Luck in bumping and robustness

Our physical world consists of matters.  A matter is mass and volume.  Mass is energy. Volume is geometry. Kinetic energy is mass and velocity.  Velocity is geometry and always relative.  Thus, kinetic energy is relative.

No single matter takes two volumes at one time. No two matters can occupy an identical volume at one time.

When two matters bump into each other, they must react because they cannot take the same volume simultaneously. Sometimes, only their kinetic energy changes without changing mass and volume. Other times, everything - kinetic energy, mass and volume -changes.  ‘Bumping and consequential reaction’ is interaction.

The force between two matters is something that impacts the frequency of bumping between them by modulating the velocity.

Life is quite similar to this. No single organism can take two spaces at one time, and two organisms cannot take an identical space at one time.

Organisms bump into their food, water, mates, and predators. Sensing is similar to the force in physics. Before bumping into actual something, change the frequency of bumping to it. Sensing is still bumping to the preceding physical events to the actual something and reactions evoked by preceding bumping to modulate the frequency of bumping to the actual something.  

Interaction- bumping and reaction – is the essence of the physical world, which consists of matters.  Nothing is different in the world of living organisms.

The immediately adjacent - the nearest proximity- is the only matter for bumping. As no two matters/individuals can occupy an identical volume/space simultaneously, none can share the identical immediately adjacent at any given time.  

Life is ‘sequence and geometry’ that govern growth, replication and reproduction. There are two types of sequence: the sequence of material units (one-dimensional order in space at one time) and the sequence of events (one-dimensional order in time at one space).

The circuital momentum of biochemical reactions is life and alive. When the momentum stops, it is the death.  The momentum alone is not life.  The circuitry momentum involving growth, replication and reproduction is life and alive.  This momentum is dictated by ‘sequence and geometry’ and its adjacent environment. All consist of molecules.

DNA consists of four nucleotides: A, C, G and T. Each has its own molecular shape. The shape is geometry. Their molecular shapes permit the formation of the pair of A-T and C-G. On the other hand, their shape also permits the formation of a DNA polymer.  A single-strand DNA polymer can hybridize with a complement second-strand polymer. This is the double-strand DNA. Although the pairing of nucleotides is constrained, the order of nucleotide polymerization has no constraint. In addition, there is no constraint on its length.  

The words ‘replication’ and ‘reproduction’ share a similar concept, but there is a fundamental difference. Replication uses a template, like a mould, which is a complementary template or an original copy. Reproduction is reproducing something with an instruction. This does not need to have replication. Life is the process of growth and reproduction in an environment based on a replicable instruction. For example, a random sequence of DNA can be replicated with its template but can barely be reproduced by chance.  The sequence is something to be replicated, but it is not easily reproduced without a template. One DNA sequence can be replicable because of the reproducible interactions of AT and CG. What permits the reproducibility of the interactions?  Their shapes – geometry.

The amino acid sequence of a protein permits the reproduction of its shape. Protein shape permits their solubility in water and the reproduction of their interaction. Solubility in water controls protein clustering, and interaction controls the formation of multiunit complexes.  The formation of clusters and complexes permits the reproduction of the geometry of proteins within a cluster and complex and between clusters and complexes. The geometry is the proximity, which is the frequency of bumping and can be the sequence of bumping events with an orientation.

A cell is a minimal unit of life. It is a sac. The cell membrane separates the inside and outer environment. This sac is not like a plastic bag you use for groceries but like a leaky braided bag—small stuff passes through it.  A cell holds its proteins inside at specific locations – geometry. The geometry controls the sequence of biochemical reactions leading to growth. Growth is the increase of the number of proteins that modulate their geometry. This also changes the sequence of biochemical reactions – called post-translational modifications. In this series of sequential events, the replication of DNA is integrated.  By untangling the double strand, each strand works as a complementary template of the other.  Their sequence is replicated.

The replicated DNA sequence encodes the amino-acid sequence of proteins that can reproduce the geometry of proteins within a cell with the inherited geometry from the mother cell and de novo production of proteins.  The cycle of growth and reproduction using the replicated sequence of DNA. This replicated sequence (one-dimensional order of material units) with a reproduction ability is called information.  However, the sequence of material units alone is not self-sufficient for reproduction. It always works with the inherited geometry and its surrounding consistent environment. They provide the context that the sequence of material units is translated into the sequence of events. Then, the sequence of events circles back to replicate the sequence of material units.  This is life: a partially open perpetual circuit of biochemical reactions.  This circuit is fully embedded in its directly adjacent environment.

Everything in the physical world is bumping and reactions. Physical proximity, i.e. geometry, is an essential matter for controlling the frequency of bumping.  The DNA sequence permits the reproduction of the geometry of proteins within a cell. The geometry of proteins permits the reproduction of the sequence of biochemical reactions leading to the replication of DNA sequence.

When this momentum stops, there are no more bumping and reactions. No more sequence of events. This is the death. The geometry degrades, and the sequence of DNA cannot be replicated.  No ‘single cause and consequence’.  Changes in sequence, geometry or environment can terminate this perpetual momentum circuit.

DNA replication has never been 100% fidelity. The geometry of proteins and the sequence of molecular events impact the fidelity. Once errors are incorporated into the sequence, they change the sequence of amino acids in a protein and modulate its shape. The changes in shape impact its function and allocation within a cell – geometry.

The geometry of proteins, organelles and non-membranous compartments is a consequence of self-organization within a cell. The molecular environment within a cell, such as pH, ion strength, protein density, fluid viscosity and so on, can impact the geometry.  This impacts the frequency of bumping and the sequence of bumping events. The fidelity of DNA replication will be compromised in this condition.   

The physical world is bumping and reaction. Life controls the frequency of bumping using ‘sequence and geometry.’ The first circuit emerged because its immediate adjacent environment provided sufficient resources for a series of sequential events forming a circuit of growth, replication and reproduction. As long as the circuit stays in this environment, this circuitry process is perpetual. On the other hand, this immediate adjacent sufficient environment inevitably constrains the frequency of bumping. Thus, the place (i.e. space) where successful cycling of the circuit occurs will be limited.

The increase in the frequency of specific bumping is equal to limiting other probabilities of random bumping  (i.e. constraint) for the sake of the successful cycling event of this circuit. However, trimming out all other probabilities to select just one makes the circuit vulnerable to small changes in internal errors and the external environment. Leaving several options (i.e. routes) as the complex network provides robustness and plasticity as multiple detours.  The 3D geometry of amino acid residues within a protein and the allocation of various proteins within a cell accommodates compensatory reactions to keep cycling the sequence of biochemical events in the circuit. This means that the DNA sequence only defines a one-dimensional amino acid sequence of the protein. The flexibility (or probability) in their 3D shape permits the range of robustness and plasticity, including errors.

Life is fundamentally the system that constrains the probability of chemical reactions to have a successful cycle of the circuit. The accidental chaotic first cycling in the resource-rich environment permits the second cycling.  The probability of all potential outcomes at individual reactions should be constrained to have successful cycling.  Enzymes are catalysts that constrain the direction of reaction outcomes. Fundamentally, the DNA sequence is essential for generating protein members (variation of catalysts) and their reproducible shape (catalytic activities).

The long random DNA sequence permits the first cycling to create a circuit accidentally.  Then, suddenly, catalysts are divided into two groups: the ones in the circuit and the others not in the circuit.  This means the DNA sequence that is part of the circuit and not part of it. This is the emergence of important and unnecessary.  The emergence of the first logic because the circuit is the path for reproducible and repetitive events.

Important or unnecessary is always dependent on and governed by the internal and external context. If the context is stable and has not changed at all, a backup plan for an internal error or an external environmental change is unnecessary. However, without a backup plan, the cycling circuitry system is fragile and vulnerable to internal and external changes.

Indeed, DNA replication is error-prone, and the external environment can change and fluctuate. No backup plan means the end of the perpetual cycling circuit when something is changed. For example, if the sequence involved in the cycling is altered, the cycling might stop. The end. Any changes that permit the circuit to keep cycling would stay. The unnecessary sequence for cycling is allowed to be changed and trimmed.

The originally long random DNA polymer that permitted the first cyclic event can be gradually trimmed down to the only essential sequence for cycling. In the original long random DNA sequence, there are many potential detours and unconnected routes irrelevant to the cyclic events. The sequence for those detours and irrelevant routes will be trimmed out. The route choice will be constrained for the sake of the cycling circuit. In this way, the probability of successful cycling is controlled and increased. The speed of cycling is not an issue, but the robustness of cycling that can accommodate internal errors and changes in immediate adjacent external environments is essential for the continuity of cycling of this perpetual circuit.

Since DNA replication is error-prone, excess backup plans are not maintained but disrupted. No backup plan is also highly vulnerable and has a high risk of termination with a slight change. The balanced equilibration between the number of detours and the reasonable usage of each detour controls the robustness of cycling of the perpetual circuit.

The evaluation of robustness is similar to the environmental test of automobiles to prepare for extreme climates and weather. The robustness is unnecessary if you drive your car only on sunny days in London. But the robustness limits you where you can drive. The robustness of internal and external challenges comes in different flavours. Internally, fewer parts and less complicated would be more robust. Think about a tricycle, a bicycle, a motorcycle and a car. Against external environments, complication is not an issue. An open car, an F1 racing car, a bulldozer, a snowmobile, a floating bus and a boat. The uniqueness permits one to take a specific space – sometimes it is the absolute necessity for survival- but the same uniqueness is irrelevant in other spaces. 

The critical point is that robustness is unnecessary if everything is stable and static. Simply, you don’t need to go out to extreme crazy places.  Just stay in the cozy and comfortable space—however, unique robustness permits exploration and survival in adjacent uncharted areas due to lethal conditions.  An environment never creates robustness. I.e. if not robust, avoid that harsh environment.  On the other hand, if somehow you are equipped to tolerate the harshness or changes of the environment, you can survive and continue.

After all, the life of organisms is not a competition at all. Only humans can create competitions.

Life is the robustness against internal and external changes that keep cycling the circuit. As I discussed at the beginning, all individuals are fundamentally unique and different from others. Survival is luck—you happen to be equipped and be where you can survive. There are various ways to be robust—almost unlimited. Therefore, the surface of Earth is occupied by various types of organisms. New ones always occupy the immediately adjacent environments that the previous ones could not take due to being too harsh and unhostile for them.

The robustness permits the continuity of cycling of the environment-dependent perpetual circuit: no competition or selection. The circuitry biochemical momentum in the individual immediately adjacent environment that was initiated a long, long time ago is still continuing. The momentum has been inherited not because it is better than others but because it is robust enough to continue and lucky enough to be at the location permitted to continue.

Life is built on the probability of bumping. This bumping could be molecules, individuals, or opportunities. But at one given moment, only the immediate adjacent space—the proximity—is the issue for the probability of bumping.

Any two matter takes one space (i.e. volume) at a time. Each matter has a unique relative reality. None of the two is identical. This is also true in any live organism. Taking one space, not the other, at a given time. This is not a competition but luck.  

Luck in bumping and robustness. They are the two essential ingredients of life.

Humans are the only organisms playing with probability.  Therefore, we own, exclude and compete until elimination.