Saturday, June 22, 2013

Seeing God in Nature

Our reference to the flow of genetic information is summarized by the famous biological flowchart DNAà RNA à Proteins. This representation is the essence of truth in the world of life forms. Knowledge of the world of biology radiates from this fundamental statement. If we experience wonder at our elementary awareness of this amazing sequence, we must keep in mind that even more extensive knowledge augments our wonder exponentially. Sometimes the wonder seems difficult to grasp, but a word of caution may be appropriate.

Carried to extremes, boundless overconfidence in our ability to “see” God and God’s actions in the natural world could amount to worship of nature. Some scientists and philosophers have erred in pronouncing that nature IS God--that the universe which surrounds us is identical with divinity. This extreme belief is termed pantheism.

We deal with the “interaction between science and Christianity” in our blog. Stated another way, we investigate “the harmony of scientific discoveries and Christian faith.” Many Christians are intimidated by this linkage for various reasons. We discuss three: (1) Intimidation may relate to simple dislike of the subjects of science and math. When my wife announces she is a math educator, it is surprising how many announce unashamedly that they did not care for math, or worse. The same phenomenon occurs with science, perhaps less frequently. (2) While interacting with our leaders in the church, we deal with various priorities ranging along their vision of gospel outreach--emphasis on conversion, social engagement, or fellowship and interpersonal relationships. (3) Lack of confidence exists in the truth of scientific conclusions ranging from the age of the earth, to evolution, to controversial findings in the field of medicine.

What shall we say to those who perceive that Albert Einstein’s exuberant pronouncement regarding his “rapturous amazement at the harmony of natural law” leads us to faith in God? In Einstein’s case, he declared his amazement to be a “religious feeling.” It is doubtful that Einstein ever developed a truly theistic worldview notwithstanding recognition of his religious feeling.

And what shall we say, then, to secular or religious friends who are not spiritually impacted by the wonders of DNA structure, RNA function, or the plethora of proteins and protein folding into particular shapes to accomplish specific bodily functions? Do we join with Einstein to proclaim our rapturous amazement without recognizing a divine Designer?

We recognize several simplified levels of awareness. One level sees nature as a god, but not the God of the Bible. At another level, fellow believers give lip service to the Creator, but other priorities prevent them from making this awareness a vital part of their apologetic scheme. At another stage of awareness, those who endorse theistic evolution may recognize God “created everything” at the beginning, but do not see the Creator taking an interventionist role since then. Finally, there are those filled with wonder at God’s creation of life, at the sudden creation events along the geologic timeline including the sudden creation of modern man in God’s image, and the phenomenal implications of DNAà RNAà Protein when fully understood.

The fourth awareness level in the paragraph above holds the most significant promise for promoting the “harmony of scientific discoveries and Christian faith.” We rely on a continuance of astonishing new discoveries to bring us ever closer to the knowledge of how the Creator of our physical universe has also acted to bring us to the knowledge of His loving plan of redemption.

Friday, June 21, 2013

Protein Fabricators

Biology textbooks summarize the flow of genetic information as follows: DNAà RNAà Protein. Our two previous posts dealt with the first two elements of this basic flowchart. Genetic inheritance begins with DNA. We did not always possess this knowledge. Arguments about the origin and flow of genetic information occurred even before the structure of the DNA molecule was discovered in 1953.

Protein had been suspected as the bearer of genetic information by many scientists in previous decades. The experiment of Avery, McCarty, and MacLeod in 1944 was reasonably conclusive that DNA was the hereditary material, but the biological world paid scant attention, occupied with other types of research. Knowledge of the trajectory of DNAà RNAà Protein has made its impact on science primarily within the lifetime of today’s baby-boomers.

If we are fascinated with knowledge of DNA’s encyclopedia of inheritance, or even with the wonder of the “messenger service” provided by mRNA and its counterparts, let us discuss our knowledge of protein fabrication as the final member of this fundamental biological trio. Perhaps it is the most fascinating member. A new term originated in 1997--proteomics--to describe the “large-scale study of proteins, particularly their structures and functions.” Knowledge of how the cells construct the proteins which comprise the structure and function of the bodies of living things is a fascinating prequel.

Imagine we were observers at a construction site, whether the building of our personal new residence or a skyscraper. Now envision a scenario where the builders do not merely fabricate the structure from previously prepared building materials such as wood, plastic, and metal already formed into shapes and sizes easily assembled. You must envision a building site where we observe the growth of the trees, learn about the manufacture of the plastics, and watch as the metal ores are refined.

Is this imaginary scenario unrealistic? Yes, it is. When we learn about the final step of protein formation in the cell, however, complexity of man-made building projects appears uncomplicated and simple by comparison. The mRNA leaves the nucleus of the cell with its coded directions for forming multiple proteins composed of just twenty amino acids. The mRNA will enter the protein manufacturing structures outside the nucleus, the ribosomes. These structures will link together the amino acids into unlimited numbers of chain structures.

Campbell and Reece in Biology, concerning the linkage of amino acids into chains, state, “The primary structure is like the order of letters in a very long word. If left to chance, there would be 20127 different ways of making a polypeptide chain 127 amino acids long. However, the precise primary structure of a protein is determined, not by the random linking of amino acids, but by inherited genetic information.” No more could we observe the processes of house-building or skyscraper-building crews and pronounce them the product of random chance than we could attribute the process of human body formation with its 100,000 or more different proteins--the correct ones--and deny the ubiquitous reality of divine intelligent design wherever we observe.

The long linear amino acid chains are manufactured and meticulously coiled and folded into specific three-dimensional shapes by the workhorse ribosomes. The biological principle of “form fits function” is a principle articulated in modern biology textbooks. The principle is thoroughly appropriate with respect to the folding of proteins. It applies to molecules, cells, tissues, organs, and complete organisms. “Form fits function” applies to every relationship between biological entities and their purpose, including the formation of proteins. Unique 3-D shapes endow the countless proteins comprising living things with a specific function.

This discussion merely scratched the outer surface of the flowchart topic DNAà RNAà Protein. Knowledge of the workings of the natural world is a good place to develop a rational apologetic for the reality of our omnipotent, omniscient, and thoroughly loving Heavenly Father.  


Tuesday, June 18, 2013

Obeying Your DNA

Many of man’s construction strategies originate from our knowledge of what takes place in the nucleus of living cells. The human DNA molecule, present in virtually every cell nucleus, is a genetic blueprint capable of replicating itself precisely over hundreds of generations. Animals and plants with short life spans have transferred their genetic information over countless thousands of generations.

DNA has the potential for affecting all activities of the organism but it does not actually build and assemble the proteins from which the body is constructed. In addition to providing structural support for the body, proteins function in everything organisms do. They speed up chemical reactions and manage storage, transport, communications, movement, and bodily defenses. This is far from a complete list. In two major leaps, however, we arrive at the building and assembling area where proteins accounting for more than 50% of the dry mass of most cells are assembled.

The first of the two major leaps is the synthesis of the RNA molecule under the direction of DNA. The double stranded DNA molecule is first pried apart. RNA nucleotides attach to one DNA strand which acts as a template for new RNA molecules. RNA is chemically similar to DNA. It usually consists of a single strand. It is a faithful replica of the important functions of DNA. This type of RNA is called mRNA, or messenger RNA. If DNA could give directions to RNA, it may say to the newly created mRNA molecule, “Now carry your protein-building instructions to the next building site: Travel out of the cell’s nucleus and find your way to the cytoplasm outside the nucleus. There, organelles called ribosomes will help assemble amino acids into the thousands of proteins needed by the body.”

The protein-building code carried by the RNA molecules occurs in the form of triplets of nucleotides (molecular assemblages). In biology the nucleotides in DNA are abbreviated A, G, C, or T. Just by chance, 64 occurrences of A, G, C, and T of any three letters could occur. GCA, for example, could occur as a nucleotide triplet followed by other triplets—all different, all the same, or repeated in any combination. But only a few dozen triplets, called codons, are needed to specify the 20 life-specific amino acids, because all proteins needed in the human body are composed of only 20 amino acids. Only a few dozen of these 20 different chemical triplets become “code” for specifying the 20 needed amino acids. All human protein is composed of combinations of these 20 amino acids.

When we speak of cracking the code of life during the 1960s, we look beyond the landmark discovery of Crick and Watson concerning the structure of DNA and its possible role in genetics in 1953. Incredible follow-up discoveries were yet to come. Determining the structure of the DNA molecule was an event of startling importance. Following this, scientists longed to discover the even more astounding physical mechanism of the cell’s ability to code for proteins. Given the knowledge that the human body contains 50,000 to 100,000 different proteins, the question of how those proteins were designated, manufactured, and assembled assumed more importance beyond mere satisfaction of scientific curiosity.

Marshall Nirenberg discovered the secret of the triplet code in 1961. Knowledge of the code for the syntheis of all the human body’s proteins from 20 amino acids was solved before the end of that decade. Hargobind Khorana and Robert W. Holley shared the Nobel prize with Nirenberg for physiology and medicine in 1968. A colorful Wikipedia entry on Khorana states, “With this, Khorana and his team had established that the mother of all codes, the biological language common to all organisms, is spelled out in three-letter words: each set of three nucleotides codes for a specific amino acid.”

We marvel at the limitless number of proteins necessary to assemble the human body. Sources quote numbers of different proteins in our bodies at far greater than 100,000. Each of millions of other species of earth life is constructed from a varied combination of proteins. Unlimited varieties of protein-forming amino acids are possible in unique linear chains. We are struck with wonder at the knowledge of the Creator who designed our planet and caused it to teem with life.


Wednesday, June 12, 2013

Information Duplicators

To prepare for this post we found ourselves chuckling about the antiquated duplicators of our childhood. In early primary grades our teachers used the ditto machine. Most copies were produced with a purple pigment. Fresh copies provided students with a captivating odor generated by the solvent used in the copying process. Perhaps my parents also used ditto worksheets. Ditto technology originated in 1910. One generation earlier my grandparents may have used practice sheets generated on a cutting edge mimeograph machine developed in 1884. A few years earlier carbon paper had made its debut and worked well with the advent of the typewriter in the 1870s.

Fast forward to the first years in my teaching career. My district provided the ditto machine for the production of classroom copies. Our school office used the difficult-to-use mimeograph machines. It produced many more copies at one sitting. Finally, in the early 1960s a close friend, using the newest equipment, produced multiple copies for me using a new Xerox copier at her place of employment. Cutting edge technology had finally provided the Xerox office printer with its ability to duplicate hundreds of copies cheaply and quickly. In a manner of speaking, the invention seemed “miraculous.” A century earlier hand copying was the only choice available.

In 1860, the year my maternal grandfather was born, the world of science knew nothing about a duplication method that all living materials had used since the creation of life. We speak of DNA--the genetic blueprint which preserves every physical feature of every living thing. It is found in virtually every cell of all creatures. On average the unraveled DNA molecule in each microscopic human cell is 2m long. Each DNA molecule has 3.2 billion base pairs, groups of molecules that function as a code for regulating the body and producing RNA which directs the fabrication of every tissue of the body from thousands of proteins. The total length of human DNA in all cells would reach from the earth to the sun and back multiple times.

Understanding the copying mechanism of DNA inspires deep reverence for the Creator. DNA information is copied to each cell as the body grows. When living things reproduce, the DNA preserves and passes on inheritance to the next generation. The fixity of species for uncounted millennia is testimony to the faithfulness of the copying mechanism. The copying mechanism of living things puts to shame the modern office technology I earlier pronounced “seemingly miraculous.” In reality, the various copying strategies of the machines in our offices and homes provide no legitimate comparison with the majesty of DNA.

The stranded double helix DNA molecule is able to “unstrand” at an appropriate time. An AP text, Biology, by Campbell and Reese, states “The two strands of the double helix are complementary, each the predictable counterpart of the other. It is this feature of DNA that makes possible the precise copying of genes that is responsible for inheritance. In preparation for cell division, each of the two strands of a DNA molecule serves as a template to order nucleotides into a new complementary strand. The result is two identical copies of the original double-stranded DNA molecule, which are then distributed to the two daughter cells. Thus, the structure of DNA accounts for its function in transmitting genetic information whenever a cell divides.”

We expand on our earlier statement that the various copying strategies of the machines in our offices and homes provide no legitimate comparison with DNA. Office machines copy information on a two-dimensional sheet of paper, but duplication of DNA results in a three-dimensional molecule identical to the original. Therefore, not only is the information duplicated, but so also is the structure. The stage is now set for discovering more wonderful processes beyond the role of DNA in future posts. The processes are summarized (1) DNA makes RNA, and (2) RNA makes protein. The hundreds of pages describing these processes in biology texts attest to the magnificence of God’s creation at the level of the micro cosmos. 


Friday, June 7, 2013

More than DNA

Radio commentator Paul Harvey (1918-2009) was famous for his “The Rest of the Story” segments. Sometimes people perceive an air of knowledge with clever emphasis on the introductory point in their discussion. We have referred to the well-known expression “It’s in our DNA.” Yes, there’s a basic glossary definition of DNA, the starting point in any discussion of genetic inheritance. But the sequel, the rest of the story, awaits discovery.

At a simple level, DNA could be described as a lengthy linear assemblage of common elements--simple atoms and molecules in virtually every body cell. This reductionist explanation is technically accurate. All physical and behavioral traits of the human body could be understood in terms of atoms of carbon, hydrogen, oxygen, nitrogen, and phosphorus, and the molecules they form. However, this account does not even come close to an explanation. The sequel to the story is a topic of majestic wonder.

We note that DNA is a nucleic acid. The DNA molecule is a macromolecule. It is composed of smaller molecular assemblages called nucleotides. Many nucleotides link together to build the polynucleotide we know as DNA. There are four types of nucleotides in DNA. They are adenine, thymine, guanine, and cytosine, abbreviated A, T, G, and C for short. These nucleotides always pair together: A with T, and C with G. Chemically, the nucleotides are bases. They are called, therefore, base pairs. AT or CG link together the two side rails of the double helix. These AT or CG pairs form “rungs” on the helix ladder, and occur in an infinite variety of sequences. The sequences may be compared with a digital code. We illustrate a two character digital code: 001101000111. Unlimited sequences of digits are possible either in our numeral example or in DNA base pairs.

As children we may have been fascinated by games using secret codes. The secret to “winning” was figuring out how to translate the meaning of the code. If we had the secret de-coder, we knew the location of a “treasure” we could not otherwise discover. The code, formerly a series of nonsense letters or symbols, became meaningful.

The base pairs of DNA macromolecules for each human are arranged in 3.2 billion “digits,” with an unlimited sequence of combinational possibilities. Bio-scientists have broken the code in the past 60 years. The code stores all genetic information for the individual, enables him or her to duplicate that information, and pass it along to the next generation. Ultimately the code provides information to build raw materials for thousands of different types of body tissues (proteins), and enables the body to assemble the materials in the correct way. This miracle occurs each time a new baby is conceived and born.

Coding DNA in the human genome provides the template for the materials of which our bodies are built. Coding DNA provides instructions for manufacturing and assembling many thousands of different proteins, the raw materials for building body tissue. Proteins are composed of twenty different amino acids. Non-coding DNA is also present in the human genome. Coding DNA is arguably the most interesting.

The majority of DNA in our bodies is the “non-coding” variety. Formerly, it was termed junk DNA because bio-scientists did not know its function. As time goes on, we know more of its function and more of the secrets of life God has authored at the level of the cell. The government supported ENCODE project, a product of the NHGRI (National Human Genome Research Institute), discovered that 80% of non-coding DNA has control and regulatory function within the cell. This trajectory of accumulated knowledge contrasts with biologists’ former belief that there was a large amount of DNA which served no function and was considered an evolutionary “left-over.” Almost all findings of molecular biology have become known in the lifetime of the grandparents of our high school and college students.

Let’s recall the traditional values communicated by Paul Harvey. Were Harvey to remark that “It’s in the DNA,” he may have expanded on the topic in his segment “The Rest of the Story.” The knowledge of DNA goes far beyond the introductory knowledge columnists and commentators provide. When the rest of the story is broadcast, we may understand that the ongoing discoveries in molecular biology point ever more clearly to the work of our Almighty God.

Our future posts will cover other small segments of “The Rest of the Story.”

Saturday, June 1, 2013

Describe or Explain?

The current blitz of 17-year cicada publicity brings to mind the desire of journalists to explain and justify their stories. What research did they access? What is the impact of the current insect outbreak? Is anything new being discovered? Very few new discoveries add to our basic knowledge of the stunning narrative of the 17-year cicada. The story has been playing out for centuries.

Some explanations for 17-year cicada behavior are speculative. Many journalists reinforce the ubiquitous proposal of evolution operating over distant eons of time. The 17 or 13 year interval supposedly conveyed an evolutionary advantage. One explanation concerns the insect’s resistance to shorter-lived parasites and predators they outlive. Both 17 and 13 are prime numbers, but what unknown meaning does this provide? Perhaps other evolutionary advantages accrued, scientists argue. It is interesting that naturalistic evolution, proposed to stand guard over life’s history like a sentry, always conveys an advantage to earth’s life forms according to the theory.

The ability to describe behavior of living things is easier than to explain it. It is more interesting to highlight unusual behavior than ordinary behavior. The 3000 cicada species and the millions of other animal species all have fascinating genetically programmed behaviors. “It’s in the genes” is an expression which realistically describes if not explains behavioral phenomena. Highly unusual animal behaviors keep the public aware of the awesome wonders of nature. It’s somewhat like a spectacular science demonstration for children designed to pique their interest in science.

Let’s return to the expression, “It’s in the genes.” Bio-scientists devote their lives to understanding genetic inheritance and how information is passed along from generation to generation. Genetic inheritance relates to (a) physical traits and (b) behavioral traits. The origin and cause of physical traits governing the appearance of a 17-year cicada are perhaps easier to attribute than the origin and cause of the animal’s behavioral traits. We recognize physical size, the red eyes, wing patterns, and the structure of its leg joints, for instance, as easier to attribute to genetic inheritance passed down from the parent than its ability to count 17 years unfailingly while tunneling underground. Manifestations of unique behaviors are not so easy to explain.

To appreciate how the flow of information in the cells of a cicada is responsible for reproducing the physical traits of a new generation of cicadas, we may compare the flow of information at the construction site of a new office building. The construction blueprint is incomprehensible to the average person. A construction engineer is able to decipher the specialized symbols and diagrams on the blueprint and translate them into a meaningful instructional tutorial for his workers. Part of the work crew will transport materials and others will assemble them into structures, but the engineer in charge oversees the project and provides guidance. The project foreman gives instructions on what, where, how, and when.

This simple analogy may aid us in over viewing the many tasks carried out by the genes of animals as simple as cicadas. Genes are discrete units of hereditary information in the cell. Gene units include DNA—the molecule from which all information for inheritance springs. Another expression indicating our understanding of inheritance, is the familiar “It’s in our DNA.”

If people are fascinated by spectacular natural phenomena, they may wish to consider the questions about which bio-scientists and bio-science journalists profess ignorance. Scientists writing about the function of genes and DNA explain how the blueprints of DNA code for the many thousands of proteins—the physical building blocks of all living creatures. Bio-scientists are at a loss to explain in detail some significant processes of protein assembly and function. What really happens and how does it happen? We end our discussion with one unanswered question: How does a special species of cicada count to 17? One journalist, writing about one such unknown, exclaimed, “It’s a trick we still do not understand.”