Chemical Tags for Our Genome

DNA contains our genetic inheritance. In the DNA molecule there exists a code for the assembly of all the proteins in our body—up to 50,000 proteins. In this way, DNA is the reference manual for the materials of which our body is composed. These chemical materials must be assembled properly or they will not become a living, properly formed, functioning human being. A multitude of additional chemical compounds tell the proteins what to do in order to achieve their proper function and formation. These additional chemical compounds comprise the epigenome, a necessary chemical supplement to the genome of DNA. It may be considered a second layer of information necessary to form a coherent living human (or any other living creature).

DNA in our bodies is wrapped in chemical “tags.” In previous posts we have mentioned  two primary tags: DNA methylation and histone modification. For this post, we deal with the second chemical “tag:” histone modification. The DNA in each human cell remains fixed for life. Chemical “tags” called histones, collections of protein molecules, influence the DNA molecule. These “tags” affect inactive genes, making them unreadable. At other times, the chemical “tags” make genes accessible and readable. Different genes are active in different types of cells at different times. My personal fascination with epigenetics currently relates to prenatal development, but epigenetic tags operate throughout our lifetime.

The NHGRI (National Human Genome Research Institute), an arm of the NIH (National Institute of Health) publishes many fact sheets, including topics on epigenetics. We quote several statements to help us understand a small part of the complexity and wonder of the human body: “…DNA in cells is wrapped around histone proteins, which form spool-like structures that enable DNA’s very long molecules to be wound up neatly inside the cell nucleus. Histone proteins attach a variety of chemical tags to DNA. Other proteins in cells detect these tags and determine whether that region of DNA should be used or ignored in that cell.”

A YouTube graphic from GSLC (Genetic Science Learning Center) illustrates what happens to the histones called “octamers.” DNA sometimes tightly wraps around these histones like “beads on a string,” making inactive genes unreadable. At other times DNA loosely wraps the histones, making active genes easily accessible.

One pillar of evolution traditionally cited by scientists has been the presence of “junk DNA” in non-protein-coding sequences. Only a small percentage of human DNA codes for proteins. The function of non-coding DNA until recently has been dubbed “junk” because it was assumed it was left over from earlier eons but no longer served any purpose. Recently the NHGRI, cited above, sponsored the ENCODE project. In the last decade, ENCODE scientists have discovered that 80% of non-coding DNA has regulatory function within the cell. Eric D. Green, Ph.D., director of the NHGRI branch of NIH says “…most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms.”

The regulatory function of this vast wealth of non-coding DNA, rather than useless “junk,” is now recognized as an epigenetic layer to enable gene expression and regulation and aid in the startling phenomenon of embryonic stem cell differentiation. Stem cells are pluripotent; they are able to differentiate into all of the 220 different cell types needed to construct the many tissues necessary to form all body organs and eventually, the integrated systems of the human body.

When we examine a newborn human baby, we notice the complexity of morphology of each baby part. Does he have all his fingers and toes? Does she look like her mother or her father? Are the dozens of internal organs present and functioning as they should? Our answers indicate but a minuscule understanding of the marvelous complexity of genetic inheritance. The more we understand, the closer we come to grasping the significance of Psalm 139:14 (NIV): I praise you, because I am fearfully and wonderfully made; your works are wonderful; I know that full well.”  

  

Epigenetics: Under the Surface

What lies under the surface? The external and internal structure and function of the human body is complex and beautiful beyond belief. According to what master plan is the human body assembled? We could devote a lifetime of study even to scratch the surface of knowledge about molecular biology. Still, our knowledge of epigenetics is in its early stages.

A few decades ago basic knowledge of genomics—the science of structure, function, and mapping of DNA—was sufficient to satisfy most laypersons’ curiosity about heritable human characteristics. In recent decades our knowledge extends far beyond DNA with its code for protein production. In particular, we speak of the astonishing phenomenon of reproduction—the assembly of DNA-produced protein substances during prenatal body development. Genomics reveals but a small portion of the complex story of reproduction of a unique new life. Epigenetics is the new buzz-word. 

At the risk of trivializing a majestic biological process with a mundane analogy, we illustrate with a culinary example. When a chef prepares a gourmet dish, all prescribed ingredients must be initially assembled. More important is the activity to follow: (1) adherence to a coherent recipe (2) use of correct utensils (3) appropriate procedure (4) proper control of necessary factors such as temperature, and (5) maintaining favorable conditions when the project is complete. We see that in addition to the initial assembly of appropriate ingredients, far more is involved in a successful gourmet production.

We transition to prenatal production of a new life—admittedly a giant leap. One important term is “gene expression.” Acquiring the biological components of the human body proteins is the initial step. But fabrication of the components is ultimately more important. The latter is a topic under the heading of epigenomics. How does the assembly process unfold? Life scientists define gene expression as the process by which information from a gene is used in the synthesis of a functional gene product. Production of a complex, unique new human life in the womb is a creative process far beyond our imagination. Gene regulation insures that genes function to produce specific cells at the proper time.

Let us consider a few molecular wonders of the reproductive process. We quote from opening statements of a lengthy Quiagen website. “It is known these non-genetic alterations are tightly regulated by two major epigenetic modifications: chemical modifications to the cytosine residues of DNA (DNA methylation) and histone proteins associated with DNA (histone modifications.)” The Quiagen site continues, “Epigenetics is one of the fastest-growing areas of science and has now become a central issue in biological studies of development and disease.”

For the remaining space in this post we discuss methylation. DNA methylation describes the addition of a methyl group containing one carbon and three hydrogen atoms. This molecule attaches to one of the nucleotides of the DNA molecule—namely, cytosine. In our previous references to the base pairs in DNA which code for proteins, CG is one of the “alphabetic letters” of the DNA protein coding scheme, along with AT. C abbreviates cytosine. The methylation of DNA may occur owing to environmental conditions. Or, it may occur as a result of naturally occurring cell processes. Whatever the cause of methylation, it may result in developmental advantages during the process of body formation during reproduction. Methylation is a disadvantage if it results in a disease state. The methylation process is heritable, even if it results from environmental factors.

Methylation of DNA is important during the many stages of fetal development in which some processes are turned on while other processes are turned off. These findings are important as they provide insight into regulatory elements guiding tissue specification that lead eventually to organ functionality.

Bioscientists are working to unlock more secrets of epigenetics. We believe that in our lifetime many more wonderful truths concerning knowledge of life processes, physical wellness, and healing will be discovered. Of the hundreds of written sources dealing with epigenetics, many state that the processes arising during fetal development are still largely unknown. 

Many personal questions concerning wonders of life are hidden with the Creator of all things. King David celebrates the omniscience of God in his majestic Psalm 139:13-16:

For you created my inmost being: you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place. When I was woven together in the depths of the earth, your eyes saw my unformed body. All the days ordained for me were written in your book before one of them came to be.      

       

Epigenetic Prologue

We have experienced a reprise of the fascination triggered when a new life enters the family. At the risk of being repetitive, we must acknowledge renewed awe of the traits and skills manifest by very young children long before the age of six months. Our visits to church, the supermarket, and other public venues supply ample observational opportunities. In the earliest months of her life we recently observed our friends’ daughter beaming exuberantly at us across the aisle during Sunday morning hymn time. On another personal level our new grandson, two months old, has been smiling and vocalizing enthusiastically for several weeks.

You may ask how epigenetics affects our knowledge of early development of human consciousness, the subject of our opening paragraph. Backing up just a few months before these children were born, one could also inquire how epigenetics relates to the marvelous sequential prenatal development of each living human. We increasingly hear medical advice on healthy lifestyles, disease prevention, and new treatments for personal health crises. Medical technology is increasingly the application of epigenetic knowledge. 

Epigenetics has entered our modern vocabulary to supplement our more traditional knowledge of genetics. (“Epi-” connotes above, beyond, or in addition to when used as a prefix.) For example, the basic physical structure, health, and function of the body may be studied under the topic of epigenetics. Therefore, we have a progression of studies—the genome, the proteome, and the epigenome. We project that our knowledge of the epigenomics is only at its beginning. What is in store for proliferation of our knowledge and enhancement of our quality of life in future decades?

Stories and examples enhance our ability to learn new concepts. After building a new home we inspect the empty dwelling to determine its initial structural integrity. We establish that the home’s blueprint was carefully followed. In the following months the home will acquire unique qualities as it is progressively finished and furnished with enhancements such as trim, color of paint, and wall decorations. These enhancement “add-ons” are not provided by the blueprint.

Application of knowledge of epigenetics, likewise, does not alter our respect for the genetic role of the DNA code. To a large degree, environment and known gene expression mechanisms are capable of effecting significant changes in human health. These are examples of epigenetics, a broadened area of inquiry we will progressively discover in coming years.

In personal continued study of epigenomics, we are often deluged with bioscientists’ relentless efforts to connect this new knowledge with an affirmation of undirected naturalistic evolution. We look forward to discussing some of the molecular basis of epigenetic processes in future posts. As we discover more astonishing design and functional features of living things and their capabilities to adapt and reproduce, the case for evolution weakens as the case for past and present acts of the Creator becomes stronger. Our God is the author of the genome, the proteome, and the epigenome!

    

Epigenetics and Phenotype

Epigenetics is a new and unfamiliar term to many non-scientists. The term signifies inherited changes to the phenotype (physical and behavioral traits) that are not caused by the genetic code of DNA. To bioscientists knowledge of epigenetics opens new medical knowledge to enhance human health and longevity. It is the next step in the lexical sequence—genomics, proteomics, and epigenetics. 

Most laypersons are familiar with the term genomics. They know that most physical traits result from DNA inheritance. Knowledge of another field, proteomics, has spun off from genomics. The human DNA code is responsible for building physical traits by  its ability to produce proteins, the building blocks of our physical bodies. Proteomics is a specialized knowledge of the composition, structure, and multiple functional roles of proteins.

We focus on two other related terms which have become part of our biological lexicon: genotype and phenotype. Our genotype is our personal genetic sequence of heritable genes making up our DNA. It provides the code for the manufacture of multiple proteins which compose our physical body. It is not dependent on any environmental factors. Personal genotypes are intrinsic to one individual.

A phenotype, in contrast, is observed as outward, physical traits. It could be influenced by environmental factors other than our DNA sequence. Unique traits and personal behavior are also considered part of our phenotype. We may see that phenotypes are dependent on genotypes to a large degree. For example, physical size and other traits such as hair and eye color trace to our genotype.

Explanation of the human architectural body plan is not simply a matter of understanding the function of DNA in inheritance. This basis of inheritance is exceedingly important, but with the passage of time we have become aware of the wonder and complexity of other factors—epigenetic factors which govern the engineering of body plans. We introduce another term in our biological lexicon. It is termed developmental biology. Epigenetics may be linked with developmental biology to create developmental epigenetics.

We introduce new vocabulary to help us focus on the cutting edge in developmental biology. Several new expressions may trigger expanded reader interest in this field: gene expression, gene regulation, cellular differentiation, and morphogenesis. All terms hold the potential for future post topics.

Our family has become aware once more of the miracle of developmental biology in a short nine months. A new grandson has joined his two-year-old brother and four-year old sister in another manifestation of the developmental wonders of the creation of a new life in less than one year. Our family has termed the event a “divine developmental miracle.”

The arrival of a new grandson inspired your blogger to create a series of posts on our family version of “developmental biology” in 2013. I link one of many posts from that sequence. You may also click on the previous four posts (older post) or the seven posts to follow (newer post).

http://jasscience.blogspot.com/2014/01/let-building-begin.html

           

More Protein Wonders

Proteins begin their lives as chains of amino acids in the body. In humans, protein-forming amino acids are either acquired in foods we eat (essential amino acids) or are manufactured in our body (non-essential amino acids). Essential and non-essential amino acids are coded by the DNA molecule to produce the proteins of the body. Twenty different protein-forming amino acids are chained together in myriad  ways according to instructions in the oft-cited DNA code. The human body operates with many thousands of different proteins.

The term DNA code is a powerfully meaning-laden term. When we were young some of our entertainments were games of code-cracking or secret code-breaking. In every case the code was devised by another person, an indicator of intelligence of the deviser of the code. They also affirm our own ability as intelligent code breakers. In the DNA code we observe that when we recognize the identity of the code author, our own sense of perception and comprehension is affirmed.

Are there limits to the number of proteins possible? Bioscientists speculate that there are as many as ten million different proteins among all living things on earth, while humans have upwards of 50,000. Proteins begin as chains of amino acids termed polymers. We highlight a fascinating capability of proteins: their ability to fold into three dimensional shapes. The three dimensional shape relates to the function of that particular protein in keeping with the biological principle of “form fits function.” In theory, there are no limits to the number of possible proteins. 

The unique three dimensional conformation of each protein, according to scientists, is dictated by the original amino acid sequence. Scientists also attribute the three dimensional structure to the mediation of other protein cells, assisted by molecular “chaperones.” These explanations point to a possible cause, but not an entirely satisfying explanation of how the cause works to accomplish the observed effect. Herein is a mystery. The line between a naturalistic cause and effect, such as the forces we exert to accomplish minor repairs of an inoperative device in our home, and a complex phenomenon such as protein folding, is not always sharply defined.

In early science lessons we learned that “proteins are the body’s building blocks,” rather like bricks and lumber incorporated into a new home. The three-dimensional conformation of complex protein molecules may help us envision the idea of “building blocks.” While this characterization of proteins is accurate, the story is incomplete. Three-dimensional protein molecules have many functions in the human body. The functions include enzyme catalysis of metabolic reactions, immune responses, cell signaling, and information processing. Each previous term could be the subject of lifetime study by specialists in bioscience. 

Where does a divine miracle end and a natural process begin as we study the astounding complexity of life—in particular, human life? We may easily perceive physical life forms and life processes as intelligently designed. We may also go further to say that human life forms are the product of a divine, transcendent miracle. As we contemplate the existing complexity of physical body structure and the functions operating to make its systems work, we are struck with wonder. God is the author of both primary causes and secondary causes. Primary causes are transcendent miracles of creation such as the beginning of our universe and the immediate creation of human life forms. Secondary causes are moment to moment transformational or sustaining miracles such as the miracles of our working bodies.

   

         

Genomics and Beyond

Citizens who have lived through World War II may contemplate a treasure of science discoveries. One favored activity is searching out timelines of discovery in science as a general field. The timelines can be broken down into many branches of specialized knowledge including life science. Advances in this field have been startling. We gain insights in our quest for truth concerning humanity. Fundamentally, knowledge of life science is far more complex than knowledge of physical science. Since the discovery of the DNA helix structure in 1953 our knowledge has multiplied exponentially.

The genetic code was deciphered in 1961. Since the 1970s scientists have perfected more efficient methods by which the partial or complete sequence of nucleotides in DNA is revealed. In 2003 a complete sequence of human DNA was published for the first time including all protein coding and non-coding genes. Protein coding has been characterized as “an incredibly detailed blueprint for building every human cell.” The familiar abbreviations of the DNA base pairs are AT and CG. They function like letters in an alphabetic code of language. This code is one of the wonders of nature and a strong argument for intelligent design. Complex codes have been acknowledged as the product of an intelligent designer. The prescribed proteins producing complex life are “coded for” and life requires nothing less.

An organism’s genome catalogs its complete set of genetic material. Genomics is a modern term introduced to the science community in 1986 even though discoveries concerning the human genome had been advancing for several decades. Only 1.5% of the human genome codes for proteins, the building blocks of life. Reusing a favorite construction analogy, we could say that when the complement of building materials for a new home or factory structure is assembled, the builder possesses the necessary “coded-for” physical components. The lack of one or more construction materials would result in an incomplete building, perhaps even a  building which has no function whatever. 98.5% of the genetic code does not code for proteins but is still expressed as a sequence of the familiar AT and CG nucleotide pairs. The sequence comprises over three billion nucleotide pairs.

Most of our discussion relates to genomics. How does our post title “Beyond Genomics” relate to our search for truth concerning human existence? Genomics is far from a complete body of truth concerning the assembly of the human organism and how it functions. In recent decades bioscientists have realized genomics is only the beginning of the story. We gain knowledge constantly and progressively. For example, we have observed a virtual revolution in genomic knowledge of 98.5% of the human genetic sequence which does not code for proteins. Much of the sequence of non-coding DNA has been termed “junk DNA,” a term currently passing into oblivion. Evolutionists had thought much human DNA was “junk,” left over as a remnant of evolution but no longer useful. Non-coding DNA has increasingly been discovered to have useful function.

The proteome is the study of the entire set of millions of known proteins. “Proteomics,” a term introduced in 1997, is an offshoot of genomics dealing with the structure and function of proteins. Another fascinating ongoing study is termed “epigenetics.” Knowledge of these fields takes us “beyond genomics.” Assembly of bodily proteins is merely the  introductory chapter in the story of how living things function. Epigenetics takes us to the realm of gene regulation which drives the operation of virtually every activity of living things. We eagerly await the additional secrets to be revealed by the new field of developmental biology. It is our considered opinion that future discoveries in developmental biology, epigenetics, gene regulation, and a host of other fields in bioscience will magnify knowledge of the role of the omnipotent Creator of life.                 

  

Wonders of Proteins

Our bio-science vocabulary is expanding. Within the lifetimes of today’s senior citizens, the molecule of DNA was named as the bearer of genetic information. By mid 20th century, brilliant discoveries about the structure of the DNA molecule were published. Soon the DNA genetic code was discovered. Inherent in DNA was a code for producing the proteins composing the bodies of living things. This century the complete human genome has been published: The term genome means the complete genetic information necessary to produce proteins composing the human body. From this information comes the knowledge of genomics. The complete human genome became available in 2003—three billion bits of coded genetic information. Genomics has been a well-known term in our bio-science vocabulary since 1986.

Knowledge of the human genome enables bio-scientists to catalog the thousands of proteins, structural building blocks of the human body. Proteins enable many other body functions. They are complex molecules formed from chains of molecules of twenty different amino acids assembled in innumerable ways. Human bodies consist of 50,000 different proteins. Millions of other species on earth are composed of many millions of different protein molecules. Proteins are chemical combinations of the elements carbon, hydrogen, oxygen, and nitrogen. The raw materials are simple, but the possibilities for their combination are virtually limitless.

It is time to introduce another vocabulary term—proteomics—a study of the structure and function of the entire set of proteins known. The term was introduced to the science community in 1997. We easily see that as our knowledge of the wonders of life forms grows, our bio-science vocabulary grows with it. With our understanding of the DNA blueprint of protein coding (genomics) fairly complete, we now turn to an issue related to the more recently discovered discipline of proteomics. How do we continue to understand the structure and function of proteins? First, we turn to the structure of proteins. We discover that form of the multiple thousands of protein molecules is related to their function. 

The principle of “form fits function” is vitally important in bioscience. Molecules, cells, tissues, organs, and complete organisms operate by the reality of “form fits function.” This principle may be initially difficult for beginning students to grasp. Therefore, without being overly pedantic, I may search for a mundane classroom example before continuing with lessons on what happens to proteins after they are produced in body cells as linear chains of amino acids.

Students have heard of the Japanese art of origami, the science of paper folding. Flat, square sheets of paper may be folded and formed into various shapes limited only by the creativity of the folder. Many thousands of forms are possible. Do we wish to create an origami airplane? The product shape (form) lends itself to its intended function—flying. Unfolded origami paper is shaped simply, usually in square sheets. The paper is composed of a few simple, basic elements. The final product, however, may manifest virtually limitless shapes and serve many purposes.  

One inquirer requested examples of “form fits function” in the world of biology on a well known question and answer website. The responder cited two: Blood cells and sharks’ teeth. Each has specific forms fitting special functions. Likewise, protein molecules which are initially produced as simple linear chains of molecules of amino acids inside the cell must fold into the correct, three-dimensional shape in accordance with their ultimate function in the body.

Specialists in proteomics have explained the protein folding process with some success. They explain what happens with respect to protein function better than how and why it happens.” We know, however, that complete knowledge of the protein folding phenomenon is in the purview of the Creator of all life forms.    

  

DNA and Body Building

Among many concerns with the truth of the evolutionary paradigm is the reality of building a new species. If evolution is true, new species made their initial appearance countless times in the history of earth life. New genetic information was necessary to produce a new species, replacing older genetic information.

Molecules of DNA are present in virtually each cell of every living creature. In living organisms the double helical structure of DNA contains four chemical bases called nucleotides. These are adenine, (abbreviated A), guanine (G), cytosine (C), and thymine (T). A and T are always paired and positioned opposite each other on the double helix as are C and G. The strands of the helix are made of sugar and phosphate molecules on which the AT and CG base pairs are affixed like rungs on a ladder. 

Each base pair, together with the sugar and phosphate molecules, is called a nucleotide. There are three billion nucleotides in every human cell. They function as a digital alphabetic code. The ATs and CGs could be represented as digital 0s or 1s. There is no limit to the length or order of the digital code. The code conveys information. Nucleotides in a certain order may function like letters and words in an intelligible alphabetic text. The “words” formed direct that a certain protein should be constructed from amino acids within the cell. In just one cell there is coding information to construct up to 50,000 proteins (complex molecules) found in the human body. The DNA code which directs manufacture of the proteins exists in several hundred thousand base pairs.  

Proteins are building blocks of life forms and have other diverse functions such as processing information and catalyzing reactions. Each species is composed of a huge assemblage of proteins coded for by DNA. There may be as many as 10 million different proteins known among the millions of species of living organisms.

We ask readers to contemplate how naturalistic evolutionary processes could produce meaningful new DNA code patterns. Evolutionary processes able to produce new proteins of coherent and viable new life forms is a scenario of astonishing incredibility. What sort of mutation could appropriately alter the DNA code to produce a viable new species? Recall that mutation degrades and destroys genetic material. Altered DNA resulting from mutation cannot produce a fundamentally new and viable organism.

The second phrase of our post title suggests a different avenue of exploration in the process of body building—the wonder of origin and reproduction of life forms. We may illustrate the concept this way: In a new building construction project, the builder could assemble all of the raw materials on the building lot site before any construction begins. The builder also has in hand the building blueprint and manuals for detailed assembly instructions. The analogy in genetics is the potential of the many thousands of protein building blocks needed before actual assembly of the living body begins. The embryo is the location of the blueprint: Assembly instructions are stored there before the body building begins.

DNA, therefore, does not accomplish all the work of body building. It is, however, the coding plan for manufacture of all the raw materials which compose living creatures. The information for body building is stored in fertilized embryos. Our body building discovery process is just beginning. Using a community building project analogy once more: we may study the complete catalog of construction materials listed in the builders’ handbook. But we may be more fascinated observing the actual construction process. We link one post from our previous series on prenatal human development:

https://www.jashow.org/articles/science/let-the-building-begin/

We close with a majestic verse from Psalms: “How many living things you have made, O LORD! You have exhibited great skill in making all of them. The earth is full of the living things you have made.” (Psalm 104:24 NET Bible)  

       

Culture Grip

Stephen C. Meyer’s interview series with John Ankerberg on the JAShow in July and August presented a conceptual and descriptive outline of the broad subject of popular evolutionary theory birthed by Charles Darwin. Meyer is primarily an advocate of the Intelligent Design paradigm. He reviewed the evolutionary proposal that earth life has progressed from simple ancestral forms to intricately complex contemporary forms. This concept grips a majority of bio-scientists owing to its creative scope and majesty. Evolutionary biologists self-congratulate in their ability to “see” the process of evolution as it has unfolded throughout life’s history on earth. Life first appeared in  the waters of earth’s oceans and is now found in virtually every segment of our planetary environment. Bio-scientists’ ability to “see” evolution in the fossil record is the source of the frequently repeated mantra that “evolution is a fact.” According to this standard, who could deny that “evolution is a fact?” Evident life forms have changed substantially. But do evolutionary biologists suffer a secret crisis of confidence?

Woven into Meyer’s primary topic of the Cambrian Explosion of sudden life were discussions of two main tenets of evolutionary theory: The theory of evolution is a bottom-up proposal of life’s development, in keeping with traditional evolutionary theory. That is to say, life advances from simple to complex. Evolutionists search for species inferred to be transitional forms. When they position their putative transitionals on theorized “tree of life” graphics (a main trunk diverging into many branches) they imply evolutionary changes are “bottom up.” Meyer disputed the concept of bottom up in the fossil record by documenting the startling results of Cambrian Explosion studies: Multiple diverse phyla appear fully formed without transitional precursors. These anomalous findings strike at the very heart of evolutionary theory. Instead, they suggest a creation event.

Another crisis of confidence may result from increasing doubts that mutation and natural selection, taken together as another pillar supporting the evolutionary model, is the driving force behind macro-evolutionary speciation. Macro-evolution is defined as the production of a new biological species. According to evolutionary theory, each of earth’s present 10 million separate species originated with the confluence of favorable mutation and natural selection. Uncounted millions of extinct species also arrived on earth through the dubious creative force of this two-segmented evolutionary support pillar. Mutation and natural selection does not enjoy its former explanatory power. Mutation is known to degrade the genetic code. It is not a beneficial, creative building process. The hypothesized operation of natural selection paired with mutation to generate speciation is uncertain at best. 

Naturalistic evolution permeates the science profession and has gripped our culture. The theory’s anomalies apparently are insufficient to deflect either naturalistic or theistic evolutionists toward a creationist or intelligent design perspective. Theistic evolutionists believe in bottom-up development of life and endorse the theorized driving process of mutation and natural selection. They claim God, the Creator of all things, endowed life with the freedom to evolve. Evolutionists of either stripe are untroubled by the evidence of top down appearances of life forms in the Cambrian and subsequent periods or the degrading propensity of mutation.

Our ruling science and educational culture is firmly gripped by belief in evolution. When we take origins beliefs in overview, many theistic commentators have stated that evolutionary origins beliefs do not impair their belief in an omnipotent God, nor are those beliefs an issue of doctrine. One friend has inquired why the issue is so important to me. I responded the same way Stephen Meyer and others have characterized belief in ID: Ultimately, the most important characterization is whether ID is true. We are constantly informed that evolution is good science. But a similar question recurs: Is evolution true?

Hard Problem of Consciousness

Philosopher/cognitive scientist David J. Chalmers formulated an expression to characterize our quest for knowledge of consciousness. In 1996 he called it “the hard problem.” The term has since become associated with the scientific subject of consciousness. Consciousness is indeed a “hard” problem. Chalmers claimed that “Consciousness poses the most baffling problems in the science of the mind….There is nothing that we know more intimately than conscious experience, but there is nothing that is harder to explain.” Understanding consciousness does not yield to the usual methods of science, analysts claim.

Many students discover the study of the phenomenon of human consciousness is esoteric—a subject for specialists. Non-scientists read definitions such as “consciousness is self-awareness” or “consciousness is the brain basis of subjective experience, cognition, wakefulness, alertness, and attention.” They nod approval, then go about their “subjective conscious experience.” We wonder whether a classroom teacher would ask students for a definition or explanation of consciousness on a science test. Many scientists specializing in systems biology may be stumped.

Scientists frequently search for “reductive” explanations in their study of the phenomena of science. This means searching for explanations in terms of causes which produce observed effects. Cause and effect is part of a reductionist explanation for ongoing events whether we prepare our meals, drive down the street in our automobiles, or attend an athletic contest. 

Human consciousness is a completely different story. It occurs within a highly interconnected neural information processing system in our brain. Does this information help us answer the “hard problem?” No, it does not. But it focuses our attention on the great unknown: What is consciousness? After reading volumes on the subject, I yield to the uncertainty of the experts. We don’t really know how to appropriately define consciousness. Our lack of knowledge, however, does not prevent scientists from researching humanity’s famous “hard problem” or producing relevant observations on the subject.

The human brain is an interface between the mental and material world. The conscious being is controlled by chemical and electrical impulses, the material basis of the conscious mind. These effects and impulses comprise the boundary between the mental and material world. Millions of words and thousands of books and commentaries have been produced without a satisfactory reductive explanation of what consciousness really is. Consciousness is clothed in mystery.

A website search for lists of scientific mysteries almost invariably includes the subject of consciousness. Another topic appearing on such lists is the origin of life. Both topics are mysterious and so far unanswerable. Science professionals will continue their search for naturalistic explanations of consciousness and the origin of life because finding naturalistic explanations is the self-defined mission of scientists. Naturalistic explanations are desirable. The Creator has produced a universe in which secondary processes occur “naturally” but are supported by God’s continuous sustaining power at the same time. Each phenomenon does not demand a supernatural, transcendent miracle. On a mundane level our life is filled with situations where natural processes sustain our life’s needs. A high level miracle is not needed, for instance, when our auto mechanic makes needed repairs on our vehicle. Auto repairs have easy reductionist explanations but there are no reductionist explanations for consciousness.

Our previous blog post on Emergence of Consciousness discussed consciousness having its origin and sustenance in a divine miracle:

http://jasscience.blogspot.com/2014/01/emergence-of-consciousness.html

A favorite scripture verse comes to mind. We do not present this verse as a “proof-text.” However, the thoughts expressed may be relevant as we contemplate mysteries such as the origin of life and the origin of consciousness: “In him we live, and move, and have our being…” Acts 17:28 (ESV). “In him we live…” could refer to the origin of life in a divine miraculous act; “…and move” may relate to physical causes and effects; and finally “…and have our being” could speak of the divine, sustaining, miracle power of God present with us from moment to moment—our conscious being.

Many in the science profession would discount supernaturalism in their study of consciousness because most scientists tolerate only naturalistic explanations for any phenomena. The subject of consciousness may never yield to a naturalistic explanation. Our blog has allowed for supernatural explanations for some phenomena where evidence points in that direction.  

            

      

    

Basis of Consciousness

When our neighborhood birds decided to engage in high-spirited, ebullient behavior, our thoughts wandered toward, “What caused this sudden display?” Description of the behavior is easy; explanation is complex and difficult.

Our previous post on “Exuberant Wildlife” described the collective antics of thirteen different bird species in the woods behind our home one recent day. Their behavior seemed to express energy, excitement, and enjoyment. Their more ordinary and deliberate activities were put on hold for roughly 45 minutes, replaced by what appeared to be an instance of simple fun. Their antics were somewhat reminiscent of playground antics of human children. We were tempted to anthropomorphize this group of animals.

The term “consciousness” may be interpreted in many ways. Without formally defining the term, we would agree that humans have a high degree of consciousness from an early age. Humans are self-aware and aware of their surroundings. What about our birds? Are they self-aware? Are they aware of their surroundings? Do they have emotions? Memories? Sensations? Human consciousness has been studied and reported on in thousands of books and articles. Consider: Do higher level animals experience consciousness in a manner similar to humans?

For this discussion we will take these aspects of consciousness: the ability to sense conditions in their surroundings and make behavioral decisions. It was obvious that each of our neighborhood birds observed their avian companions and made a “decision” to frolic with the group. Their decisions brought enjoyment to themselves and their human observers. Perhaps the individual bird’s “decision” was a reflexive expression of a mysterious group action, but we do not have full knowledge about the dynamics of this event. 

Either way, we are aware of mental phenomena in living things which result in physical responses. These mental phenomena are the basis for consciousness. What actually happens in an animal’s brain? The wondrous brain is composed of simple matter—primarily chemical combinations of a few dozen of the approximately 100 known elements we studied in Chemistry 101. Have you ever wondered how the interactions of simple atoms in a living entity produce consciousness—sensory awareness, emotion, fear, joy, pleasure, pain, response to stimuli, intelligence, memory, and freedom to make decisions and choices?

Commentators have stated that mind and matter are interconnected at the atomic level. Consciousness, whether in neighborhood bird groups or in human beings, relates in some unknown way to physical atoms and molecules. Scientists have been discussing the problem of consciousness for centuries. The literature on this topic is overwhelming, perhaps because the nature of consciousness is one of the last major unsolved problems in science.

We ask readers to contemplate the mystery of how ordinary matter in the form of atoms and molecules may come together under some conditions to produce a conscious living creature, while the same atoms and molecules could assemble in a non-living configuration. Fundamentally, this is a mystery to science, but not to the Creator.

Job 33:4 (NIV) is offered to help us contemplate the mystery of consciousness and from where it springs: “The Spirit of God has made me; the breath of the Almighty gives me life.”  

      

  

Exuberant Wildlife

Looking out across our back deck into the trees of our northwest Illinois neighborhood in autumn, our birds (I’ve called this area “bird heaven”) occasionally stage an impressive drama. Several times each fall we are favored by an event we must characterize as “exuberant bedlam.” On 10-16-09 I first called attention to this phenomenon in a post titled “Bird Exuberance,” linked here:

https://www.jashow.org/articles/science/bird-exuberance/

Since 2009 we have enjoyed these periodic reprises of exuberance. The events take place in autumn following the earlier seasons’ boisterous territorial claims and production their new generation, followed by their enjoyment of a few weeks of quieter peace, perhaps to celebrate their success in fledging young. By October our avian friends sometimes discover ways to celebrate communally with mixed species. Recently we witnessed the most extensive display of shared avian excitement we have yet experienced.

In just less than one hour, we positively identified thirteen different species of birds. Catalyzed by an immense assemblage of cedar waxwings, the following species took part in lesser numbers: blue jay, catbird, cardinal, house wren, red-bellied woodpecker, nuthatch, downy woodpecker, bluebird, chickadee, phoebe, robin, and goldfinch. We observed some birds feeding on cedar berries, but the main activity—flying here and there for no reason obvious to us—seemed to center merely on pure joy and excitement. There were no inter-species squabbles.

Another post called attention to the writings of Old Testament figure Job. His observations and insights concerning the wonders of wildlife are beautiful poetic musings. Job suggests the animals of our environment have much to teach us:

https://www.jashow.org/articles/science/wild-animals-honor-me/

We close with but one more example of collective autumn bird behavior. One recent evening we observed autumn flocking and roosting behavior of common crows, visible from the same local vantage point we described above. By our estimate several thousand crows took part in an assemblage in the sky and woods. Soon they departed to an unknown overnight roosting location. It was a scaled down, but still impressive gathering of one of our most intelligent birds. Crows have been observed to congregate in groups much larger, even up to a million. We have seen other more spectacular autumn flocking events in species such as blackbirds, but not in our local Illinois environment.

The natural world provides many other sources of wonder. Animal behavior cannot adequately be explained in human terms. Collective wildlife decision-making is a result of a mysterious ability implanted by and known to the Creator. Human explanations of causes and effects do not provide us with definitive answers.   

   

Supermoon Eclipses

Public attention is directed toward unusual and spectacular phenomena from the natural world by media accounts. The editorially injected “super” used in media descriptions generates added hype and sometimes well-deserved excitement. An example is “Superstorm Sandy,” the second most costly US hurricane which slammed into the east coast in October 2012.

Several weeks ago many world residents were alerted to a wondrous natural astronomical event not seen since 1982 and not to be observed again until 2033. A supermoon lunar eclipse would occur and would be visible to all earth residents able to view the moon during predicted hours on the evening of September 27. As a science teacher I looked forward to alerting my students to natural astronomical and meteorological wonders. In many years of teaching my subject matter received a welcome boost by comets, planetary conjunctions, eclipses, severe weather events, and other natural phenomena. These events provided natural motivation as we were temporarily relieved from our responsibility to supply classroom motivation on ordinary days.

We will now offer readers an abbreviated tutorial on this special eclipse after its occurrence: review supplements preview. Both “views” are necessary in good educational strategy.

In our solar system, motions of objects provide opportunities for one body to pass in front of another, obscuring the view of an observer. These out of the ordinary occasions add an extra dimension to already fascinating motions of solar system satellites—motions governed by physical laws. Ordinary physical laws of gravitation and motion, interesting as they may be to the science minded, are enhanced by the occurrence of unusual eclipses. A supermoon lunar eclipse? This is an example of what science instructors treasure to add mystique to their science education.

Before dealing with our recent supermoon eclipse, we remind readers that more ordinary lunar and solar eclipses occur frequently. In a lunar eclipse the earth casts its shadow on our neighboring moon. Normal sunlight is blocked from the moon. We see only a very dim, reddish lunar body during “ordinary” total lunar eclipses which occur 85 times during this century. There will be 230 lunar eclipses during the 21st century, but many of them will be partial or even less spectacular penumbral eclipses. In the 21st century there are also 224 solar eclipses, 68 of which are total with the remainder partial or in a special category termed “annular.”

The 2015 supermoon total lunar eclipse was part of a lunar tetrad: four consecutive total lunar eclipses occurring about six months apart. Tetrads occurs in groups every few hundred years. Eight tetrads occur this century but from 1600 to 1900, none occurred. 

This particular eclipse is a supermoon lunar eclipse because coincidentally, it occurs at perigee—when the moon is at the closest point to the earth in its orbit. The moon appears larger then because it is closer. The moon revolves around earth about once per month, so it is also at perigee (closest point to earth, about 226,000 miles away) about once per month, and at apogee (farthest point from earth, about 252,000 miles away) about once per month. The coincidence of the correspondence of a full moon lunar eclipse (sun, earth, and moon in line in that order) with the precise moment of perigee (moon closest to the earth) is rare indeed. If we add the coincidence of the September 27 eclipse occurring as the last of a tetrad of lunar eclipses, and also being this year’s harvest moon (the annual moon closest to the autumnal equinox) we have a series of rare and noteworthy coincidences.

We mentioned that the moon appears larger because it is at perigee. Its diameter is about 14% larger and consumes 30% more area in the sky. Consequently, it is also about 30% brighter than a more distant moon near apogee. On a comparison graphic this difference is startling on paper. The celestial view of the supermoon revealed a wonderfully large lunar orb. Our family spent several hours moon gazing with naked eye and binoculars that night in awe and wonder as we observed our special planet casting its shadow through space to our lunar companion.

If our readers wonder about the significance of the 2015 super moon in relation to Bible prophecy, we energetically dismiss any significance. The tetrad is of no prophetic significance. Tetrads have occurred for thousands of years. Many commentators have recently commented on “blood moons.” Blood moon is a dramatic description of the coppery tint present during total lunar eclipses but do not have prophetic significance. Total lunar eclipses have provided subtle colors during their occurrences for uncounted millennia of man’s sojourn on this planet.

Scriptural passages such as Joel 2:31 could have been applied to thousands of blood moons over the millennia. The term has been popularized lately by predictive utterances of mortal men. A history of failed human prophecies could fill many volumes. We should take note that future events are firmly in God’s hands. Connecting end times events with discernible astronomical events is not a gift bestowed on humans except in the general sense that future events will certainly occur and are known to God only, according to Acts 1:7 (NIV): “It is not for you to know the times or dates the Father has set by his own authority.”

As we conclude this post, we are reminded of a wonderful visual treat in the morning sky of October 2015. Planets Venus, Jupiter, Mars, and Mercury are all naked-eye visible in the eastern pre-dawn heavens. As I write on October 18, Jupiter and Mars are experiencing a spectacular conjunction, a mere one-half degree apart. We do not attribute this or any other unusual or awe-inspiring grouping to astrological or prophetic events. Rather, we give praise to the Creator who gives humanity the ability to visualize and recount past astronomical events and predict future ones within milliseconds of their occurrence according to the regularity and orderliness of God’s creation.

    

            

Cambrian Connection

Why call attention to the famous “Cambrian Explosion?” The John Ankerberg Show recently highlighted this remarkable event in the history of Earth’s life. We again invite our readers to review the full archive of Dr. Stephen C. Meyer’s seven interviews on the the Ankerberg Theological Research Institute (ATRI) website at www.jashow.org  The programs may be easily accessed under the Daystar symbol on the Ankerberg homepage.

We also call attention to one of our several past posts in which the Cambrian Explosion was cited:

https://www.jashow.org/articles/science/creationist-radiations/

Evolutionists who believe in a common ancestor and common descent for all living earth creatures are intensely challenged by the Cambrian Explosion. They recognize that new forms of life appeared suddenly. In the context of historical geology, suddenly is a relative term. It is difficult for non-scientists to imagine the 5-10 million year time frame of the explosion as a sudden event. But evolutionists would concur—it was sudden! That sweeping phylogenesis occurs in this limited frame of time, if indeed it could, is a hypothesist’s dream.    

New phyla have appeared on earth in “fits and starts.” This term is defined as repeated bursts or sudden flurries of activity.  Persuasive incidents of transitional forms of life appearing sequentially in the fossil record are not found. Stasis (a state of inactivity or equilibrium) is the rule. Gradual change in life forms is not.

The theory of evolution in our educational system and in our culture is firmly entrenched. The discussion concerning evolution has been pronounced “settled” by establishment scientists. Evolutionists connect their belief system with what they have affirmed to be the best science available and prevail upon non-scientists to accept the theory for that reason. Unique anomalies of the Cambrian Explosion must not disrupt the firmly held structure of the evolutionary paradigm. The sudden appearance of multiple new phyla of animals in a geological eye-blink is optimistically explained as having no conflict with the evolutionary model. 

For creationists and believers in Intelligent Design, the Cambrian Explosion supports their model. We propose that the Cambrian Explosion may be the single best evidence from the natural world for intelligent design theory and a creation event. Evolutionary theorists, on the other hand, are severely challenged by the Cambrian event. To a lesser extent, they are challenged by other radiations cited in the link to our post of 10-29-13.

We acknowledge that details of Cambrian events as evidence of an intelligent designer are not outlined in our current post. Likewise, details of the apologetic for evolutionary events in the Cambrian, are not included in this post. We encourage readers to research the many resources available on these topics for themselves.

In the blizzard of support for the evolutionary paradigm in our modern culture, we stress the importance of the issue for discussion in our churches, our schools, and the general public. Theistic evolutionists claim God created all things, including the ability of life forms to speciate thousands of times from the Last Common Ancestor to modern humanity within the timeline of life’s history on Earth. Sometimes this is termed “molecules to man” evolution. In the face of increasing difficulty of evolutionists to account for speciation by weakening evidence for the traditional pillars of mutation and natural selection, we propose that naturalistic and theistic evolutionists reconsider their belief system concerning the history of life.

Dr. Stephen C. Meyer has repeated many comments and questions asked by theists as well as non-theists in our day. The question is not whether Intelligent Design theory is “scientific” according to science professionals. Those science professionals would say, “Intelligent Design is not scientific.” Many scientists, however, would agree with famous atheist chemist Linus Pauling, “Science is the search for the truth.” Therefore, a more appropriate question would be, “Is Intelligent Design true?”     

        

Cambrian Fossil Mystery

In June 2013 Dr. Stephen C. Meyer’s popular volume Darwin’s Doubt appeared on bookshelves. In their fervor to uphold the proposal that 19th century Darwinian theory had been established as a prominent scientific icon of the day, many contemporary critics of Intelligent Design (ID) attacked Meyer’s treatise as “unscientific.” Believers in common descent evolution are happy to join this popular chorus. Adherents of ID such as Meyer respond that the argument between evolutionists and ID theorists is not a classification discussion concerning what is science and what is non-science. Rather, Meyer appeals that the argument should remain “on point:” The on-point question is, “Are the claims of ID true?”

In any assertion that common descent evolution is true, we search for evidence that a slow progression of life forms from simple to complex has been manifest in the fossil record in a branching pattern. Ideally, the branching tree imagery should be clearly in evidence. The single trunk represents the initial common ancestor. The hypothesized complex multi-branched tree foliage represents today’s millions of species branching away from the common ancestor. However, precursor Pre-Cambrian fossils are not in evidence. Meyer calls this the “mystery of the missing fossils.”

Meyer’s series of interview programs on The John Ankerberg Show in July and August 2015 highlighted the startling evidence for a sudden inception of a large number of phyla never before seen. The sudden event was termed “The Cambrian Explosion.” This explosion of life forms was a geologically sudden appearance of complex structures such as compound eyes, spinal cords, and articulated limbs in a metaphorical blink of an eye. If we represent the entire duration of Earth’s planetary existence on a 24-hour clock, the Cambrian Explosion of new animals occurred at about the 21st hour and lasted only two minutes. A majority of the 36 phyla (major body plans) in existence today appeared quickly in the Cambrian period beginning 530 million years ago. Most of these phyla are still extant today.

Only a few life forms had appeared prior to the Cambrian. Fossils of blue-green algae floated on the oceans very early in Earth history. Sponges (porifera) appeared much later in the Pre-Cambrian, organized into colonies of cells. Other simple life forms existed. Then, a spectacular burst of innovation and diversity in animal forms appeared. The descriptive imagery of an “explosion” is entirely appropriate. It is also as though we awaken to a foggy morning and have it quickly replaced by spectacular sudden clarity with bright sunshine after the fog dissipates.

Darwin’s doubt about evolution originated in his early experience from 1831. Geologist Adam Sedgwick was assisted by Darwin as a young student at Cambridge University before his trips to the South Seas. An apparently dramatic event initially manifest in Cambrian rocks mystified the geologists. Sedgwick and Darwin had become curious about the enigma. Darwin’s mystification persisted until the end of his life but his Origin of Species theory had gripped him and many in the scientific world by that time. Perhaps the startling discoveries of many additional Cambrian fossils in the next century would have turned the tide of Darwin’s thinking. He died in 1882. 

Geologist R. G. McConnell had discovered “stone bugs” in the rocks on the slopes of Mt. Stephen in the Town of Shield, British Columbia in 1886. They were fossilized trilobites! In future explorations of the area a plethora of unique fossils was found in the Burgess Shale. In 1909 Charles Walcott made additional startling discoveries. His studies continued in that area for many years. Cambrian animals are examples of pure innovation in multiple body plans—a study in structural and functional creativity. In the 1970s a young geologist, Simon Conway Morris, began unlocking more secrets of the Burgess Shale fossil treasures; expanded discoveries of fabulous Cambrian animal diversity still continue. Preservation of soft body parts is astonishing.

But these animals are a puzzle, even according to avowed evolutionists such as Richard Dawkins: “It is though they were just planted there, without any evolutionary history.” Advocates of evolution expect to observe a gradually branching “evolutionary tree.” Branching evolutionary trees remain literary icons of evolutionary texts. Instead, an evolutionary “lawn” is in evidence—a sudden appearance of many individual, diverse specimens with little if any evidence of predecessors or transitional forms. This scenario was inscrutable for Charles Darwin. It is still enigmatic for modern evolutionary theorists, but they remain entrenched in optimism that evolution will ultimately be proven. To the present day the theory has not been proven. With time the theory may be headed for refutation instead of proof.

I close with a personal anecdote. In the summer of 2013 the Reasons to Believe organization sponsored a “Burgess Shale Adventure” in the Canadian Rockies. Among other visits to geological sites was a visit to the famous Burgess Shale site on Mt. Stephen in the town of Field, BC. The trip was led by scholars Hugh Ross and Fazale Rana. The 900m ascent on a 9 km, 7 hour hike up Mt. Stephen to the site of this world famous geological treasure proved more than challenging for me personally. The trek is aptly described as “strenuous.” My wife and I made it half way up before turning back. We settled for splitting a slab of trilobite-bearing shale provided by the Mount Burgess Geoscience Foundation guides when the hikers returned. Our memories consist of our personal “We were there” story: We hiked to within a few hundred feet of the Burgess fossil beds—one of the most famous geological sites attesting to divine creativity and intelligent design.