God Did It

God Did It -- An Argument from Ignorance or Evidence?
“But over centuries of research we have learned that the idea ‘God did it’ has never advanced our understanding of nature an iota, and that is why we abandoned it.” (Jerry Coyne)

In a recent essay in The New Republic, evolutionary scientist Jerry Coyne asked, “Does the empirical nature of science contradict the revelatory nature of faith? Are the gaps between them so great that the two institutions must be considered essentially antagonistic?” Coyne has no doubt that the answer is yes.

Religion is so hopelessly inimical to scientific progress that any attempt to reconcile them is futile. As Coyne explains, “Accepting both science and conventional faith leaves you with a double standard.” And to make sure you are clear on what religion is at issue, Coyne adds that “rational on the origin of blood clotting, irrational on the Resurrection; rational on dinosaurs, irrational on virgin births.”

God Did It – Science-Stopper?
Is the notion that “God Did It” even allowed in mainstream science? While hallowed bodies, like the National Academy of Sciences, claim publicly that faith and science do not conflict, privately, their “dirty little secret” is that religion is a science-stopper. Their public face, Coyne lets on, is all in the interest of maintaining public trust—one that is overwhelming religious and, professedly, Christian—and with it, public funding.

To the illuminati, a believer lumbers to the edge of every frontier of knowledge, poised to retire his investigations with “God did it!” contentment. Meanwhile, dead ends caused by their own faith in scientific materialism remain unexamined—the premature designation of “vestigial” organs and “junk” DNA being two examples.

Contrary to modern criticism, the scientist who approaches the world as a product of intelligence, rather than of matter and motion, is less likely to stop short of discovery. Instead of dismissing a feature that, at first glance, appears inert, unnecessary or just plain mystifying, he is more inclined the push the envelope of investigation to unravel its function and purpose.

Rather than obstructing science, Christianity, with its emphasis on a personal Creator, inspired an age of discovery that opened the way for science.

God Did It – Igniting Discovery
The ancients generally viewed the world as an unpredictable place governed by the fates or by the whims of the gods. But once investigators understood the universe as a creation—the work of a rational God embedded with rational principles—they dared to imagine that discovery was possible. One of the first was an astronomer whose theories ignited the scientific revolution.

Speculations about a sun-centered universe had been around for some time; but challenges to the Aristotelian model refined by Ptolemy didn’t gain serious attention until the “Copernican Turn” in the 16th century.

Nicolaus Copernicus was a Christian who understood the universe as an intelligible creation that operated according to mathematically coherent principles. His initial attraction to heliocentrism was not the result of new observational data, but of his notion that the sun—symbolic of God as Light and Lamp—seemed a fitful center of divine activity. He, along with other early researchers, believed that the elegant structure observed in creation should be describable in an elegant fashion. Thus, when heliocentrism proved more mathematically simple than the reigning earth-centered model, it gained a slow following.

Like Copernicus, Johannes Kepler was a man of faith who believed that the mysteries of nature could be unlocked with the key of mathematics. Kepler put it this way: “The chief aim of all investigations of the external world should be to discover the rational order and harmony which has been imposed on it by God and which He has revealed to us in the language of mathematics.”

Kepler’s belief in the mathematical precision of the universe led to his discovery of three fundamental laws of planetary motion—the foremost, that the planetary orbits are elliptical, rather than circular as modeled by Copernicus.

While the discovery of mathematical elegance was the product of faith for these pioneers, it has been the source of faith for others. In his book, Truth Decay, Douglas Groothuis shares the account of a Russian physicist: "I was in Siberia and met God there while working on my equations. I suddenly realized that the beauty of these equations had to have a purpose and design behind them, and I felt deep in my spirit that God was speaking to me through these equations." In that moment, the young scientist stepped over the chasm from atheism to theism and, ultimately, Christianity.

God Did It – On the Shoulders of Giants
Christians using science to show that “God Did It” remained in the vanguard of scientific discovery well into the 19th century. Groundbreaking advances in electro-magnetism, microbiology, medicine, genetics, chemistry, atomic theory, and agriculture were the works of men like John Dalton, Andre Ampere, Georg Ohm, Michael Faraday, Louis Pasteur, William Kelvin, Gregor Mendel, and George Washington Carver—all believers whose achievements were the outworking of their Christian faith.

Scientists in the truest sense of the word, these were investigators who doggedly followed the evidence wherever it led, approaching the gaps of understanding not with “God did it!” resignation, but with “God created it” expectation.

Whether they realize it or not, every scientist, including Jerry Coyne, stands on the shoulders of these giants. As German physicist Ernst Mach once acknowledged, “Every unbiased mind must admit that the age in which the chief development of the science of mechanics took place was an age of predominately theological cast.”

Science and Faith

Science and Faith – Filling the Gaps of Knowledge
When exploring questions of science and faith, it has become the default assumption among the smart set that there are two non-overlapping spheres of human understanding. One sphere is Nature, where star fish, starlets, and stars are reducible to elemental forms of matter and energy. Here, direct observation and the powers of reason and science make knowledge certain.

The other sphere is Supernature, populated by soul, spirits, God, and everything else originating from human imaginings, needs and yearnings. Beyond the reach of empirical examination, knowledge here is tenuous and uncertain.

The former is the realm of Facts, the latter the realm of Faith, and betwixt them, there is no connecting thoroughfare. Such was not always the case.

The early Greeks believed in a primal source of harmony that made the universe, in its diversity, a coherent whole. (The word “universe” contains the idea of “in the many, one.”) Accepting a common rational structure for the mind and the universe, they supposed that nature and knowledge were unified. Even “things unseen” were thought to be knowable through the powers of unaided reason.

The presumption of unity held sway until “hard” empiricism jettisoned the questions of ultimate causes to the Empyrean.

Science and Faith – From Unification to Bifurcation
As science and faith started its separation, reliance on reason alone led the Greeks to many false conclusions about the universe—aether, geocentrism, and spontaneous generation, to name a few. Corrections to those errors were held back for well over a millennium until the scientific method was introduced, adding experimentation to rational analysis.

The new, empirically based approach enabled the discovery of laws and mathematical relationships that described the workings of the universe with breathtaking accuracy. And with that came a new theory of knowledge.

Inspired by the smashing success of the scientific revolution, John Locke and George Berkeley concluded that the only reliable source of knowledge was empirical. Unlike the ancient and medieval rationalists who believed that the cognitive powers of the mind were sufficient for discovering the true nature of things, Locke and Berkeley insisted that knowledge stems from sensory experience. They insisted that the mind is a blank slate with no in-built organizing architecture. It is our senses that inform our mind, not the other way around. With each new game-changing discovery of science, rationalism fell deeper into the shadow of empiricism, until fully eclipsed by the “hard” empiricism of David Hume.

Undergirding the empiricism of Locke and Berkeley was the presumption that true knowledge was possible, even for things not directly accessible by sense perception, like physical laws, and abstract mathematical concepts like infinity. But David Hume said, “No!”

According to Hume, we have no access to physical laws; they are not implanted in us from birth, or writ large in the sky for all to read. All we have is a continuing stream of experiences from which we construct associations and relationships that have no necessary bearing on what is really real. We may have experienced a sunrise every morning, but that does not guarantee the sun will rise tomorrow. Without access to the true nature of things, we are left to form working assumptions to help us order our lives. Hume’s “hard” empiricism jolted Immanuel Kant out of his dogmatic slumbers.

To rescue rationalism from the onslaught of Hume, Kant synthesized it with empiricism by proposing that the mind comes endowed with faculties that give meaning to our experiences. This synthesis, Kant submitted, makes possible the identification of laws, even the moral law. But Kant’s deliverance of reason did not include the presumption of unity upheld by the early rationalists.

In the Kant schema, reality was split asunder into the phenomenal world and noumenal world. In the phenomenal were the things of the sensible universe, Nature; in the noumenal were the ultimate causes (the logos, the good, God) and the true nature of things (ideas, forms, spirit). For Kant, certain knowledge was only possible in the phenomenal.

In time, all of Supernature and the moral law (Kant would have been pained to learn) were pushed to the sphere of faith. The resultant fact-faith split had a tremendous influence on the gatekeepers of science. Caught up in the anti-clericism of the times, they sought to liberate science from the fetters of faith by reducing its scope to “natural” explanations. The result was scientific materialism.

But as we will see, materialistic science is far from faith-free.

Science and Faith – Faith All the Way Down
The bifurcation of science and faith comes down to this: The materialist operates on the belief that “nature is all there is.” The word “belief” signifies something that is not scientifically proven. In fact, this founding proposition is not scientifically proven nor provable because, given that only natural explanations are allowed, materialistic science depends on the very premises it is trying to demonstrate. Like all worldviews, scientific materialism is founded on a faith statement. But faith is not limited to its groundwork; it comprises its superstructure as well.

Consider one of the most familiar, and basic, features of nature: gravity. Like angels, heaven, and God, we can’t see, smell, taste, or touch gravity. Sure, we feel a pull toward earth, but we also “feel” a pull toward heaven. Even the most successful theories of gravity are not explanations, but descriptions that are wildly different.

In one pitch, gravity is an invisible force, associated with matter, mediated by who knows what—some say gravitons, which, by the way, have never been isolated, observed, or measured, but, nonetheless are a convenient placeholder for our ignorance. And talk about matter—no one knows why gravity is fond of it and not other things, like photons.

In another depiction, gravity is not a force but, rather, the topography spacetime shaped by the presence of matter. As one physicist puts it, “Matter tells space how to bend and space tells matter where to go.” Again, why does matter, and nothing else, have this effect? No one knows. More fundamentally, which came first, matter or space? If space, did it have no shape? If matter, did it occupy no space? To such tail-chasing, it seems, there is never an end.

That is not to take anything away from the formulations of these theories. Indeed, they have led to many space-age advancements. Yet the gravitational phenomena we observe, and the laws and equations that describe them, are independent of their explanation or ultimate cause. Whether the orbit of the earth is the result of an invisible force, a spacetime warp, or the guiding hand of Him in whom “all things hold together,” our observations and mathematical descriptions are unaffected. The explanation we accept is an exercise of faith, not a demonstration of fact. The same goes for the common-day forces of magnetism and electricity.

When we drill down to subatomic dimensions, we enter a world of bare faith. Quarks, electrons, and muons, and the nuclear forces that control them, are foreign to anything we know from everyday experience. And the infinitesimal scales involved make direct examination impossible. Everything we “know” comes from particle accelerator—that is, “atom-smashing”—experiments.

As a working approximation, imagine riddling a steel box with an AK-47, then trying to reconstruct the mystery object inside by piecing together the resulting shrapnel. Because we do not know how the strafing affected the object in its undisturbed state, our reconstruction is based on inference. The same goes for our depictions of the atomic world, with a little fancy thrown in the mix.

For example, there is a whole category of stuff in the quantum realm labeled “virtual.” It includes subnuclear-sized particles and photons that have never been detected and, indeed, do not exist except as ethereal abstractions in the minds of physicists to make sense of phenomena that make no sense without them.

Even the quantum field, which is credited with preventing the annihilation of matter by keeping the negatively charged electron cloud from combining with the positively charged nucleus, is nothing more than a rarefied label for something (the stability of matter) that is, materialistically speaking, inexplicable.

Science and Faith – A Matter of Worldview
Indeed, science and faith coexist. From the cosmic scale of gravity down to the micro scale of the atom, faith undergirds scientific knowledge—faith in materialism. Nowhere is that more candidly expressed than in the words of evolutionary biologist Richard Lewontin: “We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises . . . because we have a prior commitment, a commitment to materialism.”

For those whose faith will not be shaken by patent absurdities, astrophysicist Robert Jastrow warns that “the story ends like a bad dream.” After their final ascent on the mountain of discovery, they peer over the horizon to see a group of theologians who have been awaiting their arrival for a long, long time.

Theory of Relativity

Theory of Relativity – A Brief History
The Theory of Relativity, proposed by the Jewish physicist Albert Einstein (1879-1955) in the early part of the 20th century, is one of the most significant scientific advances of our time. Although the concept of relativity was not introduced by Einstein, his major contribution was the recognition that the speed of light in a vacuum is constant and an absolute physical boundary for motion. This does not have a major impact on a person's day-to-day life since we travel at speeds much slower than light speed. For objects travelling near light speed, however, the theory of relativity states that objects will move slower and shorten in length from the point of view of an observer on Earth. Einstein also derived the famous equation, E = mc², which reveals the equivalence of mass and energy.

When Einstein applied his theory to gravitational fields, he derived the "curved space-time continuum" which depicts the dimensions of space and time as a two-dimensional surface where massive objects create valleys and dips in the surface. This aspect of relativity explained the phenomena of light bending around the sun, predicted black holes as well as the Cosmic Microwave Background Radiation (CMB) -- a discovery rendering fundamental anomalies in the classic Steady-State hypothesis. For his work on relativity, the photoelectric effect and blackbody radiation, Einstein received the Nobel Prize in 1921.

Theory of Relativity – The Basics
Physicists usually dichotomize the Theory of Relativity into two parts.

• The first is the Special Theory of Relativity, which essentially deals with the question of whether rest and motion are relative or absolute, and with the consequences of Einstein’s conjecture that they are relative.
  
• The second is the General Theory of Relativity, which primarily applies to particles as they accelerate, particularly due to gravitation, and acts as a radical revision of Newton’s theory, predicting important new results for fast-moving and/or very massive bodies. The General Theory of Relativity correctly reproduces all validated predictions of Newton’s theory, but expands on our understanding of some of the key principles. Newtonian physics had previously hypothesised that gravity operated through empty space, but the theory lacked explanatory power as far as how the distance and mass of a given object could be transmitted through space. General relativity irons out this paradox, for it shows that objects continue to move in a straight line in space-time, but we observe the motion as acceleration because of the curved nature of space-time.

Einstein’s theories of both special and general relativity have been confirmed to be accurate to a very high degree over recent years, and the data has been shown to corroborate many key predictions; the most famous being the solar eclipse of 1919 bearing testimony that the light of stars is indeed deflected by the sun as the light passes near the sun on its way to earth. The total solar eclipse allowed astronomers to -- for the first time -- analyse starlight near the edge of the sun, which had been previously inaccessible to observers due to the intense brightness of the sun. It also predicted the rate at which two neutron stars orbiting one another will move toward each other. When this phenomenon was first documented, general relativity proved itself accurate to better than a trillionth of a percent precision, thus making it one of the best confirmed principles in all of physics.
Applying the principle of general relativity to our cosmos reveals that it is not static. Edwin Hubble (1889-1953) demonstrated in 1928 that the Universe is expanding, showing beyond reasonable doubt that the Universe sprang into being a finite time ago. The most common contemporary interpretation of this expansion is that this began to exist from the moment of the Big Bang some 13.7 billion years ago. However this is not the only plausible cosmological model which exists in academia, and many creation physicists such as Russell Humphreys and John Hartnett have devised models operating with a biblical framework, which -- to date -- have withstood the test of criticism from the most vehement of opponents.

Theory of Relativity – A Testament to Creation
Using the observed cosmic expansion conjunctively with the general theory of relativity, we can infer from the data that the further back into time one looks, the universe ought to diminish in size accordingly. However, this cannot be extrapolated indefinitely. The universe’s expansion helps us to appreciate the direction in which time flows. This is referred to as the Cosmological arrow of time, and implies that the future is -- by definition -- the direction towards which the universe increases in size. The expansion of the universe also gives rise to the second law of thermodynamics, which states that the overall entropy (or disorder) in the Universe can only increase with time because the amount of energy available for work deteriorates with time. If the universe was eternal, therefore, the amount of usable energy available for work would have already been exhausted. Hence it follows that at one point the entropy value was at absolute 0 (most ordered state at the moment of creation) and the entropy has been increasing ever since -- that is, the universe at one point was fully “wound up” and has been winding down ever since. This has profound theological implications, for it shows that time itself is necessarily finite. If the universe were eternal, the thermal energy in the universe would have been evenly distributed throughout the cosmos, leaving each region of the cosmos at uniform temperature (at very close to absolute 0), rendering no further work possible.

The General Theory of Relativity demonstrates that time is linked, or related, to matter and space, and thus the dimensions of time, space, and matter constitute what we would call a continuum. They must come into being at precisely the same instant. Time itself cannot exist in the absence of matter and space. From this, we can infer that the uncaused first cause must exist outside of the four dimensions of space and time, and possess eternal, personal, and intelligent qualities in order to possess the capabilities of intentionally space, matter -- and indeed even time itself -- into being.

Moreover, the very physical nature of time and space also suggest a Creator, for infinity and eternity must necessarily exist from a logical perspective. The existence of time implies eternity (as time has a beginning and an end), and the existence of space implies infinity. The very concepts of infinity and eternity infer a Creator because they find their very state of being in God, who transcends both and simply is.

Origin of Species

Origin of Species - Darwin's Classic Work
Origin of Species is the abbreviated, more commonly-known title for Charles Darwin's classic, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. British naturalist Charles Darwin (1809-1882) began drafting Origin of Species in 1842, just six years after returning from his fateful five-year voyage aboard the HMS Beagle (1831-36). Heavily influenced by Sir Charles Lyell's Principles of Geology (1830-1833, a three volume work) and Thomas Malthus' An Essay on the Principle of Population (1798), Origin of Species was ultimately published in 1859.

Origin of Species - Natural Selection
In Origin of Species, Charles Darwin introduced the concept of natural selection. Natural selection is a natural process which acts to preserve and accumulate minor advantageous variations within living systems. Suppose a member of a species were to develop a functional advantage (a reptile grew wings and learned to fly: an obvious advantage his earth-bound relatives couldn't enjoy); its offspring would inherit that advantage and pass it on to future offspring. Natural selection would act to preserve the advantageous trait. Essentially, natural selection is the naturalistic equivalent to domestic breeding. Over the centuries, human breeders have produced dramatic changes within domestic animal populations simply by selecting individuals to breed. They have been able to accentuate desirable traits (given the trait is already present in the creature's genetic code) and even suppress undesirable traits gradually over time. The difference between domestic breeding and natural selection is this: rather than human breeders making the selections, nature itself is the selector.

Darwin made a keen observation but he drew a poor conclusion. He thought that since natural selection can and does produce slight variations within animal populations it should therefore be able to explain all of the variety we observe in biology. He concluded that since natural selection explains variety, all life must somehow be related, everything ultimately having evolved from some sort of common ancestor. "It is a truly wonderful fact-the wonder of which we are apt to overlook from familiarity-that all animals and all plants throughout all time and space should be related to each other…" [1] Darwinists have even gone so far as to suggest that this common ancestor somehow evolved from non-living matter (which they presume to be some kind of dirty-water soup-like composition). Well, this whole idea of the birds and bananas, the fish and the flowers, all being related, and life evolving from non-life… may have seemed remotely plausible back in the 1800s. Modern biology was still in its infancy and the living cell was still thought to be nothing more than a simple blob of protoplasm. Gregor Mendell (1822-1884) had only just begun exploring the principles of heredity and it wasn't until the late 1850's that Luis Pasteur (1822-1895) sought to disprove the abiogenesis fallacy. But thanks to the foundations laid by these great men of science (both of whom opposed Darwinian evolution) and in light of the tremendous advances we've made in molecular biology, biochemistry and genetics, especially over these past fifty years, the flaws in Darwin's theory standout quite clearly. For example, we've established that genetic barriers exist. Pigs will never fly! Yes, there are degrees of variation. Different skin tones, facial features, eyes colors, hair types, etc. You could have a big dog or a small dog, a dog with long or short hair. But no kind of dog will ever produce a non-dog! Birds and bananas aren't distant cousins! As far as life arising from non-life (abiogenesis), the mechanisms are fairly well known and the bottom line is this: certain chemical constraints make abiogenesis an impossible event.

Origin of Species - Henslow's Advice
If ever you find yourself sitting down to read Darwin's Origin of Species, keep in mind John Stevens Henslow's (1796-1861) advice to the young Charles Darwin. Henslow was one of Darwin's professors at Cambridge. In fact, it was Henslow who recommended Darwin to Captain Robert FitzRoy (1805-1865) of the HMS Beagle. Before Darwin set sail, Henslow recommended that he take Sir Charles Lyell's Principles of Geology. Lyell's book had a profound impact upon the young Charles and its influence is seen throughout Darwin's work. Henslow advised Darwin, "By all means read it for the facts, but on no account believe the wild theories." [2] We seek to pass this advice on to you. By all means read it for the facts, but on no account believe the wild theories.

DNA Double Helix

DNA Double Helix: A Recent Discovery of Enormous Complexity
The DNA Double Helix is one of the greatest scientific discoveries of all time. First described by James Watson and Francis Crick in 1953, DNA is the famous molecule of genetics that establishes each organism's physical characteristics. It wasn't until mid-2001, that the Human Genome Project and Celera Genomics jointly presented the true nature and complexity of the digital code inherent in DNA. We now understand that each human DNA molecule is comprised of chemical bases arranged in approximately 3 billion precise sequences. Even the DNA molecule for the single-celled bacterium, E. coli, contains enough information to fill all the books in any of the world's largest libraries.
DNA Double Helix: The "Basics"
DNA (deoxyribonucleic acid) is a double-stranded molecule that is twisted into a helix like a spiral staircase. Each strand is comprised of a sugar-phosphate backbone and numerous base chemicals attached in pairs. The four bases that make up the stairs in the spiraling staircase are adenine (A), thymine (T), cytosine (C) and guanine (G). These stairs act as the "letters" in the genetic alphabet, combining into complex sequences to form the words, sentences and paragraphs that act as instructions to guide the formation and functioning of the host cell. Maybe even more appropriately, the A, T, C and G in the genetic code of the DNA molecule can be compared to the "0" and "1" in the binary code of computer software. Like software to a computer, the DNA code is a genetic language that communicates information to the organic cell.

The DNA code, like a floppy disk of binary code, is quite simple in its basic paired structure. However, it's the sequencing and functioning of that code that's enormously complex. Through recent technologies like x-ray crystallography, we now know that the cell is not a "blob of protoplasm", but rather a microscopic marvel that is more complex than the space shuttle. The cell is very complicated, using vast numbers of phenomenally precise DNA instructions to control its every function.

Although DNA code is remarkably complex, it's the information translation system connected to that code that really baffles science. Like any language, letters and words mean nothing outside the language convention used to give those letters and words meaning. This is modern information theory at its core. A simple binary example of information theory is the "Midnight Ride of Paul Revere." In that famous story, Mr. Revere asks a friend to put one light in the window of the North Church if the British came by land, and two lights if they came by sea. Without a shared language convention between Paul Revere and his friend, that simple communication effort would mean nothing. Well, take that simple example and multiply by a factor containing many zeros.

We now know that the DNA molecule is an intricate message system. To claim that DNA arose by random material forces is to say that information can arise by random material forces. Many scientists argue that the chemical building blocks of the DNA molecule can be explained by natural evolutionary processes. However, they must realize that the material base of a message is completely independent of the information transmitted. Thus, the chemical building blocks have nothing to do with the origin of the complex message. As a simple illustration, the information content of the clause "nature was designed" has nothing to do with the writing material used, whether ink, paint, chalk or crayon. In fact, the clause can be written in binary code, Morse code or smoke signals, but the message remains the same, independent of the medium. There is obviously no relationship between the information and the material base used to transmit it. Some current theories argue that self-organizing properties within the base chemicals themselves created the information in the first DNA molecule. Others argue that external self-organizing forces created the first DNA molecule. However, all of these theories must hold to the illogical conclusion that the material used to transmit the information also produced the information itself. Contrary to the current theories of evolutionary scientists, the information contained within the genetic code must be entirely independent of the chemical makeup of the DNA molecule.
DNA Double Helix: Its Existence Alone Defeats any Theory of Evolution
The scientific reality of the DNA double helix can single-handedly defeat any theory that assumes life arose from non-life through materialistic forces. Evolution theory has convinced many people that the design in our world is merely "apparent" -- just the result of random, natural processes. However, with the discovery, mapping and sequencing of the DNA molecule, we now understand that organic life is based on vastly complex information code, and such information cannot be created or interpreted without a Master Designer at the cosmic keyboard.

Intelligent Design

Intelligent Design - Machines
Intelligent Design is obvious upon close examination of any machine. The concept and design inherent in a machine, whether simple or complex, is self-evident. Whether a machine is high quality or low quality, its designer is both necessary and apparent. Information Theory states that concept and design can only result from a mind. Even the diminished quality of a poorly constructed machine cannot obscure the necessity of an intelligent designer. Machines, as defined by French Biochemist and Nobel Laureate Jacques Lucien Monod (1910-1976), are "purposeful aggregates of matter that, utilizing energy, perform specific tasks." By this authoritative definition, living systems are recognized as machines. A living organism fulfills the definition of a machine all the way down to the molecular level. And yet, because of the philosophical and religious implications of life resulting from Intelligent Design, a surprisingly large portion of the intelligentsia seek to find a mechanism by which life may arise naturally by random chance. Evolutionists admit the inconsistency. George Wald, an evolutionist, states, "When it comes to the origin of life there are only two possibilities: creation or spontaneous generation. There is no third way. Spontaneous generation was disproved one hundred years ago, but that leads us to only one other conclusion, that of supernatural creation. We cannot accept that on philosophical grounds; therefore, we choose to believe the impossible: that life arose spontaneously by chance!" ("The Origin of Life," Scientific American, 191:48. May 1954).

Intelligent Design - Life
Ignoring the obvious Intelligent Design that permeates life, scientists have developed the theory of evolution in an effort to explain the origin of life via spontaneous generation. This "scientific" theory is very distinctive. Commonly, scientists observe data, interpret the data, and then formulate conclusions based upon that data. Yet, evolutionists have formulated their "scientific" conclusion without resorting to any data at all. In fact, evolutionists have steadfastly maintained their conclusion despite data to the contrary.

Intelligent Design - Education
Evidence indicating Intelligent Design is abundant and overwhelming. Since the reemergence of evolutionary thought in the last two hundred years (popularized by Darwin's Origin of Species in 1859), evolutionists have zealously sought evidence to validate their theory. Nothing has yet to stand up under the close scrutiny of an in depth scientific evaluation. And yet, curiously, evolutionary thought prevails in the mainstream. Thus, evolutionary "scientists" have disposed of true science, and replaced it with philosophy and imagination. "In fact, evolution became in a sense a scientific religion; almost all scientists have accepted it, and many are prepared to 'bend' their observations to fit with it." (H.S. Lipson, Professor of Physics, University of Manchester, UK, "A Physicist Looks at Evolution," Physics Bulletin, vol. 31, May 1980, pg.138). Since the beginning of the modern evolutionary movement, quite a few fraudulent evidences in favor of evolution have been submitted and remain in the textbooks, despite their exposure as blatant deceptions. Ernst Haeckel's work is an appropriate example. Haeckel, a German embryologist, altered drawings of various animal and human embryos, making them nearly identical. He presented his altered pictures as evidence for evolution between species, and used them as a platform to successfully promote evolution. In 1874, Haeckel's drawings were exposed as frauds by renowned embryologist Wilhelm His. Shortly thereafter, Haeckel was convicted of fraud by his own university. Yet his fallacious drawings of nearly identical embryos are still in science textbooks over 100 years later as evidence for evolution! Those drawings are being taught to kids in school today as evidence for evolution. Why? Why not present real evidence? Because there is none! David M. Raup, an evolutionist, freely admits, "In the years after Darwin, his advocates hoped to find predictable progressions. In general, these have not been found -- yet the optimism has died hard, and some pure fantasy has crept into textbooks." ("Evolution and the Fossil Record," Science, vol. 213, July 1981, pg. 289). It seems that "pure fantasy" is the politically correct term for "calculated lies."

Intelligent Design - DNA
An excellent example of intelligent design is the DNA molecule. Since its discovery by James Watson and Francis Crick in 1953, evolutionists have faced an insurmountable hurdle. Anyone who truly investigates the mystery of the DNA molecule -- this incredible micro, digital, error-correcting, redundant, self duplicating, information storage and retrieval system, with its own inherent language convention, that has the potential to develop any organism from raw biological material -- understands that life is the result of Intelligent Design. In light of recent discoveries such as the DNA molecule, the absurdity of the evolution argument is readily apparent when its basic formula is compared with that of the creation model of origins. Creation states that matter + energy + information = incredibly complex life. Evolution states that matter + energy + random chance = incredibly complex life. The theory of evolution is merely a religion that serves to discredit the Intelligent Designer Himself.

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The Cambrian Explosion

The Cambrian Explosion – Biology’s Big Bang?
The Cambrian Explosion relates to an abrupt appearance of a wide range of organisms, mainly invertebrates, with hard (fossilizable) parts in Cambrian strata which mainstream scientists date from about 540 million years ago. They were complex, well-developed organisms with many types of differentiated cells, and it is widely conceded that evolution of these organisms from unicellular precursors within such a short period of time is highly doubtful.

Now, it can be granted that organisms without skeletons will leave few if any fossils, so it should not be too surprising if one evolving line were to appear suddenly in the fossil record. It is surprising, however -- at least within an evolutionary framework -- that such a wide variety of fossilizable forms should appear at more or less the same time. The number of radically different body plans which appear in such a very short period of geological time (about 13 million years) is greater than at any other. Accounting for the abrupt and sudden appearance of these organisms is one of the leading challenges in evolutionary biology.

The Cambrian Explosion – Is it curtains for Darwinism?
There are two principle options which are invoked in an effort to account for the sudden diversity: (1) the different forms arose at the start of the Cambrian from a single common stock from which the various forms radiated, or (2) the divergence happened much earlier. If they diverged at the beginning of the Cambrian then it does some way to explaining the absence of preceding fossils but then it remains inexplicable how the wide divergence of characteristics occurred so suddenly, i.e. that the various phyla appear so different as to be unrelated. If, on the other hand, they diverged considerably before the Cambrian era (so as to allow for the divergence of various forms, then it is extraordinary that all the various lines should reach a fossilizable stage at much the same time.

One example of a Cambrian-appearing organism is the sponge. There are four classes of sponges, all of which appear abruptly in the Cambrian. Despite a relatively unspecialized structure, the classes are distinct and difficult to relate to one another. There is no sign of intermediary fossils and there is certainly no consensus as to how they could potentially have evolved from a common ancestor. Despite their primitive form, the sponges are quite separate from the rest of the animal kingdom.

Similarly, as far as the arthropods are concerned, the different subphyla of trilobites, horseshoe crabs and crustaceans arise in the Cambrian. Furthermore, the crustaceans are exceedingly diverse. All four major classes of the crustaceans and many lower taxa are found in the Cambrian; but, again, despite this multitude of fossils, no trace can be found of any transitional forms which would link the different groups to a common ancestor.

One attempt to account for the Cambrian explosion involves the proposal that there was a substantial increase in oxygen about this time which stimulated rapid evolutionary progress -- but such a suggestion ignores the sheer improbability of biological macromolecules, whether oxygen is plentiful or not. The enigma is compounded because, not only do different phyla appear suddenly, but also -- within most of the phyla -- very distinct classes arise, again at more or less the same time.

The Cambrian Explosion – Summary
In summary, what is generally proposed, is the extraordinary coincidence that these diverse types of organism with their radically different skeletons all reached fossilizable stage within a relatively short period of time. The Cambrian explosion raises the kinds of questions that occur repeatedly regarding the fossil record. First is that major new types of organism appear suddenly and abruptly. Second, many different lines, exhibiting the same sort of significant development, arise about the same time. There exists such a radical diversity that it becomes implausible that they shared a recent common ancestor. It also seems unrealistic that the same sort of advance could have arisen independently in several lines, especially simultaneously.

Scientific Method

Scientific Method – A brief history
It is often overlooked that the scientific method was actually developed in Christian Europe by men who believed that matter behaved in a rational manner because God had created an orderly universe. If the universe exists in a strictly materialistic vacuum, the product of random particle collisions, then there is no foundation upon which one can expect to observe order in nature. Many of the founders of the principle scientific disciplines (such as Newton, Galileo and Kepler), were Bible-believing Christians. Johannes Kepler -- one of the founders of the discipline of astronomy -- said that science was “thinking God’s thoughts after him.”

Scientific Method – Why is it important?
The scientific method can be divided into two primary categories: (1) empirical science and (2) historical science. Empirical science entails a systematic approach to epistemology that uses observable, testable, repeatable, and falsifiable experimentation to understand how nature commonly behaves. It finds its implementation in such disciplines as immunology, rocket science, molecular biology, etc. Historical science involves the interpretation of evidence and the deduction of past occurrences, which is normally based upon an underlying supportive paradigm.

Recognizing that every person has presuppositions that shape the way in which empirical evidence is interpreted is important. Theists and non-theists possess the same evidence; but that evidence is interpreted within a framework which corresponds to the individual’s respective worldview.

In its original form, ‘science’ could simply be defined as ‘knowledge’. Today, however, science -- in the view of an outspoken part of the scientific enterprise -- is the systematic method of gaining knowledge about the universe with reference to purely naturalistic or materialistic causation. Science in this sense automatically rules out the notion of God because supernatural claims -- it is asserted -- cannot be tested and repeated. If an idea is not testable, repeatable, observable and falsifiable, it is not considered scientific.

The problem with the above definition of science is that, even though naturalistic science claims to be neutral and unbiased, it starts with a set of basic metaphysical axioms -- that only matter and energy exist and all explanations and causes must be directly related to the laws that matter and energy follow. Many scientists have claimed that allowing supernatural explanations into our understanding of the universe would cause us to stop searching for answers and simply invoke a “god-of-the-gaps”. This is, of course, false.

The design inference is not based upon a lack of knowledge (as some would contend), but rather it is based upon our uniform and repeated experience. While we know of no naturalistic cause by which complex and specified biological information can arise from inorganic matter, we do know that in all other circumstances information originates from intelligence. Moreover, many scientists now see evidence of intelligent design in the ‘irreducible complexity’ of molecular machines and circuits in the cell, the pattern of appearance of the major groups of organisms in the fossil record, the fine-tuning of the laws and constants of physics to support complex life, the fine tuning of our terrestrial environment, the information processing system of the cell, and even the phenomenon known as ‘homology’ (evidence previously thought to provide unequivocal support for neo-Darwinism).

Scientific Method – Conclusion
While critics may disagree with the conclusions of the design arguments, they cannot reasonably deny that they are based upon commonly accepted observations of the natural world. The term ‘science’ commonly connotes an activity in which theories are developed to explain observations of the natural world, the empirical, observational basis of the theory of intelligent design provides a good reason for regarding intelligent design as a scientific theory.

RNA world

RNA world – An Introduction
The RNA world hypothesis is an attempt to provide an adequate answer to problems facing origin-of-life researchers in relation to the original information storage medium on primitive earth. DNA is responsible for housing the information that the cell requires to fold proteins into the correct shape critical to their respective function. Practically every cellular and extracellular structure is constructed from proteins. Given this importance, the information housed in DNA defines life’s most fundamental operations and structures.

When cells undergo replication, DNA and the information it stores is copied and subsequently passed on to the daughter cells. Biochemical blueprints are conveyed to the next generation through DNA replication. This process generates two ‘daughter’ molecules which are identical to the ‘parent’ DNA molecule. Once replication is complete, the two generated DNA molecules are distributed between the daughter cells produced during cell division.

Building proteins requires genetic information in DNA, but information in DNA cannot be processed without many specific proteins and protein complexes. Mutual interdependence of DNA and proteins has stood as a major stumbling block for Darwinian paradigms with regards to life’s origin since the mid-1980’s. Origin-of-life researchers even refer to this conundrum as the chicken-and-egg paradox. Because proteins are so fundamental to the means by which DNA replicates, DNA and proteins could not simultaneously arise from a primordial soup.

RNA world – A Solution?
The RNA world hypothesis has been proposed as a resolution to this paradox. This model maintains that RNA preceded DNA and proteins as the initial fundamental information storage medium. RNA can simultaneously store information (like DNA) and catalyse chemical reactions (like proteins). Thus it is contended that the RNA world eventually evolved into the DNA-protein world of contemporary biochemistry, with RNA currently functioning as an intermediary between DNA and proteins.

While the RNA-world hypothesis sidesteps the need for an interdependent system of DNA and proteins in the earliest living system on paper, in practical terms it appears largely untenable. Numerous difficulties abound for the RNA world hypothesis. For example, the formation of the first RNA molecule would have necessitated the prior emergence of smaller constituent molecules, including ribose sugar, phosphate molecules, and the four RNA nucleotide bases. It turns out, however, that both synthesizing and maintaining these essential RNA building molecules (particularly ribose) and the nucleotide bases is profoundly problematic, if not impossible to perform under realistic prebiotic conditions.

Another major difficulty confronting proponents of the RNA-world hypothesis is that naturally occurring RNA molecules possess very few of the specific enzymatic properties of proteins. Ribozymes can perform a small handful of the thousands of functions performed by proteins.

The inability of RNA molecules to perform many of the functions of protein enzymes raises a third and related concern with regards to the tenability of the RNA-world paradigm. To date, no plausible explanation has been advanced as to how primitive self-replicating RNA molecules could have made the transition into modern cellular systems which rely heavily on a variety of proteins to process genetic information. Consider the transition from a primitive replicator to a system for building the first proteins. Even if such a system of ribozymes for building proteins had arisen from an RNA replicator, that system of molecules would still require information-rich templates for building specific proteins. There is no foreseeable account of the origin of that information.

RNA world – Conclusion
In summary, RNA can perform only a few minor functional roles and even then usually as the consequence of researchers intentionally ‘engineering’ the RNA catalyst in question. Even in the face of extreme difficulty, most neo-Darwinians remain convinced that the RNA world must have existed, subsequently paving the way for the DNA-protein world. If it did not, the chicken-and-egg paradox -- from a materialistic perspective -- cannot be resolved.

Multiverse

Multiverse – A brief overview
The multiverse concept is founded upon the idea that what we have hitherto considered to be “the universe” is but a small component of a vast assemblage of universes. According to the multiverse thesis, each universe may differ with regards to their physical laws, in such a way that all conceivable constants and laws are represented in a universe somewhere. The hypothesis is intimately associated with the so-called Anthropic Principle, which states that our own existence acts as a selection principle determining which properties of the universe we can observe. That is to say, any observed properties of the universe which may at first seem to be astonishingly improbable can only be seen in their true perspective after we realize that other properties couldn’t be observed by us, since we can only observe properties of the universe which are conducive to our own existence. The Anthropic Principle is thus used by many people, often in conjunction with the Multiverse principle, to show why we shouldn’t be surprised at the astonishingly improbable fine-tuning of the universe for intelligent life.

Multiverse – The problems
The multiverse explanation is highly problematic. Perhaps the biggest difficulty is that the existence of such parallel universes can be neither verified nor falsified. The model is thus ad hoc and contrived. Second, given that the biofriendliness of the universe is in no way conducive to cosmic sustainability, no form of selection process or “cosmic evolution” can be invoked. Third, if the multiverse thesis is to commend itself as a plausible hypothesis, then a mechanism for generating such universes needs to be advanced. The concept of a ‘bubble’ of universes, each with their own fundamental constants and values, only throws the paradox back one step -- as one could easily ask who built the generator to give rise to this cosmic lottery.

Roger Penrose of Oxford University has calculated that the odds of our universe’s low entropy condition obtaining by chance alone are on the order of 1:10¹²³, an inconceivable number. If our cosmos were indeed but one member of a much vaster multiverse of randomly ordered worlds, then it is vastly more probable that we should be observing a much smaller universe. The probability of our solar system forming randomly is about 1:10⁶⁰, a vast number but inconceivably smaller than 10¹²³.

Science is founded on the notion of the rationality and uniformity of nature. The universe is ordered in a rational way, and scientists seek reasons for why things are the way they are. If the universe as a whole is without transcendency or purpose, then it exists without reason. It is therefore ultimately arbitrary and absurd. We are subsequently invited to contemplate a state of affairs in which all scientific chains of reasoning are ultimately grounded in absurdity. The concept of a cosmic order would then have no foundation. Thus, the multiverse theory undercuts the very premise upon which the scientific method is founded.

All this has been said, of course, without asking whether the multiverse itself must not exhibit some degree of cosmic fine-tuning in order to exist. If it does, as some have argued, then it is a non-starter as an alternative to design.

Multiverse – Conclusion
Without a scientifically rigorous means by which such a multiverse concept can be tested, verified and falsified, the idea remains as but a conjecture -- a fudge factor invoked merely to evade the apparent design of our cosmos. In addition, the idea suffers from a number of scientific difficulties and problems -- but a handful of which are discussed herein.

Whereas one knows that one universe exists, one does not -- nor can -- know whether more than one universe exists. Once observers exist in universe A, the theory of general relativity indicates that the space-time envelope of that universe can never overlap the space-time envelope of any other possibly existing universe. In other words, even if God made ten universes, we would forever lack the scientific means to detect any universe besides our own. The sample size of universes therefore is limited to one. Thus, the only rational option is that there exists only one universe and that God exquisitely designed the universe for the benefit of mankind.

Large Hadron Collider Experiment

Large Hadron Collider Experiment - The Purpose
The Large Hadron Collider (LHC) just outside Geneva, Switzerland, is one of the most profound scientific projects ever conceived. It is located between France and Switzerland and operated by the European Organization for Nuclear Research (CERN). Scientists from around the world hope it will be fully operational in September 2009.

The ultimate goal of the LHC is to answer huge scientific questions about the sub-atomic world, the massive cosmos, and their finely-tuned relationship. Initially, it’s an attempt to observe theoretical particles that scientists hypothesize should be there. Ultimately, it’s an attempt to understand the creation of the cosmos and the powerful complexity and design that permeates the particle realm.

Large Hadron Collider Experiment - What is Large?
The Large Hadron Collider is the largest machine in the world. The two accelerator rings are five miles in diameter and nearly 17 miles in circumference. It is the world’s largest refrigeration system with 9,600 magnets cooled to -271 degrees centigrade. It has four large detectors weighing from eleven to 25 million pounds each, and two smaller detectors.

Large Hadron Collider Experiment - What is a Hadron?
Hadrons are sub-atomic particles interacting with the Strong Nuclear Force. What is the Strong Nuclear Force? It is the strongest force in the universe, yet only operates within the nucleus of an atom. It is the force mediated by fundamental particles called gluons, which hold together three fundamental particles called quarks, which make up a proton or a neutron. The Strong Nuclear Force diminishes in strength as quarks get closer and increases in strength as they get further apart. There is no known natural phenomenon strong enough to separate the three quarks. The second order effect for the Strong Nuclear Force is to hold protons and neutrons together in the nucleus of an atom. This strong interaction is liberated during a nuclear reaction, such as what takes place in the sun, a nuclear bomb, or a nuclear reactor.

Large Hadron Collider Experiment - What is a Collider?
A collider is an underground, nearly circular, vacuum tube accelerator, in which charged particles move in opposite directions close to the speed of light. The particles are accelerated and kept at a constant energy by electromagnetic resonators. The particle beams are focused by quadrupole magnets and maintained in their orbit by dipole magnets. When the computers and detectors are ready, proton or lead ion beams are collided at four points where the two rings intersect. The two beams colliding from opposite directions doubles the energy released to an equivalent of 100,000 times the heat at the center of the sun! The detectors capture the moment of particle collision and the computers analyze the data for months and years to come.

What is the Intent?
The ultimate intent of the LHC is to help scientists understand the nature of matter at the moment the cosmos was created. Why did matter remain when matter and anti-matter annihilated each other in an energy transformation during the creation of the cosmos? What happened to the anti-matter? What makes up the 96% of the cosmos we now call “dark matter” and “dark energy?” Does the “Higgs field” (aka, “God’s boson force carrier”) that mysteriously gives mass to particles really exist? What about hidden, extra dimensions of space that quantum models show exist?

In a nutshell, the Large Hadron Collider experiment is a huge scientific effort to sneak a glimpse into the Mind of God at the moment of creation… Stay tuned!

Evolution of Sex

Evolution of Sex – The dilemma
The origin and subsequent maintenance of sex and recombination is a phenomena not easily explained by Darwinian evolution. Evolutionary mechanisms such as natural selection are not able to reveal why organisms should abandon asexual reproduction in favor of more costly and inefficient sexual reproduction. In his book, “The Masterpiece of Nature: The Evolution of Genetics and Sexuality”, Graham Bell described the dilemma in the following manner:

“Sex is the queen of problems in evolutionary biology. Perhaps no other natural phenomenon has aroused so much interest; certainly none has sowed as much confusion. The insights of Darwin and Mendel, which have illuminated so many mysteries, have so far failed to shed more than a dim and wavering light on the central mystery of sexuality, emphasizing its obscurity by its very isolation.”

Evolution of Sex – The move to sexual reproduction
Most single-celled organisms reproduce asexually. Asexual reproduction is the formation of new individuals from cells of only one parent, without gamete formation or fertilization by another member of the species. If life on earth is derived entirely from these single-celled creatures then why was this simple-yet-efficient method of asexual reproduction set aside in favor of sexual reproduction?

Why does sex exist? In his book “Evolution: The Triumph of an Idea,” Carl Zimmer concedes:

“Sex is not only unnecessary, but it ought to be a recipe for evolutionary disaster. For one thing, it is an inefficient way to reproduce…And sex carries other costs as well…By all rights, any group of animals that evolves sexual reproduction should be promptly outcompeted by nonsexual ones. And yet sex reigns… Why is sex a success, despite all its disadvantages?”

From the perspective of evolutionary biology, sex is without question ‘an inefficient way to reproduce.’ Consider all that the sexual process entails, including the complexity involved in reproducing the information carried within the DNA. From an evolutionary point of view, sex would be considered an absurdity. Yet from a design point of view, it is nothing short of incredible!
Besides the difficulties associated with the sheer rarity of beneficial mutations and their much-more frequent cousins, the harmful deleterious mutations, there is the added problem related to the two different types of cell division (mitosis and meiosis). During mitosis, all of the chromosomes are copied and passed on from the parent cell to the daughter cells. Conversely, meiosis occurs only in sex cells (i.e. sperm and eggs). During the latter type of replication, only half of the chromosomal material is copied and passed on to the subsequent generation. Meiosis results in the production of completely new combinations of the parental genes, all of them uniquely different genotypes. These, in turn, produce unique phenotypes, providing unlimited new material for the process of natural selection.
It is those very facts (that meiosis has allegedly evolved the ability to halve the chromosome count -- but only for gametes -- and that it can actually provide unlimited new material) which make the meiotic process so incredible. The mechanism of meiosis is critical for sexual reproduction. Yet meiotic sex is alleged to have evolved 520 million years ago. How could the bacteria that are supposed to be responsible for the evolution of sex have stabilized a billion years ago, and then 500 million years after the stabilization, mutate enough to ‘evolve’ the painstaking process of meiosis?
As yet, evolutionary biologists have been unable to come up with a single adequate explanation as to how somatic cells reproduce by mitosis (thereby maintaining the species’ standard chromosome number in each cell), while gametes are produced by meiosis -- wherein that chromosome number is halved so that, at the union of the male and female gametes during reproduction, the standard number is reinstated.

Evolution of Sex – Conclusion
The origin of sex remains a mystery for those committed to a purely materialistic view of reality -- not to mention the origin of the incredibly complex meiotic process that makes sex possible, or the intricate development of the embryo (which is itself an engineering marvel). At conception, the chromosomes inherited from the sperm are paired with the chromosomes inherited from the egg to give the new organism its full chromosomal complement. Naturalists would have us believe that undirected occurrences brought about this marvelously interdependent process of (1) halving the genetic information; (2) recombining it through sexual reproduction. Not only is such a sophisticated mechanism required for the production of a sperm or egg cell via meiosis, but another equally intricate process also joins the genetic information during fertilization in order to produce the zygote (which will later become the embryo). To believe that purely materialistic processes, governed by the laws of chance, could have produced such a mechanism stretches credulity beyond reasonable limits.

Endoplasmic Reticulum

Endoplasmic Reticulum – A brief overview
The endoplasmic reticulum is a complex system of membrane channels and sacs. It is made up of two regions. In the rough endoplasmic reticulum, ribosomes are associated with the outer surface of the ER membrane. The proteins made by these ribosomes are deposited into the central cavity (lumen) of the ER for further biochemical processing. The proteins transported into the lumen will eventually make their way into the lysosomes and peroxisomes, become incorporated into the plasma membrane, or will be secreted out of the cell.

Endoplasmic Reticulum – Quality Control
It is not at all uncommon for proteins in the ER lumen to become incorrectly folded or to be improperly assembled. Quality control activities ensure that proteins are properly produced and processed by the rough ER. Biochemists have discovered that proteins in the ER lumen experience both primary and secondary quality checks. Primary quality control operations monitor general aspects of protein folding. Secondary quality control operations oversee posttranslational processing unique to specific proteins.

Remarkably, the ER quality control mechanism has the ability to discriminate between misfolded proteins and partially folded proteins that appear to be misfolded but are in fact in the process of adopting their intended structures. If the quality control operations could not efficiently make this distinction, it would be catastrophic to the viability of the cell.

The ER quality control systems utilize information contained within oligosaccharides as sensors to monitor the folding status of proteins. The process begins when the ER’s machinery attaches an oligosaccharide (Glc3Man9GlcNAc2) to newly made proteins after they have been manufactured by ribosomes and translocated into the lumen of the ER. Inside the ER, two Glc units are trimmed from the oligosaccharide to form Glc1Man9GlcNAc2. This modified attachment signifies to the ER’s machinery that it is time for chaperones to assist the protein with folding.

Once folding has been completed, the remaining Glc residue is cleaved to generate the oligosaccharide Man9GlcNAc2. This attachment tells the ER’s quality control system to scrutinize the newly folded protein for any defects. If improperly folded, the ER’s machinery reattaches Glc to the oligosaccharide and sends the protein back to the chaperones to be refolded.

After this, the ER machinery removes a Man group to generate Man8GlcNAc2. This marker subsequently triggers the ER machinery to send the protein to the Golgi apparatus. If any proteins with the Man8GlcNAc2 attachment are detected as being misfolded, they are targeted for degradation. Thus, if the structure of the bound oligosaccharide does not match the expected state of the protein, either a recycling or a destruction sequence will be triggered. Proteins targeted for destruction are shuttled into the cell’s cytoplasm and coated with the protein ubiquitin, where it is destroyed by the proteasome.

Endoplasmic Reticulum – Conclusion
Only a designer who exercises thought and foresight could be so deliberate as to orchestrate effective quality control procedures. The cell’s quality assurance systems logically compel the conclusion that life’s chemistry emanates from the work of an intelligent designer.

DNA Replication

DNA Replication – A brief overview
DNA replication is the basis for biological inheritance. It is a fundamental process occurring in all living organisms to copy their DNA. This process is ‘semiconservative’ in that each strand of the original double-stranded DNA molecule serves as a template for the reproduction of the complementary strand. Hence, the process of DNA replication yields two identical DNA molecules from a single double-stranded molecule. Cellular proof-reading and error-checking mechanisms ensure nearly perfect fidelity of the DNA copies. DNA replication commences at specific locations in the genome called “origins.” The DNA unwinds at the origin to form a replication fork.

DNA replication can proceed in only one direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed to the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand in the top-to-bottom direction. For this leading strand, DNA replication proceeds continuously in the direction of the advancing replication fork.

DNA replication cannot proceed along the lagging strand, i.e. the strand with the top-to-bottom orientation, until the replication bubble expands enough to expose a sizeable stretch of DNA. DNA replication then moves away from the advancing replication fork. It can proceed only a short distance along the ‘top-to-bottom’ oriented strand before the replication process must stop and wait for more of the parent DNA strand to be unwound.

DNA Replication – The Replisome
The replisome is a complex molecular machine that carries out replication of DNA. It is comprised of a number of subcomponents, each performing a specific function during the process of replication. Helicase is an enzyme which breaks the hydrogen bonds between the two strands of DNA, thus separating the strands ahead of DNA synthesis. As helicase unwinds the double helix, it induces the formation of supercoils in other areas of the DNA.

Gyrase relaxes and undoes the supercoiling which has been caused by the helicase by cutting the DNA strands, allowing it to rotate and release the supercoil, and then rejoining the strands. Gyrase is most commonly located upstreak of the replication fork -- where the supercoils are being formed.

Primase adds complementary RNA primers to a DNA strand to begin Okazaki fragments. In addition, because DNA Polymerae can only continue (but not begin) a strand, Primase begins the leading strand as well.

DNA polymerase III is comprised of two catalytic cores -- one for replication of the leading strand and one for the lagging strand. DNA polemerase III, however, cannot stay on the DNA strand long enough to efficiently replicate a daughter strand. Hence, DNA polymerase III stays on the strands via a dimer beta clamp which contains three subunits that come together to enclose the strand -- ensuring that DNA polymerase III will remain on the strand for a few thousand nucleotides as opposed to a few hundred.

DNA polymerase I removes the RNA primers set by Primase and completes the Okazaki fragments. Because there is such a small gap remaining after the action of DNA polymerase I has continued the strand of the Okazaki fragment, ligase is required to fill in the gap. The two ends of the Okazaki fragments are subsequently connected by covalent bonds.

Single-strand binding proteins bind to the exposed bases in an effort to counteract their instability and prevent the single-strand DNA from hydrogen-bonding to itself to form dangerous hairpin structures.

DNA polymerases contain a ‘proofreading’ mechanism, commonly referred to as ‘exonuclease activity’. This removes nucleotides that have been mistakenly added.

DNA Replication – Signature of Design
DNA Replication stands as a fundamental challenge to those who seek to hold to a Darwinian worldview. As the process by which biological information is copied and passed on to succeeding generations, the mechanism is fundamental to the process of self-replication of cells. Yet self-replication of cells is necessary for the operation of any selective process such as natural selection. Thus, to attempt to explain the immense sophistication of this mechanism with reference to natural selection requires one to presuppose the existence of the very thing they wish to explain. Because of its extremely sophisticated nature, most biochemists previously reckoned that the system arose once, prior to the origin of the last universal common ancestor. In addition, many biochemists have long regarded the close functional similarity of DNA replication observed in all life as evidence for the single origin of DNA replication. Yet in 1999 researchers from the National Institutes of Health demonstrated that the core enzymes involved in the DNA replication machinery of bacteria and archae/eukaryotes (the two major trunks of the evolutionary tree of life) did not in fact share a common evolutionary origin. It thus appears as if two identical DNA replication systems have emerged independently in bacteria and archae -- after these two evolutionary lineages supposedly diverged from the last universal common ancestor.

It is phenomenal to think that this engineering marvel evolved a single time, let alone twice. There exists no obvious reason for DNA replication to take place by a semiconservative, RNA primer-dependent, bidirectional mechanism that depends on leading and lagging strands to produce DNA daughter molecules. Even if DNA replication could have evolved independently on two separate occasions, it is reasonable to expect that fundamentally different mechanisms would emerge for bacteria and the archae/eukaryotes given their idiosyncrasies. But, they did not.

Cosmological Arguments

Cosmological Arguments - Why is There Anything at All, Instead of Simply Nothing?
The core logic of the Cosmological arguments is summed-up by Alan Sandage, winner of the Crawford prize in astronomy: "I find it quite improbable that such order came out of chaos. There has to be some organizing principle. God to me is a mystery but is the explanation for the miracle of existence, why there is something instead of nothing." Stephen Hawking adds, “Why does the universe go to all the bother of existing?”

Cosmological Arguments – The Contingency Argument
The Cosmological arguments are a series of simple deductions that get us thinking about origins. Think about it; if there were no God, why would anything at all exist? There’s no necessity for it. One can imagine nothing at all ever existing. Philosophers have wrestled with the puzzle of why there is anything at all since the beginning of recorded history.

The deductions reached by the top modern philosophers on this question can be formulated as follows:

1. Everything that exists has an explanation of its existence (either in the necessity of its own nature or in an external cause).
2. If the universe has an explanation of its existence, that explanation is a timeless, personal, immaterial being of immense power.
3. The universe exists.
   
   Now what follows logically from these three premises?
   
   From 1 and 3 it logically follows that:
   
4. The universe has an explanation of its existence.
   
   And from 2 and 4 the conclusion logically follows:
5. Therefore, the explanation of the universe’s existence is a timeless, personal, immaterial being of immense power.¹

This is called “The Contingency Argument,” which makes a powerful starting case for a transcendent Cause.

Cosmological Arguments – What about an Eternal Universe?
Here, the skeptical mind might argue against the foundation of the cosmological arguments by asking, “What if the universe was always here, eternally self-existent, the same way that most people see God as self-existent?” This is a fair question. Let’s look at what would be required if this were the case, and the evidence for and against this notion.

If the universe never began to exist, then that means that the number of events in the past history of the universe is infinite. But mathematicians recognize that the idea of an actually infinite collection of things (as opposed to a conceptual infinity) leads to self-contradictions. For example, what is infinity minus infinity? Well, mathematically, you get self-contradictory answers. For example, if you take an infinite number of moments, number them all as moment one, moment two, etc., and subtract all the even-numbered moments, you have an equation where “infinity minus infinity equals infinity”. If you then take the same infinity of numbered moments, and subtract only the moments numbered higher than 3, then you have the equation “infinity minus infinity equals 3”. If you take the same numbered set of moments and subtract the entire set, you have an equation that says “infinity minus infinity is zero”. You can actually get any answer you want for the equation “infinity minus infinity” depending upon how you word the equation! This shows that infinity is just an idea in your mind, not something that exists in reality. David Hilbert, perhaps the greatest mathematician of the 20^th century states, "The infinite is nowhere to be found in reality. It neither exists in nature nor provides a legitimate basis for rational thought. The role that remains for the infinite to play is solely that of an idea."²

But that entails that since past events are not just ideas, but are real, the number of past events must be finite. Therefore, the series of past events within the universe cannot just go back forever. Rather the universe must have begun to exist.

This conclusion has been confirmed by remarkable discoveries in astronomy and astrophysics. From ancient times, many deep thinkers like Plato and Aristotle assumed that the universe had existed eternally into the past. Of course, the Hebrew and Christian cultures believed in the creation account represented in the Bible, and there were numerous non-Judeo-Christian creation accounts as well, but there were always individuals and groups who thought of the universe as eternal. Subsequent to the so-called “Enlightenment” in Europe in the 18th century (when many in Western Civilization began to drift away from biblical thinking) and even more so subsequent to Charles Darwin’s proposal of the Theory of Evolution in 1859, it became very common among scientists and university professors in the West to presume that the universe had existed eternally into the past.

This viewpoint was heavily shaken starting in 1913 when scientists Vesto Slipher, Albert Einstein, and Edwin Hubble discovered very compelling evidence that the universe was expanding. Discovery after discovery in the 20^th century affirmed that not only was the universe expanding, but that time, space, matter and energy appeared to have had a beginning in the finite past. In 1965, scientists Arno Penzias and Robert Wilson discovered the remnants of background radiation from the Big Bang. In 1968 and 1970, Stephen Hawking, George Ellis and Roger Penrose published papers that extended Einstein’s Theory of General Relativity to include measurements of time and space, demonstrating that both had a finite beginning that corresponded to the origins of matter and energy. Remarkably, their conclusion was that (causally) prior to that moment, space and time did not exist!

The astrophysical evidence indicates that the universe began to exist in a great explosion called the "Big Bang." Physical space and time were created in that event, as well as all the matter and energy in the universe. About 11 years of work by cosmologists Arvind Borde, Alan H. Guth, and Alexander Vilenkin culminating in 2003 established that this conclusion holds for all theories of cosmic origin for which there is observational evidence. This is the conclusion of modern science. Therefore, as Cambridge astronomer Fred Hoyle points out, the Big Bang Theory requires the creation of the universe from nothing! This is because, as you go back in time, you reach a point in time at which, in Hoyle's words, the universe was "shrunk down to nothing at all."³ Thus, what the Big Bang model requires is that the universe began to exist and was created out of nothing.

Now this tends to be very awkward for the atheist. For as Anthony Kenny of Oxford University urges, "A proponent of the Big Bang theory, at least if he is an atheist, must believe that the universe came from nothing and by nothing."⁴

But surely that doesn't make sense. Out of nothing, nothing comes. So why does the universe exist instead of just nothing? Where did it come from? There must have been a cause which brought the universe into being. And from the very nature of the case, this cause must be an uncaused, changeless, timeless, and immaterial being which created the universe. It must be uncaused because there cannot be an infinite regress of causes--that is to say, there cannot be a series of causes extending backwards in time to infinity past. It must be timeless and therefore changeless, at least without the universe, because it created time. Because it also created space, it must transcend space as well and therefore be immaterial, not physical.

Cosmological Arguments – The Kalam Argument
This brings us to another logical exercise in the lineage of cosmological arguments, “The Kalam Argument.” This cosmological argument is deceptively simple, but in its modern form (as developed by philosopher William Lane Craig), has never been successfully refuted:

Premise 1: Everything that begins to exist has a cause. Premise 2: The universe began to exist. Conclusion 1: Therefore, the universe must have a cause.⁵

Regarding Premise 1, notice that the classical notion of God would not be included in this category, as He never began to exist within that understanding. From that viewpoint, He is the necessary “Uncaused Cause” of the universe who created time itself, and has always existed timelessly (“eternally”). The universe, on the other hand, is believed by the majority of both secular and Christian scientists to have begun to exist at a finite point in the past.
If the Universe Began to Exist, It Must Have a Cause. Cosmological Arguments – The Inevitable Conclusion
Isn't it incredible that the Big Bang theory and the cosmological arguments fit with what the theist has always believed -- In the beginning God created the universe. Ever since indications began to surface early in the 20th century that the universe had a beginning, attempt after attempt has been made to hypothesize an eternal model to avoid the metaphysical implications of that. Some of these attempts include the Oscillating Model, the Steady-State Model, and the Vacuum Fluctuation Model, all of which have failed. The “Big Bang” models, which all have a beginning in space and time, have grudgingly become accepted by well over 90% of scientists despite their inherent metaphysical implications, due to overwhelming evidential support.
In a series of papers culminating in 2003, Arvind Borde, Alan Guth, and Alexander Vilenkin were able to prove that any universe which is, on average, in a state of cosmic expansion cannot be eternal in the past but must have an absolute beginning. This includes all universe models that honestly assess the available data. Regarding this, Vilenkin states: “It is said that an argument is what convinces reasonable men and a proof is what it takes to convince even an unreasonable man. With the proof now in place, cosmologists can no longer hide behind the possibility of a past-eternal universe. There is no escape, they have to face the problem of a cosmic beginning.

Co-option

Co-option – An Introduction
Co-option is a proposed solution to the problem of “irreducibly complex” machines inherent in living cells. Irreducible complexity relates to a characteristic of common complex systems whereby they need all of their individual components parts in place in order to impart functionality to the system as a whole. In other words, it is impossible to reduce the complexity of an irreducibly complex system by removing any of its component parts and still maintain its functionality.

The concept was popularized by Lehigh University Professor Michael Behe in his breakthrough book “Darwin’s black Box.” Behe uses the mousetrap as an illustrative example of this concept. A mousetrap consists of five interacting pieces -- the base, the catch, the spring, the hammer, and the hold-down bar. All of these must be in place for the mousetrap to work, as the removal of any one piece destroys the function of the mousetrap. In like manner, biological systems require multiple parts working together in order to function. Removal of one of the constituent parts renders the entire system non-functional.

Behe’s best known example of an irreducibly complex system from biological systems is the bacterial flagellum. An ensemble of over forty different kinds of proteins makes up the typical bacterial flagellum. These proteins function in concert as a literal rotary motor. The bacterial flagellum’s components stand as direct analogs to the parts of a man-made motor, including a rotor, stator, drive shaft, bushing, universal joint, and propeller.

Critics of the notion of “Irreducible complexity” have responded with reference to the concept of co-option. According to this hypothesis, apparently irreducibly complex systems can evolve from simpler precursors which serve other unrelated functions. One such argument that Kenneth Miller has advanced is that the basal body of the flagella is similar in a number of respects to the Type III secretion system, a needle-like structure that pathogenic germs use to inject toxins into living eukaryotic cells. The needle’s base has ten elements in common with the flagellum, but it is missing forty of the proteins that make a flagellum work. Hence, Kenneth Miller concludes that, “The parts of this supposedly irreducibly complex system actually have functions of their own.” Critics of Miller’s co-optive idea as it relates to the flagellar motor point out that analysis of the gene sequences of the two systems suggest that the flagellar motor arose first and then the pump came later. In other words, if anything, the pump evolved from the motor, not the motor from the pump.

Co-option – The challenges
In order for co-option to produce a bacterial flagellum, all of the component parts would need to be present simultaneously and in roughly the same place, and all of them must have had other naturally-selectable, useful functions. The evidence is lacking, however, that such has ever been the case.

Moreover, co-option necessitates the compatibility of the components in relation to each other. A bolt that is too large or small, or that has threads that are too fine or too coarse to match those of the nut cannot be combined with the nut to make a fastener. Again, there is a substantial lack of evidence that this interface compatibility has ever existed.

Even if all the parts are available at the same time and in the correct location, and are functionally compatible, an assemble mechanism is still required, and that mechanism must be complete in every detail -- otherwise incomplete or improper assembly will result. The assembly mechanism thus represents yet another irreducibly complex hurdle. Assembly must be timed and coordinated perfectly -- and the assembly instructions must be complete in every detail, otherwise it is inconceivable that any function will result. To date, no materialistic mechanism has been documented that is able to produce the complex and highly specified assembly instructions which would be necessary to achieve such a fete.

Co-option – Conclusion
While the concept of co-option is certainly an interesting idea, more research is required to establish its tenability as a plausible explanation for the presence of apparent irreducibly complex systems which so permeate life’s biochemistry. The co-option argument tacitly presupposes the need for the very thing it seeks to explain -- a functionally interdependent system of proteins. Until a detailed analysis is undertaken, and a plausible model constructed, the hypothesis stands as a conjecture, based not upon empirical data, but upon an a-priori commitment to a Darwinistic paradigm.

Archaeopteryx

Archaeopteryx – Introduction
It was during the dinosaur-era that the first birds appear in the fossil record, notably Archaeopteryx from Jurassic strata in Bavaria. Because it had fully developed feathers, including primaries and secondaries which were arranged on its wings in the same way as modern birds, Archaeopteryx is recognized and classified as a bird. Its skeleton, however, possessed a number of reptilian features. These included a long bony tail, claws on the digits of its fore -- as well as hind limbs, and teeth; so it is seen as a link -- showing that birds evolved from reptiles. It is widely held that birds arose from a group of dinosaurs known as the theropods. Features of the latter are their overall modest size, their bipedal stature, the long and clawed hind legs, and the three digits on their forelimb. Further, some of the theropods possessed hollow bones, and some later ones lacked teeth, with their mouth somewhat resembling a beak.

Archaeopteryx – A legitimate transition?
Despite similarities between theropods and birds, there are substantial differences which very clearly militate against an ancestral relationship. Firstly, contrary to what might be predicted, the theropods were Saurischian, not Ornithischian, i.e. they had the distinctive lizard-like pelvis rather than a bird-like one. In addition, although both theropods and birds have only three digits in their forelimbs, they are different ones: theropods have the first to third of the usual five digits, whereas birds have the second to fourth. One particularly important difference is that the theropods -- whilst having long and well-developed hind limbs -- had very small forelimbs. Such short limbs were hardly credible precursors for the extended and well developed fore-limbs of birds, including those of Archaeopteryx, which must support their wings. Also, typical of running animals, they lacked clavicles which are present in Archaeopteryx and fused to form the familiar avian wishbone (furcula) which contributes to support of the wing. Finally, Archaeopteryx had a significantly larger braincase, reflecting the need for additional sensory input and motor control required for flying.

One of the major issues with reptile-to-bird evolution is that avian lungs are completely different from those of a reptile. No models have ever been presented that demonstrate how reptilian lungs could evolve into avian lungs and still serve their intended purpose.

It might also be noted that birds have a unique arrangement for distributing air around their bodies -- to support the high metabolism associated with flying. But there is nothing to indicate that any reptile group had such a system or even anything that could be considered a precursor to it. In fact, some scientists have concluded that the theropods had a crocodilian mode of breathing, and that to convert from this to the bird system would mean going through a non-viable intermediate stage.

A further important point is that the most bird-like theropods did not arise until late in the Cretaceous period -- about 70 million years after Archaeopteryx, so could not have been its ancestor. Indeed, they come in even later than various groups of Cretaceous birds which are closer to modern birds than to Archaeopteryx.

One final point which is worth mentioning is the problem of how powered flight started. Did wings develop by gliding down from trees or by running fast along the ground? There remains no convincing evidence either way, and indeed some evidence to the contrary either way. The point is that Archaeopteryx was a fully fledged bird, capable of flight, not an intermediate running or glider.

Archaeopteryx – Conclusion
While it may be fair to conclude that Archaeopteryx was of intermediate structure (in the sense that it was a bird which shared a handful of features in common with reptiles), it cannot be regarded as transitional in terms of phylogeny. As with so many other classes of animal, the birds arise in the fossil record without any clear link to earlier creatures.