Archive for the ‘genetics’ Category

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.

 

My regrets for not being able to post the thoughts of my heart these last few months. Life’s events have managed to overtake us and we are now beginning to get back to a normal level of chaos.

I did make one major gesture to try to get myself re-oriented. I proposed a presentation for the Kirtland Symposium scheduled for October 17 and 18. The proposal was accepted so I will be on the agenda for the meeting.

The topic? Something new and different. The topic of my 90-minute session is Faith, Evolution, and Intelligent Design. This is a subject that has been working in the back of my mind for a number of years and I felt that it was the right time to speak to the questions and concerns as I worked through my crisis of faith. I plan to provide the perspective of an engineer as I analyze several key aspects of evolution and the ‘un-scientific’ intelligent design. What are the elements of the evolution of life that are problematic to me as I ponder the elements of matter, energy, and information necessary to install and proliferate living organisms? How much faith does it really require to adhere to the doctrine of a designer or to the doctrine of a natural evolution of life?

Hope you can join me in Kirtland for this event.

I had the opportunity recently to hear Leigh Anne Touhy speak at a function recently. Her effort to rescue a young black man from the streets of Memphis was immortalized in the Michael Lewis book “The Blind Side” and a movie by the same name.

Leigh Anne saw a person walking down the street in shorts and no coat on a cold day in November. She turned the vehicle around and asked the young man if they could do anything to help him. He only wanted to be dropped off at the closest express bus stop. Later, Leigh Anne, not willing to be satisfied, went to the school where this young man, Michael Oher, had recently transferred. She was told repeatedly to drop her interest in the young boy as he was a lost cause.

You probably know the story – this lost cause, adopted by the Touhy family, played football at the University of Mississippi and was drafted by the Baltimore Ravens.

In her presentation, Leigh Anne also told the story of the father and son walking down the beach after a storm. The boy was busy throwing starfish that had been washed ashore back into the water. When his father asked the boy why he thought he could make a difference, the boy replied, tossing the starfish back into the water, “I made a difference to that starfish.”

starfish on beach

She also talked of her faith in God, relaying that we are not to be the judge of those in need. God will judge those who receive our help, and God will judge us for our help or non-help of others.

As she talked of this topic, I was reminded of the scripture in the sermon by King Benjamin regarding retaining a remission of one’s sins found in Mosiah, chapter 4:

16  And also, ye yourselves will succor those that stand in need of your succor; ye will administer of your substance unto him that standeth in need; and ye will not suffer that the beggar putteth up his petition to you in vain, and turn him out to perish.

In this day, can we rightly assume that ‘the government’ will step in to help those who are in need of succor? With the great safety net provided to all who reside in our country’s borders, are there any truly needy?

17  Perhaps thou shalt say: The man has brought upon himself his misery; therefore I will stay my hand, and will not give unto him of my food, nor impart unto him of my substance that he may not suffer, for his punishments are just—

Did the person in need not try hard enough in school? Did they choose to be lazy? Were they not given the appropriate role models to understand how to be successful?

18  But I say unto you, O man, whosoever doeth this the same hath great cause to repent; and except he repenteth of that which he hath done he perisheth forever, and hath no interest in the kingdom of God.

No place in the kingdom of God if one does not help the needy? How much background information do we need before we should be willing to help?

19  For behold, are we not all beggars?  Do we not all depend upon the same Being, even God, for all the substance which we have, for both food and raiment, and for gold, and for silver, and for all the riches which we have of every kind?

What is really ours? We are born, we live, we pass away. We are not able to take any of our substance, our gold and silver and riches, with us when we move on.

20  And behold, even at this time, ye have been calling on his name, and begging for a remission of your sins.  And has he suffered that ye have begged in vain?  Nay; he has poured out his Spirit upon you, and has caused that your hearts should be filled with joy, and has caused that your mouths should be stopped that ye could not find utterance, so exceedingly great was your joy.

Does receiving a remission of our sins not bring joy into our lives? Does it ‘rewire’ our view of others? Being born again does fill our hearts with joy. It does change our view of our place in the world.

21  And now, if God, who has created you, on whom you are dependent for your lives and for all that ye have and are, doth grant unto you whatsoever ye ask that is right, in faith, believing that ye shall receive, O then, how ye ought to impart of the substance that ye have one to another.

Does becoming a son or daughter of God place us in a position of responsibility to help those around us who are in need?

22  And if ye judge the man who putteth up his petition to you for your substance that he perish not, and condemn him, how much more just will be your condemnation for withholding your substance, which doth not belong to you but to God, to whom also your life belongeth; and yet ye put up no petition, nor repent of the thing which thou hast done.

Does the beggar need to be in danger of perishing before we are obligated to help? How do we know when this is the case?

23  I say unto you, wo be unto that man, for his substance shall perish with him; and now, I say these things unto those who are rich as pertaining to the things of this world.

Who, reading this, could not be considered ‘rich’ today when those considered poor have access to food stamps and free cell phones?

24  And again, I say unto the poor, ye who have not and yet have sufficient, that ye remain from day to day; I mean all you who deny the beggar, because ye have not; I would that ye say in your hearts that: I give not because I have not, but if I had I would give.

25  And now, if ye say this in your hearts ye remain guiltless, otherwise ye are condemned; and your condemnation is just for ye covet that which ye have not received.

If one is poor relative to the things of the world and hates his neighbor who has more, they are equally condemned?

26  And now, for the sake of these things which I have spoken unto you—that is, for the sake of retaining a remission of your sins from day to day, that ye may walk guiltless before God—I would that ye should impart of your substance to the poor, every man according to that which he hath, such as feeding the hungry, clothing the naked, visiting the sick and administering to their relief, both spiritually and temporally, according to their wants.

27  And see that all these things are done in wisdom and order; for it is not requisite that a man should run faster than he has strength.  And again, it is expedient that he should be diligent, that thereby he might win the prize; therefore, all things must be done in order.

We are told in these verses that we are all beggars, that we are to share of our substance with those that are less fortunate without judgment. We cannot know what is in the heart of those people we see who are in need. As I pondered these things, my mind went back to those occasions when I was too busy to stop for a moment and provide financial help to those who are less fortunate. I asked myself if I would have taken the same steps as Leigh Anne Touhy and turned around to help a black youth on the streets of Memphis. I doubt I would have had the courage.

Rock Waterman, in his June post, http://puremormonism.blogspot.com/2013/06/of-alms-and-offerings.html, hit the nail on the head. It is easy for many of us to make the assumption that we are covered because of our donations to the church. We give our tithing, fast offerings and other items by check each month and are absolved of any need to help? I believe that is not the case. We are, as instructed, in the passage above, to help those people in need that we encounter on a daily basis. We are to give of our substance to those people who are less fortunate. We are to do it without judgment

Leigh Anne told a story of her son at a gas station. The electronics at the pump were not working so all customers had to go inside to prepay. As her son, Collin, waited to pay, the man ahead of him gave the clerk a $5 bill. Questioning, in his mind, why someone would only ask for five dollars worth of gas, Collin reached forward and added a $20 bill to the man’s request.

Outside, the man came to Collin with tears in his eyes. He didn’t have enough money to pay for gas to get to work that week. Both the man and Collin went away from the event with joy in their hearts.

We are told in the scriptures that it is our obligation to help those in need. We cannot know the true circumstances of another person, only God does. I recall, years ago, going to catch a flight at O’Hare airport in Chicago. I came across a nicely dressed man who asked me for some change to make a telephone call (this is before the era of cell phones). I gave him several coins and went on my way. The next week, I saw the same man who made the same request. I challenged him on being there a week earlier and refused to give him any assistance.

I look back now on that experience. The man was not enhungered, he did not appear to be destitute, he was wearing nice clothes.  I judged him as being deceitful and did not give him of my substance. Is there an obligation on the part of the ‘poor’ to be honest? Was it judgmental of me to not give the man more money?

There is a lot of deceit in the world today. We see scams and viruses, derivatives and pyramid schemes. We see reports of the activity of greed swirling about us. There is a natural reaction to question the motives and real circumstances of anyone who approaches us. I can only hope to rely on the Spirit to guide me in these circumstances.

If we are to ‘retain a remission of our sins’ as promised by King Benjamin, we are required to give of our substance without questioning the motive of the poor. We are to feed the hungry, provide clothing to the naked and provide spiritual nourishment to those in need.  A giver and a receiver.

In the end, all my questions are moot. There is little room for self analysis. If we are to be about God’s work, we should be looking for ways, after the poor are clothed and fed, to seek to uplift them spiritually. To expand our vision beyond our little spot on earth is very challenging. There is much hunger and nakedness in the world at large, how are we to make a difference in this vast ocean of pain, misery, hunger, disease, malnutrition, and filth?

The physician we have chosen to use locally spends much of his time in places where people are in great need. He uses the income from his practice to participate in Doctors without Borders. He collects computers and has volunteers who help him prepare them for use in areas where he visits. He has adopted a school in Haiti that takes much of his time and energy. There are others that give of their time and talents to help those unfortunate enough to be born in the ‘wrong’ place.

Is doing good healthy? In a recent study conducted by scientists at UCLA and the University of North Carolina found that there were positive immune system affects from living a ‘purposeful’ life, while a hedonistic life style had an adverse affect at the genetic level. Here is a quote from BioscienceTechnology.com:

People who have high levels of what is known as eudaimonic well-being— the kind of happiness that comes from having a deep sense of purpose and meaning in life (think Mother Teresa)— showed very favorable gene-expression profiles in their immune cells. They had low levels of inflammatory gene expression and strong expression of antiviral and antibody genes.

However, people who had relatively high levels of hedonic well-being— the type of happiness that comes from consummatory self-gratification (think most celebrities)— actually showed just the opposite. They had an adverse expression profile involving high inflammation and low antiviral and antibody gene expression.

Favorable gene expression equates to a positive health environment. So, charity is good for the immune system, as well as the soul.

What think ye?

Yesterday, I had the privilege of attending the graduation ceremony for the UC Berkeley school of Molecular and Cell Biology. The invited speaker was Dr. Bruce Ames, a noted scientist, who for decades has produced ground breaking work in genetics and how various substances impact our health at the molecular level. Dr. Ames provided a concise review of his most recent research into nutrition. According to his research, there are 40 micro-nutrients that are essential for our health and continued existence. Remove any of these 40 substances from our diet and we will weaken and die. His research points to the damage at the cellular level that occurs when any of these nutrients are missing.

He also noted that the body, when confronted with a deficiency of one of these critical nutrients, would direct its application to areas that benefit short-term performance while other body functions are deprived. This restriction leads to cellular damage that presages diseases like cancer. He cited statistics suggesting that a significant percentage of the population is deficient in some of these necessary nutrients. More information is available on Dr. Ames’ website: www.bruceames.org.

As I pondered the words of this esteemed scientist, I was struck by the thought that this idea could just as easily be applied to our spiritual health. Are there micro-nutrients that are necessary for our spiritual health? Do we, by ignoring the consumption of the proper spiritual foods, weaken our faith and set the stage for damage induced spiritual death?

Dr. Ames assailed the ‘modern’ foods made to look attractive in our day such as carbonated sugar water that contains no meaningful value and represents ‘empty calories.’ Are there activities or rituals in which we engage that represent no meaningful spiritual value yet consume a significant component of our faith diet? What represents the empty calories in our spiritual diet as a ‘soda pop saint?’

As I look around me, I see many members who are busily engaged in various activities such as home teaching, genealogy, and fulfilling their callings. While these activities can be perceived as worthwhile, do they represent the equivalent of ‘empty calories’ in a spiritual sense? Yes, it is important that we strengthen one another and perform activities that support the greater good of the congregation, but what do these activities to do our own spiritual metabolism? Are we feeding our spiritual selves the necessary nutritional elements through these activities? In many cases, I think not.

What are the essential nutrients for a healthy spirit?

First, we must seek to understand what the gospel is and apply it in our lives. I believe these nutrients are found in places like 3 Nephi, chapter 27 and D&C 33:11-12. It is not enough to simply recite that faith, repentance, baptism by water, and the sanctification through the baptism of fire and the Holy Ghost is sufficient. One must dig deeply into the meaning and substance of these spiritual concepts. We must ingest these concepts and make them available to every segment of our spirituality.

Second, we must strive to comprehend the mysteries of God. We read the following from Alma, chapter 12:

[9] And now Alma began to expound these things unto him, saying: It is given unto many to know the mysteries of God; nevertheless they are laid under a strict command that they shall not impart only according to the portion of his word which he doth grant unto the children of men, according to the heed and diligence which they give unto him.

[10] And therefore, he that will harden his heart, the same receiveth the lesser portion of the word; and he that will not harden his heart, to him is given the greater portion of the word, until it is given unto him to know the mysteries of God until he know them in full.

[11] And they that will harden their hearts, to them is given the lesser portion of the word until they know nothing concerning his mysteries; and then they are taken captive by the devil, and led by his will down to destruction. Now this is what is meant by the chains of hell.

 What else is spiritual death than the ‘chains of hell?’ One should continually strive for the essential nutrients found in the mysteries of God if they are to avoid the spiritual destruction cited in this scripture.

A great example of a mystery is, in my opinion, found in Alma 40: 3:

Now, I unfold unto you a mystery; nevertheless, there are many mysteries which are kept, that no one knoweth them save God himself. But I show unto you one thing which I have inquired diligently of God that I might know — that is concerning the resurrection.

 

The mystery that Alma then began to expound upon, the resurrection, isn’t normally considered a mystery of God. It was to Alma. How many spiritual concepts that we take for granted are truly mysteries inside? The mysteries of God are obtained through the application of diligent study and prayer. This same Alma speaks of his efforts in Alma 5:46:

Behold, I say unto you they are made known unto me by the Holy Spirit of God. Behold, I have fasted and prayed many days that I might know these things of myself. And now I do know of myself that they are true; for the Lord God hath made them manifest unto me by his Holy Spirit; and this is the spirit of revelation which is in me.

Our spiritual health depends on our continual acquisition of the essential spiritual nutrients. We must continually strive to feed our spirits, not with the empty calories of the works of man but of the bounty of the wisdom of God bestowed through the Holy Ghost

We ‘modern day Mormons’ seem to be starving our spiritual side by filling them with empty calories. The rich feast of the knowledge and wisdom of God awaits them who diligently seek these principles and strive to ingest the mysteries.

What think ye?

I am going to diverge from my usual discussion items relating to doctrines in this post. I want to spend some time rehearsing some of my thoughts on genetics and the human soul. I have a son who is finishing his PhD in Molecular Biology at Berkeley. I have been ‘forced’ to educate myself on the topic so as to be conversant with him on his research and studies.

First, please understand that I am by training a computer engineer so this relieves me of any claim of expertise in my presentation on the topic. Here is some base information on the topic. The human genome is made up of 3.2 billion base pairs. These base pairs are made up of four different sugar and phosphate-based molecules which have been identified as adenine (A), thymine (T), cytosine (C) and guanine (G). As you may know, DNA is represented by a twisted ladder with pairs of these ‘chemicals’ loosely mated together by nitrogen based compounds where adenine and thymine (A-T pair) and cytosine and guanine (C-G pair) form the steps. So, you have the 3.2 billion rung ladder that represents the set of instructions that are used to guide the operation of our bodies. These base pairs are grouped together by function into genes of which there are about 30,000 in humans. These genes are grouped into chromosomes. All living things use this same template of base pairs and genes. The number of base pairs range from about 1.8 million in the influenza bacteria to 100 million in plants to 2.6 billion in mice and up to our 3.2 billion pairs.

Every cell in our body (with the exception of sperm and eggs) contains the complete DNA string described above. Every cell also only ‘activates’ a small portion of its genetic information in the production of proteins which are necessary for the purpose of that particular cell. In the normal operation of a cell, the nucleus or center of the cell manufactures a particular protein that is then transported to the edge of the cell where it is used for some purpose. So, a liver cell has the same base information as a skin cell but they operate completely differently with selected gene being activated in each circumstance.

Hopefully that is enough background for what I would like to discuss. For those interested in this topic, I would highly recommend the book Genome by Matt Ridley.

One aspect of this topic that amazes me is how incredibly complex the process is to get us to a functioning human being. What begins as a single cell, the union of sperm and egg, results in a uber-complex body with each subsystem working off the same ‘template.’ As this original single cell begins to divide, it is only a few days before these cells are called upon to begin to specialize. The mass of cells, which were originally identical, now are called upon to form every organ, bone and muscle found in our bodies. How does one cell know what it is to do? Right now there are only theories on how a cell at one end of the mass of cells is guided to start forming the head and its components while another at the other end works of the feet and toes. How do these cells ‘communicate?’ At this time, I have only found theories that suggest the original mass of cells differentiate based on the presence of electrical or chemical markers that vary by the position in the cell mass. I find these theories woefully inadequate in explaining how my fingers and finger nails formed at the end of my arms rather than on the top of my head ;-].

The other amazing aspect of ‘life’ is commonly referred to as ‘instinct.’ Those innate abilities that we are born with that seem to be hard-wired into our brains. One example is that kittens separated from their mother before their eyes are opened will attempt to cover their fecal matter. Is there some ‘universal’ cat etiquette that is carried into the next generation?

One of my favorite examples of instinct is the cuckoo bird. There are species of cuckoo bird that do not build nests but simply lay their eggs in the nests of other birds. The cuckoo egg is ‘programmed’ to hatch before the eggs of the host nest and the young cuckoo chick pushes the other eggs out of the nest. Having removed the competition, the young cuckoo bird now is nurtured by the host. The thrush, in this picture from Wikipedia, continues to feed what is an obvious (to us) intruder. I think that the positive aspect here is that there are no bounds to the love of a parent. Looking at the size of the nest, you can get some perspective on how ‘out of context’ this situation is.


So… how does the young cuckoo bird know to push the other eggs out of the nest? It had no clues from its parents or the environment to trigger this behavior. How is this invasive species able to continue this behavior over generations?

These are only a couple examples of instinctive behavior among living beings. How does a human baby begin life with the innate ability to suckle from the breast of their mother? How does a sea turtle deposited as an egg in the sand of the beach inherently know to move toward the ocean when it emerges from the egg? How does a spider know how to create a web even though they are separated from any examples?

These are all questions related to how species-related information is transferred to offspring. Through the miracle that is the development of a living organism; basic skills are, somehow, implanted in the brain. In many cases, these implanted skills, or instincts, are necessary for survival.

So, this brings me to the crux of the matter. How can a sequence of sugars and phosphates linked by nitrogen-based chemicals govern the incredibly complex process in the development of a living entity? How can this sequence of chemicals develop into a cognitive being with certain skills imbedded in their brain?

As I peruse the available scientific literature, I find references to this information contained in what is currently called ‘junk DNA;’ segments of our genetic material that has no apparent purpose. There are other theories regarding how this information is carried in the DNA structure but none seem to satisfy the programmer in me. We share with other mammals between 70 and 90% of our genetic material. The unique material is what differentiates us physically from the mice and birds and whales in the world. I find it implausible that the same code used to build the physical body could also contain the programming.

In my mind, the argument is the same as saying a computer parts list when assembled correctly will automatically contain the operating system. As an engineer, I know that I can easily assemble a computer if I have all the physical elements needed. I also know that the computer will not be viable until an operating system is installed. The operating system is the set of instructions needed to make use of the physical components.

Our brain and the associated body are not viable without the equivalent operating system software. In my opinion, the ‘instincts’ we are born with partially represent the fundamental equivalent to this operating system. This is where I need to inject the spiritual aspect of this discussion. I hold that we, as souls or living beings, are a combination of spirit and body.  I believe the spirit which is embedded in the physical body at some point when the cells begin to differentiate carries with it the basic information needed to act in the ‘role’ defined.

It is easy for me to believe that all living things are a combination of physical and spiritual entities. The spirit of the yet to be born bird, or spider, or for that matter, any other living thing brings with it the necessary instincts and basic operating system to function in the context of its existence. We begin with this basic instinct to build our knowledge. I believe that this basic toolkit with which we are born gives us not only the basic tools but also the intrinsic uniqueness that every living thing enjoys.

As I contemplate the incredible complexity of my own body and as I have watched the process wherein new life is brought about, I find it much easier to believe in a creative God than in evolution’s process of trial and error .

From Genesis, chapter one, we read:

20  And God said, Let the waters bring forth abundantly the moving creature that hath life, and fowl that may fly above the earth in the open firmament of heaven.
21  And God created great whales, and every living creature that moveth, which the waters brought forth abundantly, after their kind, and every winged fowl after his kind: and God saw that it was good.
22  And God blessed them, saying, Be fruitful, and multiply, and fill the waters in the seas, and let fowl multiply in the earth.

The miracle of life is a testimony to me of the existence of this unseen world. There are clues all around us, if we but pay attention.

What think ye?