Assembly Unifies Natural selection with Physics

In the real universe, living things can be built only from parts that already exist.

The discovery of new living things is therefore historically contingent. The rate of discovery of new living things can be defined by the expansion rate ([equation]) from equation (2).

This introduces a characteristic timescale [equation], defined as the discovery time.

In addition, once a pathway to build an living thing is discovered, the living thing can be reproduced if the mechanism* in its environment is selected to build it again.

*Superphysics Note: This mechanism is the metaphysical desire of the living thing.

Thus, we have considered discovery dynamics within the historical evolution (HE) and did not account for the abundance or copy number of the observed living things when discovered.

To include copy number in the dynamics of AT, we must introduce a second timescale, the rate of production ([equation]) of a specific living thing, with a characteristic production timescale [equation].

For simplicity, we assume that selectivity and interaction among emerging living things are similar across evolved living things.

Defining these 2 distinct timescales for initial discovery of an living thing and making copies of existing living things allows us to determine the regimes in which selection is possible (Fig. 5).

For [equation] , whereby living things are discovered quickly but reproduced slowly, the expansion of HE is too fast under mass constraints to accumulate a high abundance of any distinguishable living things.

• This leads to a combinatorial explosion of unique living things with low copy numbers.

This is consistent with how some unconstrained prebiotic synthesis reactions, such as the formose reaction, end up producing tar.

• Tar is composed of many molecules with too low a copy number to be individually identifiable.

Selection and evolution cannot emerge if new things are generated on timescales so fast that resources are not available to make copies.

For [equation], living things are reproduced quickly but new ones are discovered slowly.

• Here, resources are primarily consumed in producing more copies

Typically, new living things are discovered infrequently.

• This leads to many living things produced by extreme constraints, which could limit the further growth of historical evolution (HE).

This illustrates how exploration versus exploitation can play out in AT.

Significant separation of the two timescales of discovery of new living things and reproduction of selected living things results in either:

• a combinatorial explosion of new living things with low copy numbers or
• high copy numbers of low evolution living things.

In both cases, we will not observe trajectories that grow more complex structures.

The emergence of selection and open-ended evolution in a physical system should occur in the transition regime where there is only a small separation in the timescales between discovering new living things and reproducing ones that are selected, for example the region located between [equation] and [equation] (Fig. 5).

To investigate discovery and production dynamics simultaneously, we introduce mass action kinetics in the framework of AT.

We unify key features of life with physics nonliving things by showing:

• how the generation of new things happen through natural selection through time.
• how measuring change identifies how much selection occurred*

*Superphysics Note: Duh. Change is the natural effect of choice or selection.

We take phenomena and impose selection in our examples. This demonstrates the foundational principles of how change quantifies choice.

To explore this, we consider a forward evolutionary process whereby the copy numbers of emerging living things follow homogeneous kinetics, together with the discovery dynamics as given by equation (2).

With the discovery of new unique living things over time, symmetry breaking in the construction of contingent evolutionary paths will create a network of growing branches within the possible evolution.

In principle, interactions among existing living things and external factors lead to discovery of new living things, expanding the space of possible future living things.

Such events can drastically change the copy number distribution of living things at various assembly indices, depending on the emerging kinetics in the formation of new living things.

By combining discovery and production kinetics in a simplified formulation, we estimate copy numbers of living things at different HE indices and show evolution of the ensemble over time at different degrees of selection.

The interplay between the 2 characteristic timescales describes how discovery dynamics ([equation]) and forward kinetics ([equation] ), together with selection (characterized by the selection parameter [equation]), are essential for driving processes towards creating higher-assembly living things. This is characteristic of trajectories within assembly contingent.

Evolution captures key features of how the open-ended growth of complexity can occur within a restricted space only by generating new living things with increasing assembly indices, while also producing them with a high copy number.

Selectivity ([equation] ) together with comparable production timescales ([equation]) is essential for the production of high assembly ensembles.

This suggests that selectivity in an unknown physical process can be explained by experimentally detecting the number of living things, their HE index and copy number as a function of time.

Considering molecules as living things and assuming that molecules observed using analytical techniques such as mass spectrometry implies a high copy number, the discovery rate and the selection index ([equation] ) can be computed from the temporal data of observed molecules at all assembly indices.

Conclusions

We have introduced the foundations of AT and how it can be implemented to quantify the degree of natural selection found in an ensemble of evolved living things, agnostic to the detailed formation mechanisms* of the living things or knowing a priori which living things are products of units of selection.

*Superhysics Note: A useful theory of evolution should explain those mechanisms. This does not.

To do so, we introduced a quantity, assembly, built from 2 quantities:

1. The number of copies of an living thing
2. Its Historical Evolution index

The Historical Evolution index is the minimal number of recursive steps necessary to build the living thing (its size).

AT allows a unified language for describing selection and the generation of newness by showing how it quantifies the discovery and production of selected living things in a forward process described by mass action kinetics.

AT unifies descriptions of selection across physics and biology, with the potential to build a new physics that emerges in chemistry in which history and causal contingency through selection must start to play a prominent role in our descriptions of matter.

For molecules, computing the assembly index is not explicitly necessary, because the assembly index can be probed directly experimentally with high accuracy with spectroscopy techniques including mass spectroscopy, infrared and nuclear magnetic resonance spectroscopy.