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A DNA repair molecule’s constant operation gives new meaning to the scripture that declares that God supports us “from one moment to another.” (Mosiah 2:21) The second article in the “It Was a Miracle” series.

The final Book of Mormon prophet, Moroni, asks a pointed question when he proclaimed “I will show unto you a God of miracles… and it is that same God who created the heavens and the earth, and all things that in them are. … Who shall say that it was not a miracle that by his word the heaven and the earth should be; and by the power of his word man was created of the dust of the earth?” (Mormon 9:11, 17)

We live in that day where the miracle of creation and the amazing adaptability, design and progression of living beings and man himself is attributed by many to arise exclusively from a source of pseudo-random mutations: without purpose, without a plan, without intelligence and definitely without miracles. 1

Joseph Smith testifies of a God of miracles, where “the light which is in all things, gives life to all things” (D&C 88:13) “upholding all things by the word of his power.” (Hebrews 1:3)

DNA:  The Controlling Molecule of Life

It was only 56 years ago last April that James D. Watson and Francis Crick published their article noting the discovery of the double helix structure of the deoxyribonucleic acid, or DNA molecule. 2


The DNA information code with its variable length double helix shape being split to make a working copy. 3

DNA is the key controlling physical molecule in living beings on earth. Since these discoveries, not only have we been able to verify that the proposed structure for this molecule that stores genetic information was correct, but we have even been able to extract out the complete sequence for the three billion DNA letter code for humans. 4 This wonderful DNA molecule, present in trillions of tiny cells in our body, microscopic cells, if unwound and stretched out would be about two meters long! 5


DNA ligase enzyme repairing a strand of DNA, needed 1,000 to 1,000,000 times a day in each cell.

This illustration shows the enzyme called DNA ligase repairing a break in a strand of DNA--color has been added to emphasize the repair enzyme’s molecules and shape. These breaks occur at the rate of 1,000 to 1,000,000 molecular lesions in each cell, every day. 6  It reminds me of the railroad track maintenance vehicles that we see from time to time keeping the railroad lines open and repaired.

It is almost unbelievable to me to see this example of how life is built upon a foundation that is so fragile.  Without this correction program constantly running, life would cease.  In an excellent example of “which came first, the chicken or the egg?” the structure of DNA ligase, essential to maintain the DNA molecule, is also specified in the DNA information code. In other words, the formula for the repair formula is found in the thing it needs to repair. 
How even more unlikely could it be for a system this fragile to come together by chance.  It is like a specially designed clean room in a microchip manufacturing center where dust must be kept to a minimum or the chips will not work. In other words, how can you build them in a clean room without building the clean room first? Those that believe that a tornado going through a junkyard can randomly create a 747, complete with microchips, don't understand that the inside of a tornado is not dust free enough to make chips. 7 

To me, this repair molecule for the long DNA strands is a powerful witness of the hand of God in creating and sustaining the universe.  It gives more meaning to the scripture:  “I say unto you that if ye should serve him who has created you from the beginning, and is preserving you from day to day, by lending you breath, that ye may live and move and do according to your own will, and even supporting you from one moment to another—I say, if ye should serve him with all your whole souls yet ye would be unprofitable servants. (Mosiah 2:21 emphasis by author) 

Complicated track maintenance vehicles such as this one from The Fillmore and Western Railroad in California keep the railroad lines open. 8

Where Do You Draw the Line?

I have talked with many Latter-day Saints about the miracle of life and the deficiencies of the Darwinian theory of evolution to explain life.  I emphasize that Joseph Smith’s restored knowledge of physical matter, spiritual matter and intelligence nullifies any need for dead physical matter to become alive.  I have been pleasantly surprised to see unanimous agreement on that point.  However, then, many say, “after creating life, don’t you think that God lets evolution take over for the details of how life progresses after His work?”
In a typical discussion, I then ask “where is the line?” Where is the boundary between the foundations of life and where evolution takes over? What about this crucial DNA repair mechanism?  Did its sophisticated programming evolve?  “No” is the reply. 

“Well,” proceeding with another question, “what about the 64 place amino acid table?"  It is a perfect design, going from RNA letter sequences to the amino acid building blocks of proteins including start and ending codes.” This table maps the letters of the DNA/RNA information code into the basic meanings to be expressed in this code. After looking at that table, people I have talked to will say: “Well, God must have been involved with that too.” 


Amino acid codon table using three bases at a time of the RNA molecule (partner molecule of DNA), with 64 slots, no holes, start and stop control sequences--a perfect design!  Note that methionine (AUG for RNA or ATG for DNA) is always the start of a gene protein sequence which then has a “start” amino acid as well as three special control codes that only indicate the ending of the protein sequence defined by the DNA gene inside of the amino acid code, another very sophisticated design feature. 9


RNA codon table arranged by amino acid instead of RNA nucleotide sequence. 10

This kind of a discussion is a challenge for many that believe firmly in evolution as it is everywhere taught and referenced in our modern society.  They may begin to see how perfectly the foundation structures of life operate, are upheld and how quickly the mutation part of the theory of evolution is left behind as a possible explanation.  And yet, since evolution is everywhere promoted as a universal natural law, they often still think that evolution “must be part of the correct explanation.” 11

From Basic Cell Engine to Language

Life is everywhere around us, complicated and beautiful, from the small inside of the cell to the highly sophisticated human thinking processes.   Especially in the context of Joseph Smith’s revelations and modern information theory, the Darwinian theory of evolution as taught today is not even close in explaining the miracles of life.  The more we understand about life, the more I believe we will realize that there is so much more to life’s foundation and progress than this theory.

We are discussing the very foundation of life, the DNA code.  We have not even moved beyond the basic cell engine that executes, as it were, this information code of life.  If this basic engine is already so far above the capabilities of the unintelligent mutation component of the Darwinian theory of evolution, then what comes next will only be more and more impossible for that component to explain.  

In my work in software development, I have worked with all different levels of programming, from low level assembly language such as scanning off a single word from an electronic file and converting upper case letters to lower case letters, to high level languages where a single instruction or subroutine call might trigger advanced processes like creating a giant multifaceted full text index of all of the patents issued by the U. S. patent office during 30 years.  As we look at any of these levels of programming, I am not trained to say:  “I wonder how this code evolved out of nothing, or randomly built upon itself to create this more complex module?”  That would be ludicrous.  I would know that the program code was created by myself or other software engineers, by the active use of intelligence to solve a problem or create some useful process.

From the foundations of DNA to the pinnacles of language as used by God and His sons and daughters--all these things require a spiritual and intelligent dimension of life.

God and His Spirit Influence the Processes of Life

As we talk about these foundations of biological life, God’s questions to Job may be appropriate: 

“Where wast thou when I laid the foundations of the earth? declare, if thou hast understanding.  Who hath laid the measures thereof, if thou knowest? or who hath stretched the line upon it?  Whereupon are the foundations thereof fastened? or who laid the corner stone thereof;  When the morning stars sang together, and all the sons of God shouted for joy?” (Job 38:4-7)

We can be assured that indeed, God not only had something to do with the foundations of life, but that He was actively involved as He has boldly proclaimed.  Even now, He “[upholds] all things by the word of his power,” (Hebrews 3:3) “which giveth life to all things.” (D&C 88:13)

 
Notes

1  Ronald P. Millett, “Joseph Smith and the Origin and Progress of Life,” Meridian Magazine, http://meridianmagazine.com/ideas/090526origin.html . May 26, 2009.

Ronald P. Millett, “Joseph Smith’s Views on the Origin of Life,” Meridian Magazine, http://ldsmag.com/ideas/090818origin.html.  August 18, 2009.

See also:  James E. Talmage, Jesus the Christ, Salt Lake City, 1915. Pp. 148-149. 

“Miracles cannot be contravention of natural law, but are wrought through the operation of laws not universally or commonly recognized.  Gravitation is everywhere operative, but the local and special application of other agencies may appear to nullify it … Achievements made possible by modern invention … --these are not longer miracles in man’s estimation, because they are controlled by human agency. … We arbitrarily classify as miracles only such phenomena as are unusual, special, transitory and wrought by an agency beyond the power of man’s control. 

“In a broader sense, all nature is a miracle. … 

“In the contemplation of the miracles wrought by Christ, we must of necessity recognize the operation of a power transcending our present human understanding.  … To deny the actuality of miracles on the ground that, because we cannot comprehend the means, the reported results are fictitious, is to arrogate to the human mind the attribute of omniscience, by implying that what man cannot comprehend cannot be, and that therefore he is able to comprehend all that is.”

2 “Double Helix,” Wikipedia Encyclopedia, Retrieved 11 Oct 2009, http://en.wikipedia.org/wiki/Double_helix.

James D. Watson and Francis Crick (1953). "A structure for deoxyribose nucleic acid". Nature 171: 737–8. See http://www.nature.com/nature/dna50/archive.html for archive copy of the April 25, 1953 paper and the followup paper on May 30, 1953 entitled “Genetical Implications of the structure of Deoxyribonucleic Acid” where “Watson and Crick follow up with largely accurate speculation on how base pairing in the double helix allows replication of DNA.”

3  “DNA replication split,” Wikipedia commons area, http://en.wikipedia.org/wiki/File:DNA_replication_split.svg. “you are free to share and make derivative works of the file under the conditions that you appropriately attribute it, and that you distribute it only under a license identical to this one.”

4   Human Genome Project Information, http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml. August 12, 2009. 

“Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others. Project goals were to (1) identify all the approximately 20,000-25,000 genes in human DNA, (2) determine the sequences of the 3 billion chemical base pairs that make up human DNA, (3) store this information in databases, (4) improve tools for data analysis, (5) transfer related technologies to the private sector, and (6) address the ethical, legal, and social issues (ELSI) that may arise from the project.  Though the HGP is finished, analyses of the data will continue for many years.”

5  Glenn Elert & Steven Chen, “Length of a Human DNA Molecule,” The Physics Factbook, 1998, http://hypertextbook.com/facts/1998/StevenChen.shtml

McGraw Hill Encyclopedia of Science and Technology. New York: McGraw Hill, 1997. [Referenced in table in this web page] with the quote:  ‘If stretched out, [the DNA molecule from a single cell] would form very thin thread, about 6 feet (2 meters) long.’ [Other quotes give other variations on the length.]

“The human genome comprises the information contained in one set of human chromosomes which themselves contain about 3 billion base pairs (bp) of DNA in 46 chromosomes (22 autosome pairs + 2 sex chromosomes). The total length of DNA present in one adult human is calculated by the multiplication of (1) (length of 1 bp)(number of bp per cell)(number of cells in the body) = (0.34 × 10^-9 m)(6 × 10^9)(10^13) = 2.0 × 10^13 meters.  That is the equivalent of nearly 70 trips from the earth to the sun and back.

“2.0 × 10^13 meters = 133.691627 astronomical units = 133.691627 / 2 = 66.8458135 round trips to the sun.”

6 Tom Ellenberger, Washington University School of Medicine in St. Louis, National Institute of General Medical Science (NIGMS), Wikipedia Commons Area Image, 2007, http://en.wikipedia.org/wiki/File:DNA_Repair.jpg

“DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. A special enzyme, DNA ligase (shown here in color), encircles the double helix to repair a broken strand of DNA. DNA ligase is responsible for repairing the millions of DNA breaks generated during the normal course of a cell's life. Without molecules that can mend such breaks, cells can malfunction, die, or become cancerous.”  Note:  DNA Ligase molecules are illustrated with colors as they encircle the DNA strand to repair the molecule.

See also:  Gwen Ericson, “Genetic repair mechanism clears the way for sealing DNA breaks,” Washington University in St. Louis: School of Medicine, October 18, 2006, http://mednews.wustl.edu/news/page/normal/8039.html

“Scientists investigating an important DNA-repair enzyme now have a better picture of the final steps of a process that glues together, or ligates, the ends of DNA strands to restore the double helix. ‘Our study shows that DNA ligase switches from an open, extended shape to a closed, circular shape as it joins DNA strands together,’ says the study's senior author Tom Ellenberger, D.V.M, Ph.D., the Raymond H. Wittcoff Professor and head of the Department of Biochemistry and Molecular Biophysics at Washington University School of Medicine in St. Louis. "The ligase resembles a wristwatch that latches around the DNA ends that are being joined.’”

7  “New Clean Room To Push Boundaries Of Computer Memory Technology,” Science Daily, September 2, 2009, http://www.sciencedaily.com/releases/2009/09/090901082709.htm.
“The University of Southampton’s Southampton Nanofabrication Centre, which opens September 9, 2009, will make it possible to manufacture high-speed and non-volatile ‘universal memory’ devices for industry within 5 years.  … the Nano electromechanical systems (NEMS) available within the new clean room will make high-speed, non-volatile and low-power computer memory a reality.

‘This high-speed, non-volatile and low-power NEMS memory will be suitable for pen drive devices for PCs and mobile applications and will mean that computers will warm up immediately when switched on and will have a sleep switch to conserve energy,’ said Dr Tsuchiya.”

8 Jon Delorey, “Rail Equipment Panorama,” Flickr.com shareable photo, 2008, http://www.flickr.com/photos/jonsphotos/2484660278/.
“The Fillmore and Western Railroad, Fillmore, CA. Yes, it's two photos stitched together. Didn't really need to but it seemed like a fun idea at the time. I'm not sure what this vehicle does exactly but I assume it is for track maintenance and repair.”

9 “Seeing codons,” Rafiki, inc.,  http://www.codefun.com/Images/Genetic/seeing/Seeing5.pdf, p. 6, 2008. See http://www.codefun.com/Index_about.htm for information on this S-corp from the great state of Indiana. “Go Hoosiers.”

“nucleic acids (64 codons X 3 nucleic acids per codon). ..... code actually assign several amino acids to each of the four nucleotide types.”

Andrzej (Anjay) Elzanowski and Jim Ostell, “The Genetic Codes,” National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A, April 07, 2008, http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi.

“Initiation Codon: AUG  ----- Alternative Initiation Codons

“In rare cases, translation in eukaryotes can be initiated from codons other than AUG. A well documented case (including direct protein sequencing) is the GUG start of a ribosomal P protein of the fungus Candida albicans (Abramczyk et al.) and the GUG initiation in mammalian NAT1 (Takahashi et al. 2005).”

10 “Seeing codons,” op. cit., p. 7.  A great paper to help visualize the amino acids from many different perspectives!  I would highly recommend looking at the great variety of meaningful graphics that were created for this paper.  You would think that being so common, the codon table would have nothing that could be improved and give new perspective on it.  That assumption would be wrong.

11  “The Link,” history.com documentary, May 29, 2009.  Transcribed by author from video.  RPM note: This is the ending quote in this documentary on the analysis of the discovery of a lemur-like animal that is widely claimed to be part of the pedigree of man.  Notice how passionately these well-respected scientists talk about the theory of evolution as a proven fact.

“Today lots of people have trouble with evolution.  Lots of people don’t want to accept evolution.  People say: ‘I don’t believe in evolution.’  And I say: ‘I don’t believe in evolution either.’  And they go ‘What do you mean?’  ‘Anymore than I don’t believe in gravity. It is fact.’  If I let go of an object, it is going to fall to the ground.  No matter how many times you do this experiment, it is going to fall to the ground.  So gravity is a law.  It’s a fact.  It is an observable thing.  And it’s the same thing with evolution.  We’ve gotten to the point now that evolution is the grand explanation for the diversity of all life that there has been, the interrelatedness of life and all the life that is and all the life that will be on this planet.  Nothing in biology makes sense without evolution.” -- Donald Johanson, Arizona State University

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© 1999-2009 Meridian Magazine.  All Rights Reserved.

About the Author:

Ron Millett and his wife Rhonda live in Cedar Hills, Utah. They are parents of six children, ages 18 to 28 and grandparents of two beautiful granddaughters. Ron is a software developer with master's degrees in computer science and linguistics from BYU. He is the inventor of ten software patents specializing in AI applications, with more patents pending. Rhonda enjoys being at home, caring for their handicapped daughter and playing the piano and organ for ward choir and church.

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