Sequences. I am attracted to that. An order and a pattern. They are the concept within the sequence. What are they? The sequence is a series of units, one-dimensionally connected like polymers. The units can be letters, numbers, nucleic acids, etc. The units also can be sounds, noises, signs and symbols. Even time is a sequence of the present. The sequence is one-dimensional, like a line. It has a direction.
The DNA sequence is the secret of life, encoding the developmental sequence of self-organized biochemical reactions. The sequence of sounds. This is the spoken language. The sequence of symbols. This is the written language. This is the secret of humans as the unique organism on the earth. We are the only organism using the sequence for communication and recognizing time as the sequence of the present.
Polymers, consisting of at least two kinds of units, can carry information with a rule. Think of a binary counting method. DNA is a perfect molecule to carry and store information. It is a polymer consisting of four kinds of units: A, C, G and T. No physical or structural constraints of their order in polymerization. A polymer has an orientation, 5’ end and 3’ end. It forms a double-strand polymer with a complementary strand. This property is essential for replication. There is no length limitation—completely random orders of four nucleotides. Without a code or rule, the random sequence is useless and meaningless. With the triplet code and uncountable trials, something auto-replicable in a sac emerged accidentally as life.
At the emergence of life, a circular random DNA sequence encoding the chaotic biochemical reactions created a unit of replication within a network of biochemical reactions. A part of a random DNA sequence suddenly became meaningful for replication. Although the replication was an accident, once it happened, it continued until it reached the equilibrated endpoint. We exist because of no equilibrated endpoint so far in the earth's history. There is no limit so far. We keep expanding.
The original circular DNA had just a random sequence. Notably, the pattern of sequences has no biochemical constraint – entirely arbitrary. It encodes random peptides in six potential open reading frames: +1, +2, +3, -1, -2, and -3. Many can be very short peptides due to short ORFs. But they can provide various 3D interphases for biochemical reactions. Each long circular DNA can carry a unique chaos of biochemical reactions.
As soon as a replication unit embedded within a network of biochemical reactions was accidentally born, the original random sequence was not meaningless anymore. It became two distinct areas, the areas encoding the peptides that are part of this network or the ones not part of it—the first distinction of Self and non-Self. Despite the original DNA having no intention, value and meaning, the accidental event, replication, generated the valued sequences for replication and non-valued within the DNA. The valued DNA sequence carries the information for replication. The essential rule to use this information is the triplet code to read the DNA sequence. Without the code, the valued DNA sequence is meaningless.
The sequence is a valuable tool to extract an order from Chaos. In the case of life, the DNA sequence was accidentally linked with replication. Life is a replication system with errors within a complex network of biochemical reactions. A highly robust evolvable system was created using the sequence.
Humans are the only organisms that can recognize and use the sequences for communication – languages are a sequence of verbal sounds. Many animals use verbal and body signs. They are usually alerting signs shared within a group. Some also use markings like smells and scratches. Those can be considered ancestral symbols. Singing of birds, dancing and displaying to attract a reproductive partner are complex signs but not languages—no flexibility in the order of sounds and variation of movements.
To my knowledge, no animal uses a sequence of signs or symbols for communication except humans. Signs and symbols alone, without their sequences, can also be used for communication. However, the amount of information you can communicate is limited, and capturing the past and future is impossible. Therefore, all animals are only living in the present. They only react to the environment, keep alert constantly, and have no plan for the future. None captures and prepares for the future. The behaviours of animals appear to be seeking something, like food and reproductive partners may not be seeking at all but wandering around. The default intrinsic behaviour of animals is wandering around and subsequent sensing and reactions—no intention but genetically embedded instincts.
Using the sequence of sounds, we can put a name on each object we see. Because we use the sequence, the available variation is infinite. We can name all objects surrounding us. Names are the symbols of the objects. They should be the first words of languages. Once we have names, we can distinguish them from others. Words are sequences of sophisticated verbal signs. Words allow us to capture the world around us and share the past with others. Before that, everything was current. Nothing in the past can be shared. Only current alerts can be.
By sharing the past, we recognize the past. By recognizing the past, we capture the future. This allows us to make predictions and preparations. We gain the sequence of time.
Names are the symbol of objects. By putting a name on something, something in three dimensions becomes a symbol. The complex 3D structure with texture is extracted to the symbol, a sequence of sounds—symbols for objects, symbols for actions, symbols for situations like morning, night, etc.
Letters are symbols, too. A sequence of letters consists of words. Each word works as a symbol, a nested information on the sequence of letters. With written words, we can have a conversation with your past thoughts.
A sequence of words can create a sentence, a further nested information of the sequence of words. A sequence of sentences is a paragraph that carries another nested information on the sequence of sentences. We can layer further as chapters and books. The nested information is created in each layer based on the sequence underneath. The striking characteristic of the sequence is that reductive approaches do not work to understand the relationship between two adjacent nested layers. A rule and code in sequences connect them. This cannot be logically reduced—simply because the meaningful sequence is the retrospective consequence. That is history, but not science.
Amazingly, in a DNA polymer within the three-dimensional molecular structure, the information for replication emerged as a sequence. The real three-dimensional molecules create the information as a sequence, not symbols like A, C, T, and G. Life replicates this information.
Biology is a discipline of science. In parallel, biology is inevitably a history of life. History forces everyone to follow the previous generations and the pre-existing rules and codes. There is no way to overwrite them completely. All living organisms are the progeny of common ancestors (not necessarily only one) – a part of history. All machinery and mechanisms in organisms are not the best in efficiency but sufficiently work to sustain and continue. Both life and human histories indicate that there is no need to be the best, but surviving with robustness would last longer on the earth. The genome carries all information on evolution, development and diseases. Yet, we need to learn how to read it as the history of life.