Information

Information is tightly linked with replication and reproduction—they are inseparable. I define information as a replicable instruction for reproduction. Information is always replicable. Information is always an instruction for reproduction. The instructions include a list of ingredients, their connections, and the procedures for their connections, with different degrees of precision and vagueness, like a cooking recipe. You may ask what is to be reproduced. The reproduction of a context that produces the logical structure within it. A context always consists of dots and connections – dots are something composed of the context (i.e. ingredients), and connections are their interactions. They are not limited to physical but of various kinds, like cognitive and virtual. A context is a network.

The dots and connections create their geometry, which reflects the order of proximity between dots. A direct connection of two dots is a path. A context is a complex network as a whole with a unique geometry. All dots are a part of the network. Geometry is the pattern of proximity of the dots within a context. A network pattern provides possible routes to connect any two dots without a direction connection. A route is a sequence of dots and paths connecting a starting dot A to an end dot B. Geometry dictates the available route possibility. The route from dot A to dot B is the logic flow between A and B.

A network emerges through direct interactions and connections of individual dots. A network grows by increasing dots and connections. Dots without connections are outside the context. They are invisible and unconceivable from inside the context because of no connection. For example, language is a network. Words are dots. Connections among individual words exist at various cognitive levels. The word ‘fruits’ represents a group of words, like ‘apple,’ ‘orange,’ and ‘strawberry,’ but not ‘fish.’ The word ‘food’ would include all of them but not ‘stone,’ and so on. The sentence ‘I like an orange’ is useful for communication if a listener knows what these words represent and how the word order (i.e. grammar) constitutes a network. Importantly, something that doesn’t have its name cannot exist in the context – it is outside of the context. As soon as it has a name, it becomes a part of the context – it can exist in the context.

Growth is an increase of new dots and new connections in a context. A new dot increases the size of the context. A new connection increases the complexity (or redundancy) of the context. With a random increase of dots and connections, the context can grow and become chaotic. Chaos is not uniform randomness. Unevenness and spontaneous orders are part of chaos. Molecules in the gas state are considered to distribute uniformly random - chaotic. However, at a global scale, they are not. That is why weather forecasts are still difficult. The molecular distribution in gas is not always uniform but can be uneven. Molecules in the liquid state are also generally considered as randomly distributed. However, at the liquid-gas or liquid-liquid interphase, they align at the boundary.  An order emerges at the boundary. At the interphase, their movement is constrained in two dimensions. The density and movement of molecules can also be uneven inside a liquid, which is why thermal convection happens.

Fluidity – the liquid property that is a free rearrangement ability of relative molecular positions. Solid has no fluidity to exchange relative positions of molecules. Interestingly, electrons behave like fluids in solid metals, which creates conductivity.

The transition of gas-liquid-solid phases creates order or disorder. Because of its physical properties, this does not need intention. Self-assembly and self-organization also occur without intention. These physical events break uniformity and evenness. There is no eternal uniformity, after all. Orders spontaneously emerge in chaos from the unevenness within chaos.

Various inanimate events in nature reproduce without any instruction but by following local physical laws like ripples on water and sand, snowflake shapes, and river patterns. Without instructions, they still reproduce the same patterns.

There is another type of reproduction based on a replicable instruction (i.e., a template) – for example, live organisms and mass industrial products in human society. They reproduce based on information, which is a replicable instruction. Information is replicable and destructible. Once destroyed, it cannot be reconstructed without a template.

Replication is a unique type of reproduction that uses a template to reproduce a new entity.

Information that is carried in a template is essential for instructed reproduction. The template is always replicable. Reproduction is producing a new context with the same geometry as the original one, based on the source information in the template – through decoding it. Information-based reproduction is producing a new context from a template.  Information is an instruction of template-based reproduction. Without template-based reproduction, the information does not exist.

Information is made from and stored in materials (i.e. polymers) or languages in sequence. The first information emerged in the first cell, as the sequence of DNA polymers. A random DNA sequence suddenly became the information of reproduction because of the accidental reproduction of a cell.  Humans are the only entities that produce information because we have developed languages.

In our daily conversations, we use the word ‘information.’ Language is primarily a sequence of sounds. Written language is a sequence of letters and words. It is a replicable template. What is reproduced based on a language-based template? The thought/experience/knowledge in one’s mind is reproduced in the receiver’s mind. A context in one’s mind is reproduced in the others. You may say the precision of reproducibility by language appears much lower than its precision in live organisms. I agree. Because live organisms always inherit the geometrical context from parents in addition to DNA polymers. In our daily conversation, we cannot inherit the cognitive geometry in the speaker’s mind. Each of our minds is an individually unique context based on own genetics and experience – phylogenical and personal history. Each of us has a unique geometry in our minds consisting of at least ten dimensions. Language can deliver information from a speaker to receivers. However, it is insufficient to faithfully reproduce the speaker’s original context. For that, the receivers actively recruit a lot of imagination and empathy to suspect the speaker’s context. Common (or shared) experiences between two are prerequisites for successfully transferring the information. 

Information is a unique property of live organisms and does not exist in the inanimate. However, live organisms are composed of inanimate materials. Biochemical organic inanimate materials accidentally created a reproducible unit based on a replicable instruction– DNA sequence. That is life. Inanimate materials created a template-based reproductive unit in a chaotic soup of abundant materials –the first cell. Once created, it cannot stop reproducing as far as the original permissive chaotic soup exists. No God. No intension. A bit of luck, although the word ‘luck’ is already hindsight from our point of view. 

Life did not start based on a blueprint and assembly. These ideas intrinsically include start, goal, and intention. Life emerges from chaotic networks of biochemical reactions by accidental reproduction. It could have a very low probability of successful reproduction, but once it started, it continued because everything was available. There must be a lot of jargon and unnecessary for reproduction in DNA at the beginning.  Imagine you inherit a messy, chaotic toy box from a neighbour. All toys like legos, dolls, dice, trains and train tracks, miniature cars and trucks, etc are in one box. You have no idea what is in it. But you can take something out and play with it. One day, you accidentally realize the box has a full set of tracks, creating a circuit for trains. It is difficult to find each piece in the chaotic box, but all pieces are there. At the end of the day, you put everything back in the box – chaos is back. The next morning, the inside of the box was too messy and confusing again, and finding the right pieces was difficult. However, as long as you keep all toys in the box, you can reproduce the track circuit. Reproducibility could be low, but it could happen if you have patience. What makes the process easier is extracting the essentials by separating them in a new box, marking them with bright colours, not disassembling the circuit or discarding all unnecessary toys. Then, the next day, it will be easy to reproduce the circuit.

Chaos was the beginning. Nothing had formed, but everything was plentifully available. Then, the first reproduction based on replication happened: the emergence of information. The reproduction continued. Extracting and trimming necessary information helped successful reproduction. Reproduction based on replicable information emerged in plentiful abundance. This is life.

This must happen at the beginning of life. Start as one accidental reproducible entity. It must have a low chance of reproducibility, but as far as staying in the same chaos, this could happen again. High error rates in DNA replication could terminate continuity if something essential is destroyed. Because the resources for reproduction are abundant, reducing error rates will support the continuity. Increasing robustness through redundancy, refinement and trimming out of extra DNA sequences helps the continuity. For example, the initial success rate was 1 in 100,000 due to DNA that was too long, error-prone replication, and too many unnecessary biochemical possibilities.  However, through errors in replication, the necessity for replication and reproduction in the abundant environment was gradually defined as genes. When individuals successfully reduce the error rate, their progeny increases in a population.

In biology, a cell is a minimal reproduction unit that consists of sequences of biochemical events that control the growth and replication of DNA. Those sequences of biochemical events are created by dots (molecules) and connections (reactions). The biochemical properties of dots generate their geometry through self-assembly, self-organization, hydrophobicity, etc. The geometry is proximity that dictates a probability of connections (molecular interactions), leading to a sequence of connections. This is the network of biochemical events in a cell. For each dot, it only interacts with adjacent neighbours. An environment for each dot is always local and adjacent but not the whole network.

In double-strand DNA polymers, each strand is a mutual template for the other. Each strand is a reverse complement of the other. In addition, each DNA strand can be a template for an RNA polymer. Only in a unique condition an RNA polymer can be a template for a single-strand DNA polymer.

Modern industrial mass production is somewhat similar—replication and reproduction. A template-based replication is like metal-based moulds for plastic products, etc. Reproduction is the process of assembling parts – building the geometry of parts. The sequence of the assembling process needs a template, too. The templates are always replicable and destructible – information.

DNA is a replicable carrier of information but not information itself.  The DNA sequence is the information. A cell is a geometrical context for biochemical reactions. In the DNA sequence, the instructions for components and their properties are encoded, but not their assembling strategies and allocation in a cell. Therefore, an inheritance of parental geometry appears to be necessary.  Parental geometry works as a seed. Cellular geometry is reproduced by biochemical properties of proteins like self-assembly, self-organization, hydrophobicity, etc. together with inherited parental geometry.

The information alone is not sufficient for reproduction. For the information to be useful, the context matters.  In a cell, the information is encoded as the sequence of DNA, thus replicable and destructible. But this is not sufficient to create life. This information is usable only in the cellular context.

The first information emerged on Earth when the first life emerged. Life is a reproduction unit supported by replicable information, inheriting the parental geometry and embedded in its environment. Except for life, nothing has information. All inanimate objects have properties but not information. Molecules exist, interact, and react—variation and complexity increase. When the first cell emerged, the first information was created as an instruction for reproduction on replicable polymers. Therefore, all live organisms have their own information.  

You might feel strange about the above statements because the word ‘information’ is often used in our daily conversation. Are we replicating something when we use it? Yes. We are replicating the knowledge that one person has in his/her mind to others’ minds using language. Humans created language as a vector of information. This was the second vector of information on Earth after DNA polymers.

Information is a replicable instruction for the reproduction of a context. It comes as a one-dimensional sequence of something, such as sounds, letters, numbers, symbols, etc. Thus, it is pseudo-two-dimensional, one infinite dimension with a second limited dimension because the sequence consists of limited selections, such as alphabets (from a to z), nucleotides (A, T, G, and C), or numbers (from 0 to 9 with digits). 

The first information on Earth was the DNA sequence of live organisms. DNA is the first information storage and vector. DNA polymers, which are the random sequence of dNTPs, suddenly became the storage and vector of information because of the first accidental replicational event. The physical material created the first information.

The second information vector is human language. Language consists of a replicable sequence of sounds. Language development allows humans to share an individual's past experiences with others—the reproduction of knowledge and experience. Only humans can do that because we have languages. Spoken languages are a vector. Humans also gain storage and vectors of information - letters.

-Information is a replicable instruction for the reproduction of a context.

The geometrical context permits DNA replication. DNA sequence permits the reproduction of the context. Eternal circuits within the local environment

Geometry is the context. Geometry is the pattern of proximity that dictates the sequence of dot connections. If something is reproduced based on replication, this will be logic. The context permits reproduction. When reproduction occurs based on replicable information, logic emerges. Not the other way around.

There are many probabilities in a route choice in a complex network context. However, one can only take one route in one linear attempt. In hindsight, there is always only one route you have taken. Whether you chose yourself or were chosen by someone else does not matter. We all are only one entity. No matter how you take your route, whenever you look back, there is only one route connecting you from birth. This is Life.