Convergent evolution 50 times with CRISPR-challenges Neo-Darwinism

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The article: ”Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12” by Han Altae-Tran, et al.(11/23), describes the TnpB protein family and its diverse roles in bacterial and archaeal genomes. The authors found that TnpB proteins are remarkably adaptable and have been recruited for a variety of functions beyond their ancestral role in transposition. The most common example of this is the development of TnpB proteins into type V CRISPR-Cas effectors, which are enzymes that defend cells against viruses and other invaders. The authors also identified other cases where TnpB proteins have been exapted for new functions, such as acting as toxins or regulators. These findings highlight the remarkable developmentally  flexibility of the TnpB scaffold and suggest that TnpB proteins may have many more undiscovered roles in biology.

Key findings of the article:

  • TnpB proteins are among the most abundant proteins encoded in bacterial and archaeal genomes.

  • TnpB proteins have been recruited for a variety of functions beyond their ancestral role in transposition.

  • The most common example of TnpB recruitment is the development of type V CRISPR-Cas effectors.

  • TnpB proteins have also been exapted for other functions, such as acting as toxins or regulators.

  • The findings of the study highlight the remarkable developmental flexibility of the TnpB scaffold.

Overall, the study by Han Altae-Tran, et al., provides valuable insights into the diversity, development, and classification of the TnpB protein family. The findings of the study have the potential to make significant contributions to a variety of fields, including biology, medicine, and biotechnology.

The recruitment of TnpB for CRISPR-Cas effector function is thought to have occurred independently on at least 50 occasions. NeoDarwinian random mutations can not explain this convergent development. This suggests that TnpB is a versatile protein that can be easily adapted for new functions. In addition to CRISPR-Cas effector function, TnpB has also been recruited for other roles, such as toxin production and regulation of gene expression.

The recruitment of TnpB for other functions is an example of exaptation, which is the process by which a trait that develops for one function is subsequently co-opted for a new position. Exaptation is a common developmentally  mechanism, and it is thought to play an important role in diversifying biological functions.

The recruitment of TnpB for other functions is a fascinating example of how developmental processes can exploit existing genetic material to create new and innovative solutions to biological challenges. This process is likely to continue to play an important role in the development of new biological functions in the future.

The convergent development of TnpB proteins into type V CRISPR-Cas effectors on approximately 50 separate occasions poses a significant challenge to neo-Darwinism. Neo-Darwinism proposes the diversity of life through gradual, incremental changes driven by natural selection. However, the repeated recruitment of TnpB for a new function, specifically as a CRISPR-Cas effector, concludes that this process is not gradual or incremental as per neo-Darwinism.    

In the case of TnpB, the catalytic site of the protein, which is essential for its original function in DNA transposition, has been repurposed to perform a completely different task: RNA-guided DNA cleavage. This repurposing has occurred independently on multiple occasions, which is not simply a matter of random mutation and natural selection. Having the same mutations 50 times is statistically impossible. Instead, it appears that the TnpB protein scaffold has some inherent properties that make it well-suited for this new function.

This observation raises questions about the role of chance and constraint in evolution. Neo-Darwinism emphasizes the role of chance mutations in providing the raw material for natural selection to work on. However, the convergent development of TnpB suggests that there are more constraints on the development  process than previously thought. The fact that the same protein scaffold has been repurposed multiple times suggests that certain structural or functional features of TnpB make it more likely to develop into a CRISPR-Cas effector.

This challenge suggests that there may be more to the evolutionary process than we currently understand. It is possible that there are other factors, besides random mutation and natural selection, that play a role in shaping the diversity of life.

Here are some specific ways in which the convergent development of TnpB challenges neo-Darwinism:

  1. It suggests that there are limits to the randomness of mutation. If mutations were truly random, we would expect to see a wide variety of different proteins evolving into CRISPR-Cas effectors. However, the fact that the same protein scaffold has been repurposed multiple times suggests that there are constraints on which proteins are more likely to develop into this role.

  2. It suggests that there are other factors besides natural selection that can influence the evolutionary process. Natural selection is often seen as the driving force behind evolution, but the convergent development  of TnpB suggests that there may be other factors at play. For example, it is possible that the structure of the TnpB protein scaffold makes it more likely to develop into a CRISPR-Cas effector, regardless of the selective pressures acting on it.

  3. It suggests that neo-Darwinism may not be able to fully explain the diversity of life. Neo-Darwinism is not able to explain all of the patterns that we see in nature. The convergent development of TnpB is one example of a phenomenon that is difficult if not impossible to explain within the framework of neo-Darwinism.

Overall, the convergent development of TnpB is a fascinating and complex phenomenon that raises important questions about the nature of evolution and suggests neo-Darwinism core concepts needs revision.

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