Junk DNA is no longer a "Slam dunk" argument for common ancestry


Researchers have found that mobile elements, also known as jumping genes, can move around the genome in a more complex way than previously thought. The findings, published in the journal Nature, could have implications for our understanding of how the genome evolves and how diseases develop.

Mobile elements (TEs below) are short pieces of DNA that can copy themselves and move to new locations in the genome. They are thought to have played a role in the evolution of life by shuffling genes around and creating new genetic combinations. However, the exact mechanism by which mobile elements move has been a mystery.

In the new study, researchers used a technique called single-cell genomics to track the movement of mobile elements in individual cells. They found that mobile elements can move in a variety of ways, including by copying themselves and inserting into new locations, or by breaking off from one chromosome and reattaching to another.

The researchers also found that the movement of mobile elements is influenced by the environment. For example, mobile elements are more likely to move when cells are dividing or when they are stressed.

For 30 years scientists claimed these elements were frozen in time making them usable to do comparative genomics showing primates split from a common ancestor 6 million years ago. This position is in question as they've discovered these elements move in real time.

The findings of the new study could help us to better understand how the genome evolves in a Lamarckian fashion and how diseases develop. For example, mobile elements have been linked to a number of diseases, including cancer and autoimmune disorders. By understanding how mobile elements move, we may be able to develop new ways to prevent or treat these diseases.

In addition to the implications for disease, the findings of the new study could also help us to better understand how the genome is organized. The genome is a vast and complex molecule, and it is not yet fully understood how all of the different genes and genetic elements are arranged. By studying the movement of mobile elements, we may be able to gain a better understanding of how the genome is organized and how it functions.

https://phys.org/news/2023-06-mobile-elements-monkeying-genome.html

Here are some examples of fast horizontal gene transfer (hgt) of TEs between primates avoiding common ancestry:

  • The LINE-1 retrotransposon family is one of the most abundant TE families in the human genome. It is thought to have originated in an ancient common ancestor of all vertebrates, but it has undergone rapid hgt in primates. For example, the human LINE-1 family contains a number of elements that are not found in other vertebrates, and these elements are thought to have been acquired through hgt from other primates.

  • Non Darwinian epigenetics controls the movement and expression of these TE's for rapid Lamarckian adaptation.

  • The HERV-K retrovirus family is another example of a TE family that has undergone rapid hgt in primates. HERV-K elements are found in the genomes of all primates, but they are most abundant in humans. This suggests that HERV-K elements have been actively transferred between primates, and that this transfer has been particularly important in the evolution of the human genome.

  • The Alu family is a class of short interspersed nuclear elements (SINEs) that are found in the genomes of all primates. Alu elements are thought to have originated in an ancient common ancestor of all primates, but they have undergone rapid hgt in recent evolutionary history. For example, the human Alu family contains a number of elements that are not found in other primates, and these elements are thought to have been acquired through hgt from other primates.

These are just a few examples of the many cases of fast hgt of TEs between primates. This hgt is thought to have played a major role in the Lamarckian evolution for rapid adaptation of the primate genome, and it has helped to shape the unique features of the human genome.

The term "junk DNA" was coined in the 1960s to describe the vast majority of DNA that did not appear to code for proteins. If it doesn't code for protein it can't change the phenotype for Darwin's Natural Selection. This the Central Dogma of NeoDarwinism. However, in recent years, scientists have learned that much of this DNA is actually functional (80% per the ENCODE project) playing a role in a variety of cellular processes, including gene regulation, DNA repair, and immunity. This is arguably the greatest failure of NeoDarwinism.

One type of non-coding DNA that has been shown to be important is transposable elements (TEs). TEs (mobile elements above) are DNA sequences that can move around within the genome, sometimes inserting themselves into genes and disrupting their function. However, TEs can also be beneficial due to epigenetic mechanisms, by providing new genes or by regulating the expression of existing genes.

The famed icon of evolution the peppered moth changed colors overnight due to a TE that was acquired by HGT and the epigenetic fixing in place. Sorry Charlie…

Another type of non-coding DNA that is important is horizontal gene transfer (HGT). HGT is the process by which genes are transferred from one organism to another, not through reproduction. HGT is common in bacteria, but it has also been found to occur in eukaryotes, including humans. When humans lived around primates in recent history they shared their microbiome. These bacteria transferred TEs via HGT giving the false impression of common ancestry.

The discovery that much of the genome is functional has challenged the idea that junk DNA can be used as evidence of common ancestry. Junk DNA is not something God created to confuse creationists as Richard Dawkins says. However, some scientists still argue that junk DNA can be used to infer evolutionary relationships.

Overall, the evidence for and against the use of junk DNA as evidence of common ancestry is mixed. More research is needed to understand the full role of non-coding DNA in evolution.

Here are some additional points to consider:

  • The term "junk DNA" is now considered to be outdated and misleading.

  • Non-coding DNA plays a variety of important roles in the cell.

  • TEs and HGT can contribute to evolutionary change.

  • The evidence for and against the use of junk DNA as evidence of common ancestry is mixed.

In short Junk DNA (TE aka mobile elements) is not a "slam dunk" argument for common ancestry anymore.

Now who would have thought of that!?



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