Shapes and Functions

In all tools and utensils, their functions come from their shape. The shape matters for their functions. Then, a name represents its functions. There is a relationship of shape-function-name.

Any object has a shape and its properties. The shape and properties of an object can create a function and give the object a name. You found a stone with a sharp edge on a river shore. You took it home and found that it can be used to cut a piece of paper. You call it a paperknife. A generic stone becomes a paperknife that is its new name and functions because of its shape.

Any object has a shape. If you find its function, it can have a name.

Probably, the beginning of tool usage in human history was like this. Any shape of objects available to you in your surroundings. You realize one can be used for something based on its shape and properties. If it is usable (i.e., it yields reproducible consequences), it becomes a tool. Then, it gains its name. Then, you start intentionally imitating and remaking it because of functionally useful for reproducing the process.

1.        The shape and properties of an object. 2. Realization of potential functions. 3. Trials of functional reproducibility. 4. Its name is placed.

A machine is the opposite. A name and potential functions come first in someone’s mind. Assembling various parts to achieve the functions. The purpose of the machine is to achieve reproducible consequences through its functions. The sequence of events within a machine, i.e. how the parts interact with each other to achieve reproducibility, is the mechanism.

A mechanism is a sequence of events supporting reproducible functions. All participants are called functional parts. They are geometrically assembled to permit the mechanism to work. 

Each part is similar to a tool. Their shape and properties are their function. One shape and one property can have multiple functions, like tissue paper. Different shapes and properties have the same function, like binding papers with a clip, clump, binder, staple, etc. 

Randomly assembling parts does not create a machine. A machine is designed to have its function through assembling functional parts at proper locations. Parts are selected from all available stock; not all available stock parts are used, but only those necessary for assembly are selected.

Prototypes and the final product can differ significantly in appearance, but the functionality and intent are likely the same. The parts necessary to assemble them are likely different, too. However, their name must remain the same.

How about in living organisms? In a cell, each gene has functions. Why? Because each gene encodes a shape and its properties. A gene is a DNA sequence. The DNA sequence is complementary copied to an mRNA sequence. The RNA sequence is translated into an amino acid sequence of a peptide and protein. The peptide and protein have a shape and properties. Their shape and properties govern their functions. The uniqueness of peptides and proteins is that their shapes are not fully fixed or determined. They are plastic and change through interactions with their environment, such as temperatures, osmolytes, pH and other peptides/proteins. Their shapes change, then their properties change and their functions change.

Importantly, all shapes have the potential to have functions because functions arise from the shape and properties of an object that can produce reproducible consequences. Thus, without any reproducible context, there are no functions. Without functions, there are no genes, despite many shapes.

A circuitry process consists of the repetition of reproducible processes. When a circuitry process emerges, functions can be identified.

A DNA sequence encoding the amino acid sequence of a peptide does not guarantee that the sequence is a gene which must have a function. Without functions, even if a DNA sequence encodes a shape and its property, it is not recognized as a gene.

Imagine many pieces of parts in a toolbox. Depending on the machine you want to make, some parts will be functional, and the rest will be unnecessary. Your decision separates the functional and the unnecessary in many pieces of parts in the box.  Your decision can swing between a watch and a radio. Maybe the box allows you to make both, but not simultaneously, because some parts overlap.  

Once you made up your mind to make a watch, the pieces for a radio or completely unusable parts are just confusing. You may mistakenly use them, leading to misassembling the real watch parts. A watch doesn’t work – it doesn't perform its functions.

If you know what you want to make, the extra parts are unnecessary and only confuse you. However, if you have no idea what exactly you want to make, the extra parts are helpful for trial and error, until an idea is solidified.

What do you think if the pieces of parts in a box are like Play-Doh? They are plastic. You can change their shape as you like. In this condition, how does a shape and its function evolve?

How did a DNA sequence become a gene?  This question is equal to how functions emerge, because gene functions are mediated by the shape of the peptide, an object.  Then, what are functions? How do we recognize any function?  My answer is a reproduced phenomenon. When a reproduced phenomenon emerges, functions are recognized in the process, as shapes and properties that support reproducibility.  This is functions.

How did functions emerge? What was the first reproduced phenomenon created functions?

Reproduction of a cell. Not the first cells (or the sacs) without reproduction capability. Only after the first two cells are formed by division, the first reproduction is recognized.

This reproduction of life is information-dependent. Information is a replicable instruction for reproduction. This information is only realized after reproduction. The bridge between two entities after life reproduction is information.

Information comes in two flavours: a replicable sequence or a replicable 3D mould, both of which serve as templates for replication.  

The amazing characteristics of DNA polymers are that they have both properties, based on the complementary double-stranded structure. The 3D mould-like interactions between A and T, and C and G. Then, this allows the one-strand sequence to become a complementary 3D template for the other.  The sequence on one strand is complementary to the sequence presented on the other strand. These characteristics make DNA polymers a replicable information carrier.

The first information carrier is DNA polymers. They act a replicable instruction for reproduction. The second information carrier is human language. Oral language is repeatable. Written language is replicable. What is reproduced by language?

The experience and thoughts in one’s mind are personal and private. No one can tell from the outside. Language is the means to reproduce one’s experience and thoughts in others’ minds. This occurs between two or more individuals, working as information. Information is a replicable instruction for reproduction.

Note: The third information carrier is photographs and videographs.

When the first reproduction (i.e. cell division) of two sister cells occurs, the first information emerges or is realized. Then, how does the information act as an instruction for reproduction?

A DNA sequence encodes the amino acid sequence of a protein. A protein is an object with shape and properties. The shape and properties control distribution patterns within a cell, based on the interactions between intrinsic properties such as hydrophobicity and environmental conditions, like osmolytes, pH and temperature. The geometry of protein distributions within a cell is reproduced based on protein products through self-organization and inheritance from a parent. The geometry creates the proximity among them. The proximity can reflect a sequence of biochemical events. Through the reproduction of the geometry, the sequence of biochemical events is also reproduced within a cell.  The sequence of biochemical events successfully replicates the material sequence of DNA polymers. A circuit of sequence (information) and geometry is established.  The system carrying cyclic momentum of biochemical reactions encompassing growth-replication-reproduction is the living organism. The momentum is geometry dependent. Geometry is sequence-dependent. Replication of the sequence is geometry-dependent. The momentum can be paused, as long as the geometry is conserved. Plants’ seeds and cryopreservation of human embryos are good examples.

When geometry is destroyed, momentum will stop. When momentum is stopped, the geometry eventually degrades. These are death.

When geometry is compromised, momentum changes but does not always stop. The momentum often finds detours. With a new geometry with new flow patterns, the momentum goes. This is cancer.

When the first reproduction occurs, the link between the parent and offspring is the information. The shapes encoded in the sequence information have functions to reproduce the geometry in collaboration with its environment and inherited geometry. Of course, there are many shapes that do not contribute to functions for reproduction in early cycles.  Similar to a box full of many random pieces of parts. Once the first reproduction, i.e. the first cycle, occurs, the random pieces are categorized into two classes: the pieces with functions for reproduction and the rest.  This means that in the sequence of a DNA polymer sufficient to conduct the first reproduction, there are two categories: the sequences encoding functional peptides, and the sequences encoding no peptides or peptides with no functions.   

It is reasonable to assume that the early replication process is erroneous. When errors occur in the functional sequence, reproduction will fail. When errors occur in the sequence of no peptide or no functions, they will be tolerated. However, the errors in those sequences can accidentally make other shapes. Extra shapes are always troublesome. Imagine a cluttered toolbox full of unnecessary materials, all mixed up. Finding the right piece takes time, and the chance of making mistakes is high.

Once you know what is needed, all unnecessary shapes and any risk of making them should be removed. Without intention, frequent errors in replication are sufficient eliminate all unnecessary and trim down to only the necessary.

As long as the surrounding conditions are unchanged, the requirements for cycling do not change. The first cycle occurs, and then the erroneous replication process handles trimming. If error rates are too high, the system does not continue. Through trimming, error rates gradually decrease. As long as in the same environment, the cycling system keeps cycling and expanding. The continuity is a probability. Through trimming, the probability can gradually increase in each progeny – lineage.

In a consistent, stable condition, all unnecessary sequences (i.e. shapes) can be fully eliminated, like an F1 racing car. Specialized for one condition. The fully trimmed entity is reasonably efficient and fragile to any change. Any backup or robustness is not needed. But this limit where the entity can continue. You cannot drive an F1 racing car on muddy gravel roads.

Before the first reproduction, i.e. before life emerged, there were chemical reactions. Chemical reactions were reproducible as long as the same molecules were encountered in the same conditions. Before the first life, all materials and their basic interactions must be available. None has functions because of no reproducing entity.

Many random materials and their interactions – the chaotic condition. Everything is available as abundant and ubiquitous, but nothing has emerged yet. No reproducible entity using information. Maybe spontaneous phenomena are occasionally due to the self-organizing activity of some molecules. No reproduction based on information.

Life emerged as reproduction based on a replicable instruction (i.e. information). This reproduction is probabilistic in its environment. Never been 100% success rate and don’t need to be. A 50% success rate in duplication (i.e. reproduction) allows a population of offspring to persist occasionally for many generations. Importantly, not always. But it can happen. As a lineage as a whole group, this continues.

The unit of survival (continuity) is not an individual but a group. i.e. a species. If one individual survives in the lineage, it is sufficient to continue. Errors occur not only in replication but also in other reactions due to misgeometry. After all, the cyclic momentum of chemical reaction flow is probabilistic. For example, a 10% success rate with 7 trials is better than a 50% success rate with 1 trial. A 1% success rate with 69 trials is better than a 50% with 1 trial.

The overall success rate can be modified by changes in the nested success rate or the number of trials.

To do something new in the physical material world, 3D objects (i.e., shapes) are always necessary. However, the extra sequences encoding additional shapes and potentially used for new shapers are all gone in prokaryotes due to trimming. In a stable, consistent environment, no extra is needed. Particularly in the erroneous system, minimal extra (minimal detours) is the least risky condition.

I imagine that the rules in transcription and translation were established to reduce the error rates, but do not need to exist from the beginning. Specifying the start and end in transcription and translation increases the consistency of the shapes of available peptides within a cell. They are not absolutely necessary for cyclic momentum, but they increase the reproducibility by minimizing detours that cannot be trimmed out. The rules and mechanisms are implemented even at the expense of extra energy because they help stabilize consistent cyclic momentum. However, when energy is in short supply, like in stressful conditions, the rules and mechanisms are compromised. Imagine a sudden blackout that disrupts traffic lights at a busy intersection. Jamming and accidents. The momentum still exists, but the flow is compromised.

Prokaryotes trimmed their DNA sequence to the minimum and implemented the rules of transcription and translation. Almost no detours in a steady normal condition - cycling of growth-replication-reproduction (i.e. duplication).

However, no environment is eternally stable. It changes. Three possibilities. First, sensing the change and pause as dormant. Second, the change cannot be sensed, thus no avoidance, but stress. The fidelity of the rules and mechanisms are weaken. Errors in replication, transcription and translation increase. Creating new shapes and exploring detours. If error-based changes accommodate the environmental change, they return to normal cycling (selected). Third, collaborate with others. One may not be sufficient to handle the change, but the two together could be. Physical proximity of the two (symbiosis) or exchanging DNA sequences (lateral gene transfer: LGT). Through LGT, new shapes are introduced, allowing exploration of detours.

Non-genic DNA sequence is a tool for exploration of detours but not needed for a stable condition. Then, trimmed. Without it, responding to the environmental change is challenging, but the reduced fidelity, due to energy shortage, releases hidden shapes in other codon frames and introduces mutations during replication.  This is my view of stress-enhanced mutagenesis. This must be happening not only in bacteria but in cancer. My bet is that many cases of drug resistance come from this cascade. Stress changes the cellular context completely. Errors increase, the process slow but everything is messy but robust.

However, due to massive trimming, the range of plasticity of prokaryotes is limited. Importantly, due to the own success of continuity of live organisms, the static local environment becomes dynamic and unstable. The production of oxygen could be one example.  Oxygen is a highly reactive gas and must be toxic for early life.  None can live in the presence of oxygen, and no extra sequence to explore new shapes for cycling under oxygen.

Fusions with others, two or more. Longer DNA sequences encode many shapes. No guarantee this will always work for a new path for cycling as a new whole. No doubt about many failures. But more shapes mean more probabilities. Unlike the first cycling on Earth, the fused entities inherit the individually functional cascades, while no one knows whether these shapes work together compatibly, collaboratively, or in conflict. 

In my view, somewhere on Earth, this occurred, and it worked.  I don’t know how many locations or how many made it work. But it worked. The first cyclic event – the first two sister cells were formed. The information was created.

Then, again, the DNA sequence is classified as necessary and not necessary for cycling. However, the environment is not as consistent as it used to be, and trimming must be incomplete. Some shapes for one condition and other shapes for another condition, for example. This plasticity within an individual allows it to continue in the previously uninhabitable areas. 

Whatever work to continue outside of the current inhabitant, then, in the first cycle, the first two organisms are created. Then, the information is defined to continue in the previous inhabitant. This is the information for a species – the genome. The genome and its environment permit enough opportunities for a sufficient number of survivors to continue as a species. The genome provides a stable and consistent range of phenotype variation and plasticity – common variation and plasticity. No guarantee of an individual’s survival because it depends on luck, “where and when one exists”. However, as a species, a sufficient number of survivors is produced in its local environment. Whoever survives, this common variation is inherited by the next generation.

I believe that a species is a stable, consistent entity with a range of common variation in morphology and anatomy. For any species, there are always uninhabited areas outside inhabited areas, because the commonality cannot create enough opportunities for a sufficient number of survivors in those areas.

If a single monogenic trait, such as a cosmetic or physiological trait, is sufficient to overcome the uninhabited reason, the trait might expand in a local population but not beyond. Of course, one trait cannot create a new species, though.

The reasons for uninhabitability are usually complex and not clear until they are overcome. Imagine why fish cannot live on land? Maybe we can tell them retrospectively now. Were any organisms aiming to? I do not think so. I believe something fundamentally changed, then the accidental changes worked.  

In the physical material world, the shape matters. Chromosomes are a very interesting object. It consists of DNA polymers and DNA-binding proteins, but they can be twisted and structurally nested. It is not a linear, straight string. The 3D structure of bendable wires. The curl, twist, and bend create structural nestedness – a relationship of outside and inside. Inside is inaccessible without opening the outside.

The DNA sequence is not uniformly presented to the accessible outer surface. Some are held inside a 3D structure. For accessing it, the structure needs to be unheld.  The structure nestedness creates the information nestedness.  Chromosomes, consisting of DNA polymers and histones, are more nested than non-chomosome DNA in prokaryotes. The DNA sequence and DNA-binding proteins further shape the 3D DNA structure within a chromosome. Shapes and properties control geometry within a nucleus and cell. The structural nestedness can control the repertoire of shapes in the nucleus and the cell. The structural nestedness can control the timing/order of information availability and the repertoire of available shapes.

Because many shapes are available, some accidentally stick out from the plasma membrane. They could attach to the extracellular structure or other cells that stick out the same peptides. The potential of multicellularity. If multicellularity opens a probability to live outside of unicellularity, this would happen.

Interestingly, the structural nestedness in a chromosome allows for cell differentiation and thus development – the nested information availability. Unlike trimming the sequence encoding unnecessary shapes in prokaryotes, the rules and mechanisms to hide them inside the structure or actively suppressing them, are used in multicellular organisms. In this regard, chromosomes have their own functions because they have their own replicable shapes. Reproducible changes in chromosome shape determine the accessibility of information that encodes the repertoire of shapes in a cell and the timing of their exhibition.

Increase of complexity and nestedness makes the whole system more complex. This means more detours at various levels. Thus, more robust, plastic and compensatory. The stable and consistent range of common variation is wider in complex organisms.

Monogenic traits are generally cosmetic and physiological phenotypic traits. They do not impact speciation but may contribute to natural selection. 

Monogenic dominant traits against a high lethal threshold could be efficiently selected and fixed. Fixation of recessive and multigenic traits is almost impossible without the founder effects. A species is not a sum of monogenic dominant traits, but it is organized as an interplay of multigenic traits that provide a stable and consistent range of common variation. Similar to human society organizations, having one person missing/replacing does not affect the structure, vision, or operations. If someone wants to change them, reorganization of organizational structures is needed, rather than an individual person changing.  

As Richard Goldschmidt discussed and perfectly captured this point. He proposed that microevolution and macroevolution operate under completely different processes. He agrees with Darwin and neo-Darwinian views that gradual changes and selection of monogenic traits. However, he disagrees with the accumulation of these small changes eventually achieving speciation. For speciation and further larger changes between phyla and families, completely different mechanisms must exist, similar to the reorganization of organizational structures.

Changes in cosmetic and physiological traits do not cause speciation, but rather a phenotypic swing within a species or a generation of subspecies.

However, generally, a species is defined as a stable and consistent range of anatomical and morphological commonality. In even two close species, their difference is not one trait but stable, consistent, subtle multiple differences. They are regulated by multiple genes and their interactions in development.

Chromosomes themselves have functions because of their dynamic shapes. Their shape controls the accessibility to information. Accessibility controls the timing and repertoire of available shapes (proteins) within a cell. The repertoire of shapes in a cell controls the geometry of shapes within a cell and cellular functions. A new repertoires of shapes in a nucleus generate a new shape of a chromosome. New information becomes accessible.

The nested structure of a chromosome controls the sequence of events on the chromosome and within a cell.  The nested structure of a chromosome is created by DNA sequence and DNA-binding proteins.  The large-scale nested layer (a upper layer) dictate the small scale nested layers (lower layers).

Nothing was planned in life’s evolution. There was no intention or will. Everything happened due to circuitry momentum and accidental errors.

Many people use the word “agency”.  Consciousness, will or intentional entity.  I must say I feel unconformable of this word.  To me, this looks like ‘straightforward momentum’ created by ‘cyclic momentum’.  If you add sensing – reaction reflection in this system, it can turn through sensing its environment without any will or intention.

Cyclic momentum creates straight, forward momentum. The environment navigates it curve. The forward momentum is not an intention nor a will, but it looks like it. Imagine a tire rolling down a hill. No intention to move forward. The cyclic momentum forces move forward. An automatic sensor detects obstacles. When the sensor senses it, turn 30 degrees left. This is not a will. Intrinsically implemented reflective responses.

Does a will or purpose exist? Yes. In the human mind, because we use language. Language is the second information carrier next to DNA. Information is a replicable instruction for reproduction. By language, one’s experience and thoughts in their mind are reproduced in others’ minds. Language is replicable (repeatable). Reproduction is receiver’s context-dependent, similar to the inheritance of the parental cell’s geometry in living organisms.  

Amazingly, language is not a physical material. No constraint in proximity and limitless. “The moon and sixpence.” Without knowing Somerset Maugham’s novel, this does not make sense. Through language, humans gained the ability for unlimited imagination.  Cognizing the present insensible exists. Inexistence in current senses can be an existence, such as a will and purpose. The emergence of the cognitive world. This is a human society.