Lamarck's Disordered proteins explains Darwin's ancient fossils

Epigenetics is a field of biology that studies how environmental factors can affect gene expression without changing the DNA sequence. In the last 10 years there have been 135,000 articles on it in Pubmed. Only 35 citations on NeoDarwinism over this time.

Epigenetics works outside of NeoDarwinism. Epigenetics works by placing tags "epi" on top the DNA whereas in NeoDarwinism mutations occur in the DNA.

 

Epigenetics works outside of neo-Darwinism by controlling site-specific transposon HGT insertion in IDR of IDP proteins. 

What is a transposon?

A transposon is a piece of DNA that can move from one location to another in the genome. Transposons are often called "jumping genes" because they can move around so easily.


What is an IDR?

An intrinsically disordered protein (IDP) has intrinsically disordered protein regions (IDR). They are polypeptide chains that lacks a stable three-dimensional structure. Instead, IDPs exist in an ensemble of conformations that rapidly interconvert. This lack of structure gives IDPs a number of unique properties.


How can transposons insert into IDRs?

Transposons can insert into IDRs in two ways. The first way is called "insertional mutagenesis." In insertional mutagenesis, the transposon inserts into the IDR and disrupts the gene. This can lead to a variety of adaptive changes. It's important to note these mutations sre not Darwinisn "single" mutations that takes eons to accumulate rather "sudden" adaptive mutations that can lead to adaptive changes dictated by the environment. It's Lamarck's "arrival of the fittest" not Darwin's "survival of the fittest."

The second way that transposons can insert into IDRs is called "reinsertion." In reinsertion, the transposon is deleted from the genome, but it then reinserts itself into the same IDR. 


Illustration of transposon insertion into IDR.

IDR regions are genomic regions that are not essential for the survival of the cell. However, they can play important roles in gene regulation and other cellular processes. When a transposon inserts into an IDR region. This can lead to a variety of rapid non Darwinian phenotypic changes, including changes in gene expression, cell growth, and cell differentiation.

The transposon inserts into the IDR and rapidly changes the gene for Lamarckian adaptation without Darwin..

Epigenetic changes can control where transposons insert into IDRs. This can affect the function of the protein, even if the DNA sequence itself is not changed. For example, an epigenetic change could make a protein more or less active.

IDP proteins can absorb mutations without changing their function over billions of years.  No Darwinian gradualistic evolution for billions of year's. 

As its being discovered that the majority of organisms proteins are IDP this explains fossils with no change over millions of years:


Horseshoe crab: These creatures have been around for over 450 million years, and their basic body plan has remained largely unchanged. 

This is because the disordered regions of these proteins are very tolerant of Darwins mutations. As a result, IDP proteins can accumulate mutations over vast time without becoming dysfunctional.

This can also  give the appearance of common descent, even if it is not the case. For example in the case of,  two species that share a common TE gained by pervasive HGT. These TE "jumping genes" can insert in the IDR region of a gene giving the phylogenetic "appearance" of common ancestry even though the two species might not actually be closely related.

The study of epigenetics is still in its early stages, but it is already clear that this field has the potential to revolutionize our understanding of evolution. Instead of Darwinian we will have Lamarckian evolution.

Epigenetic changes can provide a new explanation for how some traits are inherited, and they can also help us to understand how different species have adapted rapidly.

Here are some articles that discuss how epigenetic changes can control where transposons insert into IDRs:

  • "Epigenetic Control of Transposon Insertion" by I.R. Arkhipova and F. Rodriguez (2013). This review article discusses the role of epigenetic factors, such as DNA methylation and histone modifications, in controlling transposon insertion.

  • "Epigenetic Regulation of Transposable Elements in Human Cells" by M.A. Bannister and P.A. Bird (2007). This article provides an overview of the epigenetic mechanisms that are involved in controlling transposon activity in human cells.

  • "Epigenetic Regulation of Transposable Elements in Plants" by M.J. Matzke and A.J. Matzke (2007). This article discusses the epigenetic mechanisms that are involved in controlling transposon activity in plant cells.

  • "Epigenetic Control of Transposon Insertion in Drosophila" by S.A. Bird and A.P. Wolffe (2004). This article discusses the epigenetic mechanisms that are involved in controlling transposon insertion in Drosophila melanogaster.

  • "Epigenetic Regulation of Transposable Elements in Mammals" by J.R. Demuth and D.M. Gilbert (2006). This article discusses the epigenetic mechanisms that are involved in controlling transposon activity in mammalian cells.

These are just a few examples of the many articles that have been published on this topic. 



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