February 3, 2022 | Jerry Bergman

Life is Designed to Prevent Evolution

Another system has been discovered that corrects the
very mutations that Darwinism depends on for novelty.

 

 

by Jerry Bergman, PhD

Each year, it is becoming more obvious that cells are intelligently designed to prevent evolution. Some of the best examples are the numerous repair mechanisms that maintain DNA integrity. These systems largely negate Darwinism’s main method of generating novel genetic variation – mutations – which is at the heart of evolutionary theory. If no means of producing new genetic variety exists, evolution by natural selection cannot occur.[1]

The Cell Maintains Its Information

The ultimate source of all genetic variation from which natural selection can operate, Darwinians insist, is genetic mutations. Numerous complex cellular genetic-repair systems have been discovered, however, that ensure that the expression of mutations is extremely rare. Less than one per 100 thousand mutations gets through the repair system without correction. These repair systems pose major problems for evolution because virtually all genetic changes caused by accidental base-pair changes will be corrected (and thus not expressed), or the cell itself will be destroyed by apoptosis (programmed cell death). Genetic repair systems are estimated to be over 99.99 percent effective and, as a result, macroevolution is impossible. Much of this conclusion has already been observed from decades of studies on mutations. It is also obvious that species reproduce faithfully for many, many generations without collapsing from mutational load.

These complex genetic-repair systems effectively negate macroevolution which depends on the accumulation of mutations. Chatterjee et al. said in 2017, “Preserving genomic sequence information in living organisms is important for the perpetuation of life.”[2] Bruce Alberts, the former editor of Science, stated in his textbook Molecular Biology of the Cell (4th ed., 2002) that almost all

spontaneous changes in DNA are temporary because they are immediately corrected by a set of processes that are collectively called DNA repair. Of the thousands of random changes created every day in the DNA of a human cell by heat, metabolic accidents, radiation of various sorts, and exposure to substances in the environment, only a few accumulate as mutations in the DNA sequence. We now know that fewer than one in 1000 accidental base changes in DNA results in a permanent mutation; the rest are eliminated with remarkable efficiency by DNA repair.[3]

Scientists have discovered numerous DNA repair systems already. They are constantly at work in the nucleus to prevent mutations. These include double-strand break repair (DSB), base excision repair (BER), nucleotide excision repair (NER), mismatch base repair (MMR), homologous recombination repair (HR), and non-homologous end-joining repair (NHEJ). Additional pathways exist to repair proteins and various systems throughout the cell. Recently, another repair system has been discovered. Announced in Nature Communications January 18, 2022 by Chinese and American scientists, it is called the 53BP1 repair system.[4]

The 53BP1 protein. From Wiki Commons.

53BP1 Repair: A New Mechanism for Repairing DNA

The newly discovered mechanism involves a protein already known for repairing damaged DNA, Tumor Protein P53 Binding Protein 1 (53BP1). This system has been shown to protect the integrity of DNA in the nucleus by maintaining its proper structural shape, and repairing it if necessary. DNA (deoxyribonucleic acid), as most people know, is the informational macromolecule that stores the genetic instructions used in all living things. To function it must maintain a specific conformation.

The 53BP1 protein is a comparatively large protein that determines how cells will repair a particular type of DNA damage — the dangerous DNA double-strand break (DSB). This is when the two strands of DNA are both broken, leaving a free DNA end floating around in the cell’s nucleus. These DNA ends could inappropriately fuse, thus leading to the disruption of genetic information. Normally, cells with unrepaired DSBs self-destruct by apoptosis but, if not repaired, may begin the journey toward developing into disease, such as microcephaly with chorioretinopathy and some types of cancer.[5] As Chatterjee and Walker explained in 2017, “DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival.”[6]

In the new discovery, researchers Zhang et al. found that 53BP1 is involved in protein accumulation at condensed DNA regions in the nucleus called liquid droplets, which form structures due to mixing of dissimilar liquids. This liquid-liquid phase separation (LLPS) is similar to mixing oil with water as seen in many salad dressings. The 53BP1 protein facilitates forming liquid droplets in conjunction with other proteins. Together, they stabilize the DNA during repair within the structures, maintaining the highly condensed DNA conformation that allows other repair proteins to work.

Human 53BP1 is primarily known as a key player in regulating DNA double strand break (DSB) repair choice; however, its involvement in other biological process is less well understood. Here, we report a previously uncharacterized function of 53BP1 at heterochromatin, where it undergoes liquid-liquid phase separation (LLPS) with the heterochromatin protein HP1α in a mutually dependent manner. Deletion of 53BP1 results in a reduction in heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNA. We identify domains and residues of 53BP1 required for its LLPS, which overlap with, but are distinct from, those involved in DSB repair. Further, 53BP1 mutants deficient in DSB repair, but proficient in LLPS, rescue heterochromatin de-repression and protect cells from stress-induced DNA damage and senescence. Our study suggests that in addition to DSB repair modulation, 53BP1 contributes to the maintenance of heterochromatin integrity and genome stability through LLPS.

The result is 53BP1 stabilizes these proteins at these DNA regions, which is important for maintaining the structure, and therefore the proper function, of DNA. The authors call this “an unexpected, yet important, role of 53BP1 in maintaining heterochromatin structure and function, and consequently genome stability….” In summary, this discovery identifies a new and vital role of this protein, which works in partnership with systems of molecules that keep DNA in good working order.

Overall, we believe that our studies have revealed a previously uncharacterized layer of regulation of 53BP1 in genome stability maintenance, which is different from its canonical role in DSB repair. Nevertheless, together with recent publications, they introduced the LLPS concept to 53BP1, broadening our understanding about 53BP1’s biological function.

The 53BP1 protein adds complexity to what was already irreducibly complex. For the system to function properly, very specific environmental conditions must be met. Limits exist, and if the environmental changes are too great, the system will no longer function properly, leading to cancer or disease and death.

Conclusion

As cellular research has progressed, the cell and its parts have been shown to be far more complex and integrated than previously thought. This progression in knowledge is illustrating a higher level of irreducible complexity. The more complexity increases, the less Darwinian evolution is plausible.

Those who are able to think beyond the Darwinian box realize that evolution is becoming less and less tenable as time and research progresses. This new discovery about some of the details of the 53BP1 repair system is but one more example.

References

[1] Bergman, Jerry, The Mutational Repair System: A Major Problem for Macroevolution, CRSQ 41(4):265-273, March 2005.

[2] Chatterjee, Nimrat, and Walker, Graham C., Mechanisms of DNA damage, repair and mutagenesis, Environmental Molecular Mutagenesis 58(5):235–263, doi:10.1002/em.22087, June 2017.

[3] Alberts, Bruce, et al., Molecular Biology of the Cell, 4th edition, Garland, New York, NY, 2002, p. 242.

[4] Zhang, Lei, et al., 53BP1 regulates heterochromatin through liquid phase separation, Nature Communications 13(1), DOI: 10.1038/s41467-022-28019-y, 18 Jan 2022.

[5] Tumor Protein P53 Binding Protein 1 Gene Cards. The Human Gene Database. https://www.genecards.org/cgi-bin/carddisp.pl?gene=TP53BP1.

[6] Chatterjee, et al., 2017.


Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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Comments

  • Ben Keshet says:

    Perhaps Dr. Bergman can, in a future article, detail if such complex DNA repair mechanisms are found in blue-green algae, and other so-called “primitive” single-celled organisms. If they are, then it seems likely to me that this would signal “game over” for the viability of mutation-natural selection generating Darwin’s proposed common ancestry tree.

    • Dr Bergman replies:
      There hasn’t been as much research on DNA repair in bacteria, for example, cyanobacteria, but some repair systems do exist, including double-stranded break (DSB) repair. In fact, some biologists think higher cells evolved their repair systems from cyanobacteria! This is an area to watch. Like you say, it shows that so-called simple life is not simple at all!”

      When I taught college level microbiology, one point I stressed is bacteria were not, by any means, simple, and students typically had the most difficult time on the chapters about bacteria genetics. See Double strand break (DSB) repair in Cyanobacteria: Understanding the process in an ancient organism. August 2020 https://pubmed.ncbi.nlm.nih.gov/32795961/

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