Francis Cricks "Central Dogma is not so central due to epigenetics and Junk DNA.

The article "A revised central dogma for the 21st century: all biology is cognitive information processing" by Miller, Baluška, and Reber argues that the traditional central dogma of molecular biology is no longer sufficient to explain the complexity and dynamism of living systems. The central dogma states that genetic information flows in one direction from DNA to RNA to protein. However, recent research has shown that there is a great deal of feedback and crosstalk between these molecules, suggesting that the flow of information is more complex than previously thought.

The authors argue that a more accurate way to understand the flow of information in living systems is to view it as a process of cognitive information processing. They define cognition as "the ability to acquire, store, and use information to achieve a goal." In living systems, this goal is to maintain homeostasis and reproduce. The authors argue that all biological processes, from cell division to protein synthesis to evolution, can be viewed as forms of cognitive information processing.

The authors' argument has implications for our understanding of neo-Darwinian evolution. Neo-Darwinian evolution is based on the idea that random mutations in DNA are the source of new genetic variation. However, the authors argue that this is not the whole story. They point out that the flow of information in living systems is not random, but is instead guided by the need to maintain homeostasis and reproduce. This means that the process of evolution is not simply a matter of chance, but is also influenced by the cognitive abilities of living systems.

The authors' argument is a significant challenge to the traditional view of the central dogma of molecular biology. It suggests that the flow of information in living systems is more complex than previously thought, and that cognitive information processing plays a role in evolution. This is a promising new direction for research in biology, and it has the potential to revolutionize our understanding of life.

Neo-Darwinism is a modern synthesis of Charles Darwin's theory of evolution by natural selection with the modern understanding of genetics. The "central dogma" of molecular biology is a set of principles that explain how genetic information is passed from one generation to the next. It is essential to Neo-Darwinism because it explains how natural selection can act on genes to cause evolution.

The central dogma states that DNA is transcribed into RNA, which is then translated into proteins. Proteins are the building blocks of cells and tissues, and they play a role in many important functions, including metabolism, reproduction, and immunity.

Natural selection can act on genes because genes influence the phenotype, or physical characteristics, of an organism. Organisms with phenotypes that are better suited to their environment are more likely to survive and reproduce, passing on their genes to the next generation. Over time, this can lead to evolution.

The central dogma is essential to Neo-Darwinism because it explains how natural selection can act on genes to cause evolution. Without the central dogma, it would be difficult to explain how new traits can arise in populations and how these traits can spread through populations.

Here are some specific ways that Neo-Darwinism depends on the central dogma:

• Natural selection can only act on genes. If the central dogma did not exist, then natural selection would not be able to act on genes because there would be no way to pass genetic information from one generation to the next.

• The central dogma explains how new traits can arise in populations. Mutations, which are changes in DNA, can create new genetic variants. These variants can then be passed on to the next generation through the process of reproduction. If a new trait is beneficial, then it will be more likely to be passed on to the next generation, and it will eventually become common in the population.

• The central dogma explains how traits can spread through populations. If a new trait is beneficial, then it will be more likely to be passed on to the next generation. This means that the trait will become more common in the population over time.

The central dogma is a fundamental part of Neo-Darwinism. Without it, it would be difficult to explain how evolution works.

there are a number of ways in which this dogma is no longer valid.

• Retroviruses. Retroviruses are a type of virus that can reverse transcribe their RNA genome into DNA. This allows them to integrate their DNA into the host cell's genome, where it can be transcribed into new viral RNA and proteins.

• RNA viruses. Some RNA viruses, such as the influenza virus, can also replicate their genomes without using DNA. This is done through a process called RNA transcription, which is similar to DNA transcription but uses RNA as the template.

• Prions. Prions are misfolded proteins that can cause other proteins to misfold as well. This can lead to a number of diseases, including mad cow disease and Creutzfeldt-Jakob disease. Prions are thought to be able to replicate themselves by causing other proteins to misfold, which is a form of information transfer from protein to protein.

In addition to these specific examples, there is also evidence that suggests that the central dogma may not be as strictly one-way as originally thought.

Epigenetics is the study of changes in gene expression that do not involve changes in the DNA sequence. These changes can be caused by environmental factors, such as diet, stress, and exposure to toxins, or by internal factors, such as aging. Epigenetic changes can be inherited, which means that they can be passed from parents to offspring.

Epigenetics bypasses the central dogma by affecting gene expression without changing the DNA sequence. This can happen in a number of ways, including:

• DNA methylation: This is the addition of methyl groups to DNA. Methyl groups can silence genes by preventing them from being transcribed.

• Histone modification: Histones are proteins that wrap around DNA and help to control gene expression. Histone modifications can affect how tightly DNA is wrapped around histones, which can affect whether genes are transcribed.

• Non-coding RNA: Non-coding RNA (ncRNA) is a type of RNA that does not encode proteins. ncRNA can regulate gene expression by binding to DNA or by interacting with proteins.

Here are some examples of how epigenetics can bypass the central dogma:

• A study in mice found that exposure to lead can cause DNA methylation in the liver, which leads to changes in gene expression and an increased risk of liver cancer.

• A study in humans found that people who were exposed to famine during the Dutch Hunger Winter in World War II had different patterns of DNA methylation in their blood cells than people who were not exposed to famine. These epigenetic changes were associated with an increased risk of obesity and heart disease.

• A study in plants found that exposing plants to cold temperatures can cause changes in histone modification, which leads to changes in gene expression and an increased ability to survive cold temperatures.

These are just a few examples of how epigenetics can bypass the central dogma and affect gene expression without changing the DNA sequence.

Article snippets

A revised central dogma for the 21st century:all biology is cognitive information processing

https://doi.org/10.1016/j.pbiomolbio.2023.05.005

Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms

Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon.

A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing.

Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form

Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment

That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers

All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise.

However, the effective implementation of information is definitively a function of orderly information management.

Consequently, effective cellular problem-solving is information processing and management.

The epicenter of that cellular information processing is its self-referential internal measurement

All further biological self-organization initiates from this obligate activity.

As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.

Introduction

Alone among its scientific brethren, evolutionary biology has remained firmly wedded to 20th century dogma

Yet, there is no doubt that the general biological sciences have advanced at a remarkable rate.

microbiology has progressed rapidly, largely due to contemporary metagenomic sequencing and other innovative analytical tools.

genetic discoveries and the validation of epigenetic mechanisms have greatly impacted our understanding of the multilevel reciprocations that characterize biological systems and their relation to the environment

Yet, mainstream evolutionary and biological theories have not experienced any mirroring transitions.

within these disciplines, the consensus remains resolutely adherent to its Neodarwinian roots, tenaciously upholding that evolution predominately results from random genetic errors shaped by selective pressures and consequent reproductive advantage

This belief naturally colors how all biological phenomena are evaluated and persists despite accumulating contrary evidence.

For example, a biased non-random pattern of genomic mutations has been discovered in Arabidopsis thaliana secondary to epigenomic influences that direct biological outcomes in purposeful directions

Indeed, non-random genetic mutations are common, linked to structural factors, epigenetic impacts, and biased DNA repair mechanisms

A wide variety of non-random genetic content editors have been identified, including many virocellular interactions, transposable elements, and interacting RNA networks

One of the dominating features of 20th century evolutionary biology sprang from an influential lecture in 1957 by Francis Crick, articulating his celebrated Central Dogma and outlining his intuitive conceptions about cellular genetic and biomolecular pathways

Crick was specific that the linkage expressed within the Central Dogma between genes and proteins was a “flow of information” that directed “the flow of matter and the flow of energy” through genes as units of information

Recent advances in the 21st century have revealed deep complexities in the flow of information in biological systems.

Accordingly, a revised Central Dogma must be sought that can accommodate this contemporary stance.

Therefore, a modern revision requires a reasoned reconsideration of the nature of biological information and a thorough reanalysis of its assessment and propagation.

The crux of that difference separating Crick's Central Dogma from a modern idiom is the contemporary recognition that cellular cognition governs the flow of biological information

Consequently, this new dogma must be a cell theory, not a genetic one

Additionally, Crick's hypothesis of a unilateral directional flow of genetic information must yield to a modern narrative of the reciprocal flow of information across all biological levels and the absence of privileged levels of causation

When placed in this framework, biology must be recast in terms of the cognitive assessment of environmental cues as information, and all that follows is the productive processing and management of that information to sustain the instantiated cognitive faculties that define the living system

Section snippets

Rethinking Crick's central dogma

The major thrust of Crick's Central Dogma maintains that once “information passed into protein, it could not get out again

Notably, this concept of the flow of information became one of the “keystones of molecular biology”

Self-organization is considered fundamental to the reiterating pattern formations and regulated energy dissipation that characterize living systems, separating living organization from abiotic self-assembly

However, once it is understood that all cells are self-referential cognitive agents, it becomes apparent that self-reference cognition underlies the self-organization patterning in living systems

My own scientific career was a descent from higher to lower dimension, led by a desire to understand life. I went from animals to cells, from cells to bacteria, from bacteria to molecules. … On my way life ran out between my fingers.”

A. Szent-György

Conclusion

In the last century, Crick sought to codify biological order through a Central Dogma and an associated Sequence Hypothesis as a unidirectional and specific cellular flow of genetic information

However, relevant discoveries in the 21st century assert that biological order is not genetically encoded but instead derives from the self-referential cognitive flow of cellular information