1 - DNA double helix

With the recent publications reporting on the research of the Encyclopedia of DNA Elements (ENCODE) project, what was firmly believed to be nothing but “junk DNA” now is considered to be a complex network of regulatory switches controlling the various genes.  My previous article introducing these ground breaking discoveries entitled “What Junk DNA?” can be accessed here.

 2 - controlpanel

This panel of control switches manages a network routing system.  Imagine more than a million of these kinds of switches controlling the cell’s at least 25,000 protein-coding genes. There would also need to be some kind of connection (like a wire) between the switches and the genes.[i]

Brigham Young and other prophets and apostles have counseled us to patiently await the inevitable reconciliation of apparent contradictions between truth as discovered by science and truth as revealed by God and his prophets.[ii]

Brigham Young stated: “We differ very much with Christendom in regard to the sciences of religion. Our religion embraces all truth and every fact in existence, no matter whether in heaven, earth, or hell. A fact is a fact; all truth issues forth from the Fountain of truth; and the sciences are facts as far as men have proved them. In talking to a gentleman not long ago, I said, ‘The Lord is one of the most scientific men that ever lived; you have no idea of the knowledge that he has with regard to the sciences. If you did but know it, every truth that you and all men have acquired a knowledge of through study and research has come from him. He is the fountain [from] whence all truth and wisdom flow; he is the fountain of all knowledge and of every true principle that exists in heaven or on earth.'”[iii]

Sequencing and Analyzing the Human Genome

Just when you think that science has figured out the universe and proclaimed powerful theoretical solutions to describe it, everything still might change as science and time marches onward.  As the human genome was sequenced in 2000, the genes that have the sequences for proteins used in the body were found to constitute only about 2% (15 megabytes) out of the three billion DNA code letters (750 megabytes). 

It was proclaimed by many scientists that 90% of the genome was junk DNA code left over from ages of mostly meaningless psudorandom mutations in life’s almost endless ages of evolutionary change. In a major reversal of that theory, the ten year ENCODE project with hundreds of participatory researchers has now found that at least 80% of DNA actually consistes of a complicated network of regulatory switches that control the protein encoding genes, turning them on and off or to various control levels for various durations.[iv]

3 - DNA 3D chromatin rendering

A three dimensional model of a section of chromatin, the genome’s structural material. This 3D structure determines how the regulatory switches are linked with the genes they control. The  DNA data structures of the switches are evidently in spacial proximity with those genes. In other words, the DNA strands have to be intricately “tangled” just so in the chromosomes in order to work at all because the tangled folding of the DNA is an essential part for it to function.

3D DNA Complicated Folding has a Purpose

“Another related challenge is understanding the genome’s three-dimensional shape. Far from being arranged in a line, chromosomes are folded in fantastically complicated fractal patterns, and these topographies appear to shape network interaction.

“‘Every gene is surrounded by an ocean of regulatory elements. They’re everywhere. There are only 25,000 genes [protein-coding], and probably more than 1 million regulatory elements,’ said Job Dekker, a molecular biophysicist at the University of Massachusetts Medical School who worked on ENCODE’s structural descriptions of the genome.

“He continued, ‘It’s not just one gene touching one regulator. It can touch and interact with a whole collection of them. It must involve a very complicated three-dimensional structure. At this scale, chromosomes topography turns out to be incredibly dynamic, complex and cell type-specific.'”[v]

 “In the Nature paper, Dekker and his UMMS colleagues discovered important patterns in the three dimensional wiring of the genome, which may help researchers understand how the genome is put together and works as a system. For instance, there is a preferred order and distance between regulatory elements and their targets.”[vi]

Newly Identified Structures in DNA/RNA

“In the ENCODE data are thousands of newly identified structures known as pseudogenes, fossil genes and dead genes, which look like protein-coding genes but perform other functions. There are new pieces of RNA, the genome’s messenger molecules, and RNA that doesn’t carry messages. There are pseudogenes that act like messenger RNA.

“There are transcription factors, proteins that link these pieces together, orchestrating gene activity from moment to moment, and basic rules for that orchestration. There are also multiple layers of so-called epigenetic information, describing how the activity of genes is modulated, and how that varies in different types of cells.”[vii]

Here is a diagram by ENCODE project scientists of how genetic components are connected.  Note the many to many relationships between nodes, known to be some of the most sophisticated and complex data structures in mathematics and computer science.

4 - encode visualization 

“Visualizations of networked linkages between genetic components broadly across the human genome (right) and in a smaller, hierarchically arranged subset (left).”[viii]

A Significant Tradition-shattering Discovery

Now, if a software engineer were to start writing even a few bits into random locations of an intricately linked and interconnected executable application, he would be very likely to destroy the whole app.  It would be very, very, very unlikely for him to be able to add anything to the program’s functionality unless he had a binary map of program attachment points and data structures so a program correction or enhancement patch could be carefully made.[ix] 

Similarly, consider how significant this huge set of new tradition-shattering discoveries is as these reports come in from the ENCODE project.  Instead of mostly an evolutionary dead-end graveyard, most of the DNA is an intricately linked 3D connection structure of the network of gene regulatory switches.  Is it not much easier to see the obvious hand of God in this magnificant control structure stuffed into every tiny cell than something that is just labeled “junk DNA ” and is assumed to have no known purpose?

“In the beginning, God created the heaven and the earth.” (Genesis 1:1) 

“The worlds were made by him; men were made by him; all things were made by him, and through him, and of him.” (D&C 93:10)

Time will doubtless manifest more and more the truth of these words in the opening verse of the Bible and in this key section of the Doctrine and Covenants.  Be patient even when it may seem that there are irreconcilable differences between science and religion.

  “Truth will prevail!”[x]  Scientific discoveries of truth that seem at present to be discordant with the words of the scriptures and of the prophets will eventually, we can be assured, come into complete harmony with God’s revealed truth.


[i] Carey Goldberg, “Major Findings: Your Genes as a Panel with a Million Switches,” Common Health Section, WBUR News Radio, Boston, September 5, 2012,

 “‘The genome is like a panel of light switches in a room full of lights,’ said Dekker, ‘except there are thousands of lights and almost a million switches. We don’t know what switches turn on which lights. And some switches turn on the same lights or turn on multiple lights.’

“Over the last several years, it has become clear that one of the ways in which regulatory elements can turn genes on and off is through direct physical contact. As part of the ENCODE project, Dekker’s task was to determine where these switches and genes were touching along the genome. To do this, Dekker and his team produced the first three dimensional diagram of a section of the genome that shows which gene regulatory switches touch, and control, which genes – in essence producing a wire diagram for the genome. “These switches can be located far from the genes they regulated in the one-dimensional genome sequence but in three dimensions, the chromosome is folded so that they physically touch,” said Dekker.

“In the Nature paper, Dekker and his UMMS colleagues discovered important patterns in the three dimensional wiring of the genome, which may help researchers understand how the genome is put together and works as a system. For instance, there is a preferred order and distance between regulatory elements and their targets. Identification of more such ‘rules’ could help predict the three dimensional wiring between genes and regulatory elements for other genomes in the future and for understanding the genetics of disease.

“‘Genetic variation between individuals is often the result of differences in regulatory elements, not genes,’ said Dekker. ‘Unraveling the three dimensional wiring behind the system of switches and lights that makes up the genome will help us find genes that are misfiring because of a defect in a regulatory element that might be causing disease.’

[ii] Ezra Taft Benson, LDS Conference Report, Apr. 1966, pg. 129

“Religion and science have sometimes been in apparent conflict. Yet the conflict should only be apparent, not real, for science should seek truth, and true religion is truth. There can never be conflict between revealed religion and scientific fact. That they have often occupied different fields of truth is a mere detail. The gospel accepts and embraces all truth; science is slowly expanding her arms and reaching into the invisible domain in search of truth. The two are meeting daily — science as a child, revealed religion as the mother. Truth is truth, whether labeled science or religion. There can be no conflict. Time is on the side of truth — for truth is eternal.”

N. Eldon Tanner, LDS Conference Report, April 1978.

 “We learn from the scriptures that all truth is revealed through the light of Christ, “which light proceedeth forth from the presence of God to fill the immensity of space-

    “‘The light which is in all things, which giveth life to all things, which is the law by which all things are governed'” (D&C 88:12-13)

“Thus, the truths discovered by such men as Sir Isaac Newton, Thomas Edison, and Albert Einstein were actually revealed to them through the light of Christ. Such revealed truths have done much to free mankind from the slavery of ignorance and have extended the scope of our understanding of the universe. In like manner, through the power of the Holy Ghost, truths pertaining to the relationship of mankind to God and the mission of Jesus Christ have been made comprehendible.

    “‘The significant thing about a scientist is this: he simply expects the truth to prevail because it IS the truth. … In science, the thing IS, and its being so is something one cannot resent. If a thing is wrong, nothing can save it, and if it is right, it cannot help succeeding. So it is with the Gospel.'” (Henry Eyring, The Faith of a Scientist, Salt Lake City: Bookcraft, 1967, pp. 103, 105.)

     “To know that God the Eternal Father knows all truth and acts in accordance with it explains why he is the same yesterday, today, and forever. All that he does is in keeping with the unchanging truths of the universe. The same attributes are found in his Son, Jesus Christ, who is ‘full of grace and truth.'” (John 1:14)

    “One of the great differences between God and man is God’s greater knowledge of the truth, which makes him free to create worlds and to control the universe.”

 John A. Widtsoe, Evidences and Reconciliations, Bookcraft, 1960, pg. 139.

    “The Church, the custodian of the gospel on earth, looks with full favor upon the attempts of men to search out the facts and laws of nature. It believes that men of science, seekers after truth, are often assisted by the Spirit of the Lord in such researches. It holds further that every scientific discovery may be incorporated into the gospel, and that, therefore there can be no conflict between true religion and correct science. The Church teaches that the laws of nature are but the immutable laws of the Creator of the universe.”

 James E. Talmage, Articles of Faith, Article 8, p. 383.

 “If we compare the historical, prophetical, and doctrinal parts of the Book of Mormon with the great truths of science and nature, we find no contradictions, no absurdities, nothing unreasonable. The most perfect harmony, therefore, exists between the great truths revealed in the Book of Mormon, and all other known truths, whether religious, historical, or scientific.”

 [iii]    Journal of Discourses 14:117.

[iv] Brandon Keim, “New DNA Encyclopedia Attempts to Map Function of Entire Human Genome,” Wired.com, September 5, 2012, .

 [v] Brandon Keim, op. cit.

 [vi] Carey Goldberg, op. cit.

[vii] Brandon Keim, op. cit.

[viii] Brandon Keim, op. cit.

[ix] The DNA equivalent of knowing where to make a programming patch would include the structures and intelligence needed for “directed mutations.” See my article “Witness of God:  Information Dense DNA Mutations,” Meridian Magazine, December 19, 201

 See also:  D. Brisson, “The direct mutation controversy in an evolutionary context,” PubMed.gov, 2003, .

 “Neo-Darwinists have long held that random mutations produce genetic differences among individuals, and selection increases the frequency of advantageous alleles. In 1988, Cairns et al. claimed that an environmental pressure can cause advantageous mutations to occur in specific genes to alleviate that particular pressure. Directed mutation, as proposed by Cairns, has been all but eradicated from evolutionary thinking.However, more than a decade of research spurred by the Cairns et al. paper has cast doubt on three neo-Darwinian principles: (1) mutations occur independently of the environment, (2) mutations are due to replication errors, and (3) mutation rates are constant.

 RPM Note:  These extensive discoveries in the area of “directed mutations” that supposedly have been “eradicated” directly threaten the current “physical causes only mutations” standard view of evolution because it would force changes to the theory that would likely include spiritual and intelligent components for the mutations module. Also note that this paper is from 2003, which is the time when final touches were put on the human genome sequecing project with the widespread conclusion that 90% of the DNA is junk long before the era of the ENCODE project reports.

 To learn more about patching computer files (modifying binary versions of programs and important data such as disk file system tables) see: “SPZAP (a.k.a. Superzap): Dynamically update programs or data: Data and storage management on z/OS,” IBM.com site,

    “The SPZAP service aid has several aliases, including AMASPZAP and Superzap, the latter being the most commonly used. SPZAP allows you to patch or fix volume table of contents (VTOCs), executable programs, or almost any other disk record. In practice, it is used most frequently to patch executable programs.”

 [x] Gordon B. Hinckley, “Taking the Gospel to Britain: A Declaration of Vision, Faith, Courage, and Truth,” Ensign, July 1987.

     “Faith? Faith was all they had-faith and courage. They had no money. One of the brethren gave the coatless Heber a coat. One of the women gave him five dollars, with which he paid for passage for himself and Orson Hyde to Buffalo. …  As they came up the street in Preston, a banner unfurled before them with the words ‘Truth Will Prevail.’  This they adopted as the motto of their mission.”

     See also: “Truth Will Prevail: The Rise of The Church of Jesus Christ of Latter-day Saints in the British Isles, 1837-1987,” Edited by: V. Ben Bloxham, James R. Moss, Larry C. Porter, Reviewer: Ronald G. Watt, BYU Studies, 30:4, 

“This is a well-designed and carefully assembled book. The fourteen chapters are arranged in three sections: “The Apostolic Foundation,” “Building the Kingdom,” and “Looking Forward.” The Church of Jesus Christ of Latter-day Saints funded and published the book as part of sesquicentennial celebration of the church’s introduction into the British Isles. Apostle Russell M. Nelson wrote the forward.