Thursday, November 19, 2015

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.    


Monday, November 16, 2015

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:

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)  


Wednesday, November 11, 2015

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?

Thursday, November 5, 2015

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:

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.  




Friday, October 30, 2015

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.”  



Monday, October 26, 2015

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:

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:

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.   


Sunday, October 18, 2015

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.