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.