Are There Laws of Genome Evolution?" by Eugene V. Koonin.-Review


Summary of the article "Are There Laws of Genome Evolution?" by Eugene V. Koonin.

The article begins by discussing the two main theories of genome evolution: neo-Darwinism and the theory of punctuated equilibrium. Neo-Darwinism, which is the dominant theory, holds that evolution is driven by random mutations and natural selection. Punctuated equilibrium, on the other hand, holds that evolution occurs in rapid bursts, separated by long periods of stasis.

Koonin argues that neither of these theories is adequate to explain the full complexity of genome evolution. He proposes a new theory, which he calls the "genome evolution theory," that takes into account the following factors:

  • The vast amount of genetic variation that exists within and between species

  • The role of horizontal gene transfer (HGT) in the evolution of genomes

  • The importance of gene duplication and rearrangement in the creation of new genes and functions

  • The role of regulatory networks in controlling gene expression

Koonin argues that the genome evolution theory provides a more comprehensive and accurate explanation of genome evolution than neo-Darwinism or punctuated equilibrium. He also argues that the genome evolution theory bypasses some of the limitations of neo-Darwinism, such as its reliance on random mutations and natural selection.

One of the key ways in which the genome evolution theory bypasses neo-Darwinism is by its emphasis on the role of HGT. HGT is the process by which genes are transferred from one organism to another, even if they are not closely related. HGT is thought to be a major force in genome evolution, and it can help to explain the rapid evolution of new genes and functions.

Another way in which the genome evolution theory bypasses neo-Darwinism is by its emphasis on the role of gene duplication and rearrangement. Gene duplication is the process by which a gene is copied and then inserted into the genome in a new location. Gene rearrangement is the process by which genes are moved around within the genome. Both gene duplication and rearrangement can create new genes and functions, and they are thought to be important drivers of genome evolution outside of NeoDarwinism.

The genome evolution theory also emphasizes the importance of regulatory networks in controlling gene expression. Regulatory networks are the systems that control which genes are turned on and off in a cell. These networks can be very complex, and they can play a major role in determining the phenotype of an organism.

The genome evolution theory is a relatively new theory, but it has already generated a lot of interest among biologists. The theory provides a more comprehensive and accurate explanation of genome evolution than neo-Darwinism, and it has the potential to revolutionize our understanding of how life evolves.

In addition to the above, here are some other key points from the article:

  • The genome evolution theory is based on the following principles:

    • Genomes are dynamic entities that are constantly evolving.

    • The evolution of genomes is driven by a variety of factors, including random mutations, natural selection, HGT, gene duplication, and gene rearrangement.

    • Regulatory networks play a major role in controlling gene expression and determining the phenotype of an organism.

  • The genome evolution theory has the following implications for our understanding of life:

    • It provides a more comprehensive and accurate explanation of genome evolution than neo-Darwinism.

    • It suggests that life is more complex and diverse than previously thought.

    • It opens up new possibilities for understanding the origin of life and the evolution of new species.

The genome evolution theory is a rapidly evolving field of research, and it is likely to continue to generate new insights into the process of life.

Article Snippets

Are There Laws of Genome Evolution?

Koonin

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables

These models do not explicitly incorporate {natural} selection ; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles.

Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as “laws of evolutionary genomics” in the same sense “law” is understood in modern physics.

Darwin's concept of evolution, all its generality and plausibility notwithstanding, was purely qualitative.

in the beginning of the 21st century brought about enormous amounts of new data amenable to quantitative analysis

the formalism of population applies only to microevolution in idealized populations and falls far short of a general quantitative theory of evolution.

negative correlation between a gene's sequence evolution rate and expression level (or protein abundance)

The universality of these dependencies appears genuinely surprising

For example, the distributions of sequence evolution rate of orthologous genes are virtually indistinguishable in all evolutionary lineages for which genomic data are available, including diverse groups of bacteria, archaea, and eukaryotes.

{This means that the rate at which genes evolve is not correlated with the time since they diverged from each other.}

The shape of the distribution did not perceptibly change through about 3.5 billion years of the evolution of life even though the number of genes in the compared organisms differs by more than an order of magnitude, and the repertoires of gene functions are dramatically different as well

What is the nature of the genomic universals? Do they reflect fundamental “laws” of genome evolution or are they “just” pervasive statistical patterns that do not really help us understand biology? A related major question is, are these universals affected or maintained by selection?

The models of evolution that generate the observed universal patterns of genome evolution do not explicitly incorporate selection

any class of interacting objects can be naturally represented by nodes, and the interactions between these objects, regardless of their specific nature, can be represented by edges.

This property might be conceived as implying that the architecture of such networks represents “design."

However, this idea is no more justified than the view that the Internet was deliberately designed with the same purpose in mind.

Duplication followed by subfunctionalization is the most common route of gene evolution that does not intrinsically involve selection.

Rather, subfunctionalization is naturally interpreted as a type of “constructive neutral evolution” whereby complexity, and complex networks in particular, evolve not as adaptations but through irreversible emergence of dependencies between parts of the evolving system

The MA lines are virtually free of selective constraints, so comparison between these lines and natural isolates provides for evaluation of the contribution of selection to the evolution of various characters, in particular network architecture.

These results strongly suggest that not only general architectural properties of networks but even the position of individual nodes in networks are not subject to substantial selection.

Collectively, the ability of simple models to generate the universals of genome evolution and additional results indicating that the global architecture of biological networks is not a selected feature suggest that all evolutionary universals are not results of adaptive evolution. Such a conclusion does not imply that these universals are biologically irrelevant: beneficial properties such as network robustness may emerge “for free” from the most general principles of evolution.

a complete physical theory of evolution (or any other process with a substantial historical component) is inconceivable

Nevertheless, the universality of several simple patterns of genome and molecular phenome evolution, and the ability of simple mathematical models to explain these universals, suggest that “laws of evolutionary biology” comparable in status to laws of physics might be attainable.

The “post-modern synthesis” does posit a change of the fundamental null hypothesis of evolutionary biology: the new null hypothesis is that any observed pattern is first assumed to be the result of non-selective, stochastic processes, and only once this assumption is falsified, should one start to explore adaptive scenarios.


Comments

Post a Comment

Popular posts from this blog

Beyond the Sequence: The Epigenetic "Fingers" That Play the DNA Keyboard

Image
Imagine the keyboard itself is not a standard piano keyboard, but a modular synthesizer, capable of producing an almost infinite array of sounds. The DNA sequence, then, represents the fundamental building blocks of this synthesizer, the raw materials from which all sounds are generated. Epigenetics, our "fingers," manipulates these building blocks, adjusting parameters like volume, timbre, and rhythm, transforming the raw potential of the DNA sequence into a symphony of cellular functions. We can further refine the "fingers" analogy. Consider that each finger represents a distinct epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA.  DNA methylation, for instance, might be the "index finger," capable of precisely silencing specific genes, like muting individual keys on the synthesizer. Histone modifications, the "middle finger," could represent the ability to adjust the accessibility of the DN...
Read more

Why are Christian philosophers running towards Darwin while biologists are "running" away?

Image
As nature reveals the strength of epigenetics and the weakness of Neo-Darwinism, biologists are “running” away from the long-standing accepted theory. In The Federalist , April 2019, Benjamin Dierker reviews “Why one-third of biologists now question Darwinism”: "Current estimates are that approximately one-third of professional academic biologists who do not believe in intelligent design find Darwin’s Theory inadequate to describe all of the complexity in biology.” Dierker continues, “The important note is that these are not ideologues or religious zealots, nor do they propose a god or biblical solution.  Rather, they find problems in the lack of explanatory power of Darwin’s theory in light of modern understanding of mutation, variation, DNA sequencing and more. These expressions of doubt do not reject naturalism or evolution per se, but the rigor of the Neo-Darwinian model for explaining the development of life.” For 40 years, scientists calculated natural se...
Read more

Rewriting the Rules: Epigenomic Mutation Bias Challenges Randomness in Evolution

Image
This research challenges the long-held dogma that mutations occur randomly, irrespective of their consequences, by demonstrating a clear, epigenome-mediated mutation bias in Arabidopsis thaliana . The study meticulously unveils how mutation rates are not uniform across the genome but are significantly reduced in functionally constrained regions, particularly within gene bodies and essential genes. This discovery fundamentally alters our understanding of evolutionary processes, suggesting that mutation is not a purely directionless force. "Mutation bias reflects natural selection in Arabidopsis thaliana" This opening statement encapsulates the core finding: mutation rates are not random but reflect epigenetic pressures. The authors demonstrate that mutations are less frequent in crucial genomic regions, directly contradicting the prevailing theory of random mutation. This observation suggests an active mechanism that minimizes deleterious mutations in essentia...
Read more