriction. Child strings that were exact copies of a parent string were not allowed to live.  God discovered that if such copies were allowed, the universe would become filled with self-copiers.

7. With this rule in place, the universe worked out- producing networks of self-maintaining reactions - e.g., autocatalytic metabolisms (which could be thought of a prokaryotes).

8. At this point, God played with His universe, introducing different rules for how strings combine. The result was a variety of metabolisms.

9. These metabolisms also combined, creating other more complex metabolisms (which could be thought of as eukaryotes).

10. The metabolisms continued to combine and God rested.

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Stuart Kauffman developed a computer simulation of gene expression - how the same genome results in different types of cells doing different jobs. In his model, each "gene" was connected to two other genes - simulating the chemical means used by cells to turn real genes on and off.  The patterns he discovered confirmed his belief that there is an inherent order in networks that resulted in the development of life.

This is how it could have happened:

• Networks of molecules, with little outside influence could have organized themselves into cells.

• Networks of similar cells could have organized themselves into creatures.

• Physical networks of creatures could have organized themselves into ecologies.

• Social networks could have organized themselves into packs, flocks, tribes and states.  

• (Expanding this idea, one could imagine that mental networks, consisting of goals, memories, predispositions,  etc., might organize themselves into personalities.)  

Network Background

Networks are dynamical collections of connected parts. Actions in one part affect other parts.  One example is an array of connected light bulbs.  The condition (on or off) of one bulb causes other bulbs to switch on or off.  Another example is a cellular automaton.

The state of a network is the pattern of its parts.  In the light-bulb network, the state would be the pattern of on and off bulbs at any given moment.

Over time, the state of a network changes.  In the light-bulb network the bulbs flash on and off in a series of patterns.  The rules defining how the parts are connected determine how many states a network can have.  If each part receives input from only one other part, the network quickly settles into one static state.  If each part is connected to every other part the state constantly changes.  The network has an infinite number of states. However, if the parts are "sparsely" connected - for example, if one part receives input from two other parts (as in Kauffman's model above) , the network will cycle through a series of repeating states. If the human genome (with 100,000 genes) were such a network, it would be restricted to about 250 states - corresponding to major cell types.

The states in a Kauffman network can be viewed mathematically as basins of attraction in a fitness landscape.