Gods Gumshoe

One Man’s Tour Through the Evolutionary Debate

NOTE: The editors of The Fellowship Herald have  granted the request of the author for anonymity. 

Summer 2011 • The Fellowship Herald •


The following article offers “a tour through the evolutionary debate” from one man’s perspective. The author of the article is quite familiar with the contents of The Urantia Book, (see page this site The Urantia Book, ) which claims that the rest of the Universe refers to our planet Earth, as Urantia, and that The Urantia Book, is given to our world at this time of planetary Crisis in order to assist us in building a better world.  Although it is not the primary purpose of the article to draw parallels between current science and The Urantia Book, the article nevertheless depicts a developing consilience between recent research in evolutionary science and the key concepts relating to evolution presented in The Urantia Book.



Neo-Darwinism has been the prevailing scientific account of evolution over the past several decades. Because Neo-Darwinism is entirely reliant on material causation, chance plays an essential role. Chance processes can only proceed slowly through incremental change. The vast array of complex and diverse life forms, Neo-Darwinists claim, arose through gradual accumulations of adaptive  features.  But Neo-Darwinism’s reliance on gradual change is not holding up well in light of current research. Using tools such as genome sequencing biologists are demonstrating that evolutionary change probably did occur suddenly as The Urantia Book says:

[Life forms] do not evolve as the result of the gradual accumulation of small variations; they appear as full-fledged new orders of life, and they appear suddenly. The sudden appearance of new species and diversified orders of living organisms is wholly biologic, strictly natural. [58:6.3-4] (P. 669)


The evolutionary transitions in single celled life forms, plants and multi-cellular invertebrates and vertebrates including the predecessors of humanoids all occurred suddenly.

The higher protozoan type of animal life soon appeared, and appeared suddenly. [65:2.4] (P. 732)

It was from an agile little reptilian dinosaur of carnivorous habits but having a comparatively large brain that the placental mammals suddenly sprang. [65:2.12] (P. 732)

Slightly to the west of India, on land now under water and among the offspring of Asiatic migrants of the older North American lemur types, the dawn mammals suddenlyappeared. [61:6.1] (P. 700)


These new mid-mammals—almost twice the size and height of their ancestors and possessing proportionately increased brain power—had only well established themselves when the primates, the third vital mutation, suddenly appeared.[:61.6.1] (P. 700)


Not only did evolutionary transitions occur suddenly according to The Urantia Book, but they occurred in great leaps.

You will not be able to find such connecting links between the great divisions of the animal kingdom nor between the highest of the prehuman animal types and the dawn men of the human races. These so-called ‘missing links’ will forever remain missing, for the simple reason that they never existed.” [58:6.2] (P. 669)


Neo-Darwinism is a theory that excludes any super-material causation—no design, no guidance, no ultimate goal or purpose. Yet one of the most important findings in recent scientific research is convergent evolution—repeated evolution of similar adaptive features—not only at the organism level but also the organ and molecular level.


The Urantia Book states that there is design in life which explains the patterns in life systems and the apparent direction to evolution.

A purposeful plan was functioning throughout all of these seemingly strange evolutions of living things, but we are not allowed arbitrarily to interfere with the development of the life patterns once they have been set in operation.

[65:3.1] (P. 733)


After organic evolution has run a certain course and free will of the human type has appeared in the highest evolving organisms, the Life Carriers must either leave the planet or take renunciation vows. [65:1.5] (P. 731)


Science has no clear answer as to how inanimate matter became animated. The Urantia Book says that life was not simply a frozen accident in time or the result of a deterministic chemical pathway, but rather life was implanted on earth

by intelligent beings.


Life does not originate spontaneously... [36:0.1] (P.667)

We [Life Carriers] can and do carry life to the planets, but we brought no life to Urantia....all life appearing hereon was formulated by us right here on the planet.. [58:4.1] (P.667) [Emphasis mine]

The Urantia midwayers  (Spiritual helpers ) have assembled over fifty thousand facts of physics and chemistry which they deem to be incompatible with the laws of accidental chance, and which they contend unmistakably demonstrate the presence of intelligent purpose in the material creation. [58:2.3] (P. 665)



Life, according to The Urantia Book, is not entirely material, nor is human intellect and consciousness purely a chemical-mechanical phenomenon.

In language, an alphabet represents the mechanism of materialism, while the words expressive of the meaning of a thousand thoughts, grand ideas, and noble ideals—of love and hate, of cowardice and courage—represent the performances of mind within the scope defined by both material and spiritual law, directed by the assertion of the will of personality, and limited by the inherent situational endowment. [195:7.21] (P. 2080)


To say that mind “emerged” from matter explains nothing. If the universes were merely a mechanism and minds were unapart from matter, we would never have two differing interpretations of any observed phenomenon. The concepts of truth, beauty goodness, are not inherent in either physics or chemistry. A machine cannot know, much less know truth, hunger for righteousness, and cherish goodness. [195:6.11] (P. 2077) [Emphasis mine]


The theory that most closely parallels the evolutionary account presented in The Urantia Book is Intelligent Design. Intelligent Design seeks to expand science by incorporating non-material causation as a viable hypothesis. However, the scientific establishment has rejected such an intrusion and has adopted a strictly materialist paradigm. The article only hints at the consequences of secularism and materialism.


The Urantia Book is more explicit.

The complete secularization of science, education, industry, and society can lead only to disaster. During the first third of the twentieth century Human Beings killed more other human beings than were killed during the whole of the Christian dispensation up to that time. And this is only the beginning of the dire harvest of materialism and secularism; still more terrible destruction is yet to come. [195:8.13] (P. 2082) [Emphasis mine]


“Darwin made it possible to be an intellectually fulfilled atheist.” 1  So said Richard Dawkins, the most influential scientist and intellectual in the world. The notion that evolution is irreconcilable with belief in God in general and Christian theism in particular, may be surprising to some and perhaps a bit distressing.


By “Darwin” in the above quote, Dawkins means Darwinian evolution in its modern form, “Neo-Darwinism.” Neo-Darwinism can be viewed as a term applied to the range of viable theories given the assumption that only material causation is allowed in the explanation of natural phenomena. The secular aspect of secular

Humanism is largely dependent on the ascendency of Neo-Darwinism. Neo-Darwinism is the primary force in the conflict between religion and science and what gives rise to the impression that religion is in retreat, giving up ground under the inexorable advance of science. Religionists are seen as holding on to bits of ground only to have to surrender them under the principle of Occam’s Razor as science discovers material explanations for phenomena once attributed to Deity.

This is the so-called God-of-the-gaps fallacy materialists see religionists repeatedly succumbing to. Secular Humanism, backed by the forces of academic scientists, have laid siege to traditional values predicated on Judeo-Christian theology using Neo-Darwinism as their primary weapon. The outcome goes to the very core of what is important in human experience: whether we are the intention of a loving God, and have an eternal purpose, or merely accidents of time, alone in a purposeless, uncaring universe.


But if it can be shown that strictly materialistic accounts offered by science about the origin of the universe, the fine tuning of the universe parameters, the origin and evolution of life and the advent of sentient beings are unsatisfying, then the God-of-the-gaps fallacy is itself a fallacy. And if it can be shown that scientific advancements reveal not the signature of chance, but rather the signature of design, then the entire color of the debate changes.


 What Is “Evolution” and Why Is It Important?


Evolution means one of two things depending on the context. To some it simply means descent with modification, which refers to the theory that all creatures great and small are related—derived from a distant common ancestor. This is often referred to as “the fact of evolution.” Within the academic scientific community, the term evolution more often also encompasses the proposed mechanism of evolution. Darwin proposed that the mechanism of evolution was variation and natural selection. He was unaware of genetics at the time. In the early to mid-part of the twentieth Century the mechanism of evolution was defined more clearly with respect to “variation.” The modern synthesis, often called Neo-Darwinism, posits that the mechanism of evolution is random variation (mutation) and natural selection.


Random mutation means the raw changes that provide the input for evolutionary change are chance events—accidental changes to DNA segments which are thought to determine a living entity’s structures and functions. They are, so say Neo-Darwinists, unsolicited, and not facilitated by the organism. This means that there is no direction—no purpose—to evolution. No direction means that sentient beings are not inevitable. We are purely the result of an accumulation of chance and necessity—mutation and natural selection. How can one imagine that there is a Divine purpose to human existence if the process by which we arose is purposeless?


Nobel Laureate Jacques Monod has said: “Chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, only chance, absolute but blind liberty...Man knows at last that he is alone in the indifferent immensity of the universe, whence which he has emerged by chance. His duty, like his fate, is written nowhere”.2


An important inferential extension to this is that human intellect is purely physical—that there is no mind apart from the physical brain. If human intellect is entirely explainable as a purely physical phenomenon and the result of a purposeless process, it would seem quite unlikely that the brain would just happen, by chance, to be suitable for any sort of non-material overlay such as mind, or free will, or soul (“ensoulment”). Therefore the edifice upon which much of traditional Christianity is built, collapses; thus Richard Dawkins’ statement: “Attempts to reconcile Christian theology with evolution is to misunderstand evolution.”3


William Provine of Stanford University has said: “If evolution is true, [then] there is no God, no life after death, no ultimate foundation for ethics, no free will and no ultimate meaning in life.”4

Without a true north on an absolute moral compass there is no absolute Truth. Truth and error are ephemeral things subject to the whim of those who have seized power at the moment. They are purely human constructs. There is no barrier—certainly no persistent barrier—to behavior. Anything can be justified. And without a belief in free will—the ability to transcend the material algorithms and inclinations in the brain—there is no reasonable basis for holding individuals accountable to any human created ethics construct anyway. Thus, one of the main pillars of Western civilization collapses. As Daniel Dennett has said, “[Neo-Darwinism] eats through just about every traditional concept and leaves in its wake a revolutionized worldview, with most of the old still recognizable, but  transformed in fundamental ways”5


All variant “brands” of Humanism—e.g., Marxism— and its derivatives, socialism, and modern liberalism, are heavily influenced by this manner of thinking. The principals in the Western intellectual establishment have long ago dismissed any sort of idea of a Creator or Supreme Being, especially a compassionate, omniscient God, and are now advocating their case with greater and greater force. It has been my experience that modern secular Humanists would prefer that there be no God.


This idea is expressed artistically in John Lennon’s song Imagine—the great hymn of secular Humanism:

“Imagine there’s no heaven, it’s easy if you try.

No hell below us, above us only sky.

Imagine all the people living for today”

From song “Imagine”—the great hymn


So convinced are they of the truth of materialism and so adapted to the idea that this one life is all there is, that they have little or no interest in hearing any counter-arguments. They appear to enjoy the idea that they can dispel the myth of God and salvation from the minds of those who hope for some divine plan that provides meaning in their life. This happens in the universities in America every day. If you think this is too cynical, I encourage you to read Daniel Dennett’s Darwin’s Dangerous Idea,5 Corliss Lamont’s The Illusion of Immortality, 6 or any one of Richard Dawkins’ books. What should we make of a man such as Richard Dawkins—the most influential scientist in the world—who tells children in effect: “evolution or God kid, take your pick”?


Methodological Naturalism


The current paradigm in science is “methodological naturalism.” Methodological naturalism assumes a priori that there are no non-material influences or causes in the natural world. The renowned geneticist, Richard Lewontin, explains this in the following way:

“We [scientists] have a prior commitment…to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced

by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that

materialism is absolute, for we cannot allow a Divine Foot in the door.7


Phillip Johnson, the founder of the modern Intelligent Design movement, pointed out that if only materialistic explanations for evolution are allowed, then Neo-Darwinism, or some material-based theory of evolution, must be true.

This explains the assuredness with which Neo-Darwinists have about their theory despite its flaws.


Theistic Evolution


Theistic Evolutionists do not accept Dawkins’ conclusion that Theism and Neo-Darwinism are irreconcilable. Theistic Evolutionists are scientifically informed religionists who accept the current scientific consensus on evolution and the neo-Darwinian account of it, i.e., that we are the result of a series of fortuitous chance events within living cells coupled with natural selection. Notable scientists in this category are Francis Collins, Simon Conway Morris, Ken Miller, and Robert Russell. Theistic Evolutionists point to the Big Bang theory and the discovery that the universe seems to be very tightly tuned—adapted—to allow complex configurations of molecules, and especially living organisms, to arise, as evidence that God exists.8


What might be surprising to some is that many Theistic Evolutionists have come to accept the scientific consensus with respect to human intellect and consciousness which holds that the brain is all there is, i.e., there is no non-material overlay to the brain. Most do not, therefore, accept that there is anything like a mind or soul. Immortality is accomplished by resurrection of the physical body. Theistic

Evolutionists believe that a pseudo-mind “emerges” from the physical brain.  Emergence is a term that describes a phenomenon where the whole is far greater than the sum of its parts. But it is a term that has not been defined clearly with respect to human intellect. It strikes me as simply applying a “label to a mystery,” to use a phrase coined by Phillip Johnson.


Neuroscientists and materialist scientists have convinced Theistic Evolutionists that an interaction between a hypothetical, non-material entity (mind) and the material brain violates the laws of physics. Additionally, scientists have discovered that there are correlations between brain activity and human conscious observation. Perturbing the brain evokes predictable conscious phenomena, and conscious phenomena have predictable brain activity. I am not sure why this counts as important evidence against the existence of mind. What would the alternative be; for there to be no correlation? Clearly the brain does something.


Free will is another matter. For there to be anything meaningful about the human experience within a traditional Christian context, free will has to be salvaged. Theistic  Evolutionists speculate that interactions between the material brain and non-material aspects in human intellect can occur undetected because they operate under the radar of human detection, courtesy of the uncertainties related to quantum mechanics. Quantum mechanics, therefore, offers potential openness to an otherwise closed, deterministic system. This openness permits, or at least does not exclude, the possibility of free will. Others speculate that this openness afforded by quantum mechanics could facilitate both divine action real (ontological interpretation of quantum mechanics) as opposed to merely a limitation of our current knowledge (epistemological interpretation). The current consensus

is that quantum uncertainties are real.


The Catholic Church


What does the Catholic Church say? The first statement by John Paul in 1996 was ambiguous. It signified that evolution was a theory, not merely a hypothesis. But it did not discuss the origin of life and it did not clearly define what “evolution” is. In other words, the statement did not comment on the mechanism of evolution.9 He may simply have been referring to common descent. More recent comments have also been somewhat unclear. Comments that “true contingency” is not incompatible with the Divine plan indicate a position more consistent with what Theistic Evolutionists believe. However, other comments suggesting that evolution

has been guided by God in some way are more consistent with the claims of Intelligent Design.

Intelligent Design


Intelligent Design proponents look at the grandeur of the universe, the manner in which the physical parameters of the universe are tuned, or adapted, to  accommodate life, the complexity of life, and the marvel of human intellect, and

infer that reality is probably the result of prior intelligence. Intelligent Design theorists view their system as a superset comprising Theistic Evolutionism, Creationism, and those who accept some form of “guided evolution,” or any other

variant of teleology. Theistic Evolutionists would be aghast at being classified as a variant of Intelligent Design. Because Theistic Evolutionists accept the scientific account of evolution, it is not surprising that they are held in higher regard

within the scientific academic community than Intelligent Design proponents. The academy has nothing but scorn for Intelligent Design.


How Intelligent Design should be viewed with respect to Theistic Evolution and Creationism is an academic question. The terms have become quite muddied. The normal convention is that those who develop a school of thought get to define what it is. With Intelligent Design, Michael Behe, a molecular biologist, William Dembski, a philosopher, theologian, and mathematician, and Stephen Meyer, a historian of science, are the primary theorists, though not the originators.

In Dembski’s and Meyer’s view, Intelligent Design encompasses those who believe that intelligence was imparted at some point, any point, to effect a particular outcome whether that impartation of intelligence occurred prior to

the inception of life, at the inception of life or throughout the development of life.10


However, Creationists have also used the term Intelligent Design to describe a form of Creationism, which typically implies a belief that each species is the result of a separate Divine act. Creationists often use the term Creationism more broadly to include any belief that the universe and living creatures on earth are the result of Divine creation. A belief in guided evolution, whereby some prior act by the Creator, or those empowered by the Creator, caused an evolutionary rollout of life, could be viewed as Creationism. The fact that each new creature was an indirect act, rather than a direct act of a Creator, is an insignificant detail.


The key difference between what most Theistic Evolutionists believe, and what most non-Creationist Intelligent Design proponents advocate, is that the latter do not accept that the universe physical parameters could be tuned tightly enough by an intelligent agent to channel chemistry along a determinist “pathway” such that life would arise, or arise with a high degree of probability, let alone certainty. (A pathway in this context is simply a deterministic, step by step process whereby chemistry becomes biology.) Furthermore, even if it were the case that a chemical

pathway to biology were discovered, Intelligent Design proponents would argue, it is unlikely that such an approach to design could ensure an unfolding of life in a directed manner, i.e., a manner directed toward the inevitability of sentient beings capable of accommodating any super-material qualities such as a mind or soul.

But the demarcation between Intelligent Design and Theistic Evolution is not as clear-cut as many assume. Some notable Theistic Evolutionists, Ken Miller and Francis Collins, for example, surmise that perhaps intelligent intervention did occur at the inception of life on earth. This is virtually indistinguishable from what most non-Creationist Intelligent Design proponents believe, which is ironic, because both Collins and Miller are rather vocal critics of Intelligent Design. If Collins and Miller are prepared to admit that the origin of life may require prior intelligence, why bother with Neo-Darwinism to account for the evolution of complex features at all? Is it reasonable to think that an intelligent agent would assemble life—because chance processes could not—only to have life flounder and fail to produce anything more interesting than a few slugs?


What Happened in the Dover Case?


The 2005 court case in Dover, Pennsylvania, offers a textbook case on why it is important to define terms precisely. Proponents of Creationism on the school board wanted biology teachers to read a statement regarding evolution to freshman biology students. The statement referenced “Darwin’s theory” without clearly defining what that meant. Did “Darwin’s Theory” simply mean common descent or the mechanism of Neo-Darwinism, i.e., random mutation and natural selection? The statement also referenced a book, Of Pandas and People,11 that could be interpreted as advocating Creationism.


The case went to court and Judge John E. Jones ruled that Intelligent Design is a form of Creationism and therefore violates the Establishment Clause of the First Amendment to the United States Constitution provision. Because the statement did not specify what Darwin’s Theory was, and because the statement referenced a book that was supportive of Creationism (special creation of each distinct species),

the ACLU lawyers were able to argue the case, based on the merits of Darwin’s theory of common descent, versus Creationism. The evidence for common descent is quite strong. Arguing against Intelligent Design, by focusing on common descent, rather than also specifying the neo- Darwinian mechanism of random mutation and natural selection, is a common tactic of Neo-Darwinists, because it is a much easier thing to do. Furthermore, because the statement associated the book, Of Pandas and People, with Intelligent Design, the ACLU was able to establish a legal precedent that Intelligent Design is a subset of Creationism rather than Creationism being a subset of Intelligent Design.


The case probably would have been lost had the statement included any comment suggesting that material causes could not fully account for any and all life forms. Ultimately, a judge—not understanding the science—is going to defer to the side that has the greatest preponderance of scientific experts. Clearly, scientists advocating Intelligent Design, teleology, guided evolution—whatever you want to call it—are a small minority, unless there are many other scientists who are not speaking up, to avoid jeopardizing their careers. Advocating such a position is career impacting. Molecular biologist Michael Behe, a leading proponent of Intelligent Design, has become a pariah at Lehigh University where he teaches, despite fully accepting common descent.


Is Intelligent Design Science?


Intelligent Design rejects methodological naturalism. Why, they ask, limit the range of hypotheses before really understanding the ultimate causes of nature? Therefore, if you define science as pertaining strictly to material causation, then you could argue that at least part of what Intelligent Design proposes is not science.


Academic scientists claim that Intelligent Design is not science because it cannot be falsified. Can Intelligent Design be falsified? Yes, I believe it can. Scientists could demonstrate through laboratory experimentation that a complex feature can evolve, or has evolved, by random chance and natural selection. Alternatively, paleontologists could produce evidence of a fossil sequence showing a continuous,

gradual evolution of a complex feature. No such sequence exists. The fossil sequences they have are, however, adequate to demonstrate the truth of Darwin’s primary claim of common descent.

Can Neo-Darwinism Be Falsified?


The evidence presented by materialist scientists in support of the grand claim of neo-Darwinism—that the tandem mechanisms of random mutation and natural selection explain how all life evolved—is quite weak. But can neo- Darwinism be falsified? Since Neo-Darwinismis chancebased, its claims, in theory at least, should be able to be confirmed or falsified by the mathematics of probabilities. This is what William Dembski and others in the Intelligent Design movement have attempted to do. The scientific method requires that there be an attempt to falsify a hypothesis or theory. But materialist scientists are not highly motivated to do this because falsifying Neo-Darwinismwould likely lead to a reassessment of methodological naturalism which is required by materialism.


The Probabilities of Random Mutation


When attempting to falsify neo-Darwinism, Intelligent Design theorists focus on the probabilities related to random mutation rather than debating the powers of natural selection. They do this because natural selection is a tautology and cannot be falsified. Natural selection means “survival of the fittest.” But you define the fittest as those that survive. In other words, natural selection means: survival of those that survive. This explains why Neo-Darwinists always emphasize natural selection and speak so little about mutation. They believe that the necessary mutations will arise given enough time.


Falsifying Neo-Darwinism, through mathematical probabilities related to random mutation, is difficult to do. Why? There are two reasons. First, the power of natural selection is difficult to assess. It is hard to determine how significant the incremental benefit provided by a “mutation” has to be in order to confer minimal selective advantage, especially in comparison to other competing attributes of an organism, which are also subject to variation.


Secondly, since Neo-Darwinism is a random chance process, it does not have a target. Therefore you cannot simply calculate the probability of this or that specific molecule, molecular machine, cell system, organ, or organism evolving because there could be many other viable biologic solutions in the overall set of possible genetic configurations. And no one knows how large that set is.


Shakespeare’s sonnets are often used as an analogy to illustrate probabilities related to evolution. Imagine you were trying to calculate the probabilities of creating a Shakespeare like sonnet using random generated text and selection. In

this analogy you can think of a sonnet as a gene, each letter as a distinct amino acid.

The first point is that using a specific sonnet is a target, but since Neo-Darwinism is a random process, it has no target. Therefore, you could not simply calculate the probabilities for a particular sonnet and conclude on that basis that you could not produce a sonnet by neo-Darwinian methods— chance and selection. The more appropriate question is: Can a process using chance generation of word combinations with selection create any coherent Shakespeare-like sonnet? That is difficult to determine because the number of possible coherent sonnets that qualifies as Shakespearelike is unknown. What can be calculated—roughly—is the size of the possible combinations of words (the denominator) within which the diminishingly small set of coherent sonnets (the numerator) would reside in “probability space.” Shakespeare’s sonnets are typically about 120 words; therefore the possible number of word configurations is immense  roughly 10 to the 600th power (assuming 100,000 words in the language). But without knowing the numerator, i.e., the set of possible coherent sonnets, a final probability cannot

be established.


These are valid points that Neo-Darwinists can make. But they fall far short of settling the matter. Because of the interdependencies of living systems, there are constraints which significantly diminish the number of solutions possible, i.e., the set of overall possible genetic configurations, in an already existing system. With constraints, the numerator becomes smaller because the range of viable beneficial mutations is a smaller set. That means that there is a much smaller set of viable mutations within the overall set of possible mutations that could produce a gene whose protein product contributed to the enhancement of a minimally functioning

biologic feature. Severe constraints in effect form a target because the range of viable mutations is narrowed. As the constraints become severe, calculating probabilities becomes more plausible. Why? Let us take Shakespeare’s Sonnet 18 as an example:

Shall I compare thee to a summer’s day?

Thou art more lovely and more temperate:

Rough winds do shake the darling buds of May,

And summer’s lease hath all too short a date:

Sometime too hot the eye of heaven shines,

And often is his gold complexion dimmed;

And every fair from fair sometime declines,

By chance or nature’s changing course untrimmed;

But thy eternal summer shall not fade

Nor lose possession of that fair thou owest;

Nor shall Death brag thou wanderest in his shade,

When in eternal lines to time thou growest:

So long as men can breathe or eyes can see,

So long lives this and this gives life to thee.


Suppose that the entire sonnet had been completed except for the last line. The set of word combinations that could offer enhanced meaning to the sonnet is quite small compared to the overall set of possible word combinations because of the constraints imposed by the existing sonnet.  The words have to equate to the same number of syllables, they have to have meaning in the context of the sonnet, and the words should have that Shakespearian elegance. For an additional set of characters to have value, in this case to enhance or complete the meaning of the sonnet, it is probable that the additional line has to occur by chance in its entirety.


Natural selection cannot select on the basis of some configuration of genes/proteins based on their potential. There isn’t a scenario where you could incrementally improve the meaning word by word unless you commit the folly of invoking

a target, in other words selecting the words “So long” knowing that they would fit within the context of the target phrase “So long as men can breathe or eyes can see.” Any distinct mutation has to result in a gene whose protein product provides clear survival value at the present moment for that biologic feature. A mutation that provides some value may lead to a dead end in the long run. You may think that a small set of words has a nice ring to it and some promise for a sonnet, but you might find that once selected, it cannot be enhanced and integrated into an existing sonnet.


If the entire replacement of a line has to occur by random means by adding random words, the probability barrier is immense (roughly one in 100,000 to the 10th power [10 to the 50th power]). It is not easy to translate these probabilities to human evolution, for example, because there are a variety of other factors; but given the small population size of hominoids and the generational cycles, one chance in 10 to the 50th power would easily qualify as an insurmountable barrier. The total number of hominoids since the split from the branch leading to chimps and the branch leading to humans has been at most ten trillion individuals and probably much fewer. Ten trillion is too low of a population size to overcome a probabilities barrier of 10 to the 50th power. The analogy using a single sonnet and selecting out letters or words to simulate natural selection is greatly simplified because, in an already functioning organism there are many biologic attributes in the overall phenotype (structures and functions) of a creature that vary, and many other functions that interoperate. To carry the analogy forward, you would have to imagine a single coherent work, such as an entire Shakespearian play. As random changes are made to various acts and scenes (during republishing for example), the question arises as to which of the many varying texts of  the play are being  assessed for selection, analogous to which of the many varying attributes of a living organism are being selected, based on the improved fitness they offer. A minor incremental change in one scene of the play may be drowned out in the aggregate variation of the rest. This factor makes Neo-Darwinism less tenable because natural selection would not seem to have the acuity to select out multiple specific varying attributes. Fitness (survival) in the Darwinian sense is a binary  function; either you survive and reproduce or you do not. So an organism with one favorable novel mutation may not survive because other varying traits which regularly vary have acted to diminish its survivability, then the fortuitous mutation would have to occur again by chance. Falsifying Neo-Darwinism distills down to whether or not there are cases—many cases—where multiple (simultaneous) mutational changes are required to offer minimal selective advantage. The underlying question is: Is it reasonable to believe that complex organisms, while seeking immediate fitness through natural selection, will not often find that the genes which code for the development of a nascent feature (such as a primitive eye) become stranded, alone in genetic probability space and distant—multiple (simultaneous) mutations away—from any other viable adaptive enhancement?

If complex biologic entities cannot be built up stepwise (incrementally) using only one or a few mutational changes at a time that can be selected out—locked in—by

natural selection, then Neo-Darwinism is utterly implausible. Can biologic functions be built stepwise through random chance and selection?


App lying Probabilities to Biologic Systems


Michael Behe, a molecular biologist and proponent of Intelligent Design, uses the term “irreducible complexity” to describe molecular machines that are so complex that they cannot be assembled by random piecemeal processes such as Neo-Darwinism. The systems he cites in his books Darwin’s Black Box12 and The Edge of Evolution,13 such as the tail on the end of a bacterium, are comprised of many components—over a hundred proteins. Generally there is some slack in biologic systems, i.e. lack of specificity within each gene (not all amino acids in a protein string matter) and within an overall molecular system (not all proteins are  essential); but in the case of the cilium, many of the components appear to be essential to proper operation. The pieces are very tightly interdependent, i.e. they have a high degree of specificity.


Dr. Behe created a firestorm throughout academia by proposing that Neo-Darwinism cannot account for complex molecular machines. The entire academic biological community circled the wagons to defend against Behe’s thesis and denied there was any problem at all for Neo-Darwinism to create complex living features. Claims abound that such evolutionary scenarios have been well documented throughout the peer-reviewed literature. But when the curious began looking for these accounts, it appeared that such accounts were as common as unicorns. James Shapiro, a geneticist at the University of Chicago, agreed with Behe saying, “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful  speculations.”12 It should be pointed out that Dr. Shapiro is a secular scientist and critic of Intelligent Design.


William Dembski has used Behe’s insights about molecular machines and arrived at a tentative probability for the cilium. The calculations William Dembski has arrived at are quite unsupportive of neo-Darwinism. They are beyond the universal probability bound, which is the theoretical barrier for any stochastic (random) process. The universal probability bound is 10 to the -150th power. The universal probability bound takes into account the number of particles in the universe, the age of the universe and the smallest time increment, “Planck Time.” A much lower probability barrier—on the order of 10 to the -43rd power—is often regarded as a

more realistic limit as to what is possible, however. What makes the probabilities so poor is that when you have mutual dependencies, in other words, multiple things that have to happen simultaneously, the probabilities are the product of the two events, not the sum. And life systems are full of interdependencies.


The Neo-Darwinian Response to Intelligent Design


Many words have passed in the debate between neo- Darwinism and Intelligent Design. Most have been quite unpleasant and many downright venomous, especially those from the neo-Darwinian camp. Both sides have an agenda that results in introducing philosophy into science. Stephen Meyer points out that Neo-Darwinists who are signatories, either in letter or spirit of the humanist manifesto, are as guilty of injecting philosophy into science as Christians or Jews who advocate Intelligent Design. Their respective arguments should be assessed on the basis of the evidence they present.


Argument from Authority


Aside from ad hominem comments, and being dismissive about Intelligent Design, Neo-Darwinists often argue from a position of authority by pointing out that there is a clear scientific consensus on Neo-Darwinism. While the Intelligent Design camp can cite many hundreds of credentialed scientists who question Neo-Darwinism, Neo-Darwinists counter by presenting a longer list of scientists whose first name is “Steve” (in honor of the late Stephen J. Gould) that support Neo-Darwinism. However, many of the newer theories being advanced by researchers seek to fill in, and in some cases overhaul, Neo-Darwinism. Therefore, there is a tacit admission that Neo-Darwinism, in its conventional form, cannot explain the complexities of life. This is a claim Creationists and Intelligent Design proponents have been making for decades. Much, or most, of what Neo-Darwinists have been saying, with the greatest degree of confidence, about how we came about, appears to be incorrect. To highlight this point, I can mention that James Shapiro has  recently said that, “Richard Dawkins is a man who lives in fantasy.”15The credibility of many scientists is certainly in question. What remains to be determined is whether the credibility of science itself is in question by virtue of their strict adherence to methodological naturalism.


Conflating Intelligent Design with Creationism and

Conflating Evolution with Neo-Darwinism


A common approach by Neo-Darwinists in dealing with Intelligent Design is to conflate Intelligent Design with Creationism, and conflate evolution with Neo-Darwinism. The goal is to debate the issue in public on the basis of evolution,

i.e., common descent rather than the neo-Darwinian mechanism of random mutation and natural selection.  However, the leading Intelligent Design theorists (William Dembski, Stephen Meyer, and Michael Behe) have been very clear about what Intelligent Design is. They have pointed out repeatedly that Intelligent Design is compatible with Darwin’s principle of common descent.


Counter-arguments on Probabilities


Neo-Darwinistshave a variety of responses when confronted by evidence purporting to show the rather poor probabilities that random mutation and natural selection can account for all the wonders of life. One tactic is to point out that highly improbable things  happen every day. If you think of all the things that happen in a baseball game, for example, any particular outcome is wildly improbable. Similarly any particular outcome of a series of a thousand coin flips is wildly improbable given the number of possible outcomes (about 1 in 10 to the 300th power). Is this a valid point? No. Any specific outcome is wildly improbable, that’s true. However, some sequence is a certainty if one flips a coin a thousand times. But any one series of coin flips is as likely as any other; no outcome is unique in any way. The complexity of any outcome is low because the information content and specificity are low. There are no dependencies between each distinct flip. However, if all one thousand coin flips landed heads, do you think that would raise an eyebrow or two? Another tactic is to use some game of chance such as

dice and draw the distinction between having to roll, say, ten dice of the same number in one roll, e.g., ten sixes, which would have a very low probability, versus having to achieve ten sixes over a series of rolls of ten dice, but being able to select out each six as it occurs, thus simulating natural selection. There are a couple of problems here. First off, selecting out sixes is invoking a target, which is prohibited in contingent processes. Secondly, the threshold of selection in biologic

entities is certainly much higher than a distinct event such as a roll of six.


Deep Time”


The reason Neo-Darwinism seems plausible despite even our current understanding of the ever increasing complexity of life systems is because of the amount of time available. Random mutation and natural selection, along with “deep time,” might seem plausible. After all, mutations might be very small and could accumulate using the benefits of natural selection. Mutations can be small because there is ample time—hundreds of millions of years—for them to occur, it

would seem. But how much reliance can be placed on time, even when there is lots of it? To gain some insights into how powerless chance is, even given lots and lots of time and opportunity (population size), we can revisit Thomas Huxley’s remark that a million monkeys could type the complete works of Shakespeare given  enough time. He was quite incorrect on this unless you assume eternity. But let’s say you could marshal together, not just a million monkeys, but all the primates that have ever lived on earth—guessing about 50 trillion—and have them type away continuously on a typewriter for the entire age of the universe. Do you think they could even type just the phrase The Complete Works of William Shakespeare? The answer is No; not even close. This example uses a target, so it really is not intended to be any sort of proof. But if we were to suppose that at some point, evolution—and more importantly the development of life, which does not have the benefits of natural selection, at least in the early stages—would have encountered barriers whose complexity and constraints were comparable to that exercise, we can assess that progress toward life would have been stalled. What is really important is the population size, not necessarily time. Population size depends on the size of the organism and the reproduction rate. The parasite that causes malaria has extraordinarily large population sizes (about a trillion in each infected person, and there are hundreds of millions of infected persons a year). Yet over the course of thousands of years it hasn’t changed much. It has been able to mutate around human created medicines when there are only a few mutational changes required. But even with its enormous population sizes (and therefore great opportunity for mutation), malaria has not been able to mutate around sickle cell.13


Storytelling and Computer Models


The empirical evidence Neo-Darwinists have for how random mutation and natural selection can build an eye incrementally, for example, is quite light, to be  charitable. There are no mutations that have occurred in the lab that might offer such evidence, and no fossil sequences. The fossil record does depict a variety of eyes of varying complexity but no evidence of a sequence between them.  Therefore, neo- Darwinists have to rely on computer models supplemented with storytelling. Richard Dawkins updated Darwin’s eye story in his book, Climbing Mount Improbable14 and uses computer models which purport to show that a complex eye could evolve quite quickly. Typically these accounts are quite simplified, ignore interdependencies between other associated functions in the

eye and in the organism, and focus on higher-level gross anatomy rather than the molecular details. There is an adage that engineers commonly use: “The devil is in the details.” Using our Shakespearian play analogy it is far easier to imagine how a play might be constructed by focusing only on the Acts and Scenes rather than the dialog and character development.


Counter-arguments to “Irreducible Complexity”


Were you to Google Michael Behe and irreducible complexity, you would no doubt be inundated with information claiming that the concept has been debunked. “Debunking” irreducible complexity for Neo-Darwinists means that neo- Darwinists have been able to present a potentially plausible account as to how such complex structures could have evolved. These claims involve the phenomenon of “expatiation,” or co-option, which is the common observation that genetic components are often reused or repurposed throughout the history of life. Recent research has shown that there are far fewer genes in the genomes sequenced thus far than would have been expected given the complexity of living entities.

The reason for this is the ability of living organisms to reuse and reassemble gene components—like Legos—into new genes that code for additional complex proteins.


Neo-Darwinists claim that reuse and repurposing—  rather than the creation of new genes—supports a materialist explanation because they no longer have to explain some of the tough questions about how the many genes for a complex molecular machine or organ can be created, by modifying DNA piecemeal. Integrating many existing pieces to create complex functions may in fact be easier than assembling them anew; but it is far from easy. Using our Shakespeare example, I would not expect to be able to cobble together his complete works from a handful

of his sonnets by randomly duplicating and realigning the existing words. Intelligence is required to find and select which bits of prose are relevant, and which portions organize them in a coherent way, assemble them in one unified

piece, and then integrate them within the acts and scenes of the various plays. Beyond that, Neo-Darwinists still have to explain how the genes arose in the first place and how the mechanism for re-use arose.


Evidence for Mutation


When it comes to presenting evidence for random mutations, Neo-Darwinists say that mutations are not a problem. Yet few, if any, random mutations of any   consequence have ever been observed in the lab. Neo-Darwinists often point to mutations in antibiotic resistance as evidence for mutation, and evolution, in general. Antibiotic resistance mutations and virus mutations were all that was presented as evidence in the Darwin exhibit that was making its rounds in the various museums. The mutations associated with antibiotic resistance really shouldn’t count because, in all but a few trivial cases, there is no additional complexity (no new information content) added to a bacterium, or the eukaryote micro-organism that causes malaria, for example, when a mutation occurs that confers resistance against antibiotics. In the vast majority of cases, when a bacterium achieves resistance to an antibiotic through mutation, the mutational change is a degradation of functionality, i.e., one of its proteins or enzymes is broken in some way.


Neo-Darwinists often cite the variation seen in animals, especially domesticated animals, as evidence of the type of mutations that can generate complex features of living creatures. This is a peculiar response because the variation within a species is simply varying the existing attributes of an animal. Nothing new is created. It is like rewriting an existing novel by changing the names of the characters, the setting, the time period, and trying to pass it off as a new and important piece of work. This is plagiarism, not creativity. If anything, breeding domestic animals shows the limitations of variation in that there are limits to what you can do with

a dog, for example. They can be big, small, mean, nice, fast, slow, long-haired, short-haired, smart, and not-so-smart, but a female dog will always give birth to another lovable puppy dog.


So it seems there is reason for doubting the ability of neo- Darwinism to create these wonderfully complex features of life. However, I have found that no point made by Intelligent Design scientists, regardless of how seemingly sensible, ever

goes unchallenged; nothing is ever conceded by strict neo- Darwinists. This alone should raise a red flag.


Imperfect Design

Citing “imperfect design” is another staple of neo- Darwinists when arguing that life is the result of chance mutation and natural selection rather than design. A common claim is that the mammalian eye is configured in an imperfect way such that there is a blind spot. “No tidy engineer would design an eye in that manner,”


Neo-Darwinists claim. This claim is contested but the matter is not settled. As any engineer can point out, there are always trade-offs when trying to balance out a variety of alternatives and constraints that invariably arise in complex systems. One wonders how fragile Neo-Darwinism is, if a rather minor anomaly in our eyes is a featured item in its defense. When I reach the Pearly Gates, I may have some advice for those responsible for implementing life on earth, but offering a critique about the blind spot in my eye would not be one of them. Had I not been told about the blind spot I would not even know it existed. 


Darwinists have also noted that DNA contains a lot of chunks which do not code for proteins. They called this “junk DNA,” and pointed out that a lot of useless remnants of DNA is exactly what one would expect from a random process, but you would not expect this if life forms were designed. Richard Dawkins made much of this in his book, The Selfish Gene.15


The problem for Neo-Darwinists is that recent research is showing that a good deal of this non-coding DNA is not junk, but very useful for a variety of regulatory functions. So not only does the useful concept—useful for neo- Darwinists—of junk DNA seem to be going away, but at the same time, many of these DNA chunks are used in complex ways never imagined. The greater the complexity, the greater is the inference of design. This is a case where methodological naturalism has stalled scientific progress. Had scientists adopted a wider range of potential hypotheses, such as design, as suggested by Intelligent Design advocates, they

might very well have discovered that “junk DNA” had a useful function much sooner.

Brutality of Struggle for Existence, and Pain and Suffering


There is a general uneasiness expressed by many Darwinists about the brutality of the struggle for existence. Darwin himself made mention of this. There are some points to be made here, especially when considering that many forms of life—such as the malaria parasite—have exacted a severe toll on humanity. How can one reconcile a view that parasites such as malaria are the result of design, even if indirectly, while at the same time seeing the pain and suffering they cause? This is not an easy challenge for Theists to address. Generally, arguing against design based on the brutality of the struggle for survival and human suffering, presumes a specific knowledge about the designer and His methods, intentions and capabilities based on some assumptions that may not be accurate. Pain and suffering exist; no one denies that. But a design philosophy only has to be consistent within itself. Theism does not have to be consistent with the sentiments of a secular Humanist who views this life to be the end of our existence. From a Theistic perspective,  pain and suffering either must have a purpose (have value), must be unavoidable, must be the product of an imperfect designer, or any mix of these. The purpose and inevitability of pain and suffering is clearly lost on many of us. Perhaps only in light of one’s eternal salvation and understanding the Divine plan, could such a thing be fully understood and appreciated.


Inference of Design


What should be clear by now is that falsifying neo-

Darwinism is difficult. It may be an intractable problem. In

that case, perhaps the best we can do is to make an inference

as to how we arose. Such an inference could help us assess

whether science’s adoption of methodological naturalism is

appropriate. The relevance is that if scientists are incorrect

in adopting methodological naturalism as a paradigm, and

the universe has in fact been intelligently designed, then

adhering to such a paradigm greatly limits the array of hypotheses

to drive empirical experiments. We can expect that

scientific progress would be stalled in that case.

How could one make an inference of design versus

chance? One way would be to look at the attributes, i.e., the

structures and functions of life, and assess whether they exhibit

the signature of design or chance. There are two general

attributes to look at: 1) Complexity and 2) Causation.

What Is Complexity?

Complexity is essentially information content. One way

of understanding information content is by assessing the

amount of human text required to explain an object or system

completely and efficiently. A biology text book is a reflection

of the complexity of that which it describes. Imagine

that you were writing a comprehensive book on biology that

covered all aspects of the science in full detail. You might

first assemble all the distinct facts about biology. Distinct

facts are the phrases, sentences, or paragraphs describing a

biologic concept. You could think of them as being analogous

to genes or gene fragments in biology. There are no

doubt hundreds of thousands of such facts pertaining to


Complexity increases as these distinct facts or statements

accumulate. Assembling them is only a part of the

overall task of writing a text book, and therefore, only a part

of the overall complexity. A collection of unassociated facts

is data, but not information. The transformation of distinct

factual statements to information requires that you apply significantly

more intelligence to the enterprise in order to correlate

and associate all the data. Complexity increases as you

arrange the statements in the proper order, under the proper

heading, placed in the proper section and proper chapter.

Complexity is proportional to the amount of data and the

coherent arrangement of data into information.

Correlating data into information involves describing

the inter-associations between the data. There are various

ways in which components (or data) are inter-associated.

Some inter-associations are peer-to-peer in nature, where

interdependencies between components require that several

other components be present. There are many molecular

machines that have multiple components. Often knocking

out any one of these components causes the machine to

malfunction, or not function at all. In a text book, interdependent

facts, where you cannot understand one without

the other, would have to be covered in the same paragraph

or section and in the proper order, or the conveyance of information

would be adversely affected.

Imagine the relative complexity in describing in human

text the components of a watch that had been randomly

Summer 2011 • The Fellowship Herald • 39

placed on a table, compared to having to explain these same

components operating in a functioning watch. Looking at

this another way; imagine the relative difficulty in designing,

engineering and manufacturing a set of components for a

watch that do not have to interoperate, versus a set of components

that do have to interoperate.

The analogy of a textbook, and the biological systems

it describes, greatly understates the complexity of biologic

systems because living systems reproduce and metabolize. A

more accurate analogy between biology, and the creation of

a biology textbook, would be to write a computer program

used in a printing machine that creates a perfect bound biology

textbook, by printing each page, and making each page

from scraps of wood fed into it. Here, you have added significantly

to the complexity.

What about Causation—Final Causes?

The second major attribute to look at when assessing

whether living systems are the result of chance or design is

causation. Neo-Darwinismis a random chance process, so

its causation is said to be “contingent.” A process reliant on

contingent causation is aimless, i.e., there is no direction,

no target, no certainty of anything. Final causes—teleology—

on the other hand implies that intelligence has been

imparted into a process, or system, somewhere, that directs

the process toward a final end, or series of ends. Evidence for

causation can be obtained from research through the study

of current living forms and by examining the fossil record. A

process governed by final causes would exhibit the characteristics

discussed below.


Pattern is repeatability, i.e., the same thing(s) occurring

over and over. In the context of biological systems, pattern

would imply that the same sorts of complex living features

and entities evolved over and over again.

Final forms:

Final forms describes a phenomenon characterized by

trends toward some defined end with little change after the

end has been attained. In the context of biology this would

imply that evolution stops at some point after reaching its

final form.


Foresight describes a characteristic about the manner in

which things are constructed. Are living systems built from

the bottom up or the top down? Is there a hierarchical arrangement

in the functioning of associated living systems

within a living entity? Human artifacts and machines are

built using top-down design. An analogy to top-down systems

might be the way in which human construction is carried

out; the blueprints precede the building; framing precedes

the trim.

Modularity and Reuse:

This attribute describes the characteristic of reusing distinct

modules in various ways to assemble things. Modularity

and reuse is common practice in human engineering. Walk

into any telecom central office in the world and you will see

a series of aisles, with racks, and shelves and modules. The

same modules are reused over and over. And if you were to

open any of these modules you would find the same components:

integrated circuit chips, the same wires, and circuit

boards. And if you looked further into the virtual “construction”

of the software you would find the same programming

components used repeatedly.

Pattern, final form, foresight, and modularity are characteristics

of human engineering. It is hard to imagine that

these same methods would happen to be stumbled upon by a

chance-based process, nor were such methods ever predicted

by Darwin or any of his successors. Yet biological research

is finding these characteristics are quite common in living

systems. In fact, it is difficult to imagine how complex living

systems could function without it. Interestingly, there is an

engineering discipline whose purpose is to derive engineering

principles from biologic processes.

Let’s take a look at these two attributes—complexity

and causation—in more detail, with respect to biological entities,

to help us assess whether living systems are more likely

the result of chance or design.

Complexity in Living Systems

Living systems are highly complex. No one denies that.

Developmental biologist Sean Carroll, and many others who

have offered comment, state that living systems far exceed

the complexity of any human artifact. Dr. James Shapiro of

the University of Chicago characterizes the complexity of

even the most primitive cells as “astounding” and “unimagined.”

Bruce Alberts, President of the National Academy of

Sciences, has said, “We can walk and we can talk because

the chemistry that makes life possible is much more elaborate

and sophisticated than anything we students had ever


The origin of life is outside the scope of this article but it

is tangential to the topic of evolution. The most difficult part

of “evolution” is the origin of life because natural selection

is not available, at least initially, to assist in the development

of complexity. When asked what the best scientific explanation

for how we get from inanimate matter to the simplest

form of life, Richard Dawkins responded that, “We have

no explanation for that.”18 Harvard Systems biologist, Marc


Kirschner, says that, the novelty and complexity of the cell is

so far beyond anything inanimate in the world of today that

we are left baffled by how it was achieved.

Evolutionary biologist Eugene Koonin, for example,

claims about the origin of life:

“Origin of life is a chicken and egg problem: for biological

evolution that is governed, primarily, by natural selection,

to take off, efficient systems for replication and translation

are required, but even barebones cores of these systems

appear to be products of extensive selection…no compelling

scenarios currently exist for the origin of replication and

translation, the key processes that together comprise the

core of biological systems and the apparent pre-requisite of

biological evolution.”19

Koonin continues in describing the probabilities of assembling

a pre-requisite life form based on a quick “toy”

modeling and concludes that they are less than 1 in 10 to the

1018th power. This is well beyond the universal probability

bound. Yet if materialist scientists cannot explain the origin

of life, then not much else matters.

Complexity of the Prote ins

Even at the most fundamental level—protein synthesis

or translation—the complexity is impressive. Cells use the

genome to make proteins (enzymes) to carry out all their

vital functions and to form their structures. Amino acids

(protein building blocks) are synthesized, then DNA is copied

(transcribed) to RNA, and then transported to specific

locations within the cell for translation and assembly.

Transcription involves multiple phases, each regulated

by a large number of proteins. Transcription is accomplished

for both the protein unit itself and also the associated regulatory

proteins. Error detection and correction mechanisms,

conducted by many specialized proteins, are present to ensure


Following transcription, and before protein synthesis

or translation occurs, specialized proteins splice out the

non-coding sections in the mRNA prior to arrival at the

ribosomes for translation. Translation also involves multiple

phases—activation, initiation, elongation, and termination—

using associated enzymes.

Following translation, proteins must be folded in the

proper configuration. Protein folding into a three-dimensional

structure is essential for proper function. The process

depends on the presence of molecular “chaperones”.

Chaperones are proteins that assist the folding or unfolding,

and the assembly or disassembly, of other macromolecular

structures such as protein sequences.

Note the dependencies of multiple essential proteins

involved in the overall process. We have to ask which of

these essential and mutually dependent proteins came first.

No one knows.

Complexity of the Cell

The functions of even the simplest cells are immensely

complex. Cells have complex life cycles with many inter-associations.

Cells divide to create two new daughter cells.

First they replicate their DNA beginning at specific locations

with specific sequences. They use specialized proteins (enzymes)—

many of them—to find the correct locations to initiate

the replication process, which occurs at rate of 100 base

pairs per second, with less than one error in ten billion base

pairs in humans, for example. The cell division process has

phases which are gated by checkpoints (decision points), and

error detection and error correction. The process continues

only when things are proceeding properly. Failure to meet

the criterion of a checkpoint means the process is delayed.

All throughout this process the cell has to continue gathering

nutrients to sustain the new daughter cells and continue

to perform its functions within the overall organism.

Cell division is a cognitive process which requires central

control, precise timing, decision making, and communication

with the various processes and components throughout

the cell to ensure success. It requires the coordinated

effort of dozens and dozens of enzymes and other molecules.

Where did the high-level control algorithms come from?

How did the signaling system evolve? Which enzymes came

first, if they are all either dependent, or mutually dependent,

upon one another? How can a complex process, with all

these components and specific inter-associations, be built incrementally

as required by neo-Darwinism? No one knows.

Complexity of the Eye

Charles Darwin said to suppose that the eye with all its

inimitable contrivances for adjusting the focus to different

distances, for admitting different amounts of light, and for

the correction of spherical and chromatic aberration, could

have been formed by natural selection,20 seems, I freely confess,

absurd in the highest degree.

The basic description of how the eye works provided in

Wikipedia is quite good and to the point:

“The eye is a complex optical system which collects light

from the surrounding environment; regulates its intensity

through a diaphragm; focuses it through an adjustable assembly

of lenses to form an image; converts this image into

a set of electrical signals; and transmits these signals to the

brain, through complex neural pathways that connect the

eye, via the optic nerve, to the visual cortex and other areas

Summer 2011 • The Fellowship Herald • 41

of the brain.”

The eye uses many complex components to carry out

this complex cascade, all of which fit tightly together and

interact with multiple dependencies and interdependencies.

Not only does each part of the eye have to fit and interact

with one another, but they also have to interact with other

organ systems in the creature, and, in fact, the eye is directly

dependent on several of these systems. The function and operation

of the eye is dependent on the brain, nervous system,

the musculature system and circulatory system for its operation,

and needs to be positioned properly with respect to the

skeletal structure and skin. These systems are dependent on

one another and have interdependencies within themselves.

Which of these systems and components came first? No one


The complexity of a functioning eye is only part of the

story of the overall complexity of the eye. The organism has

to create the eye during development. Imagine the complexity

involved when an organism builds a complex organ such

as the eye as the organism itself grows. Each piece has to

grow and continue to fit, operate and interact as it grows

with other components and with other systems within the

organism. Each cell has to know what type of cell to differentiate

into, and where to locate itself in relation to all

the other components and structures in the organism. Each

cell also has to know when to stop dividing. There is a set

of master control genes that initiate the entire development

process. The process is controlled through a signaling network

between cells and a signal transduction network within

each cell. These signaling networks control events related

to the form and function of the developing organ precisely

through time and space.

The question arises: Which of these equally essential

systems and components came first, the components of the

eye—if so, which ones—the control gene that orchestrates

its development or the signaling networks used to facilitate

this control? Did the circulatory system, musculature system,

and skeletal structure, and nervous system evolve first to facilitate

an eye? No one knows.

Complexity of Development

Living systems add another dimension to complexity

compared to human artifacts in that they have to grow from

a single cell. This greatly increases the complexity. The analogy

with human artifacts is that not only do you have to

consider the complexity of the device itself but also the complexity

of the engineering, manufacturing, and maintenance

processes used to create and sustain it.

By examining the development of the common fruit fly

and other animals, scientists have discovered a complex, hierarchical

series of control genes that orchestrate the development

of not just each organ system, but the entire organism,

all from the top down. The high-level pattern is laid out

first, and gradually the development of the animal proceeds

to each distinct part. The process is controlled by genetic

regulatory components or right “toolkit.” The products of

these genes determine the fate of each cell, with intermediate

stages through spatial patterns throughout time, to create

the overall body plan, tissues, and organs. The process

involves a multitude of proteins used for communicating between

cells and defining the fate of “undifferentiated” cells

by determining which genes are expressed.

For any human engineer developing a device with even

a hint of the complexity of living systems, these problems

would be intractable. The dependencies and interdependencies

are numerous. The “morphogenesis” process has been

described as: A spectacular process and a masterpiece of

temporal and spatial control of gene expression.22 But materialist

scientists claim that to attribute this astounding

complexity to prior intelligence is to engage in a championship

level of error. Chance mutations, natural selection, and

“deep time” are all that’s needed, they assert.

In each of the examples of the complexity of core biologic

functions described above, there are many essential

proteins. The presence of multiple proteins means there are

many independencies which result in severe constraints.

Severe constraints greatly limit the range of viable mutations

that can contribute to an enhancement of a feature.

Limiting the range of viable mutations significantly reduces

the probabilities for building complex features in a chance


How Fast Did Complexity Arise?

Neo-Darwinistsoften point out that there is ample

amount of “deep time” necessary to enable very small mutations

to accumulate, using the benefits of natural selection.

Copious amounts of time could make a chance-based process

plausible. Therefore, the plausibility of neo-Darwinism

can be envisioned as being inversely proportional to a ratio

of complexity over time. The higher the ratio of complexity

over time, the greater is the inference of design. The lower

the ratio, the more plausible Neo-Darwinismis. Discoveries

that show life systems to be more complex diminish the

plausibility of neo-Darwinism. Any discovery that restricts

the time over which complex life systems evolved also makes

Neo-Darwinismless tenable. But how much time was really

available and how fast did evolution occur? The fossil record

shows that evolution occurs in fits and starts. Changes ocSummer

2011 • The Fellowship Herald • 42

cur in sudden bursts. New complex adaptations appear fully

formed in the fossil record. Stephan J. Gould referred to

“the extreme rarity of transition fossils” as the “trade secret

of paleontology.”23 He developed the theory of punctuated

equilibrium to explain these gaps. Gould claimed that evolution

occurs more quickly, and at the species level, in smaller

populations which have become isolated. Larger populations

diminish the effectiveness of natural selection and dilute

beneficial mutations through genetic drift. Punctuated equilibrium,

in my view, is really just a shell game which emphasizes

the benefits offered by natural selection in small

populations at the expense of the problems associated with

random mutation in small populations. Smaller populations,

Gould reasoned, would evolve faster and leave fewer fossils.

The problem he glosses over is that beneficial mutations in

smaller populations would be less frequent, which would

slow evolution down.

The term “transition fossils” does not imply any sort of

a gradual continuum of the evolution of a complex feature

predicted by Darwin. It is less ambitious than that. A transition

fossil is any fossil that can be used to show that this

creature is probably a descendant of this one and ancestral

to that one. While it is true that there are large gaps in the

fossil record, the record is adequate to demonstrate the truth

of Darwin’s theory of common descent.

The most notable case of rapid evolutionary change

is the Cambrian Explosion where most of the major Phyla

arose rather suddenly within a relatively short time. Phylum

is the highest level category of animals below kingdom and

above class. The short time was initially about 5 to 15 million

years. It seems some paleontologists have stretched this

a bit up to as much as 80 million years. How much of this

is real, or wishful thinking engendered by a discomfort with

a more compressed timeframe, is hard to say. In any case,

the Cambrian did usher in a rather impressive array of new

and complex animal forms. But the timeframe whether it

is 5 to 15 million years or 5 to 80 million years, is not to

imply that there is a fossil record of a gradual unfolding and

development of these creatures throughout that length of

time. Rather the 5, 15 or 80 million years is the limitation

of the granularity of the fossil record. If you were to take

the fossil record at face value, these new creatures appear

instantaneously with no evidence of a gradual accumulation

of complex features. Trilobites, for example, appeared

all at once and they had eyes, a heart and circulatory system,

digestive system, nervous systems, etc. The question arises

as to how all these organs with all their dependencies and

interdependencies arose as an ensemble without a trace. No

one knows.

While the fossil record shows a compressed timeframe

of the Cambrian Explosion where many new creatures with

complex features suddenly appeared, the extent of the compressed

timeframe may forever remain undisclosed because

of the limited granularity of the fossil record. Therefore the

fossil record is not a definitive measure of how fast complexity

arose. However, had the fossil record depicted a gradual

incremental accumulation of complex features as Darwin

predicted, that would be an important piece of evidence for


Recent research using genetic sequence appears to support

what the fossil record depicts, that complex life systems

have arisen quite suddenly. Marc Kirschner says that innovation,

such as “the first eukaryote cells, the first multi-cellular

organisms, large bilateral body plans in animals, the

neural crest cells in vertebrates…[arose] in a few waves of


Evolutionary biologist Eugene Koonin likens the evolutionary

process to Big Bang cosmology. His paper is illustrative

in that it is quite frank and honest. The following is

a quote from a technical paper authored by Koonin which

summarizes his view. Following the quotation is an exchange

between a reviewer and Koonin about the frankness

in admitting that evolutionary change, up to and through

the Cambrian, was non-Darwinian i.e., not gradual or incremental.

Referring to the origin of complex RNA molecules

and protein folds; major groups of viruses; archaea

and bacteria, and the principal lineages within each of these

prokaryotic domains; eukaryotic supergroups; and animal

phyla, Koonan says:

“In each of these pivotal nexuses in life’s history, the

principal “types” seem to appear rapidly and fully equipped

with the signature features of the respective new level of biological

organization. No intermediate “grades” or intermediate

forms between different types are detectable….There

seems to be a striking commonality between all major transitions

in the evolution of life. In each new class of biological

objects, the principal types emerge abruptly, and intermediate

grades (e.g., intermediates between the pre-cellular stage

of evolution and prokaryotic cells or between prokaryotic

and eukaryotic cells), typically, cannot be identified.”

Reviewer William Martin, University of Duesseldorf’s

comment on Koonin’s paper:

“In each major class of biological objects, the principal

types emerge ready-made, and inter-mediate grades cannot

be identified. Ouch, that will be up on Intelligent Design

websites faster than one can bat an eye.”

Koonin’s response to the reviewer:

“Here I do not really understand the concern. I changed

Summer 2011 • The Fellowship Herald • 43

“ready-made” to “abruptly”, to avoid any Intelligent Design

allusions and added clarifications but, beyond that, there is

little I can do because this is an important sentence that accurately

and clearly portrays a crucial and, to the very best of

my understanding, real feature of evolutionary transitions…

if our goal as evolutionary biologists is to avoid providing

any grist for the Intelligent Design mill, we should simply

claim that Darwin, “in principle”, solved all the problems

of the origin of biological complexity in his eye story, and

only minor details remain to be filled in. Actually, I think

the position of some ultra-Darwinists is pretty close to that.

However, I believe that this is totally counter-productive and

such a notion is outright false. And, the Intelligent Design

folks are clever in their own perverse way. They see through

such false simplicity and seize on it. I think we (students of

evolution) should openly admit that emergence of new levels

of complexity is a complex problem and should try to work

out solutions some of which could be distinctly non-orthodox;

Intelligent Design, however, does not happen to be a

viable solution to any problem.”22

This passage and exchange are extraordinarily revealing.

First off, the transitions he is talking about, the origin of

complex RNA molecules through the appearance of animal

phyla in the Cambrian, include all the really tough stuff. The

rest is “window dressing.” Secondly, note that recent science

is supportive of Intelligent Design because complexity is

being shown to have occurred rapidly—“ready made.” All

the really difficult biologic features occur abruptly. Third,

here are two scientists considering ways to describe the rapid

appearance of complexity in a manner that diminishes

(to some extent) the fact that scientific findings are supportive

of Intelligent Design and very unsupportive of any

material-based theory of evolution. Fourth, note the scorn

for Intelligent Design—“no solution to any problem”—yet

Intelligent Design is the one theory whose underlying principles

offer the best hope of explaining rapid complex changes

while the theory embraced by materialist scientists for

decades—neo-Darwinism—has suffered great harm. And

the Intelligent Design folks are called “perverse.” Finally, the

overall tone of the exchange clearly illustrates how wedded

science is to the methodological naturalism.

Final Causation in Living Systems

Final cause or teleology is another attribute by which

we can make an inference as to whether we are the result of

design or chance. Foresight, pattern, reuse, and modularity

are common engineering techniques and these same techniques

have been shown to be important features of life. The

more reuse, modularity and especially pattern and foresight

are exhibited in the way life evolved, the greater is the inference

of design.

Foresight and Final Causes Exhibited by Development

Human engineers build things from the top down,

meaning that they create the high-level design of a system

first, and then specify the underlying details. Recent scientific

discoveries show that evolution has managed to discover

a similar common sense approach to constructing complex


There are many types of eyes in the animal kingdom.

Until a couple of decades ago, evolutionists believed that the

eye evolved independently anywhere from 50 to 100 times

through the Cambrian. Recently it was discovered that there

is a control gene that initiates the development of the eye,

and this control gene is common to all animals. Given this

information, the principle of common descent requires that

all eyes must have had a common ancestor with a proto eye,

or a very primitive eye—little more than a light-sensitive

spot. This is the most primitive animal eye known to exist

prior to the Cambrian, around 540 million years ago. There

would be no other reasonable explanation from a Darwinian

perspective. So now Darwinists have to explain how it is

that a master control gene, developed in a nascent eye,

would just happen to be able to initiate the cascade of events

for all other more complex and diverse eyes that evolved


Furthermore, it is now known that the control genes for

all the various body plans introduced in the Cambrian are

common among virtually all animals. It is difficult to explain

how a layered, top-down engineering solution could

arise by a contingent process. Layered architecture greatly

increases the complexity because you have now introduced

an additional layer of dependencies. Layered engineering is

a way of controlling complexity in human engineering, and

it takes human intelligence to do so. Current research shows

that the control genes for the development of organs in animals

predated the origin of these animals themselves.23 The

instructions for the building (some of them) existed before

the building itself! These control genes are not large information-

rich genes; they specify the high level structure and

initiate the cascade of development. How can higher-level

functions appear prior to the components they control and

specify without invoking prior intelligence?

This phenomenon of highly complex features and functions,

arising prior to any obvious selective advantage, parallels

a similar phenomenon in human intellect, in that the

brain, in its current form and capabilities, evolved before

higher levels of abstract thought were necessary. David

Summer 2011 • The Fellowship Herald • 44

Berlinski, an agnostic Intelligent Design apologist, likens

this to “…discovering that the liver, in addition to being able

to create bile, can also play the violin.”24

Reuse and Rep urposing

Recent research has shown that there are far fewer genes

in the genomes sequenced thus far than would have been

expected, given the complexity of living entities. The reason

for this is the ability of living organisms to reuse and reassemble

gene components—like Legos—into new genes that

code for multiple, complex proteins, and each protein is used

for many biologic functions. For example, the proteins for

milk production in mammals were present in reptiles and

birds, and the proteins used in human neurons were also

present in much earlier organisms.

As discussed above, reuse and repurposing makes neo-

Darwinism somewhat more plausible because new genes are

not required for each new function. But reuse and repurposing

raises interesting questions. Isn’t it striking that genes

existing in primitive life would happen, just by chance, to be

suitable for the construction of complex organs in far more

sophisticated life forms, including human intellect? Human

engineers commonly reuse and repurpose existing components,

but how would a biologic cell have the knowledge to

stumble upon similar techniques by chance? Depending on

the premise one is operating from, reuse and repurposing

can be viewed as supportive of design or chance.

Convergent Evolution—Patte rn

Contingent processes such as Neo-Darwinismdo not

have targets. However, the fossil record shows that similar

complex life features evolve repeatedly, as though there were

targets or goals. This is called convergent evolution (if there

is no recent common ancestor that had the features presently

common to both). Convergent evolution is a fact.

The world’s foremost expert on the subject of convergence

in evolution is paleontologist, Simon Conway Morris,

who has written two books on the subject of evolutionary

convergence. He says that evolution shows “eerie predictability.”

Developmental biologist Sean Carroll echoes that

convergence is “…one of the most important insights revealed

by recent research.”25 Convergences at the organ level

are common. The evolution of the eye offers one of the best

examples. The eye is said to have evolved independently

anywhere from 40 to 100 times from a single primitive common

ancestor. Another example is the manner in which the

reptilian jaw bone “evolved” into the inner ear bone of mammals—

the “crown jewel” of fossil evidence. This happened

several times as well, according to Morris.

Perhaps the most stunning example at the organism

level is the similarity between various marsupials and placental

mammals. The placental wolf, for example, has a very

similar marsupial counterpart. Yet their common ancestor

did not have many of the features and attributes that are

common to both.

Scientists have known about convergences at the organ

level and organism level for quite some time. Recent evidence

from the laboratory tells scientists with equal certainty that

these same convergences exist at the molecular level, such as

the controls that regulate gene expression.

Neo-Darwinismclaims evolution is governed by contingent

causation, yet an examination of the fossil record, and

an examination of living creatures, shows that evolution repeatedly

breaks through immense barriers of complexity to

create similar adaptive solutions. How can a random process

that must, out of necessity, continuously seek immediate

gain for any incremental change, somehow manage to find

the same elegant end solutions repeatedly? It is one thing to

say that an improbable series of events occurred by chance

once; but quite another thing to say that the same complex

adaptations occurred over and over again by chance.

Pattern—repeatability—is a signature of design, not chance;

of final causation, not contingent causation. Nevertheless,

Neo-Darwinistshave welcomed this seemingly anomalous

phenomenon into their theory, claiming that the powerful

law of natural selection is such that life is directed along a

limited set of viable adaptive living forms.

Stasis—Final Causation

Stephen J. Gould offers an explanation—theory of

Punctuated Equilibrium—to the phenomenon of rapid burst

of innovation, followed by extended periods of little or no

real change—stasis. Once a wave of innovation occurs, creatures

vary in size, proportion and color, etc., but there are no

new features. This is a bit like a car model; you get a different

trim package from year to year but not much else. Virtually

all of the body plans for the animal kingdom were laid out

in the Cambrian about 450 million years ago. Stasis—like

convergent evolution—is highly suggestive of final forms or

final causes, not contingent causes. Each instance of stasis

can be viewed as a final form.

Neo-Darwinistsargue that, because most creatures have

become extinct, the argument for God based on design (“argument

from design”), using stasis as supportive of final forms

or final causes, is flawed. Arguments such as these typically

assume that those promoting this argument are Creationists

who believe that each creature was created by a divine act.

Such Creationists would not normally be advancing an

arment that is predicated on the truth of common descent.

Intelligent Design proponents, on the other hand, can cite

many examples of how human artifacts evolve from a rather

modest introduction to a solution which satisfies a vision.

The idea of scaffolding, each thing having its time and place,

is quite familiar and unsurprising in human creativity.

Stephen J. Gould was very concerned that religionists

might be heartened by the idea that evolution’s final gift—

humanity—was inevitable. He was concerned about this

because even a cursory examination of the fossil record and

life forms shows a steady gain in complexity and sophistication,

and repeatedly breaching through immense barriers of

complexity to find similar adaptive solutions. The obvious

inference is that there is a subtle way in which evolution is

guided, irrespective of what materialist scientists were claiming

about the evolutionary mechanisms themselves. Gould

rolled up his sleeves and busied himself with dispelling this

notion. He wrote two books on the subject, Wonderful

Life25 and Full House,26 attempting to show that evolution

was contingent and not directed in any way. “Rerun the tape

[of evolution]” and the result would be quite different. The

evidence says one thing; Gould claimed something else.

Challengers to Neo-darwinism

Strict Neo-Darwinistsare not without their challengers

within the scientific community. Neo-Darwinismis in

a crisis brought on by the molecular revolution. “There is a

growing feeling that Darwinism is due for another transformation,”

28 according to Eva Jablonka of the University of Tel

Aviv. Much of the debate is not visible to the public, it is buried

in scientific publications. However, in 2008 a convention

was held in Austria, the purpose of which was to assemble

notable biologists who are at least somewhat dissatisfied by

the current neo-Darwinian theory with its heavy emphasis

on natural selection. The run-up to the conference has been

documented in a book The Altenberg 16: An Exposé of

the Evolution Industry, by science journalist Suzan Mazur.

According to Mazur:

“Through the years most biologists outside of evolutionary

biology have mistakenly believed that evolution is

natural selection. A wave of scientists now question natural

selection’s relevance, though few will publicly admit it.”29

A variety of new theories have been proposed attempting

to supplement or complete neo-Darwinism. In some cases

the proposals are more of a complete overhaul than a facelift.

The common thread running through these new theories is

the emphasis on variation and, by inference, a de-emphasis

on natural selection. Also, the intelligence within the cell,

rather than the genome, becomes paramount. The Central

Dogma—the centerpiece of neo-Darwinism—apparently is

pure fiction. The Central Dogma stipulates that all hereditary

changes flow from genes to proteins through accidental

mutations, and not the other way around. If the Central

Dogma and natural selection are consigned to the historical

trash bin, then there isn’t much left of neo-Darwinism.

Facilitated Variation

Marc Kirschner of Harvard, and John Gerhart, a Cell

and Developmental Biologist from Berkeley, offer a new

theory to supplement neo-Darwinism, which they call “facilitated

variation.” The marquee principle in their theory is

that evolution proceeds in leaps by tweaks in the genetic regulatory

controls during development. New adaptive features

are constructed using existing genetic components, i.e., reuse

and repurposing. Over time, evolution—selection—has

favored creatures whose makeup is such that small changes

in the genotype can be leveraged into large changes in the

phenotype. They call this attribute “evolvability.”30

Inte rpreted Variation

Eva Jablonka, a professor of the History of Philosophy

of Science at Tel Aviv University, and Marion Lamb, former

Senior Lecturer at Birkbeck, University of London, offer a

suite of new ideas featuring non-random and non-genetic

variation to supplement neo-Darwinism. In response to certain

stressful conditions, signals from within the cell and

from the environment are processed, and cause organisms

to increase their mutation rate. These mutations are random

in the sense that they are not generated with a specific useful

function in mind, but they are non-random in two ways:

1) they are a response to environmental conditions, and,

2) they are focused on regions in the DNA that offer the

greatest promise of success. This ability to target particular

regions of the genome is part of the intelligence—“interpreted

variation”—of the cell that has been built in over time

through conventional neo-Darwinian mechanisms.

Jablonka and Lamb also detail a variety of inherited “epigenetic”

factors in evolution. Epigenetic inheritance means

changes that occur during the development process that are

inherited. These mechanisms involve feedback loops where

a protein product ensures that its genetic source is sustained,

memory systems in the cell structure, and markings in the

way chromosomes are configured. Here the research appears

to be less mature and there is more speculation about the extent

of what epigenetic mechanism may have accomplished

in evolution.

Summer 2011 • The Fellowship Herald • 46

Natural Genet ic Enginee ring

According to James Shapiro of the University of

Chicago, cells use intelligent “natural genetic engineering”

techniques to effect large evolutionary transitions. These

large evolutionary steps involve genetic rearrangements

rather than random mutational accidents. Natural genetic

engineering techniques enable an organism to respond to a

variety of inputs from within the cell, and from outside the

cell, calculate a response, and make regulatory changes that

initiate a cascade of actions that are likely to lead to a welladapted

organism. The genome is formatted using repetitive

elements, previously thought of as “junk DNA.” Natural genetic

engineering uses its knowledge of genome formatting

to target particular configurations in the genome that are

known to offer functional genetic systems.29,30

Design by Chance?

The great hope of these new theories is that there is a

free lunch somewhere to be discovered for creating complexity

rapidly. These new theories may, in fact, be more harmful

than helpful to materialist explanations for evolution.

By acknowledging that incremental mutational changes are

insufficient to create the wondrous and complex features of

life, rather than salvaging Neo-Darwinismthey may be putting

another nail—perhaps the final nail—in its coffin. The

facts these researchers present in support of their respective

theories are no doubt correct. But they can more easily be

accommodated by a theory of design, or guided evolution,

than a strictly materialistic theory. They feel differently, of


There are two fundamental flaws in each of these theories.

First, the evidence used by these researchers appears to

be limited to relatively simple adaptive changes. By extension

they hope to explain more complex adaptations. It is

one thing to say that organisms have the sophistication and

information in their repository to create simple adaptations

to changing conditions, but quite another thing to claim

that these same techniques can create an entirely different

creature with extraordinarily complex new features. It is a

matter of a difference—an enormous difference—in degree

rather than kind. Where would the foresight for generating

new complex features come from?

Secondly, they assume that the infrastructure to create

new adaptations through these enhanced variation mechanisms

is already in place. How can it be claimed that a complex

existing infrastructure is required to create relatively

simple adaptive features (because random mutation and

natural selection are insufficient), yet have to rely on these

same neo-Darwinian mechanisms to create the more complex

infrastructure in the first place? It is a bit like the joke

about how to become a millionaire: First: Get a million dollars.

Second… life systems are either the result of design or the

result of chance—not design by chance.

How do Shapiro, Kirschner, and Jablonka and others attempt

to explain how evolution created these marvelously

complex techniques? Primarily, they defer to future research.

Appealing to future research is a reasonable response. But it

seems to me that

Neo-DarwinismStill the Best Hope ?

If these new theories cannot explain the really tough

questions about evolution, then what can? The ultra-

Darwinists would suggest that the neo-Darwinian mechanisms

of random mutation and natural selection are the

only explanation. Evolution, they would say, has to proceed

by small chance mutations and natural selection. Why?

Because large coherent (functional) changes are wildly improbable,

in all likelihood near, or well beyond, the universal

probability bound. If mutational changes are not small,

it is extremely unlikely that they are random. As Richard

Dawkins has said, “We can suppose that we have some luck,

but not too much.”31 But what if “deep time” is not enough

for random mutations and natural selection to work its supposed


Infinity, The Ultimate in Deep Time

Let’s suppose science confirms that evolution and the

origin of life has occurred in such a way that extremely complex

changes or adaptations really do occur very rapidly.

Eugene Koonin’s “toy” calculation for the origination of a

barebones “replicator” (precursor of the most basic form of

life) shows a probability of 10 to the -1018th power. This is an

immense number and well beyond the universal probability

bound. How can we expect materialist scientists to respond?

A material process based on chance in the end has only a

single resource to draw upon—time. If deep time does not

offer ample opportunity, infinity surely does. If the universe

can create itself once, why not imagine that it can create itself

an infinite number of times? If there are an infinite number

of universes with varying physical parameters, not only

are highly improbable things possible, they are a certainty. In

other words, infinity trumps probabilities.

Here is how Eugene Koonin states it:

“[Therefore] the plausibility of different models for the

origin of life on earth directly depends on the adopted cosmological

scenario [my emphasis]. In an infinite universe

(multiverse), emergence of highly complex systems by chance

is inevitable.”32

Summer 2011 • The Fellowship Herald • 47

Recall that Koonin emphatically stated that “Intelligent

Design is not a solution to anything” when referring to sudden

transformations in evolution.

He and most of the rest of the academic scientific community

would rather embrace an imaginary tale of an infinite

number of universes than accept prior intelligence as

a cause for complexity because they do not want to “let a

Divine foot in the door.”

Koonin’s use of the endless resources of infinity to explain

the diminishing probabilities in the creation of life is

an extension of a technique used by materialist scientists

to explain the fine tuning of the universe. In 1973 physicist

Brandon Carter presented a paper wherein he noted the “fine

tuning” of the universe constants (the masses of the various

particles and the magnitude of the basic forces of energy).

The fine tuning is quite tight in many instances, and if some

of these parameters were to have been different by even the

slightest amount, the resulting universe would not be able to

accommodate life of any kind. Theists have seized upon this

as evidence for design: Of all the values that the physical

parameters of the universe could have, it is these.

The favored approach among materialist scientists to

counter the argument from design based on fine-tuning is to

propose a variety of multiverse theories—perhaps an infinite

number—of universes with differing physical parameters.

Surely one or some of these universes would just happen to

be such that complex living creatures could arise and exist.

The fact that we find ourselves in one of the more accommodating

universes is unsurprising, using anthropic reasoning.

A discussion of the merits of the multiverse theory is beyond

the scope of this article. It is difficult and perhaps impossible

to falsify. And this might be its most important and useful

feature and why it exists in the first place. Infinity might be

the final refuge of materialist explanations.

A Theist could adopt the idea or principle of the multiverse

theory as well. Michael Behe, the most prominent

molecular biologist in the Intelligent Design movement,

advanced such a theory in his latest book, The Edge of

Evolution. If we assume that there are an infinite number of

possible universes with varying attributes and outcomes, all

known to an omniscient God, then He is free to select and

actualize any one of them. Given that the possibilities are

infinite, anything not strictly precluded by physical laws is

a certainty. One such certainty is the very universe we find

ourselves in; the one selected by God to be actualized.

The ascendancy of multiverse theory may create an impasse

in the debate about the existence of God with respect

to the argument from design. This is true though only if we

assume that the makeup of all reality, including human intellect,

is entirely material. But if human intellect cannot be

explained strictly through material causes, then deep time

and even infinity are of no use against the argument from

design. Are there aspects to human intellect that cannot be

explained by material causation?

Human Intellect—a Zenith Point

Earlier I discussed the importance of complexity and

causation in making an inference of design. I cited several

examples of each. But there is a far more stunning example

than convergent evolution, reuse, foresight, and stasis, demonstrating

that evolution is a process governed by final causes

rather than contingent causes. There is a supreme example

of an ultimate target or zenith in evolution and one that also

demonstrates the most astounding leap in complexity. It is a

phenomenon where these two attributes—complexity and

final cause—converge.

Any Humanist would agree with the idea that nature

is transparent to human reason; it is a cornerstone of methodological

naturalism. This means that human intellect is

capable of understanding all reality which is assumed by

secular Humanists to be entirely material. If human intellect

is capable of comprehending all reality, then the complexity

of all reality is, in effect, subsumed by the complexity of

human intellect summed up in human knowledge; what it is

now and what it can be. There can, therefore, be nothing

that exceeds the complexity of human intellect. You have

to ask yourself: What are the probabilities that a random

process would just happen to assemble an organ system of

that complexity and with such uniquely special attributes, as

quickly as it did, from a handful of genes that just happened

to exist in primitive animals and to do so prior to the necessity

of such capability? I would say the probabilities of such a

thing are effectively zero. How do materialist scientists react

to the apparent final cause and extraordinary complexity exhibited

by human intellect? Some raise an eyebrow; others

wave their hand; most just shrug their shoulders.

The rather remarkable phenomenon of human intellect,

and what it represents insofar as complexity and final causes

are concerned, may be regarded by some as a “proof” of the

existence of God. I believe it to be. But such a proof may

only move a skeptic from a position of atheism or agnosticism

to Deism, and is susceptible to the argument from

infinity derived from current multiverse theories. What evidence

can be offered to carry one from Deism to Theism

that transcends chance even in light of the possibility of

an infinite multiverse? Stated another way, what qualities

of life, and specifically human intellect, transcend material

explanations? There are at least four: (1) The gulf in comSummer

2011 • The Fellowship Herald • 48

plexity between human intellect and the complexity of the

genetic components responsible for human intellect, (2) The

existence of free will. (3) The phenomenon of human identity,

what I would refer to as “the constancy of self.” (4) The

phenomenon of genuine love and compassion, what I would

refer to as “the ontology of love.” All four of these reveal a

non-material aspect to human intellect. But they are largely


Complexity of Human Inte llect vs. the Complexity of Its

Genet ic Components

Human intellect can understand (subsume) the complexity

of all reality including the interworkings of the cell

and its genome. How is it possible that the developmental

process can bring forth a phenotype—human intellect—of

such astounding complexity from the far more simple genotype?

What in the ontogeny of development accounts for the

added complexity? How can the modest quantitative differences

between the DNA of humans and chimps result in

such a qualitative gulf in intellectual capabilities?

Free Will

If Neo-Darwinistsare correct and there is no God, then

there can be no free will, either. Neo-Darwinistsdo not deny

this. “Compatibilists” claim that materialism and free will

are not irreconcilable, but they do so by demoting free will

to decision making, similar to the way computers make decisions—

algorithmically. If true free will does not exist then

that means that the human brain is essentially an organic

computer. A computer has algorithms and data. It is a system

that is entirely dependent on prior cause; it is a deterministic

system. But, if there is no free will that means that you are

really not free to do what you want. Each action is dictated

by prior events and the current configuration and state of

the molecules in your brain. The French philosopher Henry

Bergson, upon reflecting on the implications of determinism

and its requirement that each action be necessitated by prior

cause, remarked, “What a draft on credulity.” Were you to

walk out to the desert and be instructed to select one of the

many billions of grains of sand, would that act of selecting a

specific grain of sand be one of free will or only the working

out of a deterministic molecular algorithm? Could you have

selected only one grain...or any grain?

Constancy of Self

Materialism suggests that the mind is algorithmic and

that consciousness and identity arise from this. But isn’t it

peculiar that no matter how the neurological makeup of

your brain changes throughout your life, there is always the

sense that you are you? We all seem to have a unique and

immutable identity. How can that be if the underlying physical

constituents change? How can such a thing even arise

from a complex web of ever-changing neurological signals?

Ontology of Love

Is love real? Neo-Darwiniststell us love and compassion

are illusions—merely an artifact of the evolutionary process

based on reciprocity; much like Chicago politics. Darwinists

claim that altruism emanates from one’s self outward and

diminishes as genetic kinship diminishes. That’s probably

true for the most part. But is it entirely true? Only one’s own

insight can affirm whether compassion and love are genuine.

But it is not so easy to factor out the selfish effects imposed

by the limits of our existence on a finite planet and our ancestral-

animal legacy. Compassion is often interwoven with

self-interest. Do you genuinely care about others? If you had

unlimited means would you help all those that you could?

If it were in your power to do so, would you grant all decent

persons eternal salvation? If love and compassion are real,

then how can it be imagined that the God who created us,

does not also have these same attributes of love and compassion

in far greater measure?

A Modest Proposal

My own tentative proposal—which contains more than

a bit of speculation and based on limited knowledge—is that

the initial life forms were assembled by an intelligent, but imperfect

agent empowered by God. I suspect that much of the

intelligence was packed into those initial cells. The initial

cells contained much of the information necessary to effect

an unfolding of life. The major events might be random in

the temporal sense, i.e., when they occurred but not whether

they would occur. These planned macro-mutational events

may have been triggered by signals from the environment

or they could be planned to occur randomly in time and

assert themselves only if the environment were ready to accept

them—natural selection being the arbiter. Each event

could be a series of relatively simple regulatory switches that

initiate a cascade of changes resulting in a fundamentally

different creature with new, complex features using existing

genetic components.

But there is no clear evidence that all the necessary genetic

components for higher mammals were in the first cells.

And in fact, there is evidence that new genetic material has

been incorporated at key evolutionary transformations at

least through the Cambrian. Furthermore, had all the genetic

components been present but not used in the earliest cells,

they would have been subject to ruinous mutations unless

Summer 2011 • The Fellowship Herald • 49

there is some undiscovered mechanism to preserve them.

Are there natural mechanisms that may account for additional

genetic components? Yes: Horizontal Gene Transfer

(HGT). However, treatment of HGT is beyond the scope of

this article.

The unfolding of life from a few initial cells comports

with the current research, with the exception noted above,

and is beautifully homologous with the way in which a single

cell develops in the womb into a living creature. Common

descent and natural selection—to some extent—have to

be true. Common descent and natural selection are the

only way a designer can ensure that life unfolds in a way

compatible with the geological and biological environment

of the planet without requiring constant tuning and meddling.

Furthermore, evolutionary transitions particularly in

animals cannot be too abrupt, as Creationism might suggest,

especially as creatures acquire greater intelligence. A

good deal of a creature’s ability to survive is related to learning.

So there is every reason to believe, as animals become

more sophisticated and able to learn, that the evolutionary

increments could be, and should be, smaller. One would not

expect that a shrew would give birth to an elephant. Aside

from the physics of such a thing, it is hard to imagine a viable

parental lesson plan.


Neo-Darwinian evolution is a damaging philosophy, and

I suspect in the future it will be regarded as one of the greatest

intellectual canards in the history of human thought.

The only explanation for its ascendancy and persistence is

that materialist philosophy has infringed on science. And,

in fact, neo-Darwinism, or some theory very much like it,

is required by the adoption of methodological naturalism.

Methodological naturalism was a choice which has evolved

to a mandate and then to an exclusionary principle.

Science is doing what science should do: make discoveries

and modify its theories. And there is brilliant research

going on. Science is on the verge, I believe, of some of the

most important discoveries in its entire history, and perhaps

the most important discoveries ever. These discoveries have

the potential to usher in a renaissance of religion nullifying

the ascendency of secular Humanism brought about by

Darwinism—ironically. As science closes gaps in our knowledge,

they are creating larger gaps for a material-based theory

of evolution to close. The God-of-the–gaps fallacy may prove

to be a fallacy itself. As Eugene Koonin says:

“In each of these pivotal nexuses in life’s history, [origin

of complex RNA molecules and protein folds; major groups

of viruses; archaea and bacteria, and the principal lineages

within each of these prokaryotic domains; eukaryotic supergroups;

and animal phyla] the principal “types” seem to appear

rapidly and fully equipped with the signature features

of the respective new level of biological organization. No intermediate

“grades” or intermediate forms between different

types are detectable.”32

What Creationists and Intelligent Design proponents

have been claiming for decades, and Neo-Darwinistshave

been denying for decades, is apparently being confirmed.

The key question, which will become clearer over time, is

whether Neo-Darwinismor any strictly materialist explanation

can account for the complexity of life in such short

timeframes. Were it to be confirmed that living organisms

could not have evolved purely by chance physical processes,

atheism could not be sustained in large measure. The argument

from design would see a rebirth as the pendulum

swings back toward idealism away from materialism.

Scientists, currently, will not accept any theory even suggestive

of design or teleology. Only through attrition and a

new generation of more open minded researchers can a real

change in paradigm occur. But there is a role for religionists

in this dynamic. Religion should evoke action. At the very

least, religionists should be better equipped to defend the notion

that science does not preclude Belief. Religionists should

be active in bringing about the transformation from “what

things are” to “what things ought to be.” All too often, religious

individuals have sat on the sidelines waiting for Divine

help when the need for heavy lifting arises. Only through

knowledge, reason, and participation can modern religion

hope to compete with the scientism of secular Humanism.

Increasingly, in modern civilization authority on matters

of Truth is assessed to be within the domain of science

and intellectualism now dominated by secular Humanists.

If religionists cede authority on matters of Truth to secular

Humanists they risk cultural suicide. Without a firm belief

in God, and salvation, I doubt modern civilization can maintain

a true moral heading, sustain its population levels, or

defend itself. The erosion of moral standards and low fertility

rates among the advanced nations, and their acquiescence

in the face of malevolent states, is clear evidence of this.

Great and promising civilizations have passed before us.

History provides little comfort to those hopeful that Divine

intervention will spare us from a similar fate. “All that is

required for evil to triumph is for good people to do nothing”—

Edmund Burke.


1 Richard Dawkins, The Blind Watchmaker, (1986 ) Page 6

2 Jacques Monod, Chance and Necessity: An Essay on the Natural

Summer 2011 • The Fellowship Herald • 50

Philosophy of Modern Biology, New York, Alfred A. Knopf, 197 1.

3 Richard Dawkins, The Devil’s Delusion: Atheism and Its Scientific

Pretensions, (New York Crown Forum, 2008), ISBN 0-307

4 William Provine, Movie Expelled: No Intelligence Allowed, 2008.

5 Daniel Dennett, Darwin’s Dangerous Idea. Simon & Schuster,

1995 .

6 Corliss Lamont, The Illusion of Immortality, 1959 .

7 Richard Lewontin, New York Times Book Reviews, Jan 9th 1997 .

8 Robert John Russell, Nancey Murphy, Theo Meyering, Michael

Arbib, Neuroscience and the Person, Notre Dame Press, 2000.

9 John Paul, Message delivered to the Pontifical Academy of Sciences

22 October 1996

10 William Dembski, The Design Inference, Cambridge University

Press, 1998

11 Percival Davis and Dean H Kenyon, Of Pandas and People,

Foundation for Thought and Ethics, 1989 .

12 Michael Behe Darwin’s Black Box, Free Press, 1996 .

13 Michael Behe, The Edge of Evolution, Free Press, 2007.

14 Richard Dawkins, Climbing Mount Improbable, New York Norton,

1996 .

15 Richard Dawkins, The Selfish Gene, Oxford University Press,

1976 .

16 James Shapiro, Molecular Biologist University of Chicago Lecture

at Ramsey Auditorium at Fermi National Accelerator Laboratory, January

22, 2009

17 Bruce Alberts, President National Academy of Sciences Cell

Journal, 92:291-94

18 Marc Kirschner with John Gerhart, The Plausibility of Life: Resolving

Darwin’s Dilemma, (Yale University Press 2005) ISBN 0-300-10865 -6

19 Eugene Koonin, The cosmological model of eternal inflation and the

transition from chance to biological evolution in the history of life, Biology

Direct, 2007

20 Charles Darwin, Origin of Species, 1959 .

21 Marc Kirschner and John Gerhardt, The Plausibility of Life: Resolving

Darwin’s Dilemma, Yale University Press, 2005.

22 Eugene Koonin, The Biological Big Bang model for the major transitions

in evolution, Biology Direct, 2007.

23 Sean Carroll, The Making of the Fittest: DNA and the Ultimate

Forensic Record of Evolution, W. W. Norton & Co, 2006.

24 Stephen J. Gould, Wonderful Life, W. W. Norton & Co, 1989 .

25 Stephen J. Gould, Full House, The Spread of Excellence from Plato

to Darwin, 1996 .

26 Suzan Mazur, The Altenberg 16: An Exposé of the Evolution Industry, North Atlantic Books, 2010.

27 Marc Kirschner John Gerhardt The Plausibility of Life: Resolving Darwin’s Dilemma, Yale University Press, 2005.

28 Eva Jablonka and Marion Lamb, Evolution in Four Dimensions, MIT

Press, 2005.

29 James Shapiro, A 21st century view of evolution: genome system

architecture, repetitive DNA, and natural genetic engineering, Gene

345 2005.

30 James Shapiro, Revisiting the Central Dogma in the 21st Century,


31 Dawkins “We can suppose…”

32 Koonin “In each of these pivotal…”

Note: Further quotes of Richard Dawkins can be found at: www.

positiveatheism.org/hist/quotes/dawkins.htm and on Wikipedia page:

http://en.wikipedia.org/wiki/Richard Dawson