Archive for October, 2016

This post has been adapted from a presentation given at the 2016 Salt Lake Sunstone Symposium. I hope that you find it at least somewhat interesting as I have attempted to weave in the idea of faith.

Introduction

Some people may find this topic so lame. After all, isn’t it correct that only the ignorant and uneducated still hold that evolution is not a law of nature and science. It is taught in our schools as part of the foundational sciences. it is a prerequisite world view for any credible scientific scholar. The evidence is there in the rocks and in the test tube. The tree of life as illuminated by Charles Darwin can be seen in the fossils on every continent. The mechanics of evolution are demonstrated in the genetic processes of every living creature. So why even challenge the prevailing wisdom?

evolution-of-manBefore I address that question, let me relate it to a discussion often held within a belief system. For one  who was once engaged in the Latter Day Saint environment, there are likely elements of doctrine or policy that can cause dissonance. From my experience, a believing, practicing member is likely in need of a ‘shelf” to hold items that are part of the dialogue of the church but may require ‘further light and knowledge’ before the true picture can be illustrated. Items on the ‘shelf’ could be the abandoned practice of polygamy, or the policy change regarding blacks and the priesthood. It could contain doctrinal items such as our role and relevance of our Mother in Heaven or the requirement of membership to hold certain men as ‘prophets, seers, and revelators.’ It could also contain historical quandaries such as the Kinderhook plates and the origin of the Book of Abraham.

falling-shelfFor the believer, the items can become too heavy for the shelf and cause a collapse commonly known as a “crisis of faith’ Some who encounter this situation simply continue to outwardly demonstrate allegiance and anesthetize the mind and the heart.  Others who walk this path determine to reject everything they once held as ‘true’ from a religious perspective and move on to re-establish a new worldview. The rejection of all things ‘God’ appeals to those who might come to see religion as simply a means of crowd control.

celebrationAcceptance of evolution  as the cause of ‘us’ can be perceived as liberating; no more checklists, no more corporate-induced guilt, no more cognitive dissonance with answers promised at some point in the future. No more blind obedience. And, relevant to our discussion today, no more need for a shelf to hold items that have not been fully clarified… or is there?

Are there aspects of the evolution narrative that are not fully explained and demonstrable? Do we today have all the answers as to the origin of life and the diversity of living creatures we see around us? Does the embrace of evolution, as conceived by the scientific community, require any amount of what could be defined as ‘faith?’ Does this ‘faith’ bear any similarity to the faith required of believers on other discussions? To quote Alma from the Book of Mormon:

Faith is not to have a perfect knowledge of things; therefore if ye have faith ye hope for things which are not seen, which are true.” (Alma 32:21)

To bring this around to the question of evolution, are there aspects that are perceived to be true but are not seen or demonstrable? This verse contrasts ‘a perfect knowledge of things’ with a ‘hope for things which are not seen, which are true.’ I would submit that the scientific method is an example of a process to acquire a perfect knowledge. It demands that a proposed hypothesis be validated through testing and relies on repeatable verification. If the original hypothesis is not verified in the testing, one is to modify the hypothesis and continue testing.  That is the process of gaining knowledge – or to use another word – the process of coming to the truth.

Many aspects of evolution, unfortunately, are not provable by the scientific method. No one has demonstrated how man, for example, evolved from the apes. There is no repeatable scientific sequence to demonstrate how the first living organism came to exist.  detectiveAlternatively, the seeker must acquire as much data and information as possible, much like a detective at a crime scene, and infer historical events from the evidence collected.  The judicial system uses the standard of ‘beyond a reasonable doubt’ in the assessment of guilt. However, there is a continual stream of news stories regarding court convictions being overturned by new evidence, such as DNA matching. One must always consider new evidence and assess its impact on the dogma of the day.

My objective in this treatise is twofold. First, I wish to examine evolution of the theory of evolution and, secondly, to provide a reasoned analysis of the areas of evolution that may require some amount of faith from my perspective. Does the information presented take one beyond a reasonable doubt? That will be left to the reader.

But first, a note of clarification. I am approaching this question from a different perspective. I am not a biologist nor a paleontologist. I am trained as an engineer in the area of information technology, networks and systems and have built chips, boards, systems and networks.ant-and-chip My area of expertise as applied to the question at hand is what it takes to put a working entity together and the information necessary to achieve the design objective.  I will use what remains of this skill in the examination of the evidence gleaned through hundreds of hours of research and analysis of issues pertinent to the topic at hand. Again, let me clearly state that the following discussion points represent items that would find space on my ‘shelf’ as one who believed in evolution. Your mileage may vary.

Natural selection or survival of the fittest

Within two decades of the publishing of Darwin’s book, On the Origin of Species, in 1859, evolution found general acceptance within the scientific community and cleaved science from religion. darwinThe essence of the narrative of the book is that the wide variety of species found today are the result of slow, gradual adaptation to the environment from a single ancestor. Those who adapted well to their circumstances were rewarded with continued existence, those who were not able to change were left behind. In his book, Darwin states, “One general law, leading to the advancement of all organic beings, namely, multiply, vary, let the stronge live and the weakest die.” (Darwin, 1958 reprint, p. 232) To Darwin’s liking, Herbert Spencer coined the term “survival of the fittest,” representing that those creatures who are best fit for their environment will have the best chance to propagate and continue the species.

An example of evolution utilized by Jerry Coyne in his book ‘Why Evolution is True.’ dealt with the path taken to produce our modern day whale, the large mammal whose ancestors once walked on land. Here is an illustration from his book summarizing the evolution of this beast. whale-evolultionOne prevailing theory is that an organism becomes isolated and, driven by the available food or other external variables, changes it form to adapt to the environment. In the case of Dorudon, the extinct ancestor of the whale, fossils have been found in North Carolina, Egypt and Pakistan. Not necessarily constrained to a small area.

“The evolution of whales from land animals was remarkably fast; most of the action took place within only 10 million years” (Coyne, 2009, pp. 50-51). Does ‘remarkably fast’ fit the Darwin narrative? There are attempts to explain what ‘triggers’ such rapid evolutionary development but no definitive conclusion has been drawn. The other critical aspect regarding the evolution of the whale is that in there is a need to have a number of significant changes, such as the development of blubber for temperature control, skin smoothing, the movement of the sexual organs into the body along with the associated cooling mechanisms. These changes identified between the Dorudon and the Balaena, or modern whale, would have needed to occur in the last 2.5 million years. Given that this rapid evolution, not entirely in keeping with Darwin’s original hypothesis,  has not escaped the attention of the scientific community. Let’s consider what has been developed to address the ‘speed’ of evolution.

Let’s look at the implications of this from a population perspective. There are two sides to this scenario. Nature must select those individuals that exhibit the best traits and also eliminate those weaker entities from the breeding pool needed to create the next generation. J. C. Sanford, a renowned plant geneticist who is responsible for many of the genetically engineered crops in fields today, characterized three aspects of the problem:(Sanford, 2014, p. loc 979)

  • Cost of selection
  • Recognizing obscured mutations
  • Systematic reproductive elimination

The survival of the fittest has to be paired with the removal of the weak. Cost of selection represents the level of aggressiveness in the elimination of members of the group that is needed to achieve the selection of the desired mutated traits. “All selection involves a biological cost – meaning that selection must remove (“spend”) part of the breeding population. Selective elimination is the essence of selection.” (Sanford) In other words, survival of the fittest requires the elimination of those ‘not so fit.’ peopleThis selection comes with a biological cost and has to be balanced by the needs of maintaining population levels. The elimination of too many ‘undesirable’ individuals could certain hasten the selection of desirable traits in the survivors but could just as easily lead to extinction. Haldane, who suggested that 10% is the maximum biological spend that can be tolerated, presented the dilemma in this form. “…the number of deaths needed to secure the substitution by natural selection of one gene… is about 30 times the number of organisms in a generation.”  (Haldane, 1957, pp. 511-524) Could the early Dorudon become a Balaena in 2.5 million years requiring multiple simultaneous changes to occur? Haldane is not convinced.

Speaking of the work done by Haldane, which has been validated several times since the original publication, Sanford summarized the implications with a specific example:

[Haldane] calculated that, in man, it would require 6 million years to select just 1,000 mutations to fixation (assuming 20 years per generation)… Man and chimp differ by at least 150 million nucleotides representing 40 million hypothetical mutations.” (Sanford, 2014, p. 2459) His conclusion was that natural selection could not claim total responsibility for the speciation that we have today.

The second point Sanford addressed was the need to identify the mutation. Assuming the slow and gradual evolution of the species, how does nature identify and ‘select’ that individual for specific traits? In a purely random environment, this is seen as a daunting challenge. The individual with a typical subtle point mutation, favorable or unfavorable, does not necessarily stand out from the crowd and does not have increased odds of survival and participation on forming the next generation. The issue is even more complicated when there may be multiple traits that are being selected. His conclusion was that the selection based on a particular trait or set of traits does not have sufficient ‘power’ to drive natural selection.

Finally, natural selection would need to restrain non-selected individuals from the breeding population. Otherwise, the offspring would not carry the selected traits and dilute the broader population. Again, subtle changes in the genotype would not be expected to position the individual inside the breeding circle leading to a problematic explanation of how the ‘slow, gradual’ process of evolution.

Modern Synthesis

The next phase of the scientific view of evolution was triggered by a book published by Julian Huxley in 1942 which blended the recent discoveries, at the time, in genetics into the evolution equation. For the next 70 years, science saw the delivery of the DNA model and the decoding of the genome. As the work on the human genome began, scientists expected to find upwards of 2 million genes.  Today that number is estimated to be about 22,000. (The shrinking human protein coding complement: are there now fewer than 20,000 genes?, 2014). Still much is to be understood about the operation of DNA and it’s supporting cast within the cell.

Junk DNA

Let’s look at one aspect of the gene-centered story of evolution that has developed over the last several decades. As the number of identified genes and the associated content of those genes dropped dramatically, some jumped at the early findings to bolster the case for evolution.

In an article published in the Scientific American in September of 2012, Ashutosh Jogalekar wrote that junk DNA could be attributed to the mess created by millions of years of evolution.

The standard evolutionary picture tells us that evolution is messy, incomplete and inefficient. DNA consists of many kinds of sequences. Some sequences have a bonafide biological function in that they are transcribed and then translated into proteins that have a clear physiological role. Then there are sequences which are only transcribed into RNA which doesn’t do anything. There are also sequences which are only bound by DNA-binding proteins (which was one of the definitions of “functional” the ENCODE scientists subscribed to). Finally, there are sequences which don’t do anything at all. Many of these sequences consist of pseudo genes and transposons and are defective and dysfunctional genes from viruses and other genetic flotsam, inserted into our genome through our long, imperfect and promiscuous genetic history. If we can appreciate that evolution is a flawed, piecemeal, inefficient and patchwork process, we should not be surprised to find this diversity of sequences with varying degrees of function or with no function in our genome.” (Jogalekar, 2012)

Richard Dawkins, in his best seller, The Greatest Show On Earth, suggested that much of the human genome was worthless. “It is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.” (Dawkins, 2009, p. 333)

junk-dnaAs research has continued, the adage that one man’s junk can be another man’s treasure seems to be born out. While the vast majority of the genome did not directly produce the proteins, enzymes, and hormones necessary for life, it was becoming apparent that there is much more to the story. These castoffs, now called non-coding DNA, are now being shown to have a significant role in how genes are expressed or managed.

In her book titled, Junk DNA, Nessa Carey observed that “The only genomic features that increased in number as animals become more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may hold the key to evolutionary complexity.” (Carey, 2015, p. 192).

The complexity of the control mechanisms relative to gene expression is getting considerable attention today as scientists work to unravel the extraordinary activities of the areas of the genome once held to be worthless.

It has been 70 years since the redirection of evolution based on the discoveries of DNA. Is it time for another course correction? Perhaps, yes.  Research over the last ten years, as suggested by Carey, is showing that DNA information outside those sequences that are identified as genes, identified as epigenetic,  can have a significant impact on how genes are expressed and demonstrate the ability to modify the phenotype, or physical nature, of the organism.

The Finches of Galapagos

During his five weeks on a number of the islands of Galapagos, Darwin collected a significant amount of information regarding the variety of finches found there. Of most note were the color of the feathers and the shape and size of the beak. Finches that found their primary food source in hard-to-crack nuts and seeds had developed heftier beaks while those whose diet tended to softer items and smaller seeds sported slimmer beaks. Along with other examples identified on his voyage, Darwin used the variation of finches as a supporting case for natural selection.
finchesAs a follow up to the original research done by Darwin on the Galapagos Islands, Peter and Rosemary Grant spent three decades in a detailed study of the environment/ecological impact on two varieties of the Finch originally identified by Darwin. Over the course of their observation, the finches changed significantly in beak shape and thickness as well as body size.

“Natural selection occurred frequently in our study, occasionally strongly, unidirectionally in one species and oscillating in direction in the other as a result of their dependence on different food supplies.” (Grant, 2002) Interestingly, the two finch varieties studied changed their beak thickness in opposite directions with the beak size of the G. fortis actually ‘oscillating’ over several generations. It only took a few generations of finch to see significant changes to the beak, again, not the slow gradual process held as the fundamental core of evolution. So what was really happening with these birds?

Subsequent study of these finches along with the analysis of their DNA has yielded some interesting information as recorded in a recent paper, entitled ‘Epigenetics and the Evolution of Darwin’s Finches’, found in the proceedings of Genome Biology and Evolution based on a parameter called ‘copy number variations,’ which measures the changes in DNA.

There were relatively more epimutations than genetic CNV [copy number variations] mutations among the five species of Darwin’s finches, which suggests that epimutations are a major component of genome variation during evolutionary change. There was also a statistically significant correlation between the number of epigenetic differences and phylogenetic distance between finches  indicating that the number of epigenetic changes continues to accumulate over long periods of evolutionary time (2–3 Myr). In contrast, there was no significant relationship between the number of genetic CNV changes and phylogenetic distance.” (Skinner, 2014, pp. 15-16)

In other words, the changes in the phenotype, or the physical characteristics, of the finches in the study were more closely linked to the epigenetic or non-coding changes as opposed to the changes in the genes. The genes of the bird affecting the size and shape of the beak did not change, rather the non-coding area of the DNA saw changes. Again, these rapid changes within a few generations is not in keeping with the premise of survival of the fittest.

It is certainly interesting to trace of evolution of the theory of evolution since its inception in the 19th century. I would suggest that the original ‘survival of the fittest’ as characterized by Darwin, followed by the era of the gene, may well give way to yet another phase in the study of evolution, that of one centered on the implications of epigenetics.

Gene management versus the gene

The study of epigenetics represents a fascinating new avenue of research into the mechanisms employed by the cell to enable change. Dr. Assad Meymandi, an adjunct professor at the University of North Carolina at Chapel Hill, defined epigenetics as operating “very much like a switch on the outside of the genetic circuits and genome that influences the behaviors of a gene. The very prefix epi, which means to lie outside of the root structure, helps explains that, while not an integral part of an organism’s genetic code, epigenetics can influence the gene’s activities from the outside.” (Meymandi, 2010, p. 41).

One of the first characterizations of heritable genetic change came from a study of a small northern Swedish community of Norbotten that was subjected to cycles of feast and famine. The study found that males who had been exposed to famine during their pre-pubescent period produced offspring that had lower incidence of heart disease. Similarly, females who experienced famine while they were in the womb produced daughters who exhibited the same characteristic. (Marcus E Pembrey, 2006, p. 159)

mother-and-daughterA wide variety of research is now providing corroborative evidence that there are chemical genetic links between generations. For example, can alcoholic fathers influence the well-being of their offspring? The answer appears to be yes.

In the Journal of Animal Cells and Systems we find that “…paternal alcohol exposure prior to conception causes teratogenic and developmental defects in the next generation at pre- and postnatal stage. Furthermore, specific abnormalities such as agenesis [failure in the development of a body part] and exencephaly [defects in the development of the skull] were determined at the fetal stage. Transgenerational toxicity caused by paternal alcohol exposure is possibly mediated through alcohol-induced changes in sperm at the level of the sperm genome. However, the mechanisms of paternal alcohol exposure causing certain transgenerational toxicities remain to be defined.” (Hye Jeong Lee, 2013) Children born to parents, where the father was an alcoholic, showed traits of fetal alcohol syndrome just as if the mother was an alcoholic. The point? The life style of both parents can affect the offspring for several generations. The choices of the fathers can influence the health and well being of children for several generations. These changes can also be reversed as the environment of the second generation is ’embedded’ in the formation of the next generation. It is interesting to note the passage from Exodus, chapter 34, verse 7, which seems to align with this idea. “…visiting the iniquity of the fathers upon the children, and upon the children’s children, unto the third and to the fourth generation.”

Dr. Meymandi goes on the provide his assessment of the new field of study.

What is new, however, is the epidemiologic studies from Norrbotten and their defiance of Darwin’s assertion in his seminal work On the Origin of Species (1859) that evolution takes place over millions of years. The Norrbotten studies suggest that evolution and environmental influence affect genes within one or two generations. It does not take millions of years. This is heretical. Suddenly, we have evidence that Darwin was wrong. It takes only 25 to 75 years, 1 to 3 generations, not millennia, for evolution of genes to take place.” (Meymandi, 2010, p. 41)

Research into epigenetics stands to change the prevailing structure and understanding of evolution. Current findings demonstrate that the non-coding areas of DNA have a significant influence on the phenotype of an organism. However, as in the case of the Galapagos finches, that change may not have extended influence beyond several generations. Perhaps Richard Dawkins should consider writing a sequel to his book “The Selfish Gene.” An appropriate title could be “The Subservient Gene.”

Epigenetics may provide answers to a number of maladies from cancer, to lupus and diabetes, even to the effects of poor parenting. (Weinhold, 2006)

My purpose in this discussion regarding the evolution of evolution is to assert that what is espoused by the scientific community today is subject to change with new information. What our grandparents were taught regarding the origin and diversity of life diverged from what we are taught today. Likewise our grandchildren will likely be presented with new and modified theories on this topic.

Let me change direction somewhat now and address the second topic of areas that still remain uncharted from a genetic perspective. But first, a little perspective. Is it appropriate to apply aspects of engineering to the origin and development of an organism? I would suggest that it is. If evolution is to be fully endorsed as the origin of the diversity seen in all life, there must be a clear technical developmental path that can be illustrated and validated for all the required parts and functions. Any device manufactured today has detailed plans and components, a bill of materials. The device requires a defined sequence of activities in order to produce the end product. Random actions will not suffice in the process. I suggest the same is true for biological organisms.

DNA – a library of information

DNA can be considered a cookbook for proteins, enzymes, and hormones; the building blocks of our bodies. These proteins generated by transcribing the code in our DNA are used to support cellular differentiation and function. We, humans, have two strands of DNA, each of which contain about 3 billion base pairs. The analysis of the human genome has produced a variety of estimates of the number of encoding areas, or genes, typically ranging around 22,000. Comparatively, a chicken is believed to have about 17,000 genes and a grape leads with over 30,000. For us, genes represents about 2.5% of the genetic material. About 80%, perhaps going to 100%, of the remainder is identified as non-coding DNA, the stuff of epigenetics. (Parrington, 2015)

dna-stringAll life shares the same fundamental structure within the cell. All living share a common language in how these coding areas of the genome are represented. It is a sequence consisting of four bases, adenine, cytosine, guanine, and thymine, arranged along a sugar-phosphate backbone of DNA.
dna-spiralAs an information technologist, the area that is intriguing is the coding of DNA. In order to generate a protein, a defined sequence of the DNA string is transcribed to what is called messenger RNA. The messenger RNA string is then excised of non-coding items called ‘introns.’ amina-acid-codeThe ribosome is then employed to translate the sequence of bases contained in the RNA string, by sets of three, specifying a lineup of 20 amino acids which is then folded into a specific protein. Genes embedded in DNA can be represented as a data base; it is information that is stored, replicated, repaired and transcribed as needed. (Bruce Alberts, 2008) This particular database contains the information necessary to build itself; an aspect that is perplexing to an engineer. Yet, this multi-step sophisticated process is necessary for all organisms to sustain life. Click on the image below to see a snippit of a Nova presentation on protein production in the cell.

Consider the complexity of a three component code of a sequence of DNA being translated into a specific amino acid. These amino acids are then connected into a string and folded in a specific manner to assemble a protein, one sequence for each of the known genes now numbered around 22,000. The information content of our DNA represents about 18 Gigabytes of information. This multi level translation represents a level of sophistication that, from the perspective of an engineer represents a significant challenge. Could this type of process be generated by a random chemical reaction? Wow, please show me how this developed in a random gradual process over hundreds of millions of years.

Another puzzling aspect of DNA is that, within the gene, there can be multiple transcriptions from a single gene sequence. James A. Shapiro, professor of Microbiology at the University of Chicago characterizes this as a mystery. (Shapiro, 2012). Much like a crossword puzzle requires an overlapping of function, the multiple encodings found within a significant number of genes represents a significant increase in complexity. This complication would also significantly reduce the potential for a beneficial mutation given that mutation would disrupt more than one protein coding sequence. (George Montañez, 2012)

overlapping-genesWhether it be the recent discoveries around epigenetics or the research indicating the presence of multiple encodings from genes, research continues to add to the complexity of the genome. Simultaneously, the increase in complexity demands even more of the theory of natural or chemical evolution.

Human template

We have spent some time discussing DNA at a cellular level. Let us now extend out into our world. As an organism, we are more than just a collection of cells. In his book Genetic Entropy, John Sanford describes it in this way:

“A human being contains over 100 trillion cells, but we are not 100 trillion cells. I repeat – that is not what we are. we are each truly a singular entity, united in form and function and being. We are the nearly perfect integration of countless components, and as such we comprise a singular new level of reality. The separateness of our existence as people – apart from our molecules- is both wonderfully profound and childishly obvious.” (Sanford, 2014, p. LOC 2796)

We are more than the sum of our parts; the 22 square feet of skin, the 206 bones, the variety of organs, the 100,000 miles of veins and arteries or the 90,000 miles of nerves. While each of us is unique, we do share these and other common characteristics in body shape and function. This prompts the question: Where is the template stored that governs the development of our body?

Neil Shubin, in his book, The Inner Fish, asserts this answer:

It is hard not to feel awestruck watching an animal assemble itself. Just like a brick house, a limb is built by smaller pieces joining to make a larger structure. But there is a huge difference. Houses have a builder, somebody who actually knows where all the bricks need to go; limbs and bodies do not. The information that builds limbs is not in some architectural plan but is contained within each cell. Imagine a house coming together spontaneously from all the information contained in the bricks: that is how animal bodies are made. (Shubin, 2009)

brickLet me expand on this analogy. if a brick has all the information to build a house, and has the ability to change its characteristics to meet the needs of the structure we have a similar environment to the cellular development of the body. The brick in this case would need to modify its characteristics to meet the particular requirement. Not only would it need to make more bricks, but also plumbing, electrical, plaster and drywall, floor joists, etc. While each house may be slightly different in size, each has the same floors, walls, kitchen appliances, and furnace. Anyone walking through the neighborhood and seeing the houses developed in this fashion could easily spot the consistency of design. While the roof and brick may vary in color, the general layout of the house would be the same. One would easily assume that the same ‘template’ or plan was used in the construction of each house. Similarly, humans all have the same general characteristics; strongly suggesting that there is a single template for each organism. This single template is then ‘customized’ by the DNA to address physical attributes.

As has been described before most, if not all, of our genome is dedicated to the development, manufacture and control of proteins. Our DNA contains information sequences that have been analyzed for their contribution in building each type of cell needed to build and maintain our bodies. It contains information that makes our eyes brown and our hair black. But, to bring all these cells into unity of purpose, much more information is required. If the cell does contain, as Shubin states, all the information necessary to construct our bodies, where does that information reside?

In his book, Life Unfolding, Jamie A. Davis, describes one segment of the early development of the human embryo.

In organizing themselves into different specialized groups, the cells of the neural tube and somite also use cues from an asymmetrical environment. By the stage, though, most of the information involved comes, not from the geometrical properties such as a free surface, but from signaling molecules released by the other tissues. Using these molecules, adjacent tissues engage in a remarkable conversation that allows cells to organize one another into many different types, all precisely arranged.” (Davies, 2014, p. 83)

Later, Davis describes the formulation of the physical body in these terms, speaking of the development of the nervous system and the optical subsystem:

It is all very well to list the guidance cues that a particular set of growth cones [of the eye] uses to navigate, but this begs the question of how the guidance cues come to be made in such an intricate pattern in the first place. The answer – what little we yet understand of it – mirrors a process that has already been described in the context of the embryo as a whole. As cells in the central nervous system develop, a combination of cues provided by neighbouring tissues and the proteins already present in the cells determine which of their genes will be switched on and off. Some of these genes specify the production of signalling molecules that act as cues for other neighbouring cells and can affect their gene expression. In this way an initially simple and homogeneous system can organize itself to become very complicated and heterogeneous. (Davis, 2014, p. 172)

Is it simply a vastly complex choreography, sequence within sequence, of HOX genes, cell migration, and signaling proteins? The human hand, the brain, and the eye, all  represent structures of sufficient complexity to require a significant amount of direction. Yet, we humans, in large part end up with finger nails on the correct side of the finger, and amazingly, five appendages that can be trained to work in harmony.

As I see it, there are two choices. One can choose to accept the idea that the cell is ‘smart’ enough to manage the complex development of the organism, or that there is a source of information providing the extracellular guidance needed construct the complex organs from the toenail, on to  the intricate functionality of organs such as the eye and the heart, to the hair of one’s head.

blueprintHere is where the engineer in me kicks in. Information does not magically appear. Each developing cell responds in a particular fashion to stimulus, expressing or hindering the expression of genes. If the working assumption for how an organism develops,  and this information resides within the cell, one should be able to find the ‘game plan’ embedded within the cell. Again, where is it? If the current view of DNA is correct, with about 2.5% dedicated to genes and an estimated 80% associated with the epigenetic control of these genes, little or no room can be ‘assigned’ to the template of the body of the organism. If this template does reside within the cell, as Shubin and other evolutionists assert, no one has found this information.

From a genetic perspective, research indicates that the common genes between chimpanzees and humans is characterized as nearly identical at 99%, but does that tell the whole story?

Quoting from the Deeper Genome: “When used to compare the protein-coding porting of the genome, humans are seen to be 99 per cent similar to a chimpanzee, 85 per cent similar to a mouse, and, confirming the link between all life forms on the planet, even 50 percent similar to a banana. But if the whole human genome is compared to that of a mouse, the similarity is far less, only around 5%. (Parrington, 2015, p. 94)

Most of the differentiation of the genome is found in the non-coding areas, the areas that are not being identified as managing the expression or suppression of the genes. We find in the genome the information to build proteins; where do we find the information on how to construct a body?

Hardware and Software

laptopJust as a personal computer is useless without an operating system, so is most life on earth. For example, a dolphin born in the ocean must be able to swim and understand that air is required on a regular basis. In human beings, there are a variety of systems that need control such as the auditory, visual, respiratory, lymphatic, circulatory, reproductive, digestive and urinary systems.

Each of these require sensory information as well as control information in order to operate correctly. One response is that these systems are trained while the organism is in development. If so, where is the structure to direct and accumulate the control information? One example of the coordination needed to survive is the process of swallowing which requires the closely timed sequence in the activation of 50 pairs of muscles and a number of nerves to accomplish the task. (Med Central) Without such ‘software,’ as represented by the coordination needed to swallow, infants could not survive.

Where does this information, or alternatively, where is the mechanism to gather and catalog the various processed needed to maintain life? If it is housed within the cell, then, where is it?

Instinct

In his book, The Origin of Species, Darwin titled Chapter 8 as ‘Instinct,’ with this description:

“I will not attempt any definition of instinct. It would be easy to show that several distinct mental actions are commonly embraced by this term; but everyone understands what is meant, when it is said that instinct impels the cuckoo to migrate and lay her eggs in other birds’ nests.” (Darwin, 1958 reprint, p. 233)

Perhaps, this trait could be defined as “an innate, typically fixed pattern of behavior in animals in response to certain stimuli.” I would like to use the Cuckoo bird as an example of different aspect of information management. (Richard Dawkins used the same bird as a representation of ‘stealth survival’ patterns, https://www.youtube.com/watch?v=dy8Yy9nyi74) Here is a picture of a reed warbler, following its natural instincts to feed a cuckoo chick that hatched in its nest.

warbler-and-cuckooThere are a number of varieties of Cuckoo that do not build its own nests, rather it is what is called a ‘brood parasite.’  About 40% of the species of cuckoo demonstrate this trait  where the female Cuckoo will extract a single egg, while the parents are away, from the nest of a Reed Warbler, or other surrogate, and replace it with a Cuckoo egg while the Warbler is away. When the Cuckoo hatches, it pushes the other eggs or chicks out of the nest and is fed by the Reed Warbler as if it were the true chick. (Davies N. , 2015)

cuckoo-pushing-eggWhile this is an interesting example of adaptation, I would ask a different question. Somehow, the complex action and physical process of emptying the next was imprinted in the Cuckoo before the chick hatched. Given that the Cuckoo chick never saw its mother, where did the knowledge imprint come from which drives the behavior? Who taught the chick to push the other occupants out of the nest and how was this information transferred to the next generation?

This again demands that information be made available in the young that represents a significant amount of complex multicellular processes. Yet another mystery that would need to be addressed by the scientific community. Again, this information, according to the scientists of evolution, must be found within the cell. But, information does not magically appear. These types of complex behavior or processes, if indeed are housed within the cell, the ‘knowledge’ must somehow transfer from the cell to the brain of the organism. There is no logical explanation within evolution to address the inception and transfer of the knowledge to the entity.

From the perspective of the scientific community, all this information must be found within the cell. There can be no external influence needed in the development and continuation of life. The alternative, which is anathema to a scientist, is that there is an external source of information in the development of an organism’s  physical template, control structure, and imbedded information. That external source could be the ‘spirit,’ that non-physical element that, in some unknown process, provides not only the template for the physical body (customized by DNA), but also the control processes and embedded intelligence. From the Doctrine and Covenants, section 88, verse 15, we read that “… the spirit and the body are the soul of man.”  If this is the case, no answer will be forthcoming from the scientific perspective on life and the development of complex structures from a single cell.

Origin of Life

early-earthHow life began on earth is not typically treated by evolutionary theory. Jerry Coyne, author of Why Evolution is True, comments on the situation:

“Evolutionary biology deals only with what happens after life (which I’ll define as self reproducing organisms or molecules) came into being. The origin of life itself is the remit not of evolutionary biology, but of abiogenesis, a scientific field that encompasses chemistry, geology, and molecular biology. Because this field is in its infancy, and has yet given few answers, I’ve omitted from this book any discussion on how life on earth began.” (Coyne, 2009, p. 231)

While Coyne may feel justified in avoiding this fundamental question, the topic needs to be addressed. Perhaps, the best place to start is to ask the question: Have the key components of a living cell been replicated in the laboratory under conditions that could resemble the primitive earth? miller-ureyThe answer is yes and no. Most, but not all, of the amino acids used in the assembly of proteins have been manufactured in the laboratory. All of the basic components of  RNA,  as an assumed precursor to DNA, including ribose have been produced, typically in a combination of hydrogen sulfide and hydrogen cyanide excited by ultraviolet light. The manufacture of the basic components represent only the first step on the process of reaching the point where evolution is stated to take over. Ward and Kirschvink captures the essence of the problem:

…RNA is a fragile molecule, large and complicated, and thus very easily destroyed. Water attacks and breaks up the nucleic acid polymers (strings of smaller molecules) that make up RNA. In fact, it appears that there are many steps required in making RNA, and each step would require different conditions, or a different chemical environment.  (Ward, 2015, p. 55)

The coordinated development of long RNA molecules and a cellular structure to protect the easily damaged nucleotides is the theorized path in the creation of life from non-life. protocellThese molecules would then need to replicate along with the cell structure.  While theories abound, there is no clear validated path to a cell capable of replication that carried sufficient information and energy management to be considered ‘live.’

Most experiments have been done in the absence of oxygen, known to degrade these molecules fairly quickly. Likewise, most scientist hold that life developed initially in a world with little oxygen, otherwise the fundamental molecules would not have persisted.

Nick Lane, in his book, Oxygen – The Molecule that Made the World, states:

Free oxygen would have been an insurmountable problem, because any organic molecules, or incipient forms of life, would have been shredded if much oxygen was present. The fact that life did start can only mean that oxygen was not present in any abundance. (Lane, 2003, p. 18)

oxygenYet, oxygen forms the basis for energy utilization in all multi-cellular life today. The quandary still exists today. We couldn’t begin life with it and we can’t live without it.

To overcome these obstacles, Kirschvink has championed ‘panspermia,’ supporting the ‘radical notion that life not only formed on Mars more than 4 billion years ago, but that it came to Earth on meteorites..’ (Ward, 2015, p. 57) The authors came to this conclusion after a detailed review of the current range of alternatives. Unfortunately, if abiogenesis, to the development of life from non-life requires the early protocells hitchhiking on a meteor from Mars, we need to find another story.

Summary

From an evolution standpoint as a law of nature, I would have a number of items on my shelf.

The theory of evolution continues to evolve as new information is gathered and analyzed. From Darwin’s natural selection to today’s emerging epigenetic research, the complexity and information content of the genome continues to expand. It now appears the there is more to the process than the slow gradual survival of the fittest.

DNA represents a managed database of information to produce and manage the proteins necessary for sustaining life. Information doesn’t  simply spring into existence.

The structure of life, as demonstrated by human beings, exhibits a significant organization and compartmentalization in the migration from a zygote to a full featured organism. How that process is guided begs for something more than the production of signaling molecules.

There is a need for both hardware and software in the development of life. We come into this life with the basic operating system and equipped with the ability to gather and process information. If this ‘software’ can only find its source within the cell, where is it located and how does it drive development?

Finally, plausible scenarios for the origin of life require both the presence and absence of oxygen. A feat that will challenge scientists for years to come.

Perspective

As I look at the circumstances surrounding the theory of evolution, I do submit that there is plenty of room for something akin to faith as one considers the breadth of information necessary to build an organism relying solely on the information contained within the originating cell. As an engineer, the gaps in the story present a significant impediment to holding the theory of evolution as ‘true.’  One may reason that the scientific community has simply not determined that answers yet, but each successive discovery seems to require an answer even more difficult to achieve.

Bibliography

Alberts, Bruce A. J., et. al.(2008). Molecular Biology of the Cell, Fifth Edition. New York: Garland Science.

Carey, N. (2015). Junk DNA – a Journey Through the Dark Matter of the Genome. New York: Columbia University Press.

Coyne, J. A. (2009). Why Evolution is True. New York: Penguin Group.

Darwin, C. (1958 reprint). On the Origin of Species. London: New American Library.

Davies, N. (2015, June 2). Cuckoos and their victims: An Evolutionary Arms Race. Retrieved from https://www.youtube.com/watch?v=n0O6S4hDDfE.

Davis, J. A. (2014). Life Unfolding: How the Human Body Creates Itself. Oxford: Oxford University Press.

Dawkins, R. (2009). The Greatest Show On Earth. New York: Free Press.

Denton, M. (2016). Evolution: Still a Theory in Crisis. Seattle: Discovery Institute Press.

Gee, Henry (1999) In Search of Deep Time, New York: Free Press

George Montañez, R. J. (2012). Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation. Retrieved from Carnegie Mellon University.

Gitt, W. (2005). In the Beginning was Information. Green Forest: Master Books.

Goodsell, D. S. (2010). The Machinery of Life Second Edition. New York: Copernicus Books.

Grant, P. R. (2002, April 26). Unpredictable Evolution in a 30-Year Study of Darwin’s Finches. Science , p. 710.

Haldane, J. (1957). The Cost of Natural Selection. Journal Genetics 55.

Hazen, R. M. (2005). Genesis: The Scientific Quest for Life’s Origin. Washington, DC: Joseph Henry Press.

Huxley, Julian. (2010). Evolution: The Modern Hypothesis The Definitive Edition. Cambridge: MIT Press.

Hye Jeong Lee, b. J.-S. (2013, Volume 17). Transgenerational effects of paternal alcohol exposure in mouse offspring. Animal Cells and Systems .

Jogalekar, A. (2012, September 13). Three reasons why junk DNA makes evolutionary sense. Scientific American .

Johnson, P. E. (1995). Reason in the Balance. Downers Grove: InterVarsity Press.

Klinghoffer, D. (2010). Signature of Controversy. Seattle: Discovery Institute Press.

Lane, N. (2003). Oxygen – The Molecule that Made the World. Oxford: Oxford University Press.

Lane, N. (2005). Power, Sex, and Suicide: Mitochondria and the Meaning of Life. Oxford: Oxford Press.

Med Central. (n.d.). Retrieved from MedCentral.org.

Meyer, S. C. (2013). Darwin’s Doubt. New York: HarperCollins.

Meyer, S. C. (2009). Signature in the Cell. New York: Harper Collins.

Meymandi, A. (2010, Volume 7). The Science of Epigenetics. Physchology , p. 41.

Parrington, J. (2015). The Deeper Genome. Oxford: Oxford University Press.

Pembrey, Marcus E, L. O. (2006). Sex-specific, male-line transgenerational responses. European Journal of Human Genetics , pp. 159-166.

Pullen, S. (2005). Intelligent Design or Evolution? Raleigh Intelligent Design Books.

Sanford, J. C. (2014). Genetic Entropy, Fourth Edition. FMS Publications.

Shapiro, J. A. (2012, January 24). DNA as Poetry: Multiple Messages in a Single Sequence. Retrieved from Huffington Post.

Shermer, M. (2006). Why Darwin Matters. New York: Times Books.

Shubin, N. (2009). Your Inner Fish. New York: Pantheon Books.

Skinner, G. B. (2014, July 18). Epigenetics and Evolution of Darwin’s Finches. Genome Biology and Evolution , pp. 15-16.

Thaxton, W. L. (1984). The Myatery of Life’s Origin. New York: Philosophical Library.

The shrinking human protein coding complement: are there now fewer than 20,000 genes? (2014, Feb 11). Retrieved from Cornell University Library: http://arxiv.org/abs/1312.7111

Ward, P. a. (2015). A New History of Life. New York: Bloomsbury Press.

Weinhold, B. (2006, March). Epigenetics: The Science of Change. Retrieved from National Center for Biotechnology Information.

 

One of the reasons I still listen to conference is for the music. These are the songs I came to love as I grew up in the church. I am, by no means, a singer but I do try to sing parts to some of the songs. Music has a way to calm the soul and deflect the cares and tribulations of the world. Songs can evoke emotion which, I believe, is a method of communication with heaven, perhaps represented by the harps of God.

As my spiritual world shifted, my appreciation for songs and lyrics also began to broaden. I, recently, came across a song that has touched my spirit and buoyed my soul. It is called “Glory and Honor” written by Keith Lancaster, and is found, among other places, on the album Heaven and Earth by Acappella. If you haven’t heard the song, take a moment to listen.

Here are the words:

When I’m there with You in heaven

What a wondrous joy will be

Gathered with the angel chorus

Standing by the glassy sea

Such a thought is hard to fathom

In the presence of my King

And with countless ones forgiven

Gathered round the throne to sing

 

Chorus:

Glory and honor, worthy is the Lamb (worthy is the Lamb)

Glory and honor, worthy is the Lamb (worthy is the Lamb)

 

Mortal words cannot express it

All the ways You reign supreme

Even death can’t hold the vastness

Nor approach this awesome theme

You are God and to Your glory

We will worship and abide

In Your presence there forever

We’ll be happy to reside

 

Repeat Chorus

 

Ooh… (worthy is the Lamb)

 

Repeat Chorus

 

Worthy is the Lamb (worthy is the Lamb), worthy is the Lamb

The reference, of course, comes from Revelations, chapter 15. Here is the quote from the King James Bible:

And I saw as it were a sea of glass mingled with fire: and them that had gotten the victory over the beast, and over his image, and over his mark, and over the number of his name, stand on the sea of glass, having the harps of God.

And they sing the song of Moses the servant of God, and the song of the Lamb, saying, Great and marvellous are thy works, Lord God Almighty; just and true are thy ways, thou King of saints.

Some of us may have a different interpretation of the ‘glassy sea’ reverenced in the song, as section 130 of the Doctrine and Covenants illuminates.

The angels do not reside on a planet like this earth.

They reside in the presence of God, on a glove like a sea of glass and fire, where all things for their glory are manifest, past, present, and future, and are continually before the Lord.

The place where God resides is a great Urim and Thummim.

This earth, in its sanctified and immortal state, will be made like unto a crystal and will be a Urim and Thummim to the inhabitants who dwell thereon, whereby all things pertaining to an inferior kingdom, or all kingdoms of a lower order, will be manifest to those who dwell on it; and this earth will be Christ’s.

While there is much that can be discussed on this topic, my point is the song carries a deeper understanding of the need for us to overcome the beast in our lives and the  preparations needed to live on the flaming glassy sea, in the presence of the Lord.

As I pondered the messages of the October 2016 general conference, one talk that stood out to me given my current spiritual worldview was that given by M. Russell Ballard. I found that it spoke to a number of the issues with which believers struggle today. To start, I heartily agree with his plea to those whose faith is ‘faltering.’

Never abandon the great truths revealed through the Prophet Joseph Smith. Never stop reading, pondering, and applying the doctrine of Christ contained in the Book of Mormon.

Never fail to give equal time to the Lord through honest attempts to understand what the Lord has revealed. As my dear friend and former colleague Elder Neal A. Maxwell once said, “We should not assume … that just because something is unexplainable by us it is unexplainable.”

Not only should one study the ‘truths revealed through the Prophet Joseph Smith,’ but should also seek to understand how those truths are held today by the church and the general administration. Are those truths prominent today in the discourse of the church or are they, as the doctrine of the Doctrine and Covenants (also known as the Lectures on Faith) been excised from the focus of the church and replaced by the traditions of men?

Is the doctrine of Christ as contained in the Book of Mormon truly central to the message of the modern day church? Is the necessity of the baptism of fire and of the Holy Ghost as prominent in church teachings today as it is in the ‘doctrine of Christ’ found in Second and Third Nephi? The doctrine of Christ presented by the Savior as He taught the Nephites after His resurrection included this warning:

…whoso shall declare more or less than this, and establish it for my doctrine, the same cometh of evil, and is not built upon my rock; but he buildeth upon a sandy foundation, and the gates of hell stand open to receive such when the floods come and the winds beat upon them.

Does the doctrine of Christ stand in clarity as the doctrine of the church of Jesus Christ or does it have elements of the traditions of men injected into it or the core components of salvation removed from it? One must study this out and seek the direction of the Spirit or answers.

Elder Ballard then proceeded to ask some important questions that each of us must answer, my response follows:

Where will you go to find others who share your belief in personal, loving Heavenly Parents, who teach us how to return to Their eternal presence?

Are there others outside the Church,  (some by their own choice and some who had no choice) who share a belief in a Father and Mother God? Are there those who literally believe that the doctrine of Christ and other important information found in the scriptures teach us explicitly how to return to their presence? I would offer an emphatic yes. While the church offers a socially supportive environment, it does not place personal salvation in the forefront. Rather, one is called upon to support the brethren, attend the temple, pay tithing and, is time is left, do your home teaching. None of these activities are specifically mentioned in the doctrine of Christ from the scriptures.

Where will you go to be taught about a Savior who is your best friend, who not only suffered for your sins but who also suffered “pains and afflictions and temptations of every kind” so “that his bowels may be filled with mercy, according to the flesh, that he may know according to the flesh how to succor his people according to their infirmities,” including, I believe, the infirmity of loss of faith?

The scriptures speak of our opportunity to know Christ at a personal level. The promise found in D&C 93 encourages us to enter His presence and receive of His comfort. Is the church placing itself as the gate for this privilege? The role of His church should be to help members to establish this relationship on their own efforts and not rely on an intermediary for any communion with Heaven.

Where will you go to learn more about Heavenly Father’s plan for our eternal happiness and peace, a plan that is filled with wondrous possibilities, teachings, and guidance for our mortal and eternal lives? Remember, the plan of salvation gives mortal life meaning, purpose, and direction.

Go to the scriptures, go to your Father in Heaven, seek to fulfill the promise of the doctrine of Christ found in chapter 32 of Second Nephi that after we have ‘entered in by the way,’ we have the ability to speak with the tongues of angels and be guided in all we do. No apostles or general conferences are necessary. The authority to baptize historically given to the church does not extend to all communications with God.

Where will you go to find a detailed and inspired Church organizational structure through which you are taught and supported by men and women who are deeply committed to serving the Lord by serving you and your family?

Where is the inspiration recorded that authorizes this Church organizational structure in the first place? Where does the Lord establish a salaried bureaucracy under His name? Which aspect of the three-fold mission of the church supports the billion plus dollar expenditure of sacred funds for the construction of an upscale mall? Where are we told to only seek instruction from these leaders? Where are we told allegiance to this organizational structure is a pre-requisite to other benefits, such as temple attendance? The traditions of men have taken precedence over the doctrine of Christ. His organization, as characterized in Third Nephi, is made up those who acted as ministers and servants, not as rock stars deserving of the highest of obeisance.

Where will you go to find living prophets and apostles, who are called by God to give you another resource for counsel, understanding, comfort, and inspiration for the challenges of our day?

Recorded in the Old Testament is a story of a gardener who was called as a prophet to preach repentance to the established religious organization. I am sure you recall his famous saying: ‘Surely the Lord GOD will do nothing, but he revealeth his secret unto his servants the prophets.’ Is it any different today? Should we expect prophets to appear preaching repentance to those who have erred. The secret that Amos carried was that nothing short of sincere repentance would suffice for those to whom he was sent; otherwise the Lord would withdraw His protection. Are there prophets, outside the establishment, among us today who are brought before us by the Lord to preach repentance? I would offer an emphatic YES!

Where will you go to find people who live by a prescribed set of values and standards that you share and want to pass along to your children and grandchildren?

What are these prescribed values and standards that we are encouraged to live by? Do you speak of the Word of Wisdom? Do you speak of white shirts and ties required to meet the community standard? Do these values and standards bring anything other than a feeling of exclusivity to the proponents? While the church may pride itself on teaching values, it is simply not pertinent to the doctrine of Christ. There are good people outside the church who have similar values and standards without the baggage.

And where will you go to experience the joy that comes through the saving ordinances and covenants of the temple?

Which covenants and ordinances of the temple are you referring to – the Joseph Smith version, the Brigham Young version, the pre-1990’s version or today’s version? Each carries with it differences in covenants. True joy comes from the same source as Alma received it. It comes from being born again. It comes from having our sins purged and our hearts changed. No temple is necessary for that profound and life changing experience.

Brothers and sisters, accepting and living the gospel of Christ can be challenging. It has always been thus, and it ever will be. Life can be like hikers ascending a steep and arduous trail. It is a natural and normal thing to occasionally pause on the path to catch our breath, to recalculate our bearings, and to reconsider our pace. Not everyone needs to pause on the path, but there is nothing wrong with doing so when your circumstances require. In fact, it can be a positive thing for those who take full advantage of the opportunity to refresh themselves with the living water of the gospel of Christ.

I would suggest that the church can be likened to a bus that will carry you part of the way on your journey. To climb that steep and arduous trail, one must put on their own shoes (faith) and tread the trail. No bus will take you up the steep incline. I would encourage all to pause on the path they are on. Seek the Lord in humble prayer and receive of His Spirit. There is no value in relying on an organization to save you. There is no value in completing the checklist. The Lord calls upon your heart to be changed. He invites you belong to His church by repenting and coming unto Him. No more, no less.

I join Elder Ballard in this component of his testimony:

I testify that there is “no other name given nor any other way nor means whereby salvation can come unto the children of men, only in and through the name of Christ… I further testify that the Lord “inviteth them all to come unto him and partake of his goodness; and he denieth none that come unto him, black and white, bond and free, male and female; … and all are alike unto God.”

What think ye?