Epigenetic Morphospaces causes Evolution without Darwin

Waddington Diagram

An epigenetic morphospace is a theoretical space of all possible phenotypes that can be produced by a given genotype. It is a way of thinking about the potential for phenotypic variation that is encoded in the genome, but which is not necessarily realized in any given individual.

The concept of an epigenetic morphospace was first proposed by Conrad Waddington in the 1940s. Waddington argued that the genome can be thought of as a landscape, with different regions corresponding to different phenotypes. The actual phenotype of an individual is determined by its position on this landscape, which is influenced by both genetic and environmental factors.

Epigenetic morphospaces can be used to study the evolution of phenotypic diversity. For example, if two populations of organisms have different genotypes, but they are exposed to the same environment, then they will occupy similar regions of the epigenetic morphospace. This can lead to the evolution of new similar phenotypes, as the organisms in each population adapt to their environment.

Epigenetic morphospaces can also be used to study the effects of environmental change on phenotypic diversity. For example, if an environment changes, then the epigenetic morphospace of the organisms that live in that environment may also change. This can lead to the extinction of some phenotypes, the evolution of new phenotypes, or the redistribution of phenotypes within the epigenetic morphospace.

The concept of an epigenetic morphospace is a powerful tool for understanding the evolution of phenotypic diversity. It can be used to study the effects of genetic, environmental, and evolutionary factors on the range of possible phenotypes that can be produced by a given genotype.

Here are some additional details about epigenetic morphospaces:

  • They are multidimensional spaces, with each dimension corresponding to a different trait.

  • They are dynamic, meaning that they can change over time in response to genetic, environmental, and evolutionary factors.

  • They can be used to study the evolution of phenotypic diversity.

  • They can be used to predict the effects of environmental change on phenotypic diversity.

Epigenetic morphospace does not require neo darwinism, which is a theory of evolution that relies on natural selection to explain how species change over time.

Epigenetic morphospace can be explained by the idea that genes are not the only factors that influence development. Epigenetic factors, such as DNA methylation and histone modification, can also play a role in determining how genes are expressed. This means that even two organisms with the same genotype can have different phenotypes, or physical appearances.

Neodarwinism does not take into account the role of epigenetic factors in evolution. This is because neodarwinism is based on the idea that evolution is driven by changes in the genetic code. However, epigenetic factors can also cause changes in the phenotype, even without a change in the genetic code.


Ant cast with the same genotype but markedly different phenotype 

Here are some additional points about epigenetic morphospace and neo darwinism:

  • Epigenetic morphospace is a relatively new concept, and it is still being researched.

  • Neodarwinism is a well-established theory of evolution, but it is not without its critics.

  • There is evidence to suggest that epigenetic factors may play a more important role in evolution than previously thought.

Epigenetic morphospaces gives the first real explanation for convergent evolution where NeoDarwinism fails. Convergent evolution is the process by which unrelated organisms independently evolve similar traits as a result of adapting to similar environments or ecological niches. Bottlenecks are events that reduce the size of a population, such as a natural disaster or a human-caused event like habitat destruction.

When a bottleneck occurs, the genetic diversity of the population is reduced. This can lead to convergent evolution, as the remaining individuals are more likely to share the same genes for epigenetics to work with. The epigenetics can produce similar convergent phenotypes leading  to the new species.


Epigenetic morphospace explains Gould's punctuated equilibrium. 


Punctuated equilibrium is a theory of evolution that states that most of evolutionary time is spent in stasis, with periods of rapid change (punctuated) occurring only rarely. Epigenetic morphospace could explain punctuated equilibrium by providing a mechanism for rapid change in phenotype. If a population experiences a change in its environment, this could lead to changes in epigenetic regulation. These changes could then lead to the rapid evolution of new phenotypes.

For example, if a population of animals experiences a change in its diet, this could lead to changes in the expression of genes involved in metabolism. These changes could then lead to the rapid evolution of new body shapes and sizes that are better suited to the new diet.

Here are some additional points to consider:

  • Epigenetic changes can be passed down from parent to offspring, but they are not as stable as changes in DNA sequence. This means that epigenetic changes can be lost over time, or they can be reacquired by new mutations.

  • Epigenetic changes can be affected by environmental factors, such as diet, stress, and exposure to toxins. This means that the environment can play a role in shaping the evolution of a population.

  • Punctuated equilibrium is not the only explanation for the fossil record. Other theories, such as phyletic gradualism, also attempt to explain the patterns of evolution that we see in the fossil record.

The paper "Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes" by Kamaludin Dingle, Fatme Ghaddar, Petr Šulc, and Ard A Louis (2022) examines the distribution of natural RNA structures in the morphospace of all possible RNA structures. The authors find that natural RNA structures are only a small subset of all possible structures, and that this distribution is primarily due to a phenomenon known as "phenotype bias."

Phenotype bias refers to the tendency for certain phenotypes to be more likely to appear than others, even in the absence of natural selection. In the case of RNA, phenotype bias is thought to be caused by the way that RNA molecules fold. RNA molecules are made up of a sequence of nucleotides, which can be arranged in many different ways. However, not all of these arrangements are equally stable. Some arrangements are more likely to form stable structures than others. This means that some RNA sequences are more likely to fold into specific shapes than others.

The authors of the paper used a computer simulation to study the distribution of natural RNA structures in the morphospace of all possible RNA structures. They found that the distribution of natural RNA structures was very different from the distribution of all possible RNA structures. The vast majority of all possible RNA structures were very unstable and did not form any meaningful shapes. In contrast, the vast majority of natural RNA structures were stable and formed well-defined shapes.

The authors concluded that phenotype bias is the primary explanation for the distribution of natural RNA structures in the morphospace of all possible RNA structures. They argue that phenotype bias is a fundamental property of RNA folding, and that it has played a major role in the evolution of RNA molecules.

The findings of this paper have important implications for our understanding of RNA structure and function. They suggest that the distribution of natural RNA structures is not simply a product of natural selection. Instead, it is also shaped by the underlying physical properties of RNA molecules. This means that we need to take phenotype bias into account when we are trying to understand how RNA molecules function in cells.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8763027/

This means that epigenetic morphospace is a broader concept than neo darwinism. It can be used to explain how evolution can occur even in the absence of changes in the genetic code.

Epigenetic morphospaces are a relatively new concept, but they have the potential to revolutionize our understanding of evolution. By providing a way to think about the potential for phenotypic variation that is encoded in the genome, they can help us to understand how organisms evolve and adapt to their environment.

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