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Evolution – Smevolution!



An In-Depth Analysis of the Evolution Debate

Copyright 2005 Rick Harrison





Last updated 16 August 2017



*Notes: references to the appendices beyond 1, 2, 3, 6, 8, and 13 should be ignored for the moment as they are being revised and will be posted back to the Internet soon. However, if you get through all of this material, you probably won’t miss them, as you probably won’t want to read another word about evolution ever again. J
I apologize to readers who saw early drafts of my Web pages or books that were terrible products. Gulf War Illness gives me a mild cognitive impairment. This causes a lot of redundancy and word substitution errors. The short-term memory limitations and mild cognitive impairments I struggle with as a result of Gulf War Illness produce a tendency not to catch mistakes and incoherencies in real time draft writing. I apologize for any migraines this may have caused. The present version is readable (and worth a read). It will be further clarified over time with subsequent edits.



It has been an exciting time in science following the meeting of the cadre of intelligent design (ID) scientists at the home of author and attorney Phillip Johnson on a California beach in 1993.[1] Scientists have since reported unmistakable signs of intelligent design in biology. As a result, we are able to review here a volume of evidence that poses a startling challenge to the neo-Darwinian theory of accidental or godless evolution.


Evolution, yes. Accidental life, no. That is the unavoidable conclusion I derive here from the last twenty some years of scientific research. Perhaps surprisingly, at the broad conceptual level this is not really a change from Charles Darwin’s perspective. Even Darwin left the Creator in his larger theory of life as the impetus that got the evolutionary ball rolling. Roll on dude!


The way in which intelligent design (ID) theory differs from Darwin’s view is that Darwin didn’t see any concrete scientific data to support hypothesizing a Creator; ID theorists do see supporting scientific data. Darwin intuitively felt that we needed God to get things started. Call it philosophical logic, analytical intuition, or whatever, Darwin thought we needed God as Creator to set things in motion, but saw no scientific data to indicate that God took any interest whatsoever in the way things played out in the evolution of life. What we will see as the discussion develops is that Darwin’s intuition was good. He may have been right on both counts: God started the process, but started it so effectively that he didn’t have to intervene afterwards at all—the tree of life was a guaranteed result.


Now, more than 150 years later, there is a great deal of direct scientific support for the hypothesis of a Creator. Scientists are nearly unanimous in acknowledging that the evidence points to predominantly non-random processes at the heart of the origin and evolution of life. However, most of those same scientists seem to have been reluctant to go the further step and conclude that intelligent design is involved. They know that accidental evolution and accidental cosmology are out, but they are not quite sure what is in.


Because the accidental worldview is a core component of most neo-Darwinian formulations of evolutionary theory, when accident goes, neo-Darwinian theory goes with it. So my conclusion in this book will be that we can keep the basic theory of evolution, but the accidental spin that neo-Darwinists add to the basic theory must go.


For those perceptive and honest enough to admit that intelligent design now seems to be a basic truth about our world, even they seem unsure that it is the place of science to make the announcement. They may be inclined to defer to philosophy or religion. The few who might concede (in private) that it is science’s place to announce intelligent design are much less sure that the announcement should be made with their name on it. Political backlash from the materialistic core of mainstream science is a near certainty for any scientist audacious enough to attempt such a feat of intellectual honesty.


If not for the courage of a few highly educated men of integrity like Phillip Johnson, William Dembski, Michael Behe, and Stephen Meyer, we might not have been told the full import of recent scientific data for many further generations. The good news is that the struggle for truth in science continues, and there is much that is new to report.


With the advent of a new and scientifically formulated version of intelligent design (ID) theory (religious elements removed), one of the great questions of all time, the relation between God and science, has been reopened, and in grand style. Science may now have a legitimate procedure (the five scientific arguments for ID theory that are discussed a little further on) by which to decide the issue of intelligent design without having to encroach upon the turf of religion or philosophy, a procedure that preserves the empiric charter of science.


Science has long known that a myriad of critical constants, values, and parameters in physics favor life with enormous specificity. In fact, the universe is routinely described as being “fine-tuned for life.” More than 200 factors within the physics of our universe had to be fine-tuned in favor of life for our galaxy to be capable of hosting life at all![2] One of those factors, and a big one, is the specific profile of the element carbon in relation to the profile of oxygen. See Sir Fred Hoyle’s article, "The Universe: Past and Present Reflections." in Engineering and Science, November, 1981 at page 12.


Add to those 200 factors the newly discovered proclivities in natural law for forming the essential components of life (proteins), such as Michael Denton describes in his most recent book Nature’s Destiny;[3] chemical biases that favor the spontaneous formation of biotic molecules; instances of molecular selection that may slant physical processes in life’s favor; protocell self-organization; self-organizational dynamics of genomes; and nonrandom, self-transformational processes in the genome; and you have sketched out the structural backbone of a perfectly plausible candidate for cosmic purpose in nature.


Some readers may want to challenge Denton’s work merely because he is a proponent of intelligent design theory, but his scientific credentials are impeccable. It is a pointless exercise in any case because there are “mainstream” scientific journal articles on protein science that imply essentially the same thing. Michele Vendruscolo’s 2012 article in Current Opinion in Structural Biology, entitled “Proteome Folding and Aggregation” is one example. Vendruscolo tells us there, in the introduction at page 138, that “Proteins are involved in nearly all the biochemical reactions that take place in living organisms. In order to carry out their functions the majority of them fold into well defined three-dimensional native structures by a spontaneous process that is relatively robust against perturbations. The task of reaching and maintaining such native states amongst the vast multitude of possible alternative conformations that proteins can adopt is facilitated by the presence of an energetic bias towards the native states themselves.” (My emphasis) In other words, nature is strongly biased towards the building of the key elements of life, proteins. This is my conclusion, not Vendruscolo’s. However, her description of the strong biases in protein folding logically entails the conclusion.


Yes, I will say it, the ‘O’ word, long thought to be a dead theory in evolutionary science: “orthogenesis.” Orthogenesis is back. “Orthogenesis” means directed evolution, as opposed to random or accidental evolution. While the current data places the amount of direction at only moderate levels, this is enough to get the job done over time—and enough to refute the accidental worldview. It certainly reflects an enormous bias for life. The current trend also suggests that more directional factors will be found as time goes on.


Do I lean toward this view merely because I believe in God? No; the data itself suggests it, as we shall soon see. You don’t have to be a believer to see the import of the scientific data. In support of this I cite Sir Fred Hoyle, famous Cambridge astronomer and consummate mathematician. Hoyle was an atheist:


“Would you not say to yourself, 'Some super-calculating intellect must have designed the properties of the carbon atom, otherwise the chance of my finding such an atom through the blind forces of nature would be utterly minuscule. A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.' "


[Fred Hoyle, "The Universe: Past and Present Reflections." Engineering and Science, November, 1981. pp. 8–12]


While anything less than full direction may force us to concede that God is not a micromanager, it does not force us to concede there is no God. An intelligent designer of life is certainly implied by the data, and no one else has currently applied for the job. At a minimum the new data shows that accident cannot be scientifically defended as the driving force of evolution.


When one considers microbiologist Michael Behe’s point about the irreducible complexity of cells and biological systems; Professor William Dembski’s proof that an accidental process would have exhausted the resources of the universe trillions of times over before achieving life by accident; and Dr. Stephen Meyer’s point that the probabilities against accidental evolution are completely forbidding, one comes to realize that the theory of an accidental formation of life is no longer scientifically tenable.


Because of the enormous improbabilities present at each step in the evolution of life, additional constraints pointing cosmological, physical, and biological processes in the direction of our tree of life are certain to be discovered in future research. The math says they have to be there. This will likely occur in, among other places, the most obvious areas of proteomics and the sciences of the genomes.


Probably the most powerful directional factor among the many that comprise nature’s strong bias for life occurs in protein folding. Michael Denton reports on this feature of proteins in his article in the Journal of Theoretical Biology entitled “The Protein Folds as Platonic Forms.”[4] The characteristics of proteins determine the larger part of what happens inside the cell. So the discovery that protein folding is largely predetermined by natural law reveals that an enormous directional influence towards our tree of life is built into nature.


Other examples of the kinds of directional factors I am speaking of include nucleohistones, pseudogenes, and curvature-based chemical affinities in DNA strands. We have known since the 1960’s that nucleohistones influence the organization of genes into the superstructure of the chromosome. More recently, research has revealed that pseudogenes, once held to be physiological junk, are not junk DNA at all. They influence gene expression, genetic diversity, and recombination. Even the curvature of the DNA strand affects selection factors such as the bonding of the DNA strand to inorganic macromolecules.


Elements like these take much of the randomness out of biological and pre-biological events, slanting the course of natural evolution more and more heavily towards the development of life and complex genomes. We don’t yet know how much total directional bias has been embedded into natural processes, but enough bias has been revealed to show that calling life an accident is a flagrant misnomer.


Over the past thirty years science has (unintentionally for the most part) incrementally revealed a self-organizational system in nature, a partially directed and intelligently informed system used to create and evolve life. This is something we should have fully anticipated based upon life’s immense complexities and the high improbabilities involved in accidental evolution. We already knew from complexity and probability data that it is scientifically ridiculous to claim that accident could have built the tree of life within the time afforded within the history of our universe. It is therefore perfectly logical that we are now discovering piece by piece the non-random method that nature employed to create life.


Where does God fit into this new development? As intelligent design proponent Professor William Dembski explains in The Design Revolution, under intelligent design theory the designer of life doesn’t have to be the Christian (or any other) God. He/she/it might be an advanced extraterrestrial civilization, ET, for example. Or, the designer might perhaps be nature herself. The universe itself might be intelligent, having a telic principle of some kind embedded at its foundations. However, ID theory does leave conceptual room for God in science (including the Christian God) at the beginning of things at the honored place of “the Creator” where Charles Darwin first placed him in his classic work, Origin of Species.[5]


The Present State of Evolutionary Science

The naïve mutationist model of evolution is the only view of evolution compatible with pure accident. Its overly simplistic view of life has long been abandoned by evolutionary science. Science now understands that any substantial change in body form requires many time-synchronized alterations to the active operational genome, as well as closely coordinated changes to the developmental genome, gene activation markers, and the microtubule structures inside cell walls. All these changes must occur in very close proximity of space and time. Without this precise orchestration, major evolutionary change cannot occur. (We still don’t know the biomechanics of how major evolutionary change does occur. In theory, room still exists for some divine intervention at key points in evolutionary history.)


What’s a microtubule? These infinitesimally small, intricately fashioned networks of nanotubes are found inside cell walls. They may be largely unknown to lay readers, but microtubule networks are big players in biology. They comprise a sort of intricately blueprinted “plumbing” that delivers the building blocks of life to the right place at the right time.


Sounds simple—but it isn’t. On the other hand, a cell’s microtubule network does represent elegance of design in the relatively simple manner in which it accomplishes a very complex task. Given the complexities of life, even the “plumbing” of a living cell must be a very smart system to guarantee the right materials arrive when and where needed. Complex networks of microtubules are critical to assembling the structural plan of the species. In fact, they determine which species will be built. Although genes, in addition to specifying the many thousands of hugely complex proteins essential to life, also perform very complex regulatory functions, they do not directly specify which species is to be built. Species designation is hardwired into the microtubule system.


This means that the evolutionary event process must somehow coordinate many changes in the microtubule system with many other changes to the genome in order to produce a new kind of creature. Otherwise, one gets a fatal mismatch analogous to building a skyscraper out of moist chewing gum. Every part specified in the blueprint has been filled by something, but the materiel specifications are all wrong.


John A. Davison, Professor Emeritus of Biology at the University of Vermont, says that the very notion of a gradual biological form change is now meaningless, and that guiding information must be coming from somewhere, such as from the developmental genome. Davison also reminds us that the neo-Darwinian concept of gradual change requiring millions of years to observe puts neo-Darwinian theory in noncompliance with the basic principle that scientific theories must be testable.[6]


Davison’s thesis that neo-Darwinian theory is largely untestable within practical limits is a thesis with which Henry Gee, paleontologist, evolutionary biologist, and Senior Editor at Nature magazine, agrees. Gee insists that, given the “deep time” of evolution, we have too few points of evidence compared to the vast span of evolutionary history to support any narrative of lifeform evolution with confidence. One might call Gee and Davison the modern champions of pure scientific method in evolutionary biology.[7] Hurray for honesty in science! It’s about time.


According to Gee, we should abandon any and all theories of the process dynamics and narrative history of evolution, at least for the short term (and conceivably, forever). We should instead concentrate on describing the fossils and comparing the structural, functional, and genetic features of the species. From there we can evaluate alternative sets of probabilistic inferences concerning which creatures are close evolutionary relatives from the raw phylogenetic data.


Although evolutionary science can make solid inferences and highly informed best guesses as to what the family relationships are among the creatures on Earth’s tree of life, these guesses don’t equate to irrefutable facts. The limits of deep evolutionary time entail that even when we have done the best we can along these lines, it won’t, strictly speaking, be good enough. We will have probabilistically described the tree of life, yes, but we will not have infallibly mapped it, fully understood the process of its creation, or genuinely explained it.


Prior best guesses of these kinds (probabilistic phylogenetic inferences) get changed every few years. The tree of life has not been a static chart over the past few decades; it is still in transition.


Thus, while we may ultimately come to "see" the larger strokes of what happened in terms of probable species interrelationships, we will not be seeing the whys or hows of the historical evolutionary process. We will be seeing neither the full macroscopic event sequence of evolutionary history nor the microscopic biomechanical pathways of evolution—notwithstanding that the biomechanical event sequences for a few historical evolutionary events involved in the evolution of the simpler creatures may eventually get worked out to a high level of confidence.


Scientists may have grounds to make confident guesses about further large segments of the biomechanics of macroevolution, but (until macroevolution can be produced by scientific experiment) they won’t have knowledge of what the complete biomechanics of macroevolution actually were. Because the evolutionary process took millions of years to occur, the biomechanical event process required to produce a single significant event of macroevolution may well be too complex to ever replicate by scientific experiment.


The deep time of evolution means that much historical data is forever lost to science, forbidding us direct vision and complete certainty. If we could produce macroevolution in the lab we might make much more confident inferences to historical evolutionary event dynamics. But we can’t produce macroevolution in the lab. No one really seems to be trying; and there is precious little to suggest it can ever be done. There are also monumental ethical questions involved in the kind of animal experiments required to investigate the process of macroevolution.  (As a Catholic I am certainly not recommending it.)


Gee does not argue that the theory of evolution is false, only premature. In his view, which really is the pure and proper concept of scientific method, the data collection phase should remain free of any preconceptions about how it all happened. If the data itself obligates a certain view and excludes others, fine. But so long as the data is vastly incomplete and noncommittal as to process dynamics we should not commit ourselves to any one of the several theories equally compatible with the data. This is necessary to avoid producing a bias that would prejudice future research and theory evaluation.


True, smaller hypotheses must be formed to guide research, but we should not prematurely entrench ourselves inflexibly in restrictive conceptual theories of evolution or in specific historical narratives. Pretending to know the concrete biomechanics of evolution, prematurely asserting the absence of directional guidance, and pretending to know the specific historical storyline of evolution takes us well beyond what the evidence presently justifies.


In having insisted on an accidental event dynamic before much of the relevant evidence was in, neo-Darwinian theorists made this mistake, drawing premature conclusions, in a very big way. Evincing a strong materialistic bias equivalent to a major political power bloc, neo-Darwinists locked out science’s consideration of genuine candidates for the best explanatory model of evolution before the larger part of historical, genetic, and biochemical data was known.


Though Gee’s position in Deep Time is silent on the question of intelligent design, his point about premature affirmation of specific theories  absolutely pulls the rug out from under the neo-Darwinist’s frequently haughty presumption of an accidental evolutionary process dynamic. For 150 years Darwinists and neo-Darwinists staunchly issued dogmatic assertions that accidental evolution produced life on Earth. Gee, apparently without meaning to, has now exposed the neo-Darwinian dogma as a hasty and largely unsupported conclusion. ID theorists have gone further to provide data and arguments that genuinely seem to refute neo-Darwinian theory. You will see those arguments a little further on in the discussion.


After decades of insufferable atheist, materialist, and neo-Darwinist political propaganda masquerading as pure science, it is a genuine (and fully satisfying) scandal that two of our foremost scientific authorities as Davison and Gee would so cogently establish that neo-Darwinian theory is not so much an unassailable icon as a scientific prematurity, and, in Davison's case, a physical impossibility! Gradual production of radically different complex species simply cannot occur due to the ultra-complexities and interdependencies inherent in biological systems. A new germ from a germ, or a new worm from a worm by gradual accumulation of genetic accidents, maybe—but not a mammal or even a reptile from a germ.


Like the emperor’s new clothes in the fairy tale, it turns out that Darwin’s new clothes (the neo-Darwinian theory of accidental evolution) are quite an embarrassment, a scanty little ensemble indeed in terms of genuine evidential support. This embarrassment is not entirely new. Neo-Darwinian evolution has never been unassailable, contrary to what its proponents would have us believe.


Many top rank scientific experts have struck telling blows against the neo-Darwinian theory of evolution for years. One famous example is the late and much respected cell evolutionist Lynn Margulis. Margulis has long challenged the neo-Darwinists for real proof of their theory—receiving only silence in response. Legendary philosopher of science Karl Popper once dismissed the neo-Darwinian theory of evolution as merely a philosophical system, not natural science at all.


In Mathematics of Evolution, Sir Fred Hoyle reminded us that the fossil lineages of the different orders of creatures neither lead to a definite common ancestor nor fully link up.[8] Physicist and theologian Gerald L. Schroeder does the public a service in restating this now well-established truth: “Transitional forms are totally absent from the fossil record at the basic level of phylum and rare if present at all in class. Only after basic body plans are well established are fossil transitions observed.”[9] (my emphasis)


Although fully contrary to the gradualism required by neo-Darwinian theory, this basic fact about the fossil record has been known to science for more than fifty years. Michael Denton, Stephen Meyer and Duane Gish are only a few of the noted scientists who have cited this consistent anomaly in the patterns of the fossils. In addition, mainstream scientists outside of ID theory such as Harvard paleontologist David Raup; the late icon of evolutionary science, Ernst Mayr; Curator of the American Museum of Natural History, Niles Eldredge; and the late and famous evolutionist, Stephen J. Gould have also done so. Nearly all evolutionists, in fact, now concede that classical neo-Darwinian theory does not match the fossil record.[10] The fossil record establishes a non-gradual evolutionary process.


Not only do large gaps remain in the fossil sequence, but they are in all the wrong places. The gaps consistently appear where they should least likely be in a gradualist scenario. In neo-Darwinian theory, many more intermediate steps would be required to bridge the greater physiological “distance” between radically different body types than between closely related relatives of the same family.[11] Yet, few intermediates are known between the major body types, while many intermediates have been found between close relatives on the same branch. This is precisely the opposite of what Darwin’s theory of evolution via gradual accidental mutations predicts.


So, Darwin is out…and what or who is in? Punctuated equilibrium, random drift, intelligent design? Neither punctuated equilibrium nor random drift offer any real explanation of how we get the complex increments of change that evolution needs; they just say mutations occur and eventually add up. Science cannot demonstrate in the lab, or by any other means, that an accidental dynamic could generate the needed complex sets of simultaneous mutations with either of these theoretical dynamics, and the math says it is completely impossible in the time available.


Punctuated equilibrium and random drift are theories that were engendered to solve the mismatch between evolutionary theory and the pattern of the fossil record and the known lack of opportunity for natural selection to act, respectively. Both theories are actually weaker in terms of overall explanatory power than the basic neo-Darwinian theory they are designed to replace. With punctuated equilibrium the time problem already fatal to neo-Darwinian evolution is intensified in bottleneck events where evolution periodically speeds up. With random drift theory neo-Darwinian evolution’s already minimal explanatory power is reduced to nothing because natural selection is removed from the process of producing important steps in biological evolution.


This leaves intelligent design theory as by far the leading contender. There do seem to be instances of both punctuated equilibrium events and random drift events, but embedding those theories within an overall accidental dynamic leaves no chance to produce the tree of life within the historical timeline. I know what you are going to say: “But intelligent design theory isn’t science!” While that is not true, even if it was true it would not be a justification for proposing the physically impossible as the best theory science could offer to explain the evolution of life.


Let's be clear. Historically, some versions of intelligent design theory did include elements of religion. Those versions of ID theory could not qualify as scientific theories for that reason. However, most forms of modern intelligent design theory do not include any religious elements. They can therefore qualify as proper scientific theories.


We should also bear in mind that ID theory is not a replacement for the theory of evolution. It is a sub-type of evolutionary theory. Intelligent design theory retains all of evolutionary science; it only removes the accidental concept. ID is still evolution; it just adds intelligent input to the process to explain what is otherwise fully inexplicable: how to make enormously complex machines in a relatively short period of time.


For someone to find an expensive wrist watch on the beach and assert that some excellent engineer must have made it is not to assert religion. Drawing the conclusion of a watchmaker from the discovery of a watch doesn’t require a personal choice of philosophies, religions, or worldviews; it is a purely intellectual/scientific conclusion. Machines are known to be artifacts of science and technology. It is science and technology that tell us this, not philosophy or religion.


Religious versions of ID theory can be constructed by choice, yes, and some traditional versions did include elements of religion. But the core component of basic ID theory itself does not require religion, and the mainstream versions of modern ID theory don’t have religious elements. Modern intelligent design theory merely says that we need not refrain, as famous evolutionist G. G. Simpson did, in further defining the character of the “purpose” that Simpson and many other evolutionists have long admitted to be so clearly manifest in nature.


Intelligent design theory says that that “purpose” could only have originated in intelligence. That intelligence does not have to be God any more than the watchmaker we infer from finding a Rolex on the beach has to be God. Depending upon what science ultimately discovers about living systems, arguments might be made that the designer of life is or is not God.


Simpson apparently felt we didn’t have to worry about where the purpose or bias in nature comes from—sort of a, “that’s just the way nature is” concept. Some evolutionists apparently feel that it is both scientifically and philosophically acceptable to merely note that “purpose,” left largely undefined, is an inherent feature of nature and leave it at that—description without explanation.


I differ with that position. To leave a concept fully undefined as a sort of wildcard placeholder is not much different than simply ascribing the phenomenon to magic. Being conceptually undefined, and having its physical origins unexplained, G. G. Simpson’s concept of purpose in nature is not scientific. Rather, it is scientific as a report (reports can describe but don’t have to explain), but it is not scientific as a theory. Scientific theories are tasked to explain, not just describe.


If we could demonstrate that the enormous bias for life that is visible in nature arose by accident that would be different. But to do that one has to show that the universe began in chaos and that the order within our universe then emerged from that chaos by purely random event dynamics. That demonstration is known to be impossible because our universe has never been fully chaotic, not on this side of the Big Bang. We don’t, and probably can’t, know what the nature of things was on the other side of the Big Bang. Science’s own laws of thermodynamics preclude order ever coming out of pure chaos (pure entropy).


Should we just stop looking for an explanation of the origin of life and say we don’t have to know where the bias for life comes from? To me the traditions of both science and philosophy obligate us to push for a deeper explanation where the possibility of finding one remains. ID theory seems to give us that additional level of explanation. At a minimum, it gives us a promising place to look for that deeper explanation, a place that science has not yet thoroughly explored.


Behe, Meyer, and Dembski, et al. have solidly established that both direct and indirect signs of intelligence are present in biochemistry, microbiology, genetics, and the fossil record. Yet there remains this final question: shouldn’t there be more? Shouldn’t there be, not only signs of intelligent authorship, but real clues as to who the author of life is?


I go to great lengths here in Part 1 to demonstrate that there can be versions of ID theory that are purely scientific, versions that do not assert (or deny) the existence of God and which leave the identity of the designer of life a completely open question. In Part 2, however, I go further to argue that there is more, that there are purely scientific clues to the identity of the author of life, although those clues reside largely within the social sciences and psychology.


I can’t claim to have definitively proved God’s existence in this book, but I have certainly established him as a contender for being the source of the creation and evolution of life on Earth. After completing the book, I think you will agree that God is the best explanation of all the scientific data, once we include data from sociology and psychology.


The argument I advance in Part 2 that the Christian God constitutes the best scientifically defensible candidate for the designer of life presently available for consideration is (to the best of my knowledge) at least partly original in its total form and content. The same conclusion has been argued by other authors, such as Dr. Hugh Ross and Dr. Fazale Rana, et al. at Reasons to Believe, but their argument structure seems to integrate religious authority with science at points. My argument takes pains to remain exclusively within science, philosophy of science, and logical analysis.


To some readers Part 2 will, at first glance, also seem to be a religious version of ID theory, but it really is not. I do mention religious persons, events, and texts at various points and offer a few religious sentiments for inspiration—but these are not used as logical or evidential weight-bearing components of the argument.


I express my faith at points, yes. I believe God is an authority, but not a scientific authority. The Catholic view is that for his own reasons God has never deigned to teach us science. For example, in the book of Genesis God has chosen to teach us only religious principles and religious history, while allowing us to discover scientific facts for ourselves.


I think the scientific arguments of Ross, Rana and company at Reasons to Believe can probably be separated from their statements of religious authority. In fact, in some of their presentations they seem to want to emphasize the pure scientific nature of their arguments. It may be that they are not intending the acknowledgment of God’s authority in the Bible as a weight bearing part of their case, but rather a personal statement of faith. In the latter I whole-heartedly concur.


Yes, in Part 2, I actually argue that God is good science. I go a step further to argue that the Christian God is the more probable source of our world, all things considered. This is done seriously, with an attempt at philosophical and scientific rigor. I invite the reader to test my logic and data at all points and evaluate for themselves to what extent I have succeeded.


I agree that science and religion must remain separate pursuits and disciplines, but there is nothing in principle preventing the empiric data from natural science and disciplined scientific observations in social science being combined with pure logic and mathematical probability theory to support conclusions about God, either pro or con. Marxists and Communists have suggested for over 150 years that science argues against God. If science can argue against God, it can also argue for God.


Most thinkers on both sides of the accidental evolution question will consider an exploration of the question of whether scientific data can not only argue for God generally but also argue for a specific version of God to be scientific anathema, a violation of the separation of science and religion. Western cultural traditions tend to dismiss this possibility out of hand as precluded by inherent barriers that prevent natural science from tracing supernatural events.


While I agree that natural science cannot directly trace supernatural events, I think an indirect argument for God from science as the best overall explanation can still be made in a manner analogous to what goes on when the Church investigates miracles. In those cases an investigation is conducted using the tools of natural science (including forensic science) with the objective of ruling out or ruling in natural causes for the event that is a candidate for being a miracle.


Once the natural is ruled out as offering any possibility of explanation, the next question is what brand of supernatural actor seems to have been at work. If a person who was miraculously healed has a strong religious faith and reports having prayed to a particular saint for healing, it is a plausible hypothesis that the miracle was engendered by God or the saint acting on God’s behalf. Thus, the occurrence of a supernatural miracle (and the existence of the Christian God who engendered it) is a plausible conclusion to draw from natural science-based investigations of purported miracles.


Here we see that my approach to the question of arguing for God with science is not so strange after all. Each case of investigating a miracle is a small example of precisely the same form of argument. It is a simple two step procedure: rule out natural causes by means of a natural science investigation, then look for the most logical explanation among the supernatural alternatives.


Another indirect form of argument for the supernatural can be found in science’s inability to create life in the lab or to explain the first origination of life from nonliving matter. While not constituting a full proof that a spiritual element is necessary for life, science’s failure to explain and create life using exclusively physical components constitutes corroborative evidence for the thesis that a spiritual component is necessary for life.


Forensic investigation is a science as well as an art and craft. Exhaustively employing a process of elimination is a valid form of forensic investigation/argument. If, as in the case of the study of abiogenesis (creation of life from non-living substances), the instruments and methods used are purely those of natural science, then the process of elimination argument for a spiritual element of life is an argument from the “hard” natural sciences, as well as from forensic science.


After considering the knowledgebases of all the sciences, including history, sociology, and psychology as well as the fully natural sciences, if the best explanatory model science can produce includes God, then so be it. Science should go wherever the best explanation lies.


I will argue in this book that it turns out that God has signed his work after all. It’s just either a very large signature requiring us to stand back and look at all the information in science, religion, sociology, psychology, and philosophy at the same time to see; or it’s a very small signature requiring an electron microscope, a mathematical probability analysis, and an intricate review of biological complexity data to see. When God signed his work he was considerate of both the far-sighted and the near-sighted.


Not only is there, as Dr. Stephen Meyer says, an intelligent signature in the cell, but, as Dr. Hugh Ross and others have argued for years, there is a signature in cosmology—and it is the Creator’s signature. That glorious signature is in fact boldly scrawled across the larger part of nature for any rational thinker who does his or her homework to discern.[12] While the full case for God in science is, to borrow a phrase from Ernst Mayr, a long argument, it is worth the effort to work one’s way through it. In this book I try to give the reader a running start on the homework requisite to discerning God’s signature in nature and the cosmos.


The many appendices to this book concern themselves with elaborating certain interesting side topics like SETI; artificial intelligence; the multiverse theory in cosmology; testability; natural law; and natural selection. Also addressed are the many and major differences between Creation Science and ID theory; and the fact that the neo-Darwinian evolutionary argument is both a logical mess and a mammoth propaganda exercise, replete with over 100 fallacies.


But that is Part 2, and beyond to the appendices. First we must complete the objective of Part 1, which is to show that the accidental theory of evolution can now be disproved. To do that, we must dig into the biological data and describe the enormous complexity of living systems, the nuts and bolts of life. Having completed a review of biological complexity we will translate the complexity data into a probability estimate at Table 1. That probability estimate clearly rules out accident as the source of life on Earth.


Neo-Darwinian Evolution Refuted? OK, Let’s See the Hard Data


First a Summary of the Intelligent Design Argument

NOTE: Discovery Institute has provided a brief intro to ID theory at They have the PhDs, but they have very considerately kept the language simple and easy to read. It is probably a good idea to review the Discovery Institute page first before going any further here.


It will come as a surprise to many that the neo-Darwinian theory of accidental evolution can now be straightforwardly refuted—and that there is little hope of the theory’s resurrection. Yet hardly a word of this has been breathed to the news media.


In Lights in the Sky & Little Green Men, Dr. Hugh Ross identifies 115 characteristics of our universe and solar system that must be fine-tuned to astronomical levels of precision for life to exist. The probability that all these factors would occur together minus intelligent design (and this is before we get to the enormous complexities of biology) is dismissably small at 10-69. This equates to less than one chance in 100,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,0000,000,000,000.[13]


Ross presents portions of this list of fine-tuned physical values in a briefer offering entitled, “Big Bang Model Refined by Fire,” which comprises Chapter 15 of the multi-author collection, Mere Creation: Science, Faith & Intelligent Design, edited by William Dembski.  Rich Deem has conveniently replicated Dr. Ross’s data for us to review in his excellent Web page at


When we move from this mathematical bombshell in physics and cosmology to recent research in biology we encounter another explosion of zeroes in the probability figures. So much biological complexity data has been unveiled in the past forty to fifty years that intelligent design and cosmic purpose are no longer just nominally defensible personal philosophies; they are startling realities of science.


To demonstrate why this is so, let’s begin with the work of Dr. Stephen C. Meyer. Meyer is Director of Discovery Institute’s Center for Science and Culture in Seattle. He has presented a comprehensive case against the accidental origination of life in a groundbreaking article (one surrounded, of course, by political controversy) entitled “The Origin of Biological Information and the Higher Taxonomic Categories.”[14] Here Meyer cites a plethora of peer-reviewed scientific studies, and (controversy or not) presents straightforward arguments that establish a magnitude of improbability for accidental evolution that science can no longer ignore.


Dr. Meyer’s recent book, Signature in the Cell, augments that broad but convincing argument, focusing in tightly on the complex computer language-like aspects of the DNA code. Chapters 4 through 6 of Signature describe the DNA code and its transcription, transportation, and translation machinery in such clear terms that even the most casual reader can grasp the implications for intelligent design.


Meyer forgoes the misleading oversimplification one typically finds in neo-Darwinian discussions. He gives us the real meat and potatoes of how it all works. It turns out that life is not as simple as neo-Darwinists have led us to believe. It is certainly not something an accident could have thrown together.


What we see in Signature in the Cell is that the integrated genomic systems of life are unmistakably computer-aided manufacturing systems. Driving a well-defined system for the construction of a myriad of the intricate biological machines of life is a computer programming code with enormous information carrying capacity, DNA. This is only the protein/enzyme production half of the larger genomic system.


The other half, the gene regulatory system, is comprised of a different set of equally complex operations that closely govern the operation of living systems once they have been constructed. In the operational genomes of adult organisms we have a computer-aided manufacturing system, an operations control system, and a quality control-error correction and repair system. The reproductive system and the developmental genome do similar things to precisely govern the process of creating and maturing immature organisms from conception to zygote to embryo to the fully formed young of the species.


And let’s not forget the human brain. The genome is not the only biological mechanism that shows intelligent design. In his article, “Duplicating Human Intelligence is a Mirage,” computer scientist Peter Kassan informs us that a program mimicking human intelligence would have to be 25 million times the size of the largest computer software program ever written. Could an accident achieve either of these systems in the time available in evolutionary history? No.[15]


Next in the case for intelligent design comes Professor Michael Behe’s landmark book, Darwin’s Black Box, and the excellent follow-on Edge of Evolution.[16] Behe argues the irreducible complexity thesis, the argument that cells and selected other biological systems are impossible to build one small step at a time because the parts are too closely matched and their functions’ inextricably connected within a very complex interdependent living system.


Could an accidental process put such machines together with nothing more than the aid of natural selection and 4 billion years to try? The mathematical probability says “No!” Given 4 billion years, or even trillions upon trillions of years, an accidental process won’t be able to produce life. Many parts of biological systems have to be produced, preserved, and then put into place in very near proximity of time and space, all with great precision and control. This is not the kind of process traditional Darwinian and neo-Darwinian evolutionary theory has described.


Most laymen/women would agree with Professor Behe that irreducibly complex machines simply are a “sign of intelligence,” that biological machines (or machines of any kind) are always evidence of design. We have never discovered a complex machine that was made by accident. Common sense remains the hallmark of intelligence, even in the twenty-first century, though at times one might hardly know it.


Cells are too delicate and interdependent to have been formed by accident. Neither can they be accidentally modified without harm because each component is critical to function. An accidental process will inevitably break living biological systems before achieving substantial (progressive) functional change. Accidental tinkering substantial enough to make functional change will either kill the host organism outright or its gene line will be lost, vetoed by natural selection due to an inherent disability produced by the random tinkering.


Not every aspect of biology has been shown to be irreducibly complex in this way, but a central and critical core of the functions and structures of life are known to be irreducibly complex. As the reader already knows, everything in life is built around the cell, and the typical cell is, itself, irreducibly complex.


The developmental genome demonstrates the close interconnectedness or irreducible complexity of life quite straightforwardly. Every time an embryo is formed and developed into a fully formed creature a highly complex, time-synchronized, sequenced expression of thousands of different genes occurs. This process is closely orchestrated by the developmental genome. There is nothing random or accidental about the developmental process for complex creatures.


Embryonic development is the only known process available to science from which it can model the event dynamics involved in the creation of complex life forms. Science has discovered no short cuts or random substitutes to accomplishing the same thing. Cell division works for single-celled organisms, but even there you have to have life to produce life, and a management system is in place to closely control the process of cell division.


This tells us that the initial creation of simple life from nonliving substances and the later evolutionary jumps to highly complex life forms must have proceeded in a manner conceptually if not physically similar to the way the developmental genome controls embryonic development: a management and control system of some kind was required. Such systems would have to have been built into natural law and the initial state of matter and energy at the Big Bang—perhaps in very subtle ways, some so subtle that science cannot presently discover them. Alternatively, lacking a management and control system subtly hidden in nature, the creation of first life must have been supernaturally guided by a cosmic conductor who accomplished the same control functions by more direct but supernatural means.


While the creation of the first simplest form of life in a single-celled organism would be orders of magnitude less complex than producing large animals from embryos, a single living cell is still highly complex. Science hasn’t been able to produce single-celled living organisms via random processes in the lab, let alone demonstrate an accidental achievement of myriads of further steps requisite to the creation of more complex animals. This is not surprising considering that the simplest organism capable of independent life has been estimated to require approximately 1,500 genes.


To produce one standard size gene (1,000 base pairs of DNA) by accident is improbable to the tune of 1 chance in 41,000, which converts to roughly 1 chance in 10601 (‘1’ followed by 601 zeroes). To produce 1,500 genes by accident raises the improbability to 1 chance in 10901,500 (‘1’ followed by 901,500 zeroes!). The probability here is so infinitesimally small as to be scientifically dismissible, yet the materialists who have historically predominated in modern scientific and academic circles have made the theory of accidental evolution the default scientific position on the evolutionary question. It is a travesty on scientific and intellectual integrity.


In the neo-Darwinists’ accidental model of evolution abiogenesis has to somehow overcome these virtually impossible odds to get life from dust, then evolution must move the first simple organisms to the much greater level of complexity of mammals. These two tasks are almost certainly not accomplished by the same means. There are significant and obvious differences in the processes of abiogenesis and evolution. They do have one thing in common, however: they both are so hugely complex as to be impossible for an accidental process to achieve. Accidental processes may dabble a little around the edges of evolution, slightly modifying the results of various stages of life’s development, but accident is not capable of functioning as the primary engine of life’s creation and evolution.


The vast complexity of living systems recently revealed by science tell us that major biological form change evolution, like reproduction, requires an intricate management system, the functional equivalent of the developmental genome. This management system must be accidentally constructed, if we are to accept the accidental model of evolution proposed by the neo-Darwinists. In addition to needing a management system to create the first living creatures from “dust,” there seems to be no way for an accident, assisted only by natural selection, to have created the developmental genomes necessary for reproduction of the more complex creatures. These are two big problems for traditional Darwinian evolutionary theory, and its more recent cousin, neo-Darwinian theory.


How does an accidental process aided only by natural selection construct the first developmental genome? In constructing the developmental genome of an animal by accident, thousands of component steps must be hit upon by accident and sequentially locked in by natural selection. But there is nothing about the intermediate steps of such a developmental system that would give survival advantage to the host organism until the developmental genome is complete, at least complete in rudimentary form. Natural selection won’t be able to “vote” on the intermediate steps involved in constructing a developmental genome because those intermediate steps are irrelevant to the survival and reproductive fitness of the organism.


At the point where complex animals requiring a developmental genome appear in evolutionary history we see that, at least in this instance of the chicken and egg dilemma, the “egg” must come first, the developmental genome. But the neo-Darwinian theory of accidental evolution cannot get us to that “egg” because natural selection is taken out of the process. There is no time for accident to work incrementally to produce a developmental genome with or without aid of natural selection because the complex species all need the developmental genome to be immediately present in order to reproduce.


In theory, once independent simple life forms appear, the work of producing untold numbers of variations of both adult and developmental genomes could have been accomplished via the simple means of a runaway random DNA sequence generator mechanism inside the first living creatures—a biological feature that produces unending randomly generated DNA sequences. A simple transpositional mechanism then periodically substitutes the random DNA sequences into the operational genome, occasionally producing new features, and potentially even new creatures. Natural selection then only has to vote on completed adult and developmental genomes, rejecting nearly all of them, but preserving the rare few that work.


If there had been sufficient time and physical resources in the history of our universe for this method to be used (there wasn’t) it would solve the developmental genome problem, but not the problem of creating the first life forms by accident. The accidental creation of the first independent life form is so improbable that there was insufficient time and physical particles available in the history of our universe to raise the probability of the accidental creation of life to an infinitesimally small fraction of that required for scientific credibility.


Thus, the burden of proof has shifted now from those who would argue against accidental evolution assisted only by natural selection to those who would argue for it. Few in academia will acknowledge that this is so, but so it is. The immense complexity of the “higher” life forms, the requirement for a developmental genome that the neo-Darwinian process cannot produce, and the dismissably minute chance of an accidental creation of the first organism capable of independent life have shown the theory of neo-Darwinian evolution (accidental mutations assisted only by natural selection) to be an unworkable model.


To guarantee that a matching developmental genome would be available at the time each of the complex species of life emerged from the evolutionary process there must have been something like Professor Susumu Ohno’s master genome already present during life’s early development around the pre-Cambrian period before complex life forms began to emerge (at the time bacteria “ruled the earth”). The concept of a master genome is discussed further in the section entitled “A Precambrian Master Genome?” below.


But the neo-Darwinian model of the evolutionary process cannot account for a master genome being present at such an early period before most of the species themselves had appeared. There was no way for natural selection to vote to preserve the intermediate steps involved in building such a master genome (there may have been more than one master genome). Pure accident would have had to do all this work.


Once the first living organism was created, if there were manic random DNA generators in it that produced all possible DNA sequences, then a master genome wouldn’t have been required as such. What would have been present would have been, in a sense, all possible genomes. (Something like this may, in fact, be the way the tree of life began, making evolution possible.) Natural selection then chooses from among the possibilities to preserve the genomes that work in a creature’s present environment.


But there are extreme difficulties even with this wildcard quick genome generation device. Considered to be truly random, the resource exhaustion argument forbids its success: there was insufficient time and physical particles in the history of the universe to allow the system to work to successful completion. Life is that complicated. Such a system would not have remained in operation for long if it were not intelligently controlled in any case because as a marauding accidental random DNA generator it would pose a threat to the already working systems of the organisms hosting it.


From the very early years of the tree of life, evolution would have had to do things the hard way again without aid of such rapid fire random DNA sequence generating mechanisms, because natural selection would have culled out the creatures hosting the runaway DNA generators due to their own system being injured by too many random mutations. This would be true unless there were some biological dynamic that caused the manic random DNA sequence generation system to reappear periodically during the history of evolution. This, again, may in fact be the way the tree of life was created, but it doesn’t help the theory of life’s accidental creation and evolution because it doesn’t explain how to get the first living organisms. If the creation of the first living creatures hosting the manic random DNA generators is not an accident, then the evolution that follows from those creatures in not an accident either.


Neo-Darwinists prefer to call these lines of argument that defeat their theory “religion” or “non-science,” but descriptions of biological complexity and interdependent systems are science; probability computations are science; physical resource exhaustion and time limit computations are science; and the lack of observed examples of accidentally produced machines in nature is a scientific fact. The clear requirement for a developmental genome to produce complex animals, and the inability of natural selection to assist in building a developmental genome, are also scientific facts. Professor Emeritus (University of Vermont) John A. Davison's work centering on the developmental genome doesn't get as much facetime in the popular press as the work of Behe, Meyer, and Dembski, but his argument is a show-stopper for the theory of accidental evolution.


What’s the resource exhaustion argument? The accidental neo-Darwinian trial and error process would involve so many false starts and mistaken lines of development that the universe would be out of time, out of physical particles, and out of energy long before hitting upon the right combination of events. This resource exhaustion problem is one of Professor William Dembski's primary arguments for intelligent design. The resource exhaustion argument poses a formidable objection to the theory of the accidental creation and evolution of life, and no satisfactory response to it has been offered. While the vast improbability of the accidental creation and evolution of life doesn’t make neo-Darwinian evolution theoretically impossible, it does make it scientifically dismissible as our best explanation.


To absorb the full force of the modern intelligent design argument, Professor Michael Behe should be read in conjunction with Stephen Meyer as well as William Dembski. It is not an overstatement to say that, for those who invest in a careful reading, after first getting Behe and Meyer under your belt, William Dembski’s books, The Design Inference, No Free Lunch, The Design Revolution, and Intelligent Design, present the coup de grace for accidental evolution.


Much has changed since the advent of Darwin’s theory in 1859. In his close observations of nature Darwin saw only small changes occurring in various creatures. While these changes may have produced a nominal new species because, for example, the beaks and food preferences evolved to be different among certain kinds of finches, they remained finches, and they remained birds. Neither Darwin nor anyone else has ever seen macroevolutionary change occur or scientifically traced the biomechanics of such a change. No one has ever “observed” or traced the complete causal chain of biomechanical events involved in one type of creature evolving from a radically different type of creature.


True, evolutionary science can produce some very suggestive, even impressive, partial chains of fossil records of seemingly related species, but that does not give us a causal chain of events that shows how evolution operates at the biochemical and genetic level. The biomechanics of macroevolution remain mostly unknown, but we do know they are phenomenally complex.


Even if we could show that a horse evolved from a fish, without knowing the biomechanics of how it occurred it would not automatically prove that the process was accidental at its foundations. Various models of cars and motorcycles produced by the same manufacturer are visibly related to each other, sometimes by direct inheritance of components and systems, but there is nothing accidental about their design and construction.


Both gradualism and accident made sense from what Darwin could see. We now know that many key biological machines and structures can only be successfully assembled and integrated into an organism’s larger design by coordinating time-synchronized changes to ten or more genes and associated nongenetic processes. In a number of cases, very many genes would be involved, at least indirectly, and in some case nearly all genes are involved. Obviously, this kind of process is not gradualism at all—and it is not something an accident can manage


Even so staunch an opponent of purposive evolution as Richard Dawkins concedes that alteration of one gene in the active genome can at times create effects cascading through an entire living system, potentially affecting all active genes. This doesn’t mean that all genes must be changed at the same time for each evolutionary step, but it does mean that many genes will have to be changed for some steps. It also means that the resource cost will be high for many steps if accidental mutation is the engine driving the change.


Dr. Stephen Meyer’s probability estimates are derived from accurate descriptions of living systems. These system descriptions combined with standard probability theory tell us the typical resource requirements (time and physical particles) necessary to accidentally produce the known systems of biology. An accident must try half or more of the alternatives first before its success can be rationally assumed as more probable than its failure. This is required by standard probability theory.


The more complex a system is, the more physical alternative versions there are for an accidental “architect” to “consider,” that is, to work through before stumbling on one specific optimized approach. Time becomes a big factor where accident is the architect. A four year old child accidentally throwing together a functioning LEGO design having 500 parts from his older sibling’s toy chest over Christmas vacation without knowing the plan in advance is much less likely than his assembling a ten or twenty-piece design.


So, what’s the big deal? How many “LEGOs” could the human body require, anyway? Five or ten thousand, maybe? It can’t be that hard, right? Wrong. It can be hard. It can be very hard. That is what has changed since Darwin. Life has been discovered to be trillions of times more complex than the science of Darwin’s day suspected it to be.


There are some 85,000 proteins that are the building blocks of the human body alone. Each of those proteins requires additional building blocks called amino acids in unique strings ranging from several hundred to 10,000. As few changes as three nucleotides of DNA, called a DNA triplet, can affect the function of an amino acid. That’s a lot of building blocks! Matching up all possible combinations of these biological components in a matrix produces millions of trillions of possibilities.


That simple inventory of the biological building blocks merely hints at the complexity of the protein-based structural side of living organisms. Once the amino acid strings begin to fold into the ultra-complex shapes that define recognizable proteins, the newly formed proteins assume a wide variety of interactive capabilities with each other and with other types of biological components. While biological complexity is impressive at the static structural level, it expands exponentially when the multifaceted interaction of thousands of “moving parts” is considered.


There are other aspects of the operational side of things to consider: gene regulation, RNA transcription, gene translation from multiple reading frames, and DNA error detection and repair. The total genome size including both structurally and operationally concerned genes can often exceed billions of nucleotides. Here we see that the complexity of life is incompatible with the overly simplistic Darwinian model of evolution.


If the neo-Darwinian theory of accidental evolution has failed and the intelligent design argument succeeds on the basis of pure science, math, physics, genetics, and microbiology, why do the neo-Darwinists cling to an outdated model and ridicule ID theory as religion masquerading as science? There seem to be two possibilities. Either they do it knowingly, for political reasons, or they do it because they have become subconsciously influenced by the strong materialist traditions within modern science.


Politics in science? Really? Of course. All human endeavors are tainted by politics (unfortunately). For neo-Darwinists and their political and philosophical cousins in the materialist, atheist, and Marxist/Communist communities, to allow that intelligent design theory is proper science is to lose the huge influence neo-Darwinian evolutionary theory wields in world politics. The Cold War may be over in the military and intelligence arenas, but the classic struggle between atheistic Marxism/Communism and democratic political philosophy still goes on in interpersonal intellectual discussions, within the media, and at colleges, universities, and think tanks.


The theory of accidental evolution, holding the position of leading evolutionary theory as it has, tends to move naïve young students and casual adult readers of popular science to an atheistic worldview. Although Russia is now a democracy, there are still some aggressive Communist nations out there recruiting people to their cause, and there are independent Marxist groups doing the same thing. And roughly 20% of Russia is still Communist.


Having the public adopt a materialistic worldview removes the morally constraining influence of the world’s religions from the social-political chessboard. This allows violent overthrow of legitimately elected governments to be viewed as morally acceptable—something essential for the advance of Marxism/Communism.


Intelligent design theory’s arguments throw a wrench in the Marxist’s propaganda machinery by showing that neo-Darwinian evolution is a failed theory. If life is not an accident, there is more arguing for God than against him, and Marxists have a real bear of a time convincing people to accept the atheistic component of their ideology.


While it is true that ID theory tends to support belief in God, so does the Big Bang theory tend to support belief in God. Neither theory is religion as such. The latest versions of intelligent design arguments have divested themselves of all religious elements. They proceed on a purely scientific basis. And they are very convincing arguments.


Now that the scientific argument for ID theory has become so strong, scientists and philosophers with political commitments to the advancement of Marxism, or to the materialist and atheist worldviews, have no choice but to use political tactics to prevent the ID arguments from being heard within the scientific community. Once the full force of the ID argument is felt in science and philosophy, the Marxists and Communists run the risk of throwing revolutionary “parties” and having no one show up.


To preclude proper scientific consideration of intelligent design arguments, neo-Darwinists have bogusly labeled all intelligent design theory as “religion.” They have largely succeeded in this because intelligent design theory has a strong historical association with religion. Compounding the problem is the fact that ID theory’s modern proponents happen to be men and women with enough integrity not to deny their personal religious faith when challenged. But having Reverend Billy Graham propose the theory of gravity does not make the theory of gravity religion!


Yes, prior versions of the intelligent design argument did have religious components; however, most of the current versions do not. It is not all or nothing. Some versions of the intelligent design argument are religion; some are science; and some are a blend of both.


Most of the great men and women in the history of science have been people with strong religious faith. The greater part of science would have to be condemned as religion using such a standard as neo-Darwinists propose. It is a sad state of affairs that mainstream science can’t seem to drum up the political courage to get past this false “religion” label and look at the actual scientific content of the new versions of intelligent design theory.


What would happen if ID theory could get a fair hearing? If ID theory were admitted into science it would quickly supplant neo-Darwinian theory as the leading evolutionary theory. Why? Because its four primary arguments against accidental evolution visibly succeed: irreducible complexity, astronomical improbability, resource exhaustion, and the design inference—and because ID theory matches the historical data much better than neo-Darwinian theory. It has become clear both that there was seldom an opportunity for natural selection to act on nature’s proposals for the key elements of developing biological systems and that the process of producing new biological systems was for the most part not random.


The first three of the four ID arguments (we will look at the fourth in a moment) are straightforwardly demonstrable via standard scientific methods. The irreducible complexity thesis can be shown to be true by examining living systems at the genetic and biochemical level. The probability argument is proved correct by applying a standard tool of mathematical science, probability theory. And the resource exhaustion argument can be validated by mathematically comparing physics and cosmological data to the resource requirements for the creation of life via an accidental process. These are all routine applications of science having nothing whatsoever to do with religion. Do they refute neo-Darwinian theory to scientific standards? Yes, I think we have to say that they do.


Recall now that Charles Darwin’s own stated criterion for the refutation of his theory was that, should only one biological feature be shown to be impossible to originate by “numerous, successive, slight modifications,” his theory would be disproved.[17] Darwin goes on to say “But I can find out no such case.” But how could he, when he did not know of genetics and modern microbiology? Altering from ten to a thousand genes at the same time and coordinating those changes with alterations to the microtubule systems in cell walls is not a slight gradual modification.


From the beginning, the fatal weakness in Darwin’s theory was that the science of his time simply did not know the true biomechanics of life. His logic was good, but his data was not. Darwin and his contemporaries were stuck within the conceptual framework and research limitations of their time. They had no way to know what they were missing. We in the twenty-first century, however, have no excuse for maintaining such an outdated view.


The science of Darwin’s time held that the work of cells was managed by nondescript goo called “protoplasm.” They knew nothing of intricate cellular machines or the tripartite genome and associated systems. Thus, the critical unstated assumption of Darwin’s logic, that he might have found any case of a biological feature complex and interdependent enough to refute his theory, had it been present, is actually false. We cannot blame him for not knowing that, but modern neo-Darwinists, who continue to parade Darwin’s Origin of Species (which was a masterpiece for its time) as if it remained a cogent stand-alone argument for accidental evolution today, should know better.


It only takes one step in evolution invoking the simultaneous alteration of many genes or other physical components to defeat the accidental theory. What we currently know of the complexity of biological systems gives us very many candidates that are certain qualifiers under this criterion. A brief sortie into modern molecular biology, biochemistry, and genetic textbooks and related scientific journal articles quickly reveals that the clear majority of biological functions, features, and systems encounter the irreducible complexity problem. They require many precisely matched parts to be in place at the same time to function, and their overall complexity is astronomical. They cannot be produced by a gradual accumulation of genetic accidents.


The simple mathematical truth is that the improbability that any one of the major features of living biological systems would be achieved by accident is sufficiently staggering to fully imply intelligent design. The aggregate improbability of achieving all of them in sequence as manifested in the varied life forms of an estimated 100 million species, each of which has biological machines hierarchically embedded in larger machines 8-10 levels deep, as famous evolutionist G. G. Simpson conceded, simply forbids belief in an accidental process.[18] Simpson was not a proponent of intelligent design theory, but he did concede that the processes of nature involved in the formation of the tree of life were not accidental.


Astronomical improbability far beyond scientific thresholds of credibility, insufficient resources in nature to support an accidental creation of life, and specific counterexamples to the accidental model in irreducibly complex living systems all satisfy Darwin’s criterion for the refutation of his theory, albeit by approaching the question from different angles. Then there is the fourth argument, the faculty of the human mind to consciously or subconsciously recognize design, what is called “the design inference.”


The design inference argument against accidental evolution approaches the subject from the perspective of innate human cognitive abilities. The design inference argument says that humans have developed a reliable faculty of recognizing artifacts of intelligent design. We can directly see intelligent design in machines, works of art, and other artifacts of intelligent production with near infallibility, and we seem to recognize the same characteristic in living systems. We need merely look at living systems as we would a motorcycle to intuitively see that they are intelligently designed.


This argument from subjective human cognitive experience is grounded in the scientific discipline of perceptual psychology, and it is supported by the foundational principle underlying all of science, inductive reasoning. Although an experience of subjective judgment or discernment is the source of the design inference, a case built from perceptual psychology that establishes the high accuracy rate of the design inference is nonetheless a scientific case. While this form of argument is not “hard” natural science in the sense of physics and chemistry, it is natural science to the extent that perceptual psychology is natural science.


Mathematician William Dembski has broached the additional possibility that we may be able to elucidate an objective basis for these design inferences by closely analyzing the physical characteristics of objects that have been intelligently designed, including analysis by way of sophisticated mathematical tools. Such an analysis may equate to the conscious elucidation of what the human mind is doing subconsciously when it makes the design inference with extremely high levels of accuracy.


I will have more to say on this argument in Appendix 3 and in the second part of the book. It remains possible that the scientific disciplines of history, anthropology, sociology, psychology, and perhaps even mathematics, will in the future provide a combined argument to support the validity of the design inference faculty in human beings.


There comes a point in the presentation of a total case comprised of physical data, math, and logic when our human faculty of rational thought obligates a given scientific conclusion. I argue over the course of this book that we have reached and exceeded the point where this is true concerning the intelligent design conclusion. You will be seeing a great deal of the supporting data, math, and logic as we proceed further into the book. After reviewing all the data, I think you will agree that the intelligent design conclusion has now become obligatory to any rational thinker who doesn’t have a political agenda. 


There is the possibility of offering a fifth line of argument for intelligent design, one that might be called the “artificiality criterion.” This is the same criterion SETI researchers presently use while searching for signals from intelligent life in space. (see Appendix 8: SETI & ID) “Artificial” in the technical sense employed by science essentially means anything that nature is known not to do spontaneously in a specific place or situation. Artificial things don’t have to be complex, though they often are complex.


Let’s try an example. A mathematically perfect circle, square, or triangle of solid rock colored in a way that was unnatural to the mottled messy barren environment on the moon or some planet in space would be considered artificial, that is, of intelligent manufacture. These are very simple designs, yet still worthy of a conclusion of intelligent production because nature doesn’t produce those kinds of things in those locations. Since objects that do occur naturally can be relocated by intelligent beings to new environments where they don’t naturally occur, mere location of an otherwise natural object can in some cases imply intervention by an intelligent being. Those are simple examples of artificiality and intelligent intervention, things we know nature would not have produced spontaneously in the object’s current location.


Within key biological components such as the genetic system and the brain we have discovered enormously complex systems that reflect properties only found in artifacts of intelligent civilizations, such as computer programming language, Boolean logic circuits, analytical logarithms, and computer machine code. To presume that the most complex systems known in our experience (living systems), systems that employ components identical to systems that qualify under artificiality criteria everywhere outside of biology, have been created by accident when vastly simpler similar systems outside of biology are known to only be created by means of intelligent design seems to me to be an unwarranted, premature, and question-begging assumption—and a politically suspect one.


Life might be the only exception in our experience to the cognitive rules governing design inferences and artificial systems; it might just be one big coincidence. But a situation where accident creates the by far more complex machines and intelligent designers create only the less complex machines is so highly improbable as to be dismissed. Intelligent design theory must therefore become our default explanation of life and the accidental model of evolution reverted to a very long shot second place status until direct evidence is produced to support it. At present, we have no direct evidence for the accidental origin of life or accidental evolution, and much argues against both.


There is no reason to expect this situation to reverse itself based upon what science knows today. So, it turns out that the case for intelligent design in its most recent form is not one big abuse of science perpetrated by religious fanatics. It is actually an overwhelmingly convincing case built from logic, scientific data, and math, a case being smothered by Communists and materialists in academia to prevent public and academic recognition.


Nothing is given up by making the move to intelligent design theory except the ludicrous concept of an accident building astronomically complex machines. We can keep the neo-Darwinists’ reproductive variation statistics, their population studies, cladistics charts, phylogenetic inferences, and all the other impressive tools and instruments of modern evolutionary science; and we can keep religion out of science; we just can’t call life an accident.


With that brief summary of ID theory’s arguments given, let’s move on to the hard data of biological complexity.


Step 1, Abiogenesis: Life from Dust

There is a key point in the debate about the origin of life that many readers may have forgotten: evolutionary theory does not attempt to explain the creation of life at all—never has. The theory of evolution only addresses life’s subsequent transformations, not life’s origin. Since it has begun to look as if by far the hardest step in the creation and evolution of life is the first step, life from “dust” (abiogenesis), the accidental theory of evolution, and the worldview of atheistic materialism that has been traditionally associated with it, have always been a failure as a comprehensive explanation of life. An explanation that skips the hardest step is not an explanation at all.


The initial (and very naïve) assumption during the early Cold War years of the 1950s-1960s was that science would very quickly manage to produce an experiment that created life in the laboratory. That, of course, never happened. With each passing decade of exponentially increasing biological complexity data, it looks more and more certain that it never will.


Neo-Darwinian evolutionists will tell you they don’t think getting life from dirt is that hard, but they don’t put their (research) money where their mouth is…and the abiogenesis problem does remain unsolved. Neo-Darwinian evolutionists see no problems with logical consistency or intellectual integrity in beginning the study of the development of life only after the first living systems are present to generate, protect, and preserve the genetic mutations needed for biological form variation (and after the spiritual essence of life is already present). In this context, claiming that accidental processes alone can produce the tree of life is obviously a sham. Skipping all the hard parts and then declaring victory is a rhetorical propaganda tactic, not a method of science.


Creating life is not just a matter of stumbling upon an accidental rewrite of the DNA code. Creating life from nonliving materials is an entirely different kind of problem from evolving biological form change (randomly or nonrandom) from life that is already present, and present in a form that vastly facilitates further biological form evolution. Initially there is no code to rewrite, no translation system to make sense of it, no living system to protect and preserve it, and no system stable and redundant enough to tolerate mistakes—remember, the whole thing is supposed to be one big accident.


To accidentally evolve life by random genetic changes within a protected living system all that is needed is endless amounts of time. However, the amount of time required is much more than our universe has had to offer through its entire existence. Many more dysfunctional species designs would have been created than the fossil record shows if the process were accidental, even allowing that natural selection would not preserve them for the long term.


Given a steady pressure of truly accidental mutations it is not such a hard thing for mutations to eventually find their way to a new home within a protected environment inside a living creature. Some novel form or function will eventually be produced. Not hard, that is, if the process has trillions upon trillions of times the life of our universe to work, and trillions upon trillions more physical particles to work with than the history of our universe can provide.


The key to this entire discussion hinges on making a single conceptual distinction correctly: “Does the data indicate that the processes of life’s creation and evolution were random (in the sense of truly accidental) or nonrandom (showing a bias for life far too strong to be accidental)?” This book demonstrates clearly that the bias for life is far too strong to be accidental.


We will be moving to the details that show this bias to be present at many points in the biomechanical processes of life, but stepping back and looking at the total event of evolution also shows that accidental evolution can’t have happened in Earth’s history. There wasn’t the smallest fraction of the necessary time and physical particles available. As we will soon see in the complexity and probability summaries below, the bias for life in nature has to be enormous to get past the resource limits problem, and an enormous bias means the process was not accidental.


Yes, contrary to what neo-Darwinian evolutionists have been teaching for decades, evolution of the tree of life is that hard. Creating life from nonliving substances (abiogenesis) may turn out to be harder still. A large variety of unrelated independent physical conditions in Earth’s environment must be closely coordinated with each other to present all the precursors of life in close physical proximity at the same time: chemicals, prebiotic substances, and the elements and molecular compounds required for structural building blocks. Proteins and RNA sequences must be formed into very precise, delicate, and enormously complex configurations from rough materials that, in neo-Darwinian theory, have no directional or self-organizational help from Mother Nature.


But by what or whom is this coordination accomplished? Within the worldview described by neo-Darwinian theory these conditions are not produced by a purposive, at least partially guided system. In the neo-Darwinian theory of evolution it is all done by pure accident.


To generate life in the first instance, many time-synchronized events (each of which requires precise conditions involving multiple physical factors) must closely follow the other and occur in a physically constrained environment that excludes disruptive influences. It is not just about trapping gas bubbles in a permeable protective membrane. Thousands of microscopic factors are involved.


Something must string a series of thousands of nucleotides together in a meaningful pattern to achieve the writing of the original abbreviated DNA code, plus orchestrate the simultaneous construction of a DNA transcription system, a gene translation system, and a gene regulatory system.[19] Each of these systems is vastly complex in its own right. A gene regulation segment would also have to be immediately present to guide reproduction; otherwise the first life form would have quickly passed backed into nonexistence.


To accomplish the initial construction of these systems and quite a few others necessary to support the basic functions of an organism capable of independent life, a minimum of 1,500 complimentary genes (each of approximately 1,000 nucleotides) must be constructed in real time. That is a lot of code: 1.5 million characters, roughly the size of this book (which will be approximately 600 pages when the appendixes are posted back to the Web after the ongoing revision).


Page size varies quite a bit among books, but let’s say there are 2,500 characters on an average page of text. Monkeys typing randomly (as cute as they may be and despite popular writings to the contrary) will take “forever” to achieve a single page of meaningful script by accident. Achieving each of the requisite additional 600 pages by accident gets exponentially harder and harder to do with each page. Why would it get harder?


If the reader will pause to recall her game theory for a moment, she will remember that the difficulty of rolling two ‘6’s in a row with gaming dice is not 1 chance in 12, but 1 chance in 36 because there are 36 possible ways to match the values of die 1 with die 2. Similarly, rolling four ‘6’s in a row does not offer 1 chance in 24 (which would be the result of adding the probability of rolling one ‘6’ four times), it is 1 chance in 1,296. The probability of making specific sequential rolls is computed by multiplying the probabilities of each individual roll. In the case of trying to roll 4 ‘6’s in a row there are 1,296 ways to match the values of each of the 4 dice to all the other values of the other 3 dice if we recognize the individual identity of each die and not just look for the numerical total.


Imagine each of the four dice has a different color. The event outcome (not the numerical outcome) of having yellow and blue each show a ‘6’ and the others a ‘1’ is treated as a separate alternative event outcome from red and green showing a ‘6’ and the other two a ‘1’ even though the total numerical value is the same. In computing event probabilities our concern is not the numerical total of gaming dice for the purpose of winning a game, but the total number of alternative events. The event of rolling a ‘6’ on the second roll and ‘1’s on the other three rolls is treated as a different event than rolling a ‘6’ on the first roll and ‘1’s on the other rolls. So there are 1,296 alternative event possibilities when rolling 4 dice, and the probability of rolling any one specific set of values in a given sequence with the 4 dice, such as a ‘3’ followed by a ‘4’ followed by a ‘5’ followed by a ‘6’, is one chance in 1,296.


Similarly, the chance of accidentally getting a meaningful sequence of 2,500 characters of text on a page using an alphabet of 26 letters gets exponentially harder as you go (it’s hard enough to do it on purpose), starting at 1 chance in 676 to achieve the first two letters by chance and moving to 1 chance in 141 trillion just to achieve one specific sequence of text only 10 characters long! You can forget about completing an entire page of meaningful text by accident, which puts you in the neighborhood of 1 chance in 103,529. Written out in full, 103,529 would be a 1 followed by 3,529 zeroes, an enormous number. Scientists represent this chance as a probability of 10-3,529. Note the minus sign before the 3,529 indicating the negative probability. For a brief and simple refresher on how to use standard probability theory see Appendix 1.


To get the small genome of the simplest creature capable of independent life by accident, 1,500 genes at approximately 1,000 nucleotides per gene, we have to overcome the same problem: negative odds that exponentially increase with each additional step. This is true even though the alphabet of life, the DNA code, only has 4 “letters”: C, G, T, A (adenine, cytosine, guanine, thymine).


To produce only the first gene by accident we face odds of 1 chance in 41,000, which is 4 multiplied by itself 1,000 times. That is not 1 chance in 4,000 (which is roughly 4 multiplied by itself only 6 times). Four multiplied by itself merely 20 times yields 1 chance in a trillion, multiplied 30 times yields 1 chance in well over a million trillion, and so on.


Perhaps surprisingly for some, the final result of 4 multiplied by itself 1,000 times is approximately 1, 000,000, 000, 000,000,000 followed by 583 more zeroes, or 1 chance in a trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion…or 10601. That covers the improbability of accidentally creating only one standard size gene.


But to make a living creature capable of independent life requires 1,500 compatible and complementary genes. That 10601 must now be multiplied by itself 1,500 times. The improbability of creating the first independent life form by accident is then 1 chance in 10901,500. (‘1’ followed by 901,500 zeroes!)


A single attempt to throw a gene together by accident from nonliving substances obviously requires many physical particles and many seconds of time. Mathematician William Dembski has calculated that our universe has only had enough time and physical particles to produce 10150 (or less) physical events in its entire history. That calculation is based upon minutely small events only involving a fraction of a second and a single physical particle. The maximum number of larger events possible in the history of our universe is much less due to more time and particles being used in each event.


Standard probability theory requires half the alternatives to be tried before a successful random achievement of a particular result can be considered more probable than failure. In the case of accidentally generating the first independently living creature this means that a number of alternatives equal to half 10901,500 would have to be tried before we would be entitled to assign a probability greater than 50% to the accidental creation of life (half is 5 X 10901,499).


But with only 10150 particle events available in the history of our universe this is over a trillion, trillion, trillion… (“trillion” repeated over 75,112 times) the number of alternatives the universe can afford to explore. At a minimum, we are entitled to say that the accidental creation of life is much less probable than the non-accidental creation of life, but this is giving away too much to the neo-Darwinists for free. In fact, the beginning theoretical improbability for the accidental creation of first independent life (before time and physical resources are applied to the task), is so vanishingly small at 10-901,500 as to be scientifically dismissible. A 1% probability equals a mere 10-2, so the probability of creating the first life form capable of independent life by accident is one trillionth of a trillionth of a trillionth… of 1% (with trillionth repeated 75,124 times). 


Applying all of the time and physical particle resources available in the history of our universe makes no significant dent in this improbability. It only reduces it to the extent of removing 13 repetitions of “trillionth.” This leaves us with the probability of an accidental creation of the first life form capable of independent life after all the time and physical resources of our universe have been expended on the task of one trillionth of a trillionth of a trillionth… of 1% (with trillionth repeated 75,111 times!).


From the point of view of science, we are therefore justified in assigning to the hypothesis that the accidental creation of life didn’t happen an extremely high level of confidence. There are other angles from which to approach the probability computation for accidental life, but they all produce equally insurmountable improbabilities. Inevitably, such large improbabilities translate to an endless string of biomechanical obstacles to the accidental origination and evolution of life.


One such obstacle is the reversible reactions inherent in protein synthesis in water. In traditional hypotheses of abiogenesis the first proteins are believed to have been formed in solution in earth’s oceans. Spontaneously generated amino acids are assumed to have been mixed randomly in the oceans’ natural saline solution until they accidentally formed into the combinations required for biologically functional proteins. The obstacle in this case is the simple fact that proteins break down in water. Water dissolves the bonds between the amino acids and returns them back into a solution of single amino acid residues.


Thus, the lifespan of proteins accidentally hit upon in this way would be so short as to preclude anything useful being done with them to originate life and further its evolution. Proteins achieved in this manner would be mere chemical “flashes in the pan” in terms of the vast span of time required for abiogenesis to occur. They would not exist long enough to permit their assemblage into the complex biological structures necessary to support the construction or advancement of early life.


One can imagine a complex sequence of other events that might intervene to afford some protection to accidental protein creations, but doing this adds additional improbability. So, although the reversibility of protein synthesis in water does not make the accidental achievement of a few proteins fully impossible, it makes the near simultaneous accidental achievement of the set of the hundreds of key proteins needed to originate the first living organism an extraordinarily implausible hypothesis unworthy of being science’s default explanation.[20]


It is not implausible that an amino acid broth bubbling up from a steamy deep water vent or volcanic crevice saturated a location where something analogous to a PAH backbone structure held spontaneously generated nucleotides in a given sequence. Some additional accidentally constructed proteins may have immediately washed ashore at the same location, encountering a hospitable moist clay substratum where they avoid disintegration long enough to be captured by a protocell bubble containing the amino acids and PAH backbone. None of this is implausible, but it doesn’t create life. Hundreds of highly specific differentiated proteins must be developed and placed in immediate physical proximity, genetic systems must be added, and the surrounding chemical environment must be just right.


Even if we allow that a thermal vent or other phenomenon might serve as a mass-producing protein or amino acid factory that could crank them all out, we still have to remember that the price for considering the process of life’s creation to be random or accidental is that huge probability costs must be added for the production of each additional protein by accident, no matter what method nature employs.


To construct a living cell, a hundred complex proteins are required at a minimum (most involve thousands). They must interact in intricate ways with several hundred other cell components, each cell performing over two million actions per minute! Complex genomes and related genomic systems must be developed. Then 1,500 1,000-nucleotide long sequences of RNA or DNA have to be configured. Biochemical nutrients must be available. Cell walls with complex microtubule patterns must be constructed. Temperature must be controlled, and a physical threat-free environment maintained.


Yes, one can imagine an ultra-complex solution to the myriad obstacles to life’s accidental creation, but if nature is to use an unintelligent fully accidental process to create life it has to pay for each of the trillions of trial and error excursions needed to blindly stumble through that complexity gauntlet to find life’s highly improbable solution. The currency of that payment is enormous expenditures of time and physical resources in amounts trillions of times greater than Earth or its parent universe has ever had to offer.


Even if we could demonstrate that all DNA transpositions were truly accidental and unguided (hard to do when the math shows a tremendous bias for functional forms of life), we would still need complex life with a transpositional genome to first arise (from unknown causes) in order to produce evolution via random genetic transpositions. And we cannot show how an accident can produce the first independent life form with a transpositional genome from non-living materials.


Therein lies the coup de grace for the neo-Darwinian theory of the accidental evolution of life. Evolution needs the first living creature and a transpositional genome to have any chance of spontaneously producing the tree of life. It is therefore a complete travesty on the integrity of science and logic to claim that the evolution of life is accidental when the claim that the critical prerequisites to life’s evolution are accidental is known to be scientifically indefensible.


Neo-Darwinists object that their theory only looks at the development of life, not the creation of first life (abiogenesis), but if the prerequisite machinery needed to generate evolutionary change is all but certainly not accidental, then evolution is all but certainly not accidental. It is that simple. It is fine for evolutionary science to narrow its focus to life’s development after abiogenesis, but the problem is that the neo-Darwinists are claiming that the evolutionary development of life was an accidental process. Easily computable overwhelming probability figures say it clearly wasn’t an accidental process.


To allow materialists in science to continue to parade the accidental theory of evolution not only as our default explanation of life but as the vaunted flagship of modern science is a scandal of monumental proportions. As we will see, there is in fact nothing modern about the theory of accidental evolution.


As we touched on in the introduction, in addition to enormous improbability, resource exhaustion, and irreducible complexity, abiogenesis, the production of the first single-celled creature from non-living chemicals, has another problem: the chicken or the egg dilemma. In chapter 5 of Signature in the Cell, Stephen Meyer reminds us that there are a number of highly specialized proteins and other biological products (approximately fifty) that must be present for the gene transcription system to function, but the gene transcription system is itself the only method known to science that is able to produce those particular biological products.


True, experimenters have discovered that a handful of proteins can be produced spontaneously under the right environmental conditions, but they do not include all the key proteins necessary for life or even for gene transcription (there are some 200,000 or so proteins requisite to building the tree of life). Thus, abiogenesis of the first living cell remains an enormous obstacle for the accidental view of life.


To produce the full tree of complex life forms from the first simple organism many different cell types must be evolved or created. There are 120 different types of cells in basic vertebrates,[21] and about 200 types of cells in humans. Additional improbability (and a lot of it) is added to the total cost of creating life by accident to cover the differentiation of the original cell into the 200 or so different cell types necessary to complete the accidental evolution of the tree of life. Thousands of different kinds of proteins not contained in the first cell must also be produced.


Step 2: Proteins for 100,000,000 Highly Varied Species[22]

As most readers already know, very little happens in living systems without critical assistance from proteins of one form or the other. This is especially true of enzymes. Enzymes are proteins that have the unique ability to induce life-essential chemical reactions. Could all of the required proteins/enzymes have been produced by accident?


Recent studies say almost certainly not. The effect of accidental tinkering on biological machines is no longer an unknown. Random mutations to amino acids and proteins, the key structural components of life, have recently been scrutinized with scientific rigor for the first time. According to Dr. Stephen Meyer, citing the foundational work of Dr. D. D. Axe, the probability of getting even the most rudimentary biologically viable protein (just one) by chance from nonliving sources is no more than 1 chance in 10125, and the improbability of creating biologically useful proteins randomly within a living system is roughly 1 chance in 1077. [23] This estimate is not a guess; it is based upon peer-reviewed scientific research.[24]


A full inventory of all animal proteins has not been completed—or of all animals for that matter. However, the human body alone is estimated to use, at a minimum, 85,000 different proteins.[25] Total estimates for living creatures range to the hundreds of thousands. Physicist Paul Davies estimates the improbability of evolutionary protein generation at 10-40,000, 1 chance in 1040,000.[26] This is a huge number, but, even so, Davies must have made some allowance for nature’s bias for life, or for reuse of amino acid sequences obtained in earlier proteins for the creation of later ones, because a strict computation from the Meyer/Axe figures gives a much larger improbability (figures not available to Davies at the time his estimate was issued).


Perhaps Davies was following his mentor and doctoral advisor, Sir Fred Hoyle, in his identical estimate. However, Hoyle’s estimate, given in his classic book, Evolution from Space, was for the random synthesis of only 2,000 enzymes. “Life cannot have had a random beginning...The trouble is that there are about 2000 enzymes, and the chance of obtaining them all in a random trial is only one part in 1040,000, an outrageously small probability that could not be faced even if the whole universe consisted of organic soup.”


If we assumed true randomness (as an accidental worldview would require) and assumed no reuse of amino acid components at all, the improbabilities of generating each kind of protein of the full complement of 85,000 would have to be multiplied in sequence: 10-77 times 10-77 repeated 85,000 times. This yields a super immense improbability of roughly 1 chance in 106,545,000! That’s a big number! And it only encompasses the proteins needed to create the human species.


Many new proteins have to be generated and integrated into new systems, structures, and organs for each step up the evolutionary ladder. The problem of protein solubility in water eliminates much of the useful protein production from the external environment, as does the fact that, once bacteria were present, they would rapidly consume or biodegrade any accidentally produced proteins and other biotic components existing outside the protective confines of living systems. This leaves us with internal generation of new proteins from living organisms as the primary source for evolutionary progress. While internal generation of new proteins via random mutation is easier than nature building them from scratch outside a living system, it is still exorbitantly hard.


In Table 12.2 of their fascinating book, Origins of Life,[27] Fazale Rana and Hugh Ross employ a probability computation formula similar to those we have just used. There they compute the improbability of arriving at the first living creature by accident. To simplify, they used a single protein as typical instead of wrestling a long list of different values for different kinds of proteins. They used Hubert Yockey’s estimate of the odds for random production of the common protein cytochrome-C, which is 10-75, and multiplied that by itself 1,500 times.[28] Here the odds of achieving the 1,500 gene minimum thought to be requisite to first independent life (a simple bacterium-like creature) is given as 10-112,500, or 1 chance in 10112,500. This is much smaller than the estimate I give above because it is not based upon the assumption of purely accidental processes; it starts with what Mother Nature has provided in terms of a given state of physical events and the laws of chemistry and physics. Those natural laws and the existing physical state of matter and energy already embed a large bias for life that goes a long way towards taking the bulk of the work out of the process of building life, work that pure accident would have to otherwise do the hard way by purely random trial and error.


In essence, the problem with the accidental production of life is that proteins are super-complex (as is the genome that codes for them). They are so complex, in fact, that the dice of life have to be considered to have 1077 numbered faces, not just six! That is one hundred thousand trillion, trillion, trillion, trillion, trillion, trillion faces on just one die. Several hundred thousand such dice (different proteins) are required to construct the tree of life!


I bring to the reader’s attention the fact that the improbability of generating the complete inventory of human proteins (the improbability of each multiplied by the other) has been reduced by as much as 4,080,000 orders of magnitude simply by moving the process of protein construction from outside a living creature to inside.[29] While it is not surprising that a living system produces its own building blocks, it is interesting to note that already in the first two steps of life’s construction we see incremental increases in the bias for constructing our tree of life—and an enormous bias it is.


This phenomenon has the effect of refuting accidental neo-Darwinian evolution because here we see that the early organisms were not just built to survive, as natural selection choosing from random mutations would have done; they were built to evolve, to produce many new proteins and DNA sequences currently of no help to the host organism but which form the blueprints and building blocks of future new life forms. That is not to preclude evolution’s having some help from events occurring outside the organism, but the bulk of the biological evolution task seems to have been accomplished via internal biological mechanisms.


Given Michael Denton’s work on predetermination of protein forms and the enormous improbability of our tree of life having been created without a preexistent blueprint to guide evolution, a plausible hypothesis to make is that many proteins already have segments of a master blueprint for the tree of life somehow embedded into their structure, a structure apparently largely defined by natural law.[30] It appears that nature somehow employed a procedure (yet to be discovered by science) for unwrapping and translating that blueprint incrementally during the evolutionary process. My hunch is that the blueprint for life, or at least a significant section of it, is hidden somewhere in the enormously complex folded structure of proteins.


The complexity of protein structure allows for an enormous data storage capacity. A single protein can contain as many as 10,000 amino acid residues, with approximately 100 amino acids linked in an average protein. The enormous complexity of creating a precisely folded three-dimensional protein structure of typically from 50 to 300 amino acids, each amino acid with many functionally relevant properties of its own, is one thing (between them the 20 biologically useful amino acids have 437 properties relevant to determining function).[31] However, the full complexity of protein interactions in the cell, termed “systems proteomics” by Gabriel Waksman, is so complex that even our most state of the art computer simulations cannot represent it without employing shortcuts and simplifying assumptions.[32]


The exact nature of the fold is what imparts viable biological function to proteins. Even electromagnetic properties of amino acids are involved in protein folding. The full determinants of protein folding characteristics of amino acids are traceable down to the atomic level!


The configurational complexity of biomolecules means the entropic contribution to the free energy is a significant factor in their behaviour, requiring detailed dynamical calculations to fully evaluate. Computer simulations capable of taking all interatomic interactions into account are therefore vital. However, even with the best current supercomputing facilities, we are unable to capture enough of the most interesting aspects of their behaviour to properly understand how they work.[33]


As Waksman’s book, Proteomics and Protein-Protein Interactions, and the new volume, Protein Folding: New Research, edited by Tony R. Obalinsky, make abundantly clear, we know a lot about proteins, but only a fraction of what there is to know. Protein science is still in its infancy and already the complexity is off the charts, literally, for we have no way to fully model it.


Protein folding, key to all the processes of life, involves complexity so vast that it parallels the search for life in outer space. The public has been recruited to sign up potentially millions of home computers to help scientists process protein folding data, much like SETI@home does in using volunteers to scan data on their home computers to find intelligent signals from space. They are not doing this just for fun. They are doing it because they need the additional computing horsepower to have any hope of ultimately completing the task.[34]


Proteins configure themselves into folded patterns so intricate that it takes an average computer an entire day to accomplish in simulation what the protein has done in one billionth of a second!


The chief difficulty in simulating protein folding is time, explained Vijay S. Pande of Stanford University. Proteins fold on a time scale of microseconds (millionths of a second), but it takes an average computer about a day just to simulate the folding over a single nanosecond (one billionth of a second). At that rate, it would take almost three years to simulate a microsecond of folding and perhaps a decade or two of computer time to analyze the folding of a single protein. This is hardly a practical way to resolve the problem.[35]


Step 3: Constructing Cellular Machines—the Astounding Complexity of the Cell & Irreducible Complexity

Beyond the complexity of proteins and the DNA code itself is the actual day-to-day operation of the cell, which involves a myriad of complex machines. Professor Scott Minnich of the University of Idaho says the assembly instructions for cellular machines are even more complex than the protein coding instructions contained in DNA.[36]


The ribosome is one such machine, a critical organelle that manages the protein assembly process. To construct a ribosome, in addition to the basic protein composition of its two-part structure (20-21 proteins, and 31-35 proteins for the respective parts), several copies of ribosomal RNA must be created and added to the structure. In neo-Darwinian theory (which this book argues is clearly wrong), the RNA coding sequence must first be achieved by accident. That accident must precisely configure 1500 base pairs (bp) of nucleotides for the small unit and 3,000 bp for the large unit. It must also assemble 50 or more structural proteins into two functional subunits.


To get a better idea of just how complex even these deceptively simple miniscule protein tunnels are known to be, see Kathleen L. Triman's article, "Mutational Analysis of the Ribosome." Note particularly the bibliography, and the text she recommends by Liljas, Structural Aspects of Protein Synthesis,[37] both of which loudly proclaim that what seems so simple a task on the surface, to merely string amino acids together in line, turns out to be enormously complex when all the required biochemical interactions are considered.


For the sake of simplicity, if we estimate the improbability of accidentally creating only the smaller portion of ribosomal DNA, involving a sequence of 1500 base pairs, as the improbability of accidentally creating one functional protein (10-77) we are being fairly conservative.[38] (If the process were truly random the improbability would be 4-1500, or roughly 10-902—big difference! (Note: What the estimate for 10-77 represents is the odds of an already living system with a transformational genome and with occasional externally induced mutations spontaneously producing a new biologically functional protein that the system is not already built to code for. Living systems already have a large bias to produce such proteins, as we can see from the enormous difference in these two probability figures; so it is not a genuinely accidental process at that point.)    


Another biological machine is the cellulosome. The cellulosome is a two-component machine composed of what scientists call a dockerin sequence and a cohesion module. Bacteria use it to degrade polysaccharides on the cell walls of plants. The dockerin sequence is composed of approximately 70 amino acid residues, while the cohesion module requires around 150 residues. The genetic information required to create a cellulosome is approximately 6,000,000 base pairs.[39] Again, the 6,000,000-long nucleotide sequence must be configured by accident under neo-Darwinian theory. The improbability of generating the cellulosome by accident can then be roughly estimated as 4-6,000,000, an enormously small probability equating to 1 chance a trillion, trillion, trillion, trillion…with “trillion” repeated many hundreds of times.                                     


There are plenty of other machines involved in life. The famed biological clock, for example, perhaps thought by some (young persons) to be mythical, turns out to be quite real, and quite complex. The circadian clock is found in all complex creatures and some bacteria. It has been studied for 50 years and all of its mysteries and mechanics are still not fully understood. In a creature as simple as the fungus it involves 11 proteins and a very complex system of interactions with many auxiliary components.


Christian Heintzen and Yi Liu describe the circadian clock in amazing technical detail in a fascinating article, "The Neurospora crassa Circadian Clock," revealing feedback loops and a variety of regulatory actions, data input and output channels, etc. These clearly mark the clock as an intricately designed machine. (Heintzen and Liu neither advance nor deny the inference to intelligent design; they simply describe the clock.)


There are a variety of biological clock functions in humans and other creatures. There are apparently clocks in each cell, or at least most cells, which would amounts to trillions in a single human body. These intricate timekeepers interact with the genome and the overall metabolism to keep everything in tune and in time.


Hundreds of clock-controlled genes have been identified in a wide variety of creatures. Gene expression feedback circuits are involved in the generation of circadian rhythms,[40] and another of the important functions of the circadian clock only recently discovered is to govern the timing of DNA excision and repair. This is in addition to managing sleep, eating, blood pressure, heart rate, hormone production, and cholesterol synthesis. John B. Hogenesch has even remarked in a recent PNAS article that it begins to appear that everything is timed.[41]


A fourth biological machine that has gotten a lot of attention is the bacterial flagellum. Professor Michael Behe describes this intricate machine in Darwin’s Black Box. To get a more detailed view of the complexity of the flagellum ion powered motor, see Robert M. Macnab’s Annual Review of Microbiology article entitled “How Bacteria Assemble Flagella.”[42] The bottom line is that these are complex machines with very closely matched parts. They are, in fact, outboard motors, having rotor, bushing, and bearings, very intricately powered and controlled by miniscule electronic impulses. (See Access Research Network’s animations of the flagellum  here  and  here.)


In addition to such overt machines, there are other kinds of complex systems within the physiology of life that seem well beyond the reach of accidental construction. Many of these systems exist at microscopic levels. Acclaimed science writer, Boyce Rensberger (The Washington Post) gives a masterful account of some of the truly amazing things cells can do in his 1996 page-turner, Life Itself.  Here we learn that “cells have the biological equivalent of a containerized cargo system,” and many other complex mechanistic systems.[43]


It should not come as a surprise that extreme biological complexity at the genetic level is mirrored in visibly intricate cellular machinery.[44] However, the genetic code doesn’t encompass all elements affecting biological complexity. The functional attributes of these machines can be determined by nanoscale factors at the molecular, atomic and even subatomic levels!


In Darwin’s Black Box, Professor Michael Behe presents examples of a handful of biological systems that have been currently described by science to such an extent that we can very confidently analyze them. Within these closely-studied systems every component has been found not only to be essential to its function but very closely matched to each other in design. Behe calls these systems “irreducibly complex” because they can’t be reduced by even one component without destroying their function. These systems are too sensitive to deviation to permit accidental mutations that alter function; and the requirement for each part to be in place precludes accidental assemblage one piece at a time.


Behe’s thesis is that irreducible complexity is typical enough of living systems to preclude accidental evolution. Dr. Michael Denton claimed very much the same thing in his book, Evolution: A Theory in Crisis,  in 1986.[45] I think Behe’s point is undeniable. It is also a point that provides innumerable instances of biological systems satisfying Charles Darwin’s own criterion for the refutation of his theory: a biological feature that could not have been built by a series of small accidental variations.


The developmental genome, essential to reproduction of complex organisms, seems to be a very large and key system of life that is irreducibly complex, at least in its most rudimentary form. Proteomics represent another key irreducibly complex system of life.


Proteins are the elements largely responsible for almost every key activity of living systems. Construction of these proteins requires the presence of many quality control elements in the biochemical environment to enable correct folding of each protein into a precise and enormously complex 3-dimensional structure that determines the protein’s function. Proteins interact in a hugely complex interconnected system within the body in such a way that the essential functions of life cannot be sustained minus the simultaneous presence of hundreds of interrelated components. For a good discussion of the interconnected nature of key protein reactions in living systems see Michele Vendruscolo’s 2012 article in Current Opinion in Structural Biology, entitled “Proteome Folding and Aggregation” (Vol 22, pages 138-143).


It is clear that an accident could not have thrown life together one step at a time because the smallest living unit of life, the cell, requires many parts to be in place simultaneously, as does the reproductive system, and the proteomic system. All the essential systems of life are themselves irreducibly complex.


With irreducibly complex designs, random changes (accidents) seriously impair existing functions. Even should the mutation occur in a reproductive cell that will then pass on the change to future offspring, the future cell line becomes dysfunctional. It will not survive long-term culling by natural selection.


Irreducible complexity doesn’t have to be a universal truth about all living systems and components to defeat the neo-Darwinian theory of accidental evolution. We only need one example of a living system that is irreducibly complex to defeat Darwin’s theory—and there are many.


The Tip of the Iceberg

There are thousands of biological machines and systems that must be constructed accidentally under neo-Darwinian theory.[46] Much more complex than unitary biological machines are biological systems that integrate thousands of those machines into an inter-cooperative network.


For example, the complexity of the human immune system is often marveled at in both popular and technical writing. The adaptive immune system can recognize approximately a trillion threats, and can construct defenses against future man-made antigens that do not yet exist.


Professor Michael Behe gives us a glimpse of the hidden workings of the immune system in Chapter 6 of Darwin’s Black Box; Boyce Rensberger expands that in Chapter 11 of Life Itself; and the rest of the story is beautifully laid out in the recent textbook The Immune Response, by Tak W. Mak and Mary E. Saunders, a glorious work of 1194 pages.[47]


As impressive as the human immune system is, our central nervous system far exceeds it in complexity, performing operations of much greater sophistication. The brain, of course, is our paradigm for biological complexity, but we still don’t know how complex it really is. There are 100 billion neurons in the human brain and spinal cord that make up the central nervous system, each with thousands of connecting fibers.[48] In addition, there are nine times as many glial cells in the brain as there are neurons. While glial cells were long thought to fulfill only structural roles, Peter Kassan reveals that in 2004 researchers discovered glial cells had functional as well as structural roles.[49]


The cerebral cortex alone has 10 billion neurons and 60 trillion synaptic connections. But it is what those trillions of connections do interactively in real time that is so amazing. Francis S. Collins, director of the Human Genome Project for fifteen years (later the director of the National Institutes of Health), tells us in The Language of Life that the brain expresses every gene in the genome at some point in the human lifespan. One particular gene that is activated in the brain expresses 36,000 proteins.


Much of the detail of how our own perceptual/cognitive functions actually work remains to be elucidated by science. We have only recently discovered two additional and very fundamental methods the brain employs for intercellular communication (in addition to the usual axons, synapses, junctions, and extracellular fluid channels): roamer type microvesicles and tunneling nanotubes.[50]


Sir Roger Penrose suspects the explanation of the microtubules’ part of brain activity will go well into the quantum levels of physics.[51] Dr. David Faust of Brown University Medical School has this to say on the subject of brain complexity, citing J. C. Eccles 1977 book, The Understanding of the Brain. Eccles seems to have prophetically anticipated Penrose’s assertion that new kinds of mathematical models are required to understand the brain.


If anything, I believe the case for complexity has been understated. Anyone who wishes to glimpse the complexity of processes needed to manage the sensory world might find current studies of the human brain illuminating. Eccles…a prominent researcher in this area, makes the following statement when discussing human perception:[52]


Before the cerebral cortex is involved in the necessary complex patterned reaction to the sensory input so that it gives a conscious perception, there will be activity of this immense, unimaginable complexity…it will be necessary to develop new forms of mathematics, as yet unimagined, in order to cope with such immense patterned complexities.[53]


Coming back to genetic systems, we cannot restrict our estimate of biological complexity to genes and proteins alone. There are a multitude of functions involved, each highly complex. [54] As with the brain, we have yet to fully understand and describe the workings of the genome, though there are already volumes of description on file.


Dr. Robert Pollack, in his excellent and gracefully aging primer on genetics, Signs of Life, explains that the process of translating genetic information into functioning bodily systems is extremely complex, going well beyond the task of simple protein production and assembly.[55] A myriad of various and subtle contexts within bodily systems, many yet to be fully scrutinized by science, alter the way a given gene will finally be expressed. Multiple genes interact in governing each other in an ultra-complex system of rules. Simple models have been devised to illustrate the general concept of gene interactions but, as this excerpt from Astrobiology Magazine makes clear, the process of gene activation and regulation is not simple.


Unfortunately, real systems are vastly more complicated. More than two genes may be involved in activating a single gene. In the case of three controlling genes, there are already 256 different rules. And in a system of 25 genes, the number of possibilities is greater than the number of atoms in the known universe.[56] (My emphasis)


In humans alone, there are approximately 19,000 genes. Other species’ genomes extend to many thousands more. Though a typical gene only expresses a few proteins, many express several thousand different instructions to cells for protein building or gene regulation, and, as we just learned in discussing the brain, in some cases a single gene can express as many as 36,000 proteins.[57]


 “But,” one might object, “I thought we had already mapped the genomes?” Yes, we have mapped a few of them. But it is important to note that mapping a genome is not the same thing as describing its functions. Basic mapping is merely a list of the multiple locations for the many component sequences of nucleotides for a single gene. This yields nothing more than a still preliminary chart of gene segments within the chromosome. Mapping as such does not cross-reference a gene to its functions, though studies are beginning to do that. Nor does mapping explain the complex machinery involved in translation, transposition, error correction, repair and duplication, protein synthesis (transcription), and biological systems regulation. The mere fact that we have “mapped” the genomes of a few creatures does not mean that we have fully described or understood genome functions.[58] (See Professor Jakubowski’s webpage on Proteomics and Wiley's Essential Biochemistry Chapter on Proteomics.)  


New, substantial, and even basic discoveries about genetic mechanisms continue to be revealed with each passing decade. The gene regulatory task for the human body is enormous. It requires precise regulation of trillions of cells each doing millions of tasks per minute, with many organs, systems, tissues and body parts all working together in near perfect concert to maintain the functions of life. Expression of particular genes is turned on and off in real time within each of these trillions of cells.


Only recently have we realized that the classic concept of the gene as being a contiguous string of nucleotides consolidated in the same spot on the chromosome is quite wrong. Many segments of a gene are scattered around the chromosome with hundreds or thousands of nucleotides intervening between them.


While there are only 19,000 genes in the human genome, roughly 85,000 proteins are employed in human anatomy. One gene obviously codes for more than one protein. As recent research reveals, one way this gap can be bridged is through alternate reading frames where the sequence of nucleotides can be read from more than one frame of reference. The truth is that we currently understand only a fraction of the total operations of the genome.


The complexity of DNA repair systems alone is extreme. A recent textbook devoted entirely to that subject goes over 800 pages, describing an astoundingly complex system, for which we still do not know the full details. Many readers will already be familiar with basic DNA transcription and repair tasks, but more complex functions are being discovered as research proceeds. Even the straightforward task of translating a gene into a protein has hidden complexities.[59]


Way back in 1971 one of our most famous biologists, G. Ledyard Stebbins, offered a simplified chart of the interactive complexity of biological systems based upon the concept that more than one gene and multiple gene expression tags are involved in regulating or directing protein synthesis for any one biological function.[60] In Stebbins’ chart, one can trace 10 different junction points on the road to gene expression resulting in a functional phenotypic feature. In light of more current research (Stebbins’ book is now 45 years old) this has become an underestimate, as Stebbins already acknowledged being likely in 1971.


The expression of a single gene can involve up to 100 gene expression markers scattered around neighboring sequences up to many thousands of nucleotides away. A single gene can generate up to several thousand instructional sequences directing cellular activity, and can be read from more than one reading frame.[61] 


Only a few of the hundreds to thousands of expressed sequences generated by a gene are used for protein building. The rest have regulatory functions. The enormous complexity of gene regulatory mechanisms pushes the improbability estimate for accidental evolution far beyond the previous figures based upon DNA sequences or protein synthesis alone, though the prior figures were already sufficiently large to decisively refute the theory of accidental evolution. 


Beyond the sheer complexity of the genome lies another, perhaps, more important point: DNA is a language, and language is a sign of intelligence. As Professor Emeritus James W. Valentine tells us in chapter 3 of his enjoyable textbook On the Origin of the Phyla, DNA qualifies under all the technical requirements to be a language: “letter” symbols, rules of syntax or organization, standard dictionary, consistent translation, punctuation, etc. Valentine does not infer intelligent design from this, but there are no known instances of language originating outside of an animal intelligence.


The brain, the genetic system, protein complexity, cellular systems, and the immune system are the five big guns of biological complexity. But the complexity of even the most basic biological machines clearly signals the larger difficulty of the evolutionary task. Some simple organisms have thousands of ribosomes in one cell (the simple bacterium E. coli can contain as many as 72,000 ribosomes).[62] Nor do we know absolutely everything regarding ribosome construction. Substantial questions remain unanswered, and current research reveals the construction process for even “simple” machines like the ribosome to be enormously complex.[63]


So, where have we got to in sketching out the complexity of life:


*     A genomic system complex beyond any hope of an accident putting it together

*     Two or three hundred thousand proteins, each of which is so complex that an accident can only assemble it one time out of 1077 tries, even given a living system to work with

*     Proteins necessary for life that can only be produced by life (the chicken and egg dilemma)

*     Protein interactions so complex that our best computers cannot model them

*     The human brain, so complex that it would take a software program 25 million times the size of the largest computer program ever written to match its computational power (if we had the mathematics necessary to model the brain’s processing patterns at all—still waiting on Penrose for that)

*     A circadian clock in potentially every cell

*     Up to trillions of cells per creature each having many biological machines and hundreds of proteins critical to their operation, each cell performing two million life-sustaining actions per minute.

*     Hierarchically integrated whole-body designs that embed systems within systems to nine or ten levels deep and keep them working flawlessly together in real time


Does that sound like an accident to you? No way. In humans, complex interactions of trillions of cells have to be organized and regulated to ensure the proper function of systems, organs and tissues. The entire body plan of the organism must somehow make all these components work together to provide integrated body-wide functions.[64] The improbability of creating the tree of life by accident vastly exceeds any rational standard for scientific credibility.[65]


Epigenetic Showstoppers

Scientists have observed varied instances of epigenetic factors (factors other than the DNA sequence) that determine biological form since 1964.[66] The most commonly discussed epigenetic factors are the chemical gene activation markers, but they are not the most startling.


Dr. Jonathan Wells reports that scientists have discovered three- dimensional control structures inside of cell membranes, a sort of patterned network of plumbing for cell product distribution and cell component assembly. These microtubule networks, much like Willy Wonka’s chocolate factory, will ensure that a specific well-defined result comes out the back end if you put the right ingredients in at the front. Some of these microtubule systems function as developmental control factors that act independently of DNA. Such microtubule arrays occur in animal cell membranes and, particularly relevant to our purpose here, in the cell membrane structures of egg cells.[67]


According to Wells, recent research in developmental biology reveals that DNA does not directly control species determination in animals: the microtubule arrays in egg cell membranes control species determination. Placing the DNA of species ‘A’ into the egg of species ‘B’ does not change the species from that of the ‘B’ egg to species ‘A’, and the result will not likely survive. This is because the 'B' form and structure defined by the microtubules is being supplied with an improper list of proteins, the wrong building materials (the materials for the 'A' species).


The microtubule species-determination function alone would seem to complicate the origination of new species sufficiently to refute the theory of accidental evolution. Gene activation markers complicate accidental evolution somewhat further. Gene activation markers must also be managed by evolution because they can at times be stable enough to be passed on to the next generation, affecting the biological form assumed by the offspring.


A 2003 Wistar Institute study suggests that gene activation itself is much more complex and dynamic than previously thought. Gene activation involves a whole series of preparatory alterations to the histones by adding ubiquitin, and the precise sequence of multiple steps seems to be critical to the result. DNA methylation and histone methylation must often be coordinated, and factors as elusive as diet can influence the result.[68]


Thus, in addition to getting a new complex DNA sequence correctly configured for an evolutionary advancement, an accidental evolutionary process must closely coordinate simultaneous changes to at least these two other areas of an organism’s physiology to ensure a workable result from any attempt at macroevolution. Barring the future discovery that reproductive cells harbor a hidden parallel development of a second complete microtubule system for a new species, science is stuck with a complex microtubule system changeover occurring in the extraordinarily brief moments of cell reproduction, as well as many simultaneous alterations to chemical gene activation markers. Such a whole system conversion is impossible to achieve by accident in such limited time.


One can see here that there are really only three choices for producing macroevolution:


*     Orthogenesis (dumb form), a system of directional features inherent in the universe that set things up in advance so all this could occur in a brief moment of time

*     Orthogenesis (intelligent form), a similar system of directional features was built into nature by an act of intelligent design

*     An out and out miracle, a supernatural intervention to create the new genome and microtubule system in a few moments and cause them to transfer into the new cell during cell reproduction.


None of these options are compatible with neo-Darwinian evolutionary theory, which says that life was created by accidental mutations assisted only by natural selection. Given these kinds of biological complexities, we can see that the small unitary changes of neo-Darwinian evolution won’t work fast enough to allow an accidental achievement of macroevolution. There is far too much to do in too little time, too little odds that the right genetic and epigenetic combinations will be found by accident, and there is nothing in an accidental process to ensure that the achievement of multiple necessary components is synchronized. The physical impossibility of accidentally producing macroevolution in real time from any known available event conditions is a showstopper for neo-Darwinian theory—game over!


Bottlenecks in Time: The Cambrian Explosion, et al.

The Cambrian Period, which began some 530 to 570 million years ago, is a significant time bottleneck for evolution. Here the vast majority of the animal body plans that have ever existed evolved within only five to ten million years.[69] The Cambrian explosion means that the full lifespan of the earth (4.45-4.6 billion years) was not available for the completion of the bulk of the evolutionary task. The basic body forms that appeared in the Cambrian gave rise to at least nineteen and as many as thirty-five of the forty different animal phyla we have today.[70] Having practically all the primary animal body forms evolve in only ten million years as opposed to billions dramatically increases the odds against it happening by chance—and the accidental thesis was already scientifically incredible.


Other historical timeline bottlenecks occur in the spurts in evolution referred to as “punctuated equilibrium.” Each spurt significantly adds to the difficulty for an accidental dynamic. For example, Baylor University surgeon Joseph A. Kuhn, who has recently written an article called “Dissecting Darwinism,” reveals that the move from ape to human would have required an “incredibly rapid rate of mutation leading to formation of new DNA, thousands of new proteins, and untold cellular, neural, digestive, and immune-related changes….”[71]


Both the internal biomechanics and the external event dynamics necessary to birthing a substantially different kind of organism produce time-related obstacles. A mutated creature must first somehow integrate the changed feature with the rest of an immensely complex system in a way that does more good than harm. However, the standard mutation rate is so slow that the integration task will never be accomplished within the lifespan of the creature hosting the newly evolved feature.


The species subpopulation hosting the new feature must survive reimmersion and disappearance back into the host gene pool. It must move into physical isolation from the host gene pool community so that the new species/sub species can remain phylogenetically distinct and evolve further. In very many cases this won’t happen, the trait will be lost as the new species interbreeds with prior forms and its new gene line is reimmersed in the old. Much time is consumed awaiting circumstances fortuitous enough to allow their escape from the host population.


If a creature having a new feature gets past the lifespan bottleneck and somehow quickly integrates a new biological feature with its overall physiology, and survives reimmersion into the host population gene pool, it must then produce a population large enough to give the newly modified species a chance to compete successfully against prior forms of the same species as well as against other species that are competitors and natural enemies. In some cases this could be done, but doing it eats up quite a lot of time, at least where large animals with extended gestation periods are concerned.


So, in addition to the probability hurdles of sheer biological complexity and the rarity of biologically useful genes and proteins, any newly proposed biological feature faces additional hurdles in time and improbability inherent in the species birthing process.


Interruptions to Evolutionary Progress

There have been at least seven major disruptive events, ice ages or mass extinctions, that would have cost evolution a significant amount of time. These catastrophes would almost certainly have "vetoed" many of natural selection's choices, removing thousands of previously favored species, at times compelling a nearly full restart on an entire branch of the tree of life. For example, ninety-six percent of marine animals were lost during an extinction occurring toward the end of the Permian period.[72] Major extinction events have also occurred within the last eighty million years, extending all the way up to the last ice age less than two million years ago. A large portion of evolutionary development was certainly lost in these catastrophes. The lost progress further increases the workload and derivative improbability of an accidental evolutionary process.


Symmetry and Fine Art in Biological Machine Design

Symmetry is a striking characteristic of most biological machine designs. The presence of substantial, even near perfect, symmetry is a hallmark feature of living things. Symmetry is easy to achieve in biomechanical terms because the biological information that directs it need merely be placed at a very early point in the embryonic construction process. The code merely needs to “say” that whatever is done for the left of the torso segment should also be done for the right, or for the top the same as the bottom, etc.[73] Nonetheless, in my view, symmetry is something randomness is incapable of producing with consistency initially, that is, prior to natural selection's evaluating the symmetrical performance profile on the battlefield of life. Swimming and flying, even walking and crawling, creatures would eventually move to symmetry for efficiency of movement, but they need not have begun that way in an accidental process.


Symmetry in body form is useful for balance, stability, agility, grasping with counter pressure, efficient swimming, flying etc. Clearly, natural selection would preserve symmetry in these applications, once achieved. And the symmetrical design option would probably be offered up for approval fairly quickly because it is not a difficult coding change to achieve by mutation. But why did an accidental process so unanimously and quickly hit upon symmetry in all the right places throughout all of evolutionary history without first creating some imbalanced designs that were temporarily survivable, asymmetrical creatures that survived long enough to create fossils?


In the early years of life, the first complex biological form innovations out of the chute, as it were, for each level of advancement on the tree of life would in many cases have no direct competition; they would be at the top of the food chain in a niche without predators or heavy competition, at least for a while. Thus, selective pressures favoring symmetrical over asymmetrical forms would often not have been present for some time.


One might propose UCA (universal common ancestor) as the solution. Some UCA, probably a bacterium, had symmetry so all the other creatures of life simply inherited it. Natural selection would have no reason to cut it out. Soft-bodied creatures would not make many if any fossil imprints, so that’s why the accidents don’t show in the fossil record.


Sounds good, so it must be true, right? No. It might be true, but there are no demonstrated links between a given ancient bacterium having code for symmetry and the complete inventory of more complex creatures in the fossil record, and this explanation doesn’t cover all the bases. The problem is that accident tinkers with everything, good designs and bad. When accidental tinkering fouls up something already well-designed, natural selection will eventually cull out the mistake, yes—but not immediately. Natural selection may take decades or centuries to work, leaving plenty of time for fossil records of asymmetrical creatures produced by accident.


Even if we allow inheritance, inheriting DNA segments that code for symmetry from a bacterial genome doesn’t preclude symmetry popping up in all the wrong places in the more complex animals that inherited the UCAs simple genome. The UCA didn’t have arms and legs. Given only an accidental mutation process to find where to stick the code in the more complex follow-on animal genomes, why don’t we see populations of creatures with symmetrical torsos and asymmetrical limbs, creatures with tails on both ends, etc.? We see birth defect type mutations of these kinds in individuals, but we don’t see evolution trying them out in whole populations. Why did symmetry, even if it was inherited from a simple creature, initially appear in all the right places if the genetic mutation process was truly accidental?


Where are the fossils of the failed attempts at asymmetrical design that should be there at the beginning? Granted, they would rarely, if ever, be competitive, and the symmetrical variations would dominate quickly once they occurred. But “quickly” in evolutionary time could be 500 to 10,000 years. Not every environmental niche has intense competition or scarcity of resources. Given the neo-Darwinian assumption of an accidental process, there should be a discoverable if not a substantial record of asymmetry—but it’s not there.


Do not be misled by the occasional examples of a tendency to symmetry in certain simple structures of basic chemistry.[74] The same natural laws that govern chemistry do not constrain random mutations of DNA to a symmetrical result. In a truly accidental mutation process symmetry is easily avoidable.


Beyond symmetry, there is the undeniable presence of art in nature, and, of course, symmetry is a major element of art. The presence of dramatic beauty in nature has long been an argument for intelligent design. Art in nature perhaps reaches its peak in tropical birds, tropical fish, and flowers, though it can be found almost anywhere, from wondrous microscopic structures to panoramic landscapes to glorious cosmological vistas.


The argument for design from magnificent, living, moving, and growing works of art is simple: we know art when we see it. This remains true despite the fact that an accident could achieve substantial variations of color and pattern much more easily than it could achieve complex mechanisms.


And it is true that colors can have functional purposes that natural selection would preserve. Color patterns obviously add functional advantage in brilliant mating displays, camouflage, attraction of pollinating birds and insects to flowers, etc. So selective advantage apparently does explain some simple aspects of color variation; but it does not explain overall artistic quality. The argument here is not just “Oh, look at all the pretty colors!” but “That is real art.”


In most cases the average person can immediately distinguish scribbling and junk design from good human art. Most people would concede that at least some of the magnificent works of nature easily outclass the bulk of human art. Take a look at some of the YouTube videos on birds and nature and you will see what I mean.


Keep in mind that flying bird art far exceeds sitting bird art, the same as human dance exceeds human sitting in artistic value. Even when some creatures are not great examples of divine art in terms of color, they are in terms of elegant motion, or even literal dance. Others certainly are fine art in terms of color. Some just aren’t art at all; but humans are intelligent designers and we don’t do art in everything we do. Yet when we do art that human art is evidence for the existence of human artists.


If nature didn't contain real art, why would bird watching and nature viewing be the world’s most popular hobby? Many creatures display a superbly elegant form of art in motion (not all). Perhaps God felt that there must be something positive in favor of cute little multicolored feathery birds that offset their carrying lice and crapping all over the patio. And there certainly is: that something is fine art, and it is in fact glorious art in many cases. There are even elements of music, dance, aerial and water ballet involved in many animal behaviors. They may or may not perceive it (though some very likely do), but we can.


Any doubts one may have about the artistic merits of nature are easily dispelled. Simply stop philosophizing for a moment and observe; buy a good pair of binoculars and get out of the house and into the field. Go to the ocean, the mountains, the lakes, and rivers (take precautions against turbulent weather, animal attack, and human crime, however). Look at the video documentaries, the nature books and magazines. Films like Richard Attenborough’s Life on Earth,[75] come to mind, in addition to Science and Nature magazines, National Geographic, and Discovery Channel documentaries. Look at the field guides to the tropical birds and flowers in the nature area of your bookstore, the birding magazines. Or better yet, go to the high-end pet stores or zoos; see the real thing. (PS: While you are out and in the nature appreciation mood, stop by the local animal shelter and save a loveable creature from being killed.)


Simultaneous Development of Complimentary Traits

Here is an additional problem for neo-Darwinian evolution in terms of resource costs and probability hurdles. An accident won’t be able to synchronize the creation of a set of features that must work closely together, features that would individually convey no obvious advantage. The set of characteristics in birds comes to mind: acute long distance vision, wings, a lightweight frame, rapid flight capable reflexes, and feathers. At a minimum these features would have had to appear in the right order. Otherwise they would pose an explicit vulnerability to the organism.


For example, moving to such a fragile frame would be a decided disadvantage if the bird could not first get off the ground to escape predators or run like an ostrich. A non-flying "welter weight" creature would lack the necessary strength and weight to stand and fight, and the fragile frame would not be sufficiently rugged and durable to withstand periodic (otherwise non-lethal) injuries from combat. Alternatively, agile flight at high speed without improved vision and fast reflexes would be accident prone, and so on.


Traditional discussions have dispensed with this objection by citing imaginary routes to evolving a related set of complementary traits.[76] While such routes are theoretically possible, they are vastly improbable. Achievement of those complex imaginary routes via accidental processes adds substantial improbability and additional time and physical resource requirements. An accidental process is not likely to manage such a complex transition efficiently. Thousands of tries are required, each of which consume time and resources.


Before modern microbiology and genetics revealed exactly how complex the physiology of eye-brain-wing coordination must be to allow rapid flight, imaginary routes to developing the necessary complimentary traits seemed plausible. The underlying biomechanics were being ignored as largely irrelevant to the problem. What we now see is that the underlying biomechanics are too complex to be ignored.


The high efficiency and the resource economy that we see in the historical record of evolution, despite a seemingly wandering path toward the creation of humanity, strongly suggests intelligent design. The fact that evolution first “wandered” about creating a magnificent support system, a beautiful life-sustaining garden full of fellow creatures with which mankind can compassionately share the planet, hardly rebuts intelligent design. It may simply be a matter of preparing our place before we were placed into it. We do as much for the puppies we bring home from the pet store (or the pound J).


Given the rapid microtubule system production that must match a whole set of new genes to produce an event of macroevolution, it remains true that we still don’t know that a miracle wasn’t required to create each radically different type of creature. I am not saying each step of macroevolution was definitely a miracle; I am saying that at the present state of science we can’t demonstrate that it wasn’t a miracle. What we can demonstrate is that the creation of the tree of life was far too difficult for an accident to manage.


Convergence: Achieving Similar Design by Multiple Independent Routes

Simon Conway Morris, a popular modern evolutionary writer, is Professor of Evolutionary Paleobiology at Cambridge University. His book, Life’s Solution: Inevitable Humans in a Lonely Universe, gives a fascinating account of the many and varied cases where evolution uncannily converged on the same design through multiple independent pathways.[77] For example, the camera-type eye common to humans and octopi has evolved separately in at least six different creatures. Other features that have evolved independently in multiple instances include olfaction (smell), hearing, the trachea, myoglobin, anti-freezing mechanisms, photosynthesis, social organization, and quite a few others, almost certainly to include hemoglobin and even intelligence. Morris goes so far as to say that convergence is found practically everywhere in nature.


In cases of convergence, extreme similarity cannot be explained by the standard Darwinian mechanism of inheritance because the creatures having the feature in common do not share ancestors on the tree of life. They may or may not turn out to have bacteria or other single-celled organisms as a common ancestor, but bacteria don't possess any of the features in question.


This suggests either that the features achieved via convergence were pre-established goals of evolution, or that an unexpressed or dormant master genome containing instructions for these complex features was already in place early on, perhaps with bacteria. Another possibility is that equivalent design information for the convergent features was coded into nature in another, perhaps more subtle form.


The neo-Darwinian logic used to establish relationships on the tree of life itself suggests that this is true. Neo-Darwinists argue that creatures with many similar traits are almost certainly related due to inheritance. Implicit in this argument is the view that creatures achieving such similarities by chance is so improbable as to be scientifically dismissible.


Thus, convergence really does pose a serious logical dilemma for neo-Darwinian theory. In cases of convergent features, where inheritance is known not to have occurred, the presence of closely similar or identical features must be held to be non-accidental by the neo-Darwinists own logic. But, if inheritance is not available as the explanation, what was the non-accidental cause of the similarity?


And there is an overt contradiction in neo-Darwinian thinking. They say that the phylogenetic similarities that ground their proposed trees of life can be ruled out as being accidental—too improbable. However, they recommend the much greater improbability of the accidental construction of the entire tree of life as our default theory of evolution.


Intelligent design is strongly implied in cases of independent achievement of complex biological features (called “convergence”). How does an accidental process manage to generate a hugely complex design proposal again and again in nearly identical fashion without benefit of inheritance? An early master genome, perhaps. But the presence of a master genome early on takes natural selection out of the genome-building process. At a minimum, a large bias in nature for the repeated design solution is indicated even where there are noticeable variations on the theme.


Convergence does not disprove that inheritance frequently happens, but it does add enormous obstacles to the already lagging credibility of an accidental evolutionary process. Dr. Gerald Schroeder, a noted physicist and applied theologian, author of Genesis and the Big Bang, The Science of God, and The Hidden Face of God, (properly) estimates the probability of convergence at a magnitude well beyond what could be randomly achieved within the lifetime and resources of our universe. That, in itself, rules out chance as the architect of life.[78]


What’d Ya Say?—Issues with the DNA “Dictionary”

Why do all creatures use the same biological language of DNA? Why do they use the same 4-letter code, the same DNA/RNA molecular structure for biological coding, and the same dictionary to translate the code? As many readers will know by now, there are four letters of the language of DNA: C, G, T, and A. Any given combination of them could be used to stand for different things in the biological architecture where a triplet of nucleotides specifies which amino acid is to be built.


In theory, different DNA dictionaries might be used that associate different three “letter” strings of nucleotides with different amino acids. They would all work as long as the method was consistent. If the mechanisms of life were hit upon by sheer chance, why do all creatures “speak” the same physiological language when a chance process should have focused on all biological dictionary options more or less equally? Why do all use the same dictionary?


Obviously creatures using the first system that gets a good start would have a competitive advantage over those using a fledgling new experiment that still has "bugs" in it, at least where competition was present. Increased efficiency gained through years of being polished by natural selection could easily be decisive. But all creatures do not compete with all others. Nor is there competition in all niches at all moments in time. But even where there was competition the process of natural selection takes time. The fossil record should show traces of attempts to use alternative genetic systems, even if they quickly proved noncompetitive. 


Darwinists say the single DNA dictionary and single genetic structure phenomena prove inheritance from a common ancestor, and that is a plausible explanation in this case. Having the same designer is an equally good explanation. Some of both, perhaps, is best.


The historical record suggests the absence of a universal ancestor more than the presence of one, although it also suggests a great deal of inheritance did occur via a number of separate phyla and family trees. Because a truly accidental process would have tended to try other possibilities for the DNA dictionary (and there is nothing to prevent them from working), only the confirmation of a genuinely universal ancestor will save neo-Darwinian theory from this objection. The single DNA dictionary problem does not constitute a stand-alone refutation of accidental evolution, but it does add additional improbability to a theory already well across the threshold of being scientifically dismissible.


Nobel laureate Francis Crick offered a related but slightly different solution to the UCA (universal common ancestor). He theorized that life came here (on purpose) from outer space. Such an occurrence would explain not only the single DNA dictionary but the consistent structure of DNA.


Coming full circle to his groundbreaking discovery of DNA's structure, Crick wondered, if life began in the great "primeval soup" suggested by the Miller/Urey experiment, why there wouldn't be a multitude of genetic materials among the different life forms. Instead, all life on Earth shares the same basic DNA structure.[79]


Crick’s theory remains an open question. It also remains possible that other DNA structures and dictionaries were tried on other planets. However, there is substantial evidence that life arose on Earth.


But, hold the phone…a few exceptions to the standard DNA dictionary have been recently discovered. Universality of the DNA dictionary is no longer the sure assumption it used to be. After decades of Darwinists flaunting the universality of the DNA dictionary as indisputable proof of inheritance, it turns out that the DNA dictionary is not universal after all.


Geoffrey Zubay, professor of prebiotic chemistry at Columbia University, tells us in his book Origins of Life on the Earth and in the Cosmos, that exceptions to the standard DNA dictionary have been found.[80] The universality argument has now been overcome by events and must be updated. What remains to be determined is whether the type and quantity of the exceptions imply anything significant for the evolutionary debate.


The newly discovered variations of the DNA dictionary occur predominantly in very primitive organelles like chloroplasts and mitochondria. They may be the remnants of true alternative systems that never quite got off the ground, or they may result from alterations that occurred after inheritance of the otherwise universal system. The occurrence of variations of the DNA dictionary exclusively in very primitive organelles that originated at the very beginning of the tree of life is suggestive. The harder question is what does it suggest? My guess would be that it suggests a complexity barrier.


In being restricted to only simple systems in very simple creatures, these alternative DNA dictionaries may be evidence that accident can do only very simple things. In other words, the rare variations on the DNA dictionary found in simple life forms could have been, at least in part, accidental, but that was as far as an accident could go. Perhaps accident needed a living system to work from to do even that much. It seems to me that the most cogent explanation is that the DNA dictionary and architecture was initially supplied by orthogenesis/intelligent design and then accident turned out these minor variations as the best it could do.


Probability theory strongly argues that such a complexity barrier exists. By implication, the existence of such a complexity barrier to the development of alternative DNA dictionaries or architecture means that the successful standard DNA dictionary that went on to drive the construction of the larger tree of life faced a similar complexity barrier, and therefore its successful creation was apparently no accident.


The existence of such a probability barrier is not just my personal conjecture; it is supported by basic math and has been endorsed by very notable scientific geniuses over the years, including Sir Fred Hoyle, the famous Cambridge astronomer. In his book Evolution from Space, co-authored by Chandra Wickramasinghe, a Cambridge mathematician, astronomer, and astrobiologist, Hoyle instructs us that "The notion that not only the biopolymer but the operating program of a living cell could be arrived at by chance in a primordial organic soup here on the Earth is evidently nonsense of a high order....the probability of life originating at random is so utterly miniscule as to make it absurd."


The discussion of the DNA dictionary is also interesting from the perspective of the history of the evolutionary debate. Darwinists/neo-Darwinists used to (and still do) assert the theses of phylogenetic inheritance and universal common ancestor based upon the huge improbability of so many closely similar traits in a visible pathway evolving without inheritance, and the huge improbability of a presumed to be accidental evolutionary process achieving multiple independent origins of life. Those two scenarios, according to the Darwinists, would be too improbable. (Note the Darwinists’ acceptance of the probability argument here.)


When evolutionists such as W. Ford Doolittle or Richard Dawkins dismiss the probability argument used in the case for intelligent design as of no consequence they are therefore contradicting the Darwinian’s own historical position in the evolutionary debate. They are also contradicting the standard practice of science. If probability is good for the goose, it is good for the gander. Once we accept standard probability theory (and science does accept it everywhere else), intelligent design theory is firmly established as by far the most probable theory of the origination and evolution of life.


No Explanation for Macroevolution

The late Ernst Mayr (1904-2005) was one of the best writers and thinkers on their side of the debate, one who candidly admitted that lack of intermediate fossils poses a serious challenge to Darwinian Theory. He was also likely one of the best writers and thinkers that world literature has to offer on any subject. Nonetheless, in What Evolution Is, we find Mayr offering a single unevidenced phrase to address what is the only real point of contention between intelligent design and neo-Darwinist theories, how to originate complex biological information: “Even though all new genes are produced by mutation…”[81] That’s it.


That is the entire neo-Darwinian explanation of the origin of meaningful biological information repositories comparable to whole libraries of books: it happens by "mutation." I may only have a bachelor’s degree, but I feel confident is asserting that a single word “mutation” does not offer a satisfactory explanation for the writing of a book, let alone an entire library. (Ironically, it is an apt description of my confused early drafts of this book! J)


Obviously mutations of some kind are involved; something has to make a change to the nucleotides. But why should we presume the process to be accidental?


In changing the content from a prior book's text to the present printing job one character at a time, re-setting the typeface on an old printing press for a new book is a form of mutation—but it is not accidental. Certainly, when such mutations produce 300-600 coherent and meaningful pages virtually overnight (electronic typesetting) we are not entitled to assume that an accident caused the change even if we haven’t caught the printer’s assistant in the act of doing it. To be logically consistent, we should admit that the same is true of the evolution of 100,000,000 species, where the genome of each is the rough equivalent of five or more full-size books.


Expending the entire 4.6 billion years of the Earth’s existence to do the job only allows 9.2 years per book. Granted, that is longer than the average author of mildly technical nonfiction takes, but accident can’t touch it. And the tripartite genome is not mildly technical. It is much more complicated than a simple number representing the genome size indicates.


Given the extreme complexity already built into protein structures by the laws of nature even before the genome starts building them, the closest analogy we have to that level of complexity would be a rigorous mathematical exposition of theoretical physics, or a detailed textbook on, you guessed it, genetic science.


Thus, the 9.2 years is actually close to what an intelligent human would require to produce a book of that complexity, if his or her mind could reach that far at all. Any forensic investigator stumbling upon such a large and complex typesetting change at a printing press, let's say at a museum of the Gutenberg Press that had been closed and later reopened, would be entitled to assume with confidence that someone had been in there and made the change, even if the change occurred over centuries.


In everyday life we all know that once certain thresholds of complexity are passed, accident can no longer be our default explanation. Yet neo-Darwinists cling to accident as the default explanation for the evolution of life even though the tree of life has turned out to be the most complex thing in our experience by many, many, many orders of magnitude.


"Surely you exaggerate," you may challenge. "There must be more to the neo-Darwinian explanation than that." Just, “mutations?” No; it is not an exaggeration, not that I could discover in twelve years of research.


Am I glossing over the true depth of expertise of neo-Darwinian scientists concerning the explanation of the origin of genes and biological information? You be the judge. Here is the entire section of Ernst Mayr’s discussion on the subject excerpted from What Evolution Is.


The Origin of New Genes

A bacterium has about 1,000 genes. A human has perhaps 30,000 functional genes. Where did all these new genes come from? They originate by duplication, with the duplicated gene inserted in tandem in the genome next to the sister gene. Such a new gene is called a paralogous gene. At first it will have the same function as its sister gene. However, it will usually evolve by having its own mutations and in due time it may acquire functions that differ from those of its sister gene. The original gene, however, will also evolve, and such direct descendants of the original gene are called arthologous genes.


Additions to the genome come not only by the duplication of single genes, but sometimes through the duplication of groups of genes, whole chromosomes, and entire chromosome sets. For instance, a special mechanism, involving kinetochores, can lead to a duplication of chromosome sets in certain orders of mammals, leading to highly variable chromosome numbers in these orders. Lateral transfer is another way for addition to the genome.[82] 


We need to note several things about this “explanation.” First, it doesn’t explain the creation of meaningful new biological information, it merely explains the easy part of genome evolution, creating new bulk material. How that material can be reconfigured in astronomically complex, biologically meaningful ways in real evolutionary time is not explained.


Mayr also does not address how to originate the first set of genes at a time when there were none to duplicate. Ultimately, this kind of explanation is guilty of the logical fallacy of equivocation. It confuses the physical mechanism that produces a change with the guiding influences that determine which extraordinarily precise change is produced. The neo-Darwinian explanation is like saying that the fingers of the typesetter for Gutenberg's press were the form-determining force behind Shakespeare's Macbeth or Tolstoy's War and Peace instead of the authors’ minds.


The hard part here is simply assumed by Mayr, not explained. Such over-simplified explanations, though transparently deficient, are typical of evolutionists across the board. Neo-Darwinists don’t know how new meaningful genes are created, so they merely tell us how copies of genes are created—it’s not the same thing.


Gene duplication is not totally irrelevant to the hypothesis of accidental evolution. It does add redundancy, and, at least once evolution gets to complex creatures, plenty of it—but it doesn't add new complex biological information. Duplication of a printed text plus printer’s errors does not equal a new book. Neo-Darwinian evolution has no explanation for the larger and harder part of evolution: the creation of new highly complex biological information.[83]


Two other things should be considered in regards to considering gene duplication with random mutation as the explanation of life. First, complex life has already been achieved before the process of gene duplication comes into existence. Thus, gene duplication cannot be used to explain the origination of complex life, for it is itself dependent upon the preexistence of complex life. Second, this view offers no explanation of how to randomly integrate a new feature into a complex organism where many features critically interact with others to which they are very closely matched.


Why does the larger system (in complex creatures, at least) not incur many conflicts when the new gene starts operating prior to overall integration with the rest of the system? Remember, this new gene was not intelligently designed according to neo-Darwinist theory; it's an accident. In their theory, it is completely blind to the requirements of the rest of the system. Darwinists don’t say how successful integration of new genes and features can occur by accident, yet this is the “fully satisfactory explanation” proposed by acknowledged experts like Ernst Mayr and Richard Dawkins: genes split and mutate. We need only wait a few million years and it's all done. Walla Booby! Abra cadabra! Presto chango! Accidental evolution proved! Right? No. Not even close.


"Not so fast," we should be objecting, and “Show me the money.” What have we actually seen accidental mutations accomplish? The answer: not much. We may have seen a handful of simple degradations of existing genes that can still do something useful after incurring a mild injury; some alterations to genes that are created by removing a segment of DNA already present; or a few very simple changes in bacterial genes. That’s it!


We have never seen the accidental origination of a new set of genes sufficient to generate new complex functions in a complex organism. Nor can we randomly create or substantially progress a gene or set of genes in the lab to produce a macroevolutionary advancement—the complexity barrier again.


To see just how little evidence there is for the accidental generation of new beneficial genes, go to the Wikipedia Web site and review the entries for “genetics” and “mutation.” Look for “beneficial mutations.” The sparseness of evidence will amaze you. Ask yourself “Is this enough to explain the entire tree of life?”


If that doesn’t convince you, go to a biosciences library and ask for information on beneficial mutations and the origin of new genes, the genetics of evolution, etc. You will be very disappointed, probably frustrated, and perhaps even angry at the politicized exaggeration of the evidence that has gone on now for decades.


The evidence for accidental origination of new genes sufficient to explain evolution is simply not out there. For 150 years science has merely assumed that the creation of the tree of life happened by random mutation. They have never demonstrated this assumption, nor have they even substantially evidenced it. All the while massive evidence has accumulated against the possibility of truly random (accidental) mutations producing complex new genes in real evolutionary time, and evidence against a truly random process successfully integrating those genes into a living system.


True, recent modifications in statistical modeling techniques have left neo-Darwinian theory impressively arrayed with new conceptual tools. To give credit where credit is due, the modern neo-Darwinian toolkit is impressive to look at. Neo-Darwinian theory has become extensively enhanced, but it has not been concretely defined; it has not been significantly confirmed; and it has been largely refuted.


Neo-Darwinian theory is largely an abstract concept with no substantive biomechanical content. It doesn’t answer the hard questions, such as “How does macroevolution occur in biomechanical terms?” or “How can an accidental event dynamic accomplish any of the major steps in the creation and evolution of life within the time available in the historical record?”


Inheritance between creatures is pretty well established—yes, we all admit that much. Neo-Darwinists roll out endless genetic sequence comparisons demonstrating that living creatures frequently have much genetic sequencing in common, and some of the hypothetical pathways between creatures do seem to show step by step transitions. However, intelligent construction of a series of mechanisms often does the same thing: reuse components that work and progress new designs incrementally from the original. The patterns we see in genetic sequences and phylogenetic trees does not distinguish between intelligent or accidental authorship; either might have produced the same pattern. It would all depend upon the purpose of the designer as to whether he or she needed to micromanage the details of evolution or not.


Modern evolutionary science has added some fancy bells and whistles: population studies, cladistics charts, phylogenetic inferences, mathematical mutation models, and so on. But it’s not enough. If accident is the primary engine of life, we need to be able to explain how life was first created by accident, and then how the big steps we see in the fossil record were accomplished by accident within the time available. To merely say that a self-evolving transpositional genome can do such things is not to prove accident is the architect of those genomes and the living creatures that host those genomes.


The only way to prove accident is capable of such changes is by using standard probability theory applied to full and correct descriptions of the physical systems involved—or to produce a laboratory demonstration. This is where the accidental thesis dramatically fails. The event process of evolution is too big for the lab, so probability computations are all we have to answer the question—and the neo-Darwinists dismiss probability computations as irrelevant!


While neo-Darwinian evolutionary models are interesting intellectual exercises, they lay out no actual biomechanical sequence of events that connects one type of creature to another. That’s right, science still cannot do this. We do not know the biomechanical events that produce macroevolutions.


If we were intellectually honest, we would admit that events of macroevolution, given our current state of knowledge, look more like miracles than anything else. But the culture and traditions of Western science forbid our admitting this. We merely assume that further research will dispel the mystery and that materialism will prevail in the end. But that is just a politically and culturally-driven assumption; it is not an assumption science can presently justify.


Despite modern enhancements of the abstract theory, macroevolution is not a known biomechanical event process; it is merely a theoretical label for a still mysterious phenomenon. For such radical changes in living creatures to occur in real time seems clearly to require intelligent guidance and control, yet, the neo-Darwinists still say otherwise. However, they cannot show or demonstrate otherwise.


While the new fancy math formulas guess at genetic mutation rates with such precision that one would think that science must surely have some absolutely rock-solid evidence stored away somewhere, some known and specific sequences of randomly generated events that produce viable and advantageous mutations leading to the necessary macroevolutions between branches of the tree of life—it hasn’t. Nothing of the kind is out there in science’s toolkit or knowledgebase; we are still looking at a mystery and a seeming biomechanical impossibility in macroevolution.


Already we can discern that the process dynamics of human developmental and transpositional genomes, which are the only plausible engines of evolution, show far too much information and process control to be truly random in the sense of coming from an unguided or undirected process. Thus, for those who are willing to face the import of what we now know, it has become clear that an accidental process doesn’t drive evolution. Accident is fully out, but evolutionary science is politically and conceptually grappling with the dilemma of what to recommend as its replacement.


The Destructive Nature of Random Mutations

During the first (and primary) evolutionary synthesis of the 1950s, just prior to the discovery of the double stranded DNA molecule in 1959,[84] scientists modified Darwin’s original theory in an attempt to incorporate the basic concepts of the primitive Mendelian genetic science of the day. They knew, or hypothesized, that there were genes, but had no clue how those genes functioned. From roughly Darwin’s time it had been claimed that accidental changes in the vital substance of life (protoplasm), were the source of the variations that natural selection chooses from to evolve new forms of life. Later this hypothesis was updated from protoplasm to the genetic material (as yet unanalyzed) that the Catholic monk, Gregor Mendel, discovered. Finally, evolutionary scientists posited accidental or “random” point mutations of single nucleotides as the driving force of evolution. This early version of evolutionary theory, called “naïve mutationism,” is now considered refuted, since point mutations cannot be shown to have accounted for any significant amount of evolutionary change.


All of these antiquated, overly simplistic hypotheses contrast starkly with the reality of what is now known to be required for macroevolution: highly complex transpositions of whole sets of genes and gene segments that occur in closely orchestrated series, transpositions that are somehow synchronized with corresponding changes in the microtubule networks residing inside the walls of reproductive cells. So, why does current mainstream science continue to deny biological reality and push an overly simplistic theory onto the public? Politics, of course: personal preferences for political or metaphysical philosophies, specifically atheistic materialism, either in generic form or of a Communist/Marxist variety.


Here, in a 1941 article, Time magazine reviews Columbia University Assistant Professor of History Jacques Martin Barzun’s book, Darwin, Marx, Wagner, in the process revealing that the godless accidental worldview was in fact built into neo-Darwinian theory. To be clear, Charles Darwin did not do this; his successors did.


Darwin's discovery was "evolution by natural selection from accidental variations." The dynamite, says author Barzun, was in the phrase "from accidental variations." Reason: it denied the role of God in the universe, ruled out a purpose in existence, made men mere puppets of mechanical forces.[85]


While it is true that Darwin’s successors read atheistic materialism into his theory, there are problems read and with the wording in this quote. Darwin, himself, allowed that God did have a role in the universe: starting creation off on its course and instilling the initial breath of life into his creatures. That means that there would certainly be a purpose for our existence if God was our creator even if he didn’t micromanage the process of nature after he set the evolutionary ball rolling.


It is true that Darwin could detect no further guidance being exerted on the processes of nature from that point forward, but his theory left room for both God and a purpose for human existence. Darwin’s successors, at least many of them, adopted atheistic versions of Darwin’s worldview that no longer invoked God. They did that as a personal or political preference, not from scientific or logical necessity. Merely saying that evolution occurs from “accidental variations” does not logically entail atheism or a meaningless human existence. One may still allow that God started the evolutionary process going and then left it to its own largely accidental dynamics, while being able to omnisciently forecast a successful achievement of the tree of life. Even with the physical event process of evolution being largely accidental, by adding the human soul at the appropriate point, God nonetheless injects meaningful aspects into life such as love, justice, aesthetic beauty, and the moral dimension that grounds ethical behavior, rule of law, and human rights.


Of course, the entire point of this book is to demonstrate the process of evolution now appears not to have been accidental at all. And let’s be clear on something else. Darwin did not “discover” evolution by natural selection from accidental variations; he merely hypothesized it. It now appears that evolution doesn’t work that way at all, so Darwin did not make a discovery; he offered an explanatory hypothesis.


Science subsequently adopted Darwin’s hypothesis as the leading theory of the creation of the tree of life because it seemed to explain well given the limited scientific knowledge of the time. However, in light of what we now know of genetic science and microbiology, the accidental part doesn’t work. Things have become so complex that it is hard to imagine natural selection getting the opportunity to act at the appropriate times when key elements of biological systems are being built. Therefore, to say that Darwin “discovered” evolution from accidental variations preserved by natural selection is saying too much. It implies that the theory of accidental evolution is known to be true, when it now seems clear that it is not true.


Darwin’s perception that God does not manage/micromanage the course of nature may or may not turn out to be correct. Even it is correct, it does not mean that God cannot predict or control nature’s course using less restrictive methods that nonetheless assure the eventual achievement of his ultimate objective. For example, when a bowler releases a bowling ball, if he or she is expert, a strike is predictable seven, eight, or even nine times out of ten. While many observers cannot predict that strike from merely observing the ball in motion after its release (some can), the strike is still certain to occur when the ball is thrown in that way 70-90% of the time. The bowler doesn’t micromanage the course of the ball in real time during its transit down the lane, but having once set it on its way in an informed and skillful fashion, the bowler can still be confident in the result.


Human bowlers will themselves be mistaken in a small percentage of bowls, but God or a super-advanced ET civilization that approaches our concept of God need not ever be mistaken (in God’s case) or nearly so in the case of advanced ETs. How much more than a human bowler could God, being fully informed and all-powerful, set nature on its course and instill the breath of life in such a fashion as to insure that our tree of life is the result without to have to constantly intervene in real time? Bowl on dude!


Darwin’s thesis about accidental transformations of life was merely a theory; neither Darwin nor any Darwinian scientist who came after him knew or could prove that accidental changes or a series of single point mutations could produce major life form evolution. They had not seen it; they could not demonstrate it; they merely hypothesized it. They felt confident in that hypothesis because, under the simplistic protoplasm-era biology of the day, it seemed very explanatory given what little they could see on the macroscopic level minus the aid of modern genetic science and microbiology. They could not yet see inside the cell.


In retrospect, the whole enterprise of confidently asserting a specific model of what occurred in life’s evolution must be considered vastly premature. Nonetheless, many of the scientists, writers and commentators of the 1950s and 1960s onward until today have continued to throw the entire weight and confidence of science behind this unevidenced and outrageously implausible 1860-vintage assumption of an accidental process having produced the biological evolution of complex life.


In the mid nineteenth century, neo-Darwinists positing randomness in the strong, truly accidental sense as the source of biological form variation seemed to offer a powerful explanation. But we had not as yet observed the destructive effects of random mutations in practice through gene mutation studies. And, again, in 1860 scientists mistakenly thought life was relatively simple compared to what we now know it to be. Thousands of mutagenesis experiments later the accidental hypothesis has turned out to be a problem. In the experimental lab, random mutations have proved themselves, with only the rarest and insignificant exceptions, exclusively destructive or neutral.[86] 


These test results match perfectly with what we now know of the intricately interdependent nature of living systems at the microbiological level. Professor Michael Behe, author of Darwin’s Black Box and Edge of Evolution, points out that the designs of living systems involve so many critical interrelationships that many changes must be made at the same time for the system to advance. This means that, contrary to the undemonstrated beliefs of neo-Darwinists and random drift theorists, small changes that do not have conspicuous effects are not comprehensive enough to accomplish any progressive evolutionary change. They may produce an occasional triviality: color change or something fully irrelevant to the complex internal mechanics of an organism, such as scaling up or down the overall size of the creature. But when such small changes do finally accumulate sufficiently to cause a change in internal functions, the effect once again becomes destructive due to the inevitable occurrence of a conflict among the closely matched interrelated parts of an irreducibly complex system.


Dr. Robert Pollack who worked with James Watson, co-discoverer of DNA’s structure, at Cold Spring Harbor Laboratory, says that major alterations to the DNA of embryonic cells caused by environmentally induced mutations are normally tragic.[87] Dr. Jonathan Wells confirms that in the developmental genes that govern embryonic development random mutations never produce beneficial changes, and typically lead to death or deformity.[88] But the developmental genes are precisely where major body type evolution must occur, else it cannot occur at all.


Enter yet another impassable barrier for neo-Darwinian theory: developmental sensitivity to random mutation. This is another show-stopper for the theory of accidental evolution, with the developmental genome essentially representing an example of intensified irreducible complexity. This poses a sort of catch-22 for the accidental mutation theory of evolution. Mutations occurring outside of reproductive cells do not get passed on to the next generation; those that do alter reproductive cells are invariably harmful or have no effect. Therefore, with the relatively trivial microevolutionary exceptions noted, the only macroevolutionary result accidental mutations appear capable of producing is a destructive or degrading effect, though many are neutral.


It is not surprising that random mutations show no beneficial effect. Remember, there is an enormous amount of DNA for random mutation to have to sort through (the rough equivalent of 600 round trips to the Sun).[89] Reports of modern genetic research reveal that the available options for new biologically viable DNA sequences are so rare within the vast library of total DNA sequence options, the distance between them so great, that the odds are overwhelmingly against random search ever finding an alteration that works to advance the organism.[90] That’s how complex life is. Darwin and his contemporaries had no clue about this, though through no fault of their own.


Contrary to the approximate rule of thumb that seems to be casually implied in some of the neo-Darwinian literature, namely that one could expect roughly one in a thousand mutations to be beneficial, the protein synthesis research of D. D. Axe cited by Stephen Meyer indicates the true ratio to be closer to 1 out of 1077. Trillions of trillions of trillions of trillions of trillions of trillions of useless or harmful mutations must occur to get one beneficial change at the “simplest” level of biological construction, the protein. How many would be needed to produce the sets of multiple genes that must work in concert to construct a new biological function or structural feature? The increase would be exponential due to the rules of probability theory, in other words, something on the order of 1077 X 1077 X 1077 X 1077, or 1 mutation event out of 10308 might be of use to macroevolution. But, as we discuss in Appendix 2, Professor William Dembski has informed us that there are only enough resources in the history of the universe to generate the smallest fraction of that number of mutations.


A Mickey Mouse Operation

Neo-Darwinian theory makes the outrageous claim that nature has, while blindfolded, and with no blueprint in mind, successfully tinkered with the Mickey Mouse watch (a bacterium) without stopping the watch or malforming it beyond natural selection’s standards more than 1,500,000,000 times (the approximate number of nucleotides in the non-“junk” portion of the human genome, which has been, by the way, steadily increasing).[91] It claims that an accident has inconceivably succeeded in advancing the Mickey Mouse watch design to the complexity equivalent of the Space Shuttle (a human being), while never giving us an explanation of how the original watch was created in the first instance.


Well, there was a long time to do it, right? No, not so much as one might think, not in relation to the size of the task. The historical fossil record, in fact, now reveals that the larger part of the work of evolution was done in the brief 5-10 million years of the Cambrian explosion, and the various bottleneck phenomena we have discussed above requires much of the work to have been done in periods ranging from years to moments. Simply put, such a thing seems both physically and mathematically impossible.


Darwinists respond to this objection with an oversimplified and, therefore, fallacious, logic. They note that bacteria can, and clearly do, generate “useful” mutations each year, for there are trillions of them and they mutate all the time. Granted, bacteria do come up with some “useful changes” every day, but they are only useful for bacteria. There is no evidence that these changes ever exceed a very simple threshold of form change. What little credibility the neo-Darwinian argument has ever had relies fully upon the fallacy of using a creature that is atypical of nature in terms of simplicity (the bacterium) to model what is claimed to be the typical evolutionary process for the entire tree of life, which is vastly more complex—clearly a flawed argument. In fact, this mistake is so glaring as to be politically suspect.


Can we now in the laboratory, while simulating the Cambrian and post-Cambrian environments of earth regarding mutagen prevalence and delivery, and with true random targeting of nucleotide base pairs, generate two or three ultimately progressive form and function mutations per year?[92] No. We cannot produce any. We can only demonstrate that under limited conditions creatures with genetic features quite unique in nature (bacteria) can produce varied changes of the simplest form and function within a definite and very limited set of options, useful only to themselves, at no time yielding a new type of organism outside the family of bacteria. 


The Phylogenetic Tree from Hell

Darwinists are fond of holding up tree diagrams as proof of evolution. One wants to ask, specifically, “Where is the tree full of documented viable progressive results from random mutations?” “Where is the tree of the requisite steps that must be accomplished to move between the known species?” For every newly evolved animal type there must have been thousands of mutative steps along the way. Where are the examples from nature and the lab that such frequently needed occurrences do in fact occur and that they link up in real time to form cumulatively progressive results? Where is the biomechanical chain of events involved in each of the series of mutational events hypothesized to lead to a significant development of macroevolution?


There is, of course the unfortunate fruit fly with a leg on its head, a poor dog turned into Cyclops, and the fly with broken wings that replace its flight stabilizers, thus fouling up flight dynamics. Aberrant deformities, genetic illnesses, regressive changes, and malfunctions are practically the only documented form-changing mutations we have on record![93]


The only exceptions to this rule are simple changes that don’t require integration with an organism’s complex internal functions, and which do not evidence a change in form and function significant enough to be a step towards macroevolution. The fact that there are no known mutations that are exceptions to the intelligent design claim that accident cannot do what is required for evolution suggest that the complexity barrier to accidental evolution is real.


Noted evolutionist Professor Douglas Futuyma notes two kinds of simple changes as proof of evolution: a bacterium that gains the ability to metabolize new organic chemicals, and the fruit fly becoming more efficient in the use of food. He also notes that hair color and height vary continuously across the spectrum in humans.[94] While this is true, such things are the simplest, least problematic, alterations to make. They pose no integration challenges to the complex internal machinery of the body for they are minor variations on a physiological theme already in place. And they don’t constitute significant building blocks of a new kind of creature.


The known results of accidental mutations would indeed fill a tree, but it would be a horrible thing to behold, with monstrous deformities and birth defects hanging from every limb. I challenge any scientist or team of scientists to construct an evolutionary tree from the known results of accidental mutations, or to show anything that has been produced via accidental mutations that led to an instance of beneficial progressive macroevolution vice an exhibit from a chamber of horrors. It can’t be done.


The practice of good hard-data-based objective science requires us to hypothesize not that accidental evolution can produce large changes in complex biological functions resulting in the entire tree of life, but, that accident can, at best, produce only the small simple changes that we have actually seen. We should stick to the evidence.


Where Are the Billions of Deformed Fossilized Species an Accidental Process Would Produce?

In a truly accidental process most early “competitors” would be stumbling and fumbling around with substantial design flaws. One competitor would be more or less as equally inept as the other. If evolution were truly accidental, in those early days, a predatory act would be something like comedian Tim Conway going to Harvey Korman as his dentist. The dentist would be just as likely to lose a tooth as the patient. Early predators would have been more akin to Wily Coyote than T-Rex. Each attempt at a meal could potentially turn into a genuine comedy of errors.


Granted, the fossil record would reveal to us only a small portion of failed designs. Some birth defects would preclude a creature’s living to reproduce. More minor to moderate defects, however, would impair the long term survivability of the species, but not its immediate reproduction. Certainly, we would be entitled to expect less occurrences in the fossil record than if the species had lived a fuller term, but we should still find myriads of malformed yet survivable designs in the fossil record for the simple reason that there would be so many of them produced by an accidental process.


There might only have been a few thousand mutant creatures created by any given imperfectly designed species, but, if the process were accidental, the math says that to get to the present elegant and complex biological systems by accident, trillions upon trillions of imperfect species designs must have been tried first. The sheer number of defective species designs based upon standard probability computations would in aggregate equate to an enormous combined population, in fact dwarfing the total of all other fully functional species combined. Bottom line: massive fossil evidence for an accidental design process would have been produced in the form of deformed species, but that evidence is not in the fossil record.


Mutant fossil occurrence should also be relatively uniform across the geographic and ecological strata because the random process of neo-Darwinian theory is presumed to be ubiquitous. Paleontologists and paleobiologists could not, then, easily miss the myriad of defective fossils that an accidental process would have created. A trillion, trillion, trillion, trillion bacteria may fit in a few thimbles of solution and therefore be overlooked in fossil sampling, but a trillion, trillion, trillion, trillion antelope with horns on their rump (or a variety of other disabilities and disfigurations) do not fit in a thimble, and their hard bony skeletons are easily preserved. Where are the mutants in the fossil record?


When fossils are found, in most cases it is not a case of finding an individual occurrence of a single fossilized species, but rather whole communities of species are found entombed together. Helmut Mayr tells us in his nice little book, A Guide to Fossils, that, because of the hit and miss nature of the geophysical forces that produce fossils, we should only expect to see the most abundant species in the fossil record. While this is true, it is still a mistake to assume that the “most abundant” rule applies only to species.


As a mathematical truism it also applies to any characteristic whatsoever. If microscopic creatures are more abundant, microscopic creatures will be most often found in the fossil community, vice macroscopic creatures. If swimming creatures are more abundant in relation to crawlers, their fossils will appear the most, etc., assuming conditions where fossilization can in fact occur. This rule holds for absolutely any characteristic or criteria one can devise to differentiate members of a population, including the presence or absence of a dysfunctional design feature or physical deformity.


If, as D. D. Axe has discovered, the odds against achieving even a single functional protein by accident are 1077 to 1, the odds against accidentally achieving a complex functional design feature requiring several if not hundreds of proteins must be at least as great. If only a single individual survived with each of the possible dysfunctional features that would have resulted from an accidental process, approximating that limit of 1077 defective designs for each success in design improvement, visibly dysfunctional aberrant designs would not just be present in the fossil record, they would strongly predominate.


Here we see evidence that either evolution was definitely an intelligently guided process or there was some kind of filtering system (perhaps built into the developmental genome) that was active in the evolutionary process, a filtering system that precluded inefficient and disabled designs from surviving the developmental/reproductive process or birth. Natural selection cannot perform this function; it must wait until the creature has competed in the natural environment and been found wanting. It must score the various attributes relevant to overall fitness such as biological efficiency, reproductive rate, competitiveness for scarce resources, physical hardiness, defense mechanisms, etc. That scoring process takes time, and during that time fossil records are made of the species that eventually get eliminated.


While granting, as modern evolutionists frequently remind us, that there is no bias that requires an evolutionary change to match the organism’s requirements in its present environment, there is clearly another kind of bias that is present: a bias for avoiding disabling mutations. The bias for mechanical soundness in nature manifested in the overall success rate of evolution is overwhelming. Bias and accident, by definition, cannot coexist. What the fossil record suggests, then, is that the evolutionary process, although occasionally marred by accident, or even assisted in minor ways by accident, does not have accident as its foundational dynamic.


“Show Me the Money!”

Neo-Darwinists cite minor changes to the already completed genomes, so called “random mutations,” as convincing evidence for accidental evolution. However, they can’t give even one example of a mutation or series of mutations that can be demonstrated to be both truly random and shown to have led to a significant step in progressive evolution. In fact, they can’t give a definite concrete causal explanation of any kind, random or otherwise, for even one major step in evolution. “The process is too big” seems to be their defense.


Neither Darwin, nor any Darwinian, has so far given an actual causal explanation of the adaptive evolution of any single organism or any single organ. All that has been shown…is that such explanations might exist (that is to say, they are not logically impossible).[95]


In scientific writing about evolution the allusion is often made to “beneficial mutations.” Typically, studies documenting the referenced mutations are not cited, nor is it even made clear what the term “mutation” in that context fully implies. Are the referenced mutations confirmed by observation, or are they, rather, merely theoretical assumptions? Are we speaking of mutations beneficial in some minor way to one species, or mutations that can be demonstrated to link with others to advance the creature towards a more complex organism on the tree of life? Are they truly accidental point mutations caused by toxic exposure or replicative error, accidental chromosome relocations caused by physical or chemical injury, or are they not so accidental allele substitutions, reproductive mixing of genes, genetic transpositional element-induced changes, or genetic marker changes closely managed and shepherded by governing mechanisms within the living cell?


The answer makes all the difference in the world to the question before us: accident or purpose? Yet no effort is made to give the reader the information they need to properly evaluate the neo-Darwinian claim of an accidental process when these references to “beneficial mutations” are given.


One can find selected biomechanical aspects of some of these types of mutations discussed in genetics texts in descriptive terms, but documented and observed examples of instances of truly accidental mutations leading to evolutionary advancement are not to be found. Demonstrably accidental mutations known to have led to a major evolutionary advancement are the unicorns of biology. They are believed in; they are imagined; they are hypothesized; they are celebrated, but they have never been seen.


Recently Dr. Jerry Bergman accomplished an exhaustive search of the scientific literature and did not find any genuine examples of information-gaining gene mutations at all. The few examples that did anything useful for an organism generally required an unusual circumstance to be beneficial and were otherwise injurious. Dr. Bergman’s paper recounting that search, entitled “Darwinism and the Deterioration of the Genome,” is available online at True Origin and also at the Creation Research Society Quarterly journal online.


In order to locate all alleged examples of beneficial mutations, I carried out a computer search of the literature.  My review covered all published scientific studies that dealt with beneficial mutations. The definition of beneficial mutation used was a mutation that was regarded as beneficial by the authors surveyed. Key words used in the computer search included synonyms of beneficial, such as “favorable, helpful, usable, valuable, adaptive, good, advantageous, supportive, positive,” etc.  The search of two databases totaling 18.8 million records found that, of all articles discussing mutations, only 0.04 percent, or 4 in 10,000 articles on mutations, were located that discussed beneficial or favorable mutations. Some overlap exists in the databases searched, consequently the actual total number of records searched was less than 18.8 million. The overlap in the search was estimated by extrapolating from the records found.  Assuming that the same level of overlap exists in the entire database, a total of approximately 16 million records was searched. These searches may have missed some relevant articles but are useful to indicate trends.


All of the 126 examples located were then reviewed, focusing on evidence for information-gaining beneficial mutations.  It was found that none of them contained clear, empirically supported examples of information-gaining, beneficial mutations.  Most “examples” of actual, beneficial mutations were loss mutations in which a gene was disabled or damaged, all of which were beneficial only in a limited situation.[96]


I have myself made a much less exhaustive search through two of the electronic academic journal services by obtaining a user account at the local university and could find nothing reflecting any viable mutations that might lead to evolutionary advancement. There is apparently no central databank of “beneficial” mutations leading to progressive evolution maintained for the common use of researchers and the public. But why not? There is a databank for absolutely everything else.


If beneficial mutations exist in such abundance and neo-Darwinian theory so critically depends upon them, why haven’t they been traced and recorded with the greatest of care? Why don’t pro-Darwinian articles wave this alleged multitude of progressive evolutionary mutations around in public view as a great victory for their theory? Certainly they have tried to do more with less. The obvious conclusion is that they don’t have anything beyond the trivial to present.


Evolutionists explain the process of evolution to students and the public in the simplest of terms as if the process were child’s play, easy as pie, implying that any fool can see how it happens. But when pressed to demonstrate real examples of specific mutations that have led to evolution they protest that it is an unfair demand because of the enormous size and complexity of the event process, and the trillions of small gradual changes involved. However, when one looks at the fossil record one sees that the changes were neither small nor gradual.


“OK fine,” we can respond. “We can agree on this much. Evolution is not simple. Which complex set, then, of accidental changes must occur in sequence or conjunction in order to create a specific recognizable step in macroevolution? Just give us one complete set of accidental mutations for just one substantial step in macroevolution as an example. Then we can test that hypothesis in accordance with proper scientific method, critique it with peer reviewed studies, and so on. We can ask other researchers to try to replicate those steps in the lab while taking care to preserve the randomness aspect essential to neo-Darwinian theory. We can do the math and see what the resource requirements would be to get the job done within the realm of scientific credibility, etc. This is how science works, after all.”


The Darwinists protest again. “We can’t do that. We don’t know a complete set of mutations sufficient to accomplish any specific macroevolutionary step, and, even if we did, attempting to randomly generate enough useful mutations to produce a new complex feature in biology would exceed the budget of all of science for millenniums! (They don’t add, as they should, “If it could be done at all.”) The entire process is too big.”


What they fail to recognize, though their objection is in other ways well grounded (the process is enormous), is that implicit in their own objection is the truth that accomplishing all of the needed complex new features and function changes required for the evolution of the tree of life by accident exceeds more than the budget of science, it exceeds the total budget of the universe in time and materiel by untold trillions of orders of magnitude. The same truth makes neo-Darwinian evolutionary theory untestable, and therefore not a proper scientific theory.


“Well, how about this?” they may say. “Let us break something for you. We can do that easy enough. No trouble at all. We can make a fly that doesn’t fly; oh, and a one-eyed dog. How about that?” “No, thanks,” we politely demure. “Any fool can break something; but evolution is the process of building more and more complex forms of life well fit to survive in their environment. To demonstrate evolution you have to demonstrate forward progress, not major malfunctions and regressions.”


Yes, it’s true; all that science can do in the genetics lab to this day, is break things (or produce trivia); it cannot progress biological designs via accidental mutations. What this whole fiasco demonstrates is that progressive evolution is not a simple matter of a few accidental point mutations, but rather an enormous closely guided process involving multitudes of time-coordinated changes affecting the many interrelated parts of highly complex integrated systems.


If life is not irreducibly complex as Professor Michael Behe claims, if it is all simple and easily thrown together as the neo-Darwinists say, why can’t we reproduce these easy steps in the lab? Some Darwinists, of course, claim that new genes are created by the bushel every single day, and that beneficial mutations are everywhere. But they are not everywhere documented. They are not everywhere in the textbooks and science journals. They are only everywhere hypothesized without proof.


The next time you confront a Darwinist say “Show me the money! Where are the specific documented mutations that have generated the difficult steps of evolution toward the complex forms of life?” They will only produce a few bacterial changes that go nowhere beyond bacteria, regressions of genes that go backward in functional capacity, genetic illnesses, horrific defects, changes in color, changes in size, and trivial changes requiring no substantial integration with the complex internal design functions of the organism.


Beware the word game. Consider the following quote from Douglas Futuyma:


So is it true, as the creationists claim, that good mutations are vanishingly rare? Certainly it is true that many, many mutations are harmful. But if even only one hundredth of 1 percent of all mutations are beneficial, 20,000 of them should crop up in the gypsy moths of Long Island just this year. Moreover, the early geneticists significantly underestimated the proportion of beneficial mutations, because they studied a biased sample of possible mutations, the ones that drastically change an organism instead of modifying it only slightly.[97]


In my opinion the wording here is very misleading in several ways. First, “if even only one hundredth of 1 percent of all mutations are beneficial”—is this a generous figure as Futuyma clearly suggests? Hardly. Do we have any hard research indicating such a figure is in fact generous? No. The only concrete research we have is quite to the contrary. D. D. Axe’s protein synthesis research (which, in fairness, was completed after Futuyma’s statement was published) has revealed that the proportion of useful mutations in the sense of being able to produce at least one biologically viable protein (the minimum change to have a significant effect on the organism’s design structure) is not 1 one hundredth of 1 percent but rather a trillionth of a trillionth of a trillionth of a trillionth of a trillionth of a trillionth of that, or one part in every 1077!


Thus we should expect, not 20,000 beneficial evolutionary changes in the gypsy moths of Long Island each year, but only one beneficial evolutionary change to occur in the Long Island gypsy moths every 10,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 years; that’s it. But the universe is only 20,000,000,000 years old!


Thus, the truth is not what Futuyma implies, that there are more than sufficient numbers of beneficial mutations to ground accidental evolution. Rather, we should expect no beneficial random macroevolutionary change whatsoever. We should also go check to see if the gypsy moths of Long Island have really been rapidly progressing in form and function, given all those supposed beneficial mutations they have been having. I will guarantee you they are not doing anything of the kind.


Finally, nothing is said here as to whether the mutations are accidental in any real sense, but, since no delimiting characteristic is given, Futuyma is apparently considering all types of mutations taken together. It remains an open question whether internal genetic transpositions should be considered random or not. The only undisputedly random mutations are the toxic exposure-induced ones, and they are the ones that produce the horror stories previously discussed. They are also the ones that scientists have already conceded (including Futuyma) produce no significant impact on evolution.


Why aren’t the examples of new randomly produced genes that effect evolutionary advancement in the textbooks if we get 20,000 beneficial mutations per species per region per year? One thousand nucleotide mutations roughly correlates to a gene totally rebuilt from scratch, which yields roughly 20 new genes per species per region per year. Where are they in the text books? This would be the best evidence neo-Darwinian theory could produce, rapid generation of new genes with beneficial results.


All we see in the text books and science journals are deleterious mutations such as Sickle-cell Anemia, Downs syndrome, Cystic Fibrosis, Muscular Dystrophy, wings that don’t work, a leg in place of an antennae, regression in the capability of a gene, etc. A collection of mistakes and regressions, no matter how elaborate, will never assemble themselves into an evolutionary advancement of a complex living machine. These are not real scientifically documented beneficial mutations Futuyma is referring to; they are imaginary, and his imagination is based upon mathematics formulae fully out of touch with recent research.


It is time for the public to put the neo-Darwinists on the spot: show us the new genes, show us that they make substantial progressive change, and demonstrate that they were evolved by accident! Then link a set of them together to show a real step in macroevolution, one phylum evolved from another, one class evolved from another. Then replicate the process in the laboratory. This would be proof of accidental evolution, and only this—and accidental evolution will not be a fact, as neo-Darwinists have prematurely claimed for decades much to the eternal embarrassment of science, until these things are done. But don’t hold your breath; it will never happen.


Let’s visibly catalog those alleged new gene evolutions and place the complete data before the public where it can be rigorously scrutinized to see if it adds up to an achievement of new, complex, and highly integrated biological systems. This would comport more with the presumed integrity and known method of science, as opposed to what is presently occurring, that is, casually referring to volumes of evidence that exist only in the interpretive imaginations of the neo-Darwinists.


I guarantee you that, when produced, the so-called evidence will comprise a thin catalog indeed, consisting of front cover, back cover and a single insert saying TBD (to be determined by further research). If the quality of the evidence was as good as Darwinists have claimed, we wouldn’t have to publish in the nation’s leading science journal studies of regressive change as proof of progressive evolution.


A catalog of beneficial mutations would be the best, certainly the most direct, evidence neo-Darwinian theory could conceivably offer. Professor Futuyma says there are plenty of instances of beneficial mutations. Why not lay them out for inspection and see what they add up to? Frankly, I just don’t believe it. I think the neo-Darwinists’ extreme faith in evolutionary theory has blinded them to the truth. Their theory has explanatory power only in the abstract, that is, in the imagination, so that is where all of their arguments reside, and their so-called “evidence.” Neo-Darwinists have no concrete objective evidence for accidental evolution. The rhetorical support they offer for accidental evolution requires us to interpret data through the lens of neo-Darwinian theory; it is a circular argument.


Neo-Darwinists may reply that gradual random mutation-based changes that lead to macroevolution take too much time to be observed. This may be true; but that makes the events key to supporting their claims unobservable. It makes neo-Darwinian theory unscientific because it can’t be tested.[98] Neo-Darwinists are asking us to take their theory on faith, all the while dismissing intelligent design theory evidence as religion, when it is honest mathematics, genetic science, and microbiology!


This is a huge scandal in science, and very ironic. Scientists influenced by an academic power structure comprised largely of individuals practicing the pseudo-religion of atheistic materialism have succeeded in having the legitimate science offered by intelligent design theorists dismissed as religion because it challenges their religion of materialism, a religion they have succeeded in substituting for objective science in Western cultures.


If science is to survive this assault from pseudo religion, it will have to stick to the objective evidence. The implications of the mutations we can observe are very different from the assertions of neo-Darwinian theory. Truly random mutations are observed to consistently degrade the efficiency of the organism, or even destroy it—cancer and birth defects being cases in point. The neo-Darwinist objection then amounts to “The beneficial changes that support our theory are too big to be observed, but the destructive changes that argue against neo-Darwinian evolution are small enough to be seen all the time.” That is rather a dubious claim, and it is hard to see how it helps their case.


Granted, if random mutations could produce beneficial change, it would take them longer to make a sophisticated biological machine than to break it. But this does not further the neo-Darwinist case. Quite the opposite. It places the neo-Darwinists in a logical pin, or checkmate. It amounts to an implicit admission that biological machines should break long before they constructively evolve under the influence of random mutation.


The Mutation Factor: Not Good Enough

Could the beneficial mutagenic rate be high enough to make neo-Darwinian theory credible? Genetic science, unavailable to Darwin, now says no. According to Dr. Stephen Meyer, citing Dr. Susumu Ohno, the scientist who discovered the link between cancer and genetic mutation, a random mutation rate of 10-9 per nucleotide base pair per year is taken to be a reasonably liberal assumption. That is one mutation per billion base pairs per year and includes all types of point mutations: harmful, beneficial and neutral.


Other scholarly sources confirm the standard mutation rate and there is general agreement upon it.[99] As Dr. Ohno indicates, a standard mutation rate of 10-9 would correspond to only a 1% change in DNA over 10 million years, almost all of which would be destructive or neutral.[100] How then were 48%-87% of our elegantly functional body types evolved during the Cambrian period (lasting 5-10 million years) in the time that, if the standard mutation rate is correct, should have generated only predominantly destructive changes to genomes and produced no new viable body types? A similar unanswered question is, “How was the evolutionary process accelerated far beyond the standard mutation rate to produce the evolutionary progress that occurred during the time bottlenecks of punctuated equilibrium?”


“So what,” you may want to say, “no big deal. So there are a few mysteries left in the history of life; that is to be expected. All we need to know is how long it takes to achieve one beneficial mutation, and of those few that are beneficial, how many and how long are required to generate a complex new feature that goes further to contribute to advancement of the macroevolution of a radically different highly complex species?” That’s an excellent point. The only problem is no one knows the answer. We have never seen any randomly generated mutations that can be positively linked to the development of a significant new body form or a beneficial complex functional innovation—not one.


That may be because we haven’t been looking long enough. It may be because the process is simply too big and too complex for empirical science to ever complete the linkage. Or it may be, as complexity analysis, probability theory, and mutational studies suggest, because there aren’t any accidental mutations that lead to macroevolution.


Where we do see phenotypic changes arise within a species in nature, they are minor microevolutions that do not lead to a significant change of body form—and these have not been linked to external/toxin-induced (accidental) mutations as their source.[101] Rather, nontrivial biological form change appears to be coming exclusively from the internal shuffling of increments of already highly configured meaningful genetic information.


Preexisting increments of meaningful genetic information are both randomly and non-randomly rearranged inside living organisms on a regular ongoing basis.  Various processes accomplish the rearrangements: allele substitutions; modification of gene expression tags that turn on or off a complex design module that is already complete; transpositional mechanisms that move genetic components around based upon the built-in rules of the genome (in part still poorly understood but on the surface nonrandom); and the well-known variations that result from reproductive recombination. Even the most random of these elements are not fully accidental in that they are harnessed within a nonrandom living biological machine. The units of information being moved are already meaningfully formed so very little of accident is involved. That is clear enough, but it is the recently discovered role of transpositional elements and mechanisms that I wish to highlight here.


Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms…Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons.[102]


Mobile group II introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the intron-encoded protein. After DNA insertion, the introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage.[103]


The variation of genetic recombination rate along a chromosomal arm is shaped, not only by the distribution of simple repeats, retrotransposons, DNA transposons, and nucleotide substitutions, but also by the functions of genes contained, especially those with multiple functions, suggesting that variation of genetic recombination along a chromosomal arm is the result of interactions among the components constituting local genome structure, function, and evolution.[104] (My emphasis)


The rapid genetic shuffling required for macroevolutionary form change is apparently driven largely by such transpositional processes. Just how much of the genetic transpositional process is truly random remains to be established, but the process is nonrandom in the larger sense of being closely shepherded within the living cell’s larger mechanism.[105] As the Lambowitz and Zimmerly quote says, host damage is minimized.


The problem of intelligent authorship of the books that govern the designs of living creatures remains unsolved, but here we see a hint that the vast information-storing capacity of folded protein structures is likely the key to the mystery of life’s evolution. Such genetic transpositions apparently produced the unthinkably complex form and function changes that occurred in relatively short time periods through evolutionary history. The only potential source of input for guiding information of the scale necessary seems to be proteins, which we see in the second of the three quotes above (Lambowitz and Zimmerly, 2004) are interacting closely with genetic transpositional elements.


The enormous statistical improbabilities for unguided evolution, combined with the vast information storing capacity of folded protein structures, suggests a new theory of evolution: the hypothesis that the evolution of life is a non-random process guided by the release of protein-stored biologically meaningful design information. Certainly this hypothesis is vastly more plausible than that the entire thing is one big accident.


Most scientists presently follow Francis Crick’s 1958 vintage hypothesis that information cannot travel back from proteins into RNA or DNA, but, if Susumu Ohno can hypothesize a master genome at the beginning of the Cambrian Period that we have no direct evidence for because it explains things otherwise inexplicable, I can hypothesize this for the same reason. We may not find a protein-to-RNA/DNA information transfer mechanism in living systems today, but that doesn’t mean it wasn’t there “yesterday,” perhaps even as far back as the Cambrian. Such a mechanism may in fact be the source of Ohno’s master genome. That mechanism, something like a reverse ribosome, may even have been alive: a bacterium that functioned as a living reverse ribosome. It consumed proteins and spit out RNA sequences corresponding to the folded protein structure.


An early presence of a LRR (living reverse ribosome) or RRS (reverse ribosome system) would explain how we could get the tree of life in real evolutionary time, something we cannot presently do. However, as long as materialists, atheists, and Communists dominate the modern scientific culture very little research will be directed at this question because it implies that accident was not the driving force of evolution.


Natural selection would indeed be a powerful player again in an evolutionary scenario driven by the periodic release of design information from folded protein structures into living genomes via protein interactions with transpositional genetic elements. Here we have a nearly Darwinian model where spontaneously occurring but complex pre-designed biological form variations arise from the unfolding of a master plan (if only a fuzzy and flexible plan) encoded into proteins. These variations generate evolutionary advancements that are then confirmed or rejected by natural selection. The only differences between this model and traditional Darwinian theory are that the design information preexists in protein structures and “spontaneous” in this theory does not equate to “accidental.”


The Bacterial Cavalry: Hurray! Here Come the Germs!

But don’t panic yet, you die hard neo-Darwinians; here come billions upon billions of gene-transferring, hyper-reproductive bacteria and viruses to save the day. Hurray for germs!


There are undeniably an astounding number of them (70,000,000,000,000 in your intestines alone[106]), and they reproduce at amazing rates. Bacteria do carry spare genetic information around with them in “sacks” called “plasmids” that spontaneously mutate the organism via recombinant DNA processes.[107] Walla Booby, accidental neo-Darwinian evolution will be proved this time for sure! Right? No.


Bacteria are visibly exceptional to all other creatures in nature in that they carry spare bags of genetic material around, material clearly designed to be periodically integrated into their simple genome in routine ways. And bacteria are exceptional in being ultra-simple compared to the larger part of the tree of life. Bacteria’s extraordinary reproductive rate is not typical of nature. What accidental genetic substitutions can do for bacteria they cannot do for more complex creatures due to complexity and probability barriers.


Ultimately, the unique success rate of bacteria in adaptive gene substitutions may derive from two very simple things: the rate at which bacteria try substitutions, which is astronomically high, and the fact that it is not hard to do what they do, that is, it is not hard to decompose things, to tear things apart. It is always easier to break something (in this case to break it down) than to construct it.


The bacterial enzyme-based digestion/defense mechanism has a simple unitary function and operates on the exterior of the organism’s design. It requires neither close nor complex interaction with other components. Like a piece of a jigsaw puzzle with a single simple standard node that plugs into the puzzle from the exterior border, there is practically nothing to conflict. Genes of more complex animals that govern critical internal processes, on the other hand, have multiple functions and are additionally cross-referenced to a very sensitive developmental genome. They therefore correspond to a highly complex internal piece of the puzzle with multiple irregular nodes. There is more to conflict.


In more complex creatures, necessary modifications might cascade in a chain reaction that extends to as many as several vertical levels in the hierarchy of the organism’s design, and to several additional interacting systems laterally. A new genetic change, the effect of which is simple and routed solely to the exterior of the organism, however, as is the bacterial defense mechanism or digestive enzyme, avoids the necessity for a cascading series of modifications, and is thus much easier to implement.


Mutations of plasmid DNA have only demonstrated the capacity to do simple things like add antibiotic resistance or generate a new enzyme to breakdown an additional source of food. No plasmids are known to routinely transfer from bacteria to complex organisms and the cells of complex creatures are not able to pick up free DNA as readily as bacteria do.[108] Once again, the problem of equating the process of microevolution in one atypical species with the very different processes of macroevolution across the entire tree of life must be avoided.[109] To say that because bacteria can evolve and transfer simple enzyme-affecting DNA segments that they can evolve and transfer absolutely everything else necessary to generate the entire tree of life is not just ungrounded speculation; it is scientifically reckless.


Genetic transfers from bacteria to other species, if they happen at all, are not the norm, but the rare exception. Therefore we do not have benefit of the enormous numbers of bacteria and their fantastic reproductive rate to create trillions upon trillions of mutations of all types that might solve Darwin’s lack of time problem. Bacteria may have constructed the initial master genome(s) but they most likely have not been the instruments of each subsequent step in evolution by way of transfer of genetic material.


Even if germs could in theory produce massive numbers of useful mutation events, we have already seen that there is not enough time and physical particle events available in the history of our universe to “fund the effort,” as it were. Standard probability theory tells us that if germs did produce the massive numbers of progressive mutations necessary to build the complex machinery of life in real evolutionary time, then the process used to manage, direct, and assemble those mutations into viable form and function evolutions could not have been driven by random or accidental dynamics.


Even if large numbers of bacterial gene transfers to other species could take place, transferring in many genes from simple creatures does not make a complex creature. As Peter Kassan tells us in his refreshingly candid discussion of the failed attempt to duplicate human intelligence by artificial means,[110] transferring in 3,000,000 cockroach genes doesn’t equate to the functionality of a human, it equates to the functionality of a colony of cockroaches.


One aspect of the genome that indirectly forms a barrier to accidental recombinant DNA substitutions in complex organisms is alternative splicing or alternative reading frames. Alternate splicing is used on as many as three quarters of the genes of complex creatures. Those genes are “read” or edited in several different ways in order to produce more than one protein from the same gene. In addition, in complex creatures, a single gene tends to be involved in regulating multiple processes, not the single process of biodegrading one substance as is the case with the simple bacterial genes. Gene substitutions that work for bacteria are no longer so simple for other creatures. Advancing one of the multiple gene functions with a nucleotide mutation stands to degrade or destroy one or more of the other functions.


Instead of effecting a simple change in immunity to a standard threat, the substitution of a single gene in complex creatures can, hypothetically, alter the development of the embryo causing children to be stillborn; remove cancer protection; and flatten the arches of the foot all at the same time. Consequently, one cannot say with confidence that the ability of bacteria to spontaneously evolve new antibiotic resistance demonstrates any real potential for evolution across the taxonomic inventory of more complex forms of life.


For the substitution of a gene from bacteria to be less than catastrophic in the far more complex variably-read machinery of a mammal, for example, the entire mammalian genetic system would have to be regressed to remove the developmental genome and the alternate reading frame mechanisms. At that point mammals can neither reproduce successfully nor complete the large part of complex biological systems maintenance and regulation needed to keep them alive—hardly an improvement.


Bacterial gene transfer may have played a part in evolving bacteria and primitive creatures, but it is of little or no use in promoting further advancement and differentiation of mammals. Bacteria’s big contribution was more likely an early symbiosis that led to the creation of complex eukaryotic cells, master genome(s), and our present system of genetic transpositional elements. But, in mammals and other highly complex creatures, those advanced cells and transpositional elements are now harnessed by and integrated into a vastly more sophisticated machine.


In light of the against-the-odds progress of evolution itself, which mathematically entails the use of a nonrandom process, we are not entitled to merely assume that internal genetic transpositions are random; we have to demonstrate they are random. The math alone says that our transpositional genomes are not completely random, else the rate of genetic illness would be astronomical and evolution would still be working on troglodytes.


True, the relative simplicity of bacterial design taken together with their closely circumscribed plasmid-based enzyme-altering mechanism may explain our strong suspicion of successful horizontal DNA transfers among prokaryotes (very simple organisms).[111] But it simultaneously invalidates the larger evolutionary inference that the same thing could be routinely accomplished with higher eukaryotic organisms, which are too sophisticated to tolerate such a primitive tool. In short, bacteria are set up to handle such transfers, while other creatures are not.


All that we can safely conclude is that some microevolutions in bacteria may be promoted by DNA transfers. We may not safely conclude the ability to move from one type of creature to another via DNA transfers.[112]


Retroviruses, do, in a sense, routinely alter the DNA of the host, but the transfer of viral DNA isn’t going to cause an advancement or a continuing series of advancements; it is simply going to make the host ill, as is commonly seen. Good evolutionary science like good police work should confine itself to the facts, and to valid logical inferences from those facts. All we truly know to have resulted from naturally occurring bacterial and viral exposures are infectious or genetic diseases and birth defects.


The use in the laboratory of germs as gene vectors, that is, delivery vehicles, may seem to suggest the usefulness of gene transfers via bacteria as a tool of accidental evolution, but these laboratory procedures are not accidental. For lab transfers a genetic sequence is analytically chosen by scientists and then carefully edited. All the troublesome aspects are (hopefully, but not necessarily) cut out or cropped off. The carefully prepared gene segment is then placed by an expert scientist into a germ already known to be a suitable receiver. The germ is then introduced into the recipient cell via a substantially controlled procedure. Nothing about this procedure is random or accidental.


Such procedures tell us that, under artificial, intelligently-guided conditions, germs can effect a beneficial genetic change to an organism within certain limits. It does not demonstrate that an accident can do the same thing. It certainly does not demonstrate that an accident can do absolutely everything that macroevolution requires within the historical timeline. To date it has not been possible to achieve the radical biological form changes needed for macroevolution (any of them) even with intelligently guided laboratory procedures.


The amazing adaptations of germs and the adaptive capacity of bugs to pesticides, when compared to the dramatically smaller adaptive capacity of higher life forms suggest that there is an inverse relationship between complexity and the ability to rapidly evolve viable biological form change. It also suggests that the adaptive options are primarily/exclusively limited to those options predetermined by the overall design of the organism, such as the generation of antibiotic and pesticide resistance and the creation of new biodegrading enzymes.


The germ plasmid gene substitution routine is a good example of a random generator program built into a larger highly ordered and constrained design, a design that does not have unlimited capacity to generate novel change. Rather it can only run through a list of predetermined options, many of which are “preflighted” to work but cannot, as it were, step outside of their programming to do anything truly novel in terms of macroevolutionary form change.


Even where such gene substitutions have occurred in bacteria they are substitutions of a precomposed gene selected from a preexistent set of such genes containing at least some genes that convey an advantage. It is not a case of visible evolution from scratch where fully accidental mutations are demonstrated to have constructed a new and useful gene in real time. Yes, there might be one or two exceptions to this rule, but they would involve very few mutations being made to an already existing gene sequence.


It is almost certainly not a coincidence that the only thing the human body does comparable to the bacterial ability to rapidly generate new genetic information (viz. antibody production by our immune system) also routes the results to the “exterior” dead end of an event chain, a point in the process architecture where an ensuing cascade of design changes is not required. After the human antibody is produced, like the bacterial enzyme, it then confronts an exterior threat, an invader. It attacks the external enemy with a chemical attack that destroys design structures (the invading organism), which is much easier than interacting with a complex design or progressing a complex design. Such examples seem to me to more precisely describe the limitations of accidental genetic substitutions than to demonstrate their unevidenced hypothetical capability to generate new complex life forms.


While almost always destructive to living systems, it is (in theory) possible that an accidental process might (rarely) achieve a simple system, such as a bacterium, from nonliving components, given sufficient time and a highly improbable and complex set of conditions. It may seem odd to allow that an accidental process might achieve a bacterium but go no further, but bacteria are both uniquely simple and, in many ways, simply unique. As such, they may be a genuine dead end for accidental evolution. Bacteria may represent the upward delimiting boundary of the capabilities of an accidental process in biology. It is possible that accident can do that much but no more.


[Note: As a Catholic, of course, I assume that bacteria, as living creatures, also have the spirit of life added by God. But that is not something science can speak to directly. Although I personally believe that, if accident could successfully throw together a bacterium’s physiological structure, that structure would not spontaneously come to life, there is no scientific argument I can give you to support that position beyond the larger argument for God as the creator of life that I give in Part 2.]


Whole gene or large DNA segment substitution events, such as occur with bacterial plasmid substitutions, as opposed to single or multiple nucleotide change events, don’t qualify as true examples of novel design origination. In these cases the existing design merely rotates preexisting design modules within a common interface. New complex design modules are not originated; they are shuffled around within a machine interface already designed to facilitate the shuffle. Many of the plasmid gene substitutions harm or kill the individual host organism, but the larger process of having these substitutions go on improves the survival ability of the species.


It is like turning a multi-lens microscope to a higher magnification or moving between slides during a slide show on your home computer. The high power lens is not created on the spot; nor is the next slide; its design is already present, made available by a prior intelligently designed process. A feature of the microscope’s design permits alternating between preexisting components, but it does not generate those components in real time. So it is with bacterial plasmid gene transfers. This is not a case of visible evolution in real time, but a case of an existing design performing a preexistent rotation function.


Contrary to popular belief, bacteria do not solve the bulk mutation numbers problem for accidental evolution. If we allowed 10 billion species of bacteria (microbiologists presently estimate only approximately 10 million bacterial species)[113] each with a trillion population sites and a trillion, trillion germs at each site mutating at the standard mutation rate of 10-9 per year extending back through 4 billion years, this still only accounts for a maximum of 1046 mutations. Based upon D. D. Axe’s studies that show a probability for randomly achieving biologically viable proteins of 1 chance in 1077, this is the smallest fraction of what is needed.


This estimate of total bacterial population would seem to be generous, however. A very well-designed analysis by the University of Georgia in 1998 estimated the current bacterial population at only 5 million, trillion, trillion; my estimate here allows for a current population of 10 billion, trillion, trillion, trillion—surely a safe overestimate.[114]


There are three unknowns that could alter the estimate for historical bacterial populations potentially relevant to producing key biological mutations: (1) the margin of error in current estimates extends to many orders of magnitude;[115] (2) while the number of past bacterial species was possibly less than at present, the total bacterial populations during past millennia may nonetheless have been much greater, and; (3) some of the mutational product of huge extraterrestrial bacterial populations may have found its way to Earth. None of these possibilities seem very likely, but they are possible.


The possibility of a gross underestimate of current bacterial populations and the difficulty in estimating past bacterial populations mean the numbers could be much larger, but even if we allow for another trillion, trillion greater overall bacterial population it still does not get the mutation total quite to the level required to make the accidental achievement of even one biologically viable protein plausible. Given the standard mutation rate we can confidently rule out the accidental achievement of even a handful of biologically viable proteins via predominantly bacteria-induced mutations—and the tree of life needs two or three hundred thousand proteins!


Even allowing a much more generous assumption of much greater numbers of bacteria we would not scratch the surface of the number of mutations needed to generate 200,000 proteins, genomic systems and related necessary components. We wouldn’t have solved the time synchronization problem for simultaneous appearance of interdependent components, and we wouldn’t have solved the problem of how to integrate sets of new biological elements into a living system in real time.


OK, let’s suppose the standard mutation rate is wrong; the bacterial population estimate is too small; and something anomalous occurred to cause bacteria to start doing plasmid substitutions at a frantic rate while infecting or being in a position to infect other creatures causing an enormous amount of random lateral trans-species DNA transfers and internal DNA transpositional events. That would, in theory, produce enough mutations but, as we discussed above, if the process is truly random before the third biologically useful protein was achieved randomly the universe would have completely exhausted its resources in time and particle events. The remaining 99.9999999…% of evolution would be cancelled due to lack of resources. So much for bacteria as the engine of accidental evolution.


A Precambrian Master Genome?

But neo-Darwinists never say “die.” Here’s another proposed solution to Darwin’s lack of time problem. It is a truly ingenious one belonging to the late, much loved, and highly respected Professor Susumu Ohno. Ohno proposed that at some time in the distant past, probably during the Precambrian period, a creature or creatures somehow accumulated a genome containing such a large set of the core genes essential to the tree of life. These genes were sufficient, given some further rapid mutations, to quickly generate the advanced features of many more complex organisms, as well as most of the major body types that evolved during the 5-10 million-year surge of evolutionary development that is called the Cambrian Explosion.[116]


In Ohno’s view, most of the creatures of the early Cambrian or Precambrian somehow came to possess the same or similar master genome, or significant components of such a genome. Later variations in biological form, including most of the major body types of the animal kingdom, were produced from the master genome(s) by rapid altering of gene expression and gene silencing tags. Thus, in Ohno’s master genome hypothesis we have a plausible explanation of the rapid explosion of life form variation in the Cambrian period.


Ohno calls this master genome the “pananimalia.” One virtue of his theory is that it allows for a more reasonable period of time to develop the first comprehensive set of genes: the three billion plus years preceding and including the Cambrian, as opposed to the mere ten million years of the Cambrian explosion.


Explanatory power is another virtue of Ohno’s hypothesis. The pananimalia genome can explain things otherwise fully inexplicable except by intelligent design or otherwise heavily directed evolution (orthogenesis): how to accomplish the jump from bacteria to the first complex invertebrates and how to rapidly develop thousands of radically divergent vertebrate and invertebrate forms without leaving fossil traces of intermediate transitional stages. The pananimalia master genome hypothesis generally explains how to accomplish so much in so little time without making a complete mess of the attempt.


Ohno’s proposal goes as far towards the solution to the time problem presented by the Cambrian Explosion as anything else of a concrete nature that has yet to be proposed—and precious little has been proposed. Ohno’s theory remains to be corroborated by direct evidence. We have not discovered any solid indications of a master genome in the early Cambrian/Precambrian.


It is a very useful hypothesis in regards to the progression of evolutionary theory generally. However, when employed as a neo-Darwinian argument for an accidental process, Ohno’s pananimalia master genome hypothesis only goes so far before encountering insurmountable obstacles. The most glaring of these obstacles is the fact that natural selection would be largely irrelevant to the formation of Ohno’s master genome. In the pananimalia scenario, the new genes must either originate within the inactive portion of the genome or quickly become inactive after they are originated. If the widely varied genes of the pananimalia were all actively expressed, the pananimalia creatures would have been bizarre mixed-genre many faceted chimeras of which the fossil record gives no evidence.


Since the new and complex sets of genes were not expressed actively in the host organisms within which they were developed, natural selection had no chance to vote to preserve them. Thus, the standard neo-Darwinian model that posits very gradual changes locked into place by natural selection doesn’t apply.


Another problem, not necessarily insurmountable, is that accident would have continued to alter the inactive genetic sequences of the master genome even after they were perfected. Without natural selection to squirrel away the good stuff via the survival of those with superior fitness quotients, useful genes once constructed could quickly be deconstructed, degraded by further accidental mutations. This doesn’t mean a master genome might not be preserved due to rapid reproduction rates of bacteria making thousands of copies before random mutations started to disassemble it again, but it does decrease the odds.


Another problem with Ohno’s master genome viewed as a random or accidental product is that it wouldn’t just create the good stuff; it would also create genomes producing dysfunctional, deformed, and disabled creatures that would live long enough to make imprints in the fossil record. It is reasonable to presume many fossils would not be created for nonfunctional designs that perished almost immediately after creation, if not immediately, but many mutant or chimeric designs would be temporarily survivable. They would create fossil records. Since the biologically viable, largely flawless designs are much more rare and harder to achieve accidentally, by far the larger part of the design output of such randomly/accidentally produced master genomes would be disabled, dysfunctional, and deformed creatures. But the fossil record indicates that no such massive population of deformed creatures ever existed.


Ohno’s theory doesn’t explain how we get organisms with master genomes not having serious defects prior to natural selection having millions of years to work out the flaws. It doesn’t explain the creation of life, or the hard parts of constructing genomes by accident. It only explains what might have caused the Cambrian explosion of rapid evolutions of many new body plans. It is therefore not a savior for the astronomically improbable accidental theory of evolution.


Take the accidental dynamic of neo-Darwinian evolution out of it, convert Ohno’s hypothesis into a form that allows for intelligent design or some other type of orthogenesis (directed evolution) and it becomes the absolute most explanatory theory we have, hands down. Partially developed novel genome segments and some of the associated integration work for use in a later design, could, in theory (in this case not by accident), be perfected in inactive DNA prior to implementation.


With inactive DNA, modifications to an inactive genetic sequence still in development place no wrenches into the working machinery of the organism. Once the inactive code was perfected including gene sequences necessary to integrate the new genes into an existing organism, gene expression tags could be quickly changed to active and the creatures could start to differentiate into the fifty different major body types of the animal kingdom and then on to a myriad of additional diverse species. Thus, Ohno’s theory of the pananimalia taken in a non-accidental and non-neo-Darwinian form is hugely explanatory of the Cambrian explosion. Science has no other explanation for the Cambrian explosion.


Why couldn’t there have been an accidental version of gene expression tag placement within an enormous accidentally created master genome that was nearly complex enough to represent all possible genomes? First of all, creating all possible genomes is far outside the resource range of our universe. But let’s say the accidental manic DNA generators got “close,” that is, close enough to create the good genomes representing those in Earth’s tree of life plus a larger amount of junk and disabled genomes. How would an accidental process know when to switch which gene expression tags in which combinations? If gene expression markers were being moved around in a truly random manner, as neo-Darwinian theory requires, one would expect to see both odd chimeric forms and nearly all the intermediate variations that the DNA of the host creature could theoretically produce in the fossil record—if the creatures could survive the accidental tinkering at all. Those intermediates are not present in the fossil record. And again, deformed and disabled creatures would be the numerically predominant result, but fossils of those creatures are not in the fossil record either.


It is highly improbable that an accident could reset thousands of gene expression markers in very complex interrelationships with such precision for even one species in one generation so that no fossil record of the flawed intermediates is created. Then there is the problem of how an accidental spate of gene expression marker changes could create genomes that seem to have the ability to look forward, to contain the future genomes of millions of additional species, which flowered from the original master genomes, as opposed to randomly evolved.


It is, technically speaking, theoretically possible for such a remotely possible complex series of accidents to have occurred. But, minus direct proof, it is not scientifically proper to assert or believe that such an event happened by accident due to the staggering improbability. Once again, the crux of the matter lies in just how enormous that improbability actually is. It is not just mildly improbable; it is incomprehensibly improbable.


The math says not just that an accidental process would have tended to produce more intermediates as well as disabled and dysfunctional creatures, but that it would have produced them en masse, that is, in enormous numbers. Their absence from the fossil record indicates either that the intermediates were not survivable; that some counter-veiling event occurred to preclude fossil imprints being made; or that a built-in (nonrandom) filter of some kind ruled out most of the options being tried.


A random/accidental process would have produced the entire range of possibilities, including millions of flawed intermediates that were survivable. There is no evidence for an event that would have prevented the making of fossils, and we in fact have many fossils from the Cambrian period. The last possibility, a filter system that precludes the production of non-viable designs is not compatible with an accidental process.


The sensitivity of the developmental genome to mutation suggests there may have been such a filter. A built-in filter that eliminated some biological form change proposals and allowed others at early points in development is one tool an intelligent designer might use to funnel the evolutionary process towards a set of predetermined goals. Having preset filters that rule out the majority of alternatives that a random process would otherwise produce makes the process at a minimum strongly nonrandom (non-accidental) and therefore an example of orthogenesis, not of neo-Darwinian evolution.


Because a pananimalia genome would explain so well at a key point (the Cambrian Explosion) where science has no other explanation, one cannot, by any means, rule out its existence. On the other hand, it is clear that any process that built the pananimalia received little or no aid from natural selection and that the intermediates and dysfunctional forms that accident would have produced are not in the fossil record in the requisite numbers. It is not within the range of scientific credibility to believe that such a large genome/set of genomes could have originated in inactive mode completely by accident without enormous unmistakable signs in the fossil record that accident had been at work.


Ultimately, the deciding evidence for or against the pananimalia master genome hypothesis will have to come from the fossil record, including fossilized DNA from ancient creatures,[117] and comparative studies of the genomes of early life. Although the evidence currently presented by fossilized and comparative DNA studies of living organisms shows a lot of similar sequences going back to bacteria, thus hinting at common ancestry, it falls a long way short of demonstrating an early master genome—and it says nothing whatsoever in favor of accidental evolution.


My own best guess, which I describe further on in this book, is that the “master genome” was not so much literal, as virtual: a very sophisticated and closely orchestrated dance of a multitude of factors reaching perhaps even to the subatomic level within biotic molecular structures. These factors may have included Michael Denton’s Platonic protein forms, rules of biochemistry set in natural law that facilitate self-organization of life in a plethora of different ways, and a mass of information hard-wired into protein structures that is yet to be elucidated, all combined to allow the creation of first life from inert chemicals and guide evolution towards (at least roughly) preset goals.


While it does appear that there must have been either a master genome similar to what Ohno has suggested or some functional equivalent of the same thing more subtly built into natural law and the state of the physical elements, to assert that accident was the dynamic that produced such a genome is scientifically indefensible.


The Fossil Record

As of 1985, 250,000 species of complex life forms (Cambrian forward) were represented in fossil records.[118] However, an insignificant number and range of transitional forms between major body types and between phyla were present in these fossil records to support neo-Darwinian theory.[119] Michael Denton, an Australian medical doctor, research geneticist, and author of Evolution: A Theory in Crisis and Nature’s Destiny, points out that although the fossil record was far from complete as of 1986 it had systematic problems in relation to Darwinian theory, problems so extensive that the significance is noteworthy despite the fairly low rate of fossil sampling.


What Denton is pointing to is the fact that there are consistently fewer intermediates between the larger branches on the tree of life than between the smaller. For example, there are many intermediate forms between an ancient and a modern horse, but relatively few between land mammals and whales.[120]


Ultimately, Denton's argument boils down to the fact that, whatever the level of sampling reliability of our fossil record may be, in at least the majority of cases (and probably all) we should have seen many more intermediate forms between the originating and terminating creatures of a presumed large evolutionary jump, including between the phyla, than between the smaller jumps that separate the lower divisions and represent smaller physiological “distances.” D. M. Raup reports that even Darwin acknowledged this.[121] Yet we have not seen this anomaly remedied in any case of the larger “distances” between any two radically different creatures—not once.


Raup, writing in an official NASA publication on evolution says “…the basic evolutionary tree of life has been worked out and it is not likely to change very much as a result of further study.”[122] Other scientists have more recently suggested that now, more than twenty years later, our fossil record is substantially reliable, albeit still incomplete. Nonetheless, Denton’s objection that there is a systematic problem in the fossil record remains: while we have fossils of many intermediates between closely related species, there are insufficient fossils of intermediate species between major divisions on the evolutionary tree to support an accidental evolutionary process.[123] 


We have only 40 phyla and over 250,000 fossilized species. While granting that there are many legitimate unknowns that remain to be discovered in the evolutionary process, the one thing we are entitled to affirm is that the fossil record should reflect more intermediate species between the phyla than between the species and the genera if the neo-Darwinian theory of accidental evolution is true.


This point Denton makes about systematic problems, though seemingly an elementary one, is quite formidable. Despite its simplicity, it is crucial to understanding the weight of the fossil evidence. It flatly contradicts the predictions of neo-Darwinian theory, equating to a failed test of the theory of accidental evolution.


Given that there are at least 100,000,000 species presumed to have existed through the history of life (estimates vary, ranging to 2,000,000,000 or higher),[124] having only 250,000 represented in fossil records raises a concern about incomplete or nonrepresentative sampling. It might be said that the missing links could all still be out there because we are missing 400 fossil species (possibly many more) for every one that we have. While this is true, it is scientifically invalid to presume the nature of the evidence prior to its discovery. Instead of filling in the gaps, future fossil and fossilized DNA discoveries could pose new problems for neo-Darwinian evolutionary theory, or, as is most likely, further corroborate the patterns already present.


Critics of the completeness of the fossil record rightly point out that soft- shelled and invertebrate creatures are rarely preserved as useable fossils. Though this is true, fossil evidence of invertebrate history is not fully lacking. Invertebrates compose some 90% of the species on the planet. Given their enormous numbers, despite the comparative infrequency of fossil creation from soft-bodied creatures, invertebrate fossils are still frequently found.


The fossil database at The National Center for Ecological Analysis and Synthesis (NCEAS) in Santa Barbara, California has a substantial number of invertebrate fossils. Their fossil catalog consists of over 110,000 taxonomic occurrences, with an emphasis on marine invertebrates. Although critics of the presumed inadequacy of the fossil record have made much of the slight representation of invertebrates, the marine invertebrates clearly have a substantial presence in the fossil record. The global marine invertebrate database either grounds or supplements more significant modern studies than any other; so we obviously trust our marine invertebrate fossil sampling enough to draw certain types of scientific conclusions—and much progress has been made in sampling reliability.[125]


With this in mind, it is not surprising that, in Problems of Phylogenetic Reconstruction, C.R.C. Paul tells us that the "fossil record is much less incomplete than is generally accepted. Its incompleteness is largely irrelevant to the sequence of preserved fossils and hence to phylogenetic reconstruction provided only that we confine our phylogenies to known organisms. We ignore the fossil record at our peril.” David Woodruff echoes the same belief in his May 1980 Science article, "Evolution: The Paleobiological View" in saying "Evolutionary biologists can no longer ignore the fossil record on the ground that it is imperfect." Michael Denton’s criticism of the systematic problems the fossil record displays in regards to neo-Darwinian theory therefore survives against the incomplete fossil record challenge and remains a genuine show-stopper to the theory of accidental evolution.


Some of the gaps are more telling on neo-Darwinian theory than others. In The Fossils Still Say No! Professor Duane Gish leaves little room for doubt that intermediates between single-celled organisms and complex invertebrates have not been found in the fossil record.[126] Given the absence of an explainable link between the various phyla and what would otherwise be presumed to be a common ancestor at the base of the evolutionary tree (bacteria-level prokaryotic organisms); given the absence of intermediate links between the phyla (the main branches of the tree of life); and given an approximately reliable fossil record; we are forced to conclude that if anything like Darwinian evolution occurred, it accomplished approximately forty partial restarts: one at the beginning of each phylum.


As Dr. Jonathan Wells tells us in Icons of Evolution, that is exactly what the evidence suggests: many of the phyla appeared abruptly and fully formed.[127] NASA scientists’ study of the fossil record echoes a similar theme suggestive of independent origins of the phyla in acknowledging that “…multicellularity appeared independently in many different lineages…Fossil records of the first evolutionary steps in the development of multicellular animals are lacking.”[128]


The necessity of duplicating the jump between single-celled and multicellular organisms some forty times over increases the already enormous improbability of neo-Darwinian accidental evolution. Furthermore, as Dr. Jonathan Wells points out, according to the fossil record, the phyla essentially did the equivalent of coming out of nowhere.


It certainly is not the pattern expected from an accidental process, but it is fully consistent with the problems we see in generating macroevolutionary jumps, given the need to produce a completely different network of microtubules to match a novel genome. A close politics-free examination of the data reveals that the tough points in evolution remain unexplained and seem to border upon the miraculous.


Arguments have been made that the 3% representation of primate species in the fossil record is too small to ground a criticism of Darwinian theory because randomly placing 3% of the primate species on a tree diagram doesn’t yield a single instance of the known fossils of even two creatures occurring in immediate proximity on the same branch.[129] The objection that there are too many missing links is, Darwinists say, therefore, shown to be premature; we should wait for the discovery of more fossils. But this same inadequacy in the fossil record argues just as strongly that we have far too little fossil evidence to solidly ground any theory of evolution, let alone an accidental one.


The similarities in genetic sequence among species does strongly suggest inheritance, but until we can sketch the tree of life with confidence and show concrete biomechanical pathways and definite historical routes between phyla and between species, we remain “light years” away from having sufficient evidence to affirm any specific narrative or biomechanical theory of evolution, including, and especially, the accidental theory, which is so heavily impugned by astronomical improbability.


To be consistent, if we are to wait for more evidence from the fossil record to draw conclusions, then all of our conclusions should await that evidence, not just those that tend to argue against the atheist, materialist, and Marxist worldviews. Otherwise, we are violating the standards of science by anticipating what the nature of new discoveries will be. And we are being politically biased in selecting when to apply rules governing the drawing of scientific inferences and when not to apply them.


“We don’t yet know” is an answer scientists are not reticent to give anywhere in science where the evidence is inadequate or ambiguous—except evolutionary science. Where huge political stakes exist, as they clearly do in the evolutionary science battlefield between atheistic materialism/Communism and God-fearing worldviews and the democratic nations that host them, “We don’t yet know” is frequently eschewed for fear of giving the political opposition an opening to win the minds of the public via propagandized rhetoric.


By far the strongest case that has been made for restraining the unbounded imagination of the neo-Darwinists and sticking to a strict cladistic description of the fossil record is made by Henry Gee. Gee discloses in his recent paradigm shattering, In Search of Deep Time, that there are no grounds for evolutionists to presume to assert why or how (or even when in many cases) creatures have emerged through history as they have, but only to describe the record of that emergence in an objective way. Over an extended and convincing course of argument grounded in the concrete but very limited facts of the fossil record, Gee demonstrates that to say more is to arbitrarily import and impose sociological or philosophical preconceptions onto the objective data.[130]



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[1] This seminal meeting is documented in a fascinating video entitled Unlocking the Mystery of Life, from, Illustra Media (DVD), Many of the primary intelligent design team members make significant appearances in this video, such as Scott Minnich, Michael Behe, Jonathan Wells, Phillip Johnson, Jed Macosko, and Dean Kenyon. Law professor and attorney Phillip Johnson is the author of one of the early trailblazing works on intelligent design, Darwin on Trial (Downers Grove, IL: InterVarsity Press, 1991), as well as The Wedge of Truth: Splitting the Foundations of Naturalism (Downers Grove, IL: InterVarsity Press, 2000) and Defeating Darwinism (Downers Grove, IL: InterVarsity Press, 1997). For those who would like a brief and clear introduction to the subject of intelligent design, William A. Dembski and James M. Kushiner’s (editors), Signs of Intelligence: Understanding Intelligent Design (Grand Rapids, Michigan: Brazos Press, 2001) is a good choice.

[2] Fazale Rana and Hugh Ross. Origins of Life: Biblical and Evolutionary Models Face Off. Colorado Springs, CO: NavPress, 2004, 222; also see Witham, By Design, ch.3.

[3] Michael J. Denton, Nature’s Destiny (New York: The Free Press, 1998).

[4] Denton, Michael J. “The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law.” Journal of Theoretical Biology. Vol. 219, no. 3 (2002): 325-342.


[5] Charles Darwin, The Origin of Species, 1st ed., (New York: Barnes & Noble Books, 2004), 210, 525. The second edition adds a third reference to the Creator as he who breathed life into creation. This appears in the very last sentence of the book.

[6] John A. Davison, “Instant Evolution” Rivista di biologia. Vol. 96, Issue 2 (May-Aug, 2003): 203-6.

[7] Henry Gee, In Search of Deep Time: Beyond the Fossil Record to a New History of Life (Ithaca, NY: Cornell University Press, 1999.)

[8] Fred Hoyle, Mathematics of Evolution (Memphis, TN: Acorn Enterprises, LLC, 1999), 107.

[9] Gerald L. Schroeder, The Science of God: The Convergence of Scientific and Biblical Wisdom (New York: Broadway Books, 1998), 10.

[10] David Raup, “Conflicts between Darwin and Paleontology," Field Museum of Natural History Bulletin, vol. 50, no. 1 (1979): 22–29; Ernst Mayr, What Evolution Is, (New York: Basic Books, 2001), 14. Large gaps in the fossil record have long been universally acknowledged in evolutionary science and paleontology. It is an undisputed fact, and these two experts are only mentioned as representative of the broad consensus.

[11] If you have trouble remembering the taxonomic divisions, kingdom, phylum, class, order, family, genus, species try the mnemonic trick, “King Phillip Came Over From Great Spain,” or have a go at the amusing student’s songs at

[12] Hugh Ross, The Creator and the Cosmos: How the Greatest Scientific Discoveries of the Century Reveal God (Colorado Springs, CO: NavPress, 1992); Hugh Ross, Creation and Time: A Biblical and Scientific Perspective on the Creation-Date Controversy (Colorado Springs, CO: NavPress, 1994); Hugh Ross, The Fingerprint of God (New Kensington, PA: Whitaker House, 2000); Hugh Ross, Beyond the Cosmos: What Recent Discoveries in Astrophysics Reveal About the Glory and Love of God, 3rd ed. (Kissimmee, FL: Signalman, 2010). It is Hugh Ross’s science that I am lauding here; his theological argument seems based upon a reading of scripture that is not Catholic (as I am) and I cannot give it a blanket endorsement without further study.

[13] Hugh Ross, Kenneth Samples, and Mark Clark. Lights in the Sky & Little Green Men: A Rational Christian Look at UFOs and Extraterrestrials (Colorado Springs, CO: NavPress, 2002), Appendixes A and C; Mere Creation: Science, Faith & Intelligent Design (Downers Grove, IL: InterVarsity Press, 1998). Another of Hugh Ross’s relevant offerings on this subject, written with co-author Dr. Fazale Rana, is Origins of Life: Biblical and Evolutionary Models Face Off (Colorado Springs, CO: NavPress, 2004). Also, see Paul Davies’, The Accidental Universe (Cambridge, UK: Cambridge University Press, 1982).

[14] Stephen C. Meyer, “The Origin of Biological Information and the Higher Taxonomic Categories,” Proceedings of the Biological Society of Washington 117, no. 2 (2004): 217.

This article is available on the Web at There is a heavily politicized controversy concerning the peer review status of Meyer’s article, which was oddly withdrawn after its publication. The editor who approved it was fired. All of this, of course, is highly nonstandard, but the neo-Darwinists assure us no politics were involved whatsoever. In any case, the research Meyer cites in his article is peer-reviewed, and the logic of his argument is transparently valid. A brief synopsis of the controversy is given on page 2 of Meyer’s new book, Signature in the Cell: DNA and the Evidence for Intelligent Design (New York: HarperCollins, 2009).

[15] Peter Kassan, “Duplicating Human Intelligence is a Mirage,” in Artificial Intelligence, edited by Sylvia Engdahl (Farmington Hills, MI: Greenhaven Press, 2008). Also, see Appendix 2 for a detailed presentation of this case, what has been called the resource exhaustion argument. This is my own reformulation in terms of the historical biomass of the Earth and should not be read as an explicit restatement of William Dembski. It begins from Dembski’s resource limit computations and extrapolates a similar line of argument using cumulative biomass instead of total number of atomic particles.

[16] Michael J. Behe, Darwin’s Black Box (New York: The Free Press, 1996); Michael J. Behe, The Edge of Evolution (New York: The Free Press, 2007).

[17] Charles Darwin, The Origin of Species, 1st edition, (New York: Barnes & Noble Books, 2004), 210.

[18] G. G. Simpson, This View of Life: The World of an Evolutionist (New York: Harcourt, Brace & World, Inc., 1964), 71, 202.

[19] Barbieri, Marcello. The Organic Codes: An Introduction to Semantic Biology. Cambridge, UK: Cambridge University Press, 2003.

[20] Russell Grigg, “Could monkeys type the 23rd Psalm?” published to the Answers in Genesis Internet site at

[21] Eva Jablonka and Marion J. Lamb, Epigenetic Inheritance and Evolution: The Lamarckian Dimension (Oxford: Oxford University Press, 1995), 202.

[22] See Paul Davies, The Fifth Miracle (New York: Simon & Schuster, 1999), 271. Paul Davies here cites a debate between Carl Sagan and Ernst Mayr published as "The Search for Extraterrestrial Intelligence: Scientific Quest or Hopeful Folly?" Planetary Report, vol. 16 (1996): 4. Mayr indicates that the number of species in Earth's history may be as high as 50,000,000,000. Estimates of the number of species offered by different scientists have varied widely over the past fifty years but appear to have been steadily declining. The only significance of the figure I use here is that it is a visible underestimate. There is no consensus on the best estimate of the number of species in the history of life, or even on the number of living species. Current estimates of the number of species still living range from 4 million to 100 million. In a recent Huffington Post article, Richard Dawkins pegs the number of species that ever lived at a billion. So we are in the ballpark. Timothy Shanahan, in The Evolution of Darwinism, reflects the prevailing opinion that 99.99% of all species that have ever lived are extinct.

[23] Meyer, “Biological Information,” 220; D. D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, vol. 341, no. 5 (2004): 1295-1315.

[24] Stephen C. Meyer, “Word Games,” in William Dembski and James M. Kushiner, eds., Signs of Intelligence: Understanding Intelligent Design, (Grand Rapids, MI: Brazos Press, 2001), 110; Axe, D. D., “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, vol. 341 (2004): 1295-1315.

[25] D. B. Davison, “Brute Force Estimation of the Number of Human Genes Using EST Clustering as a Measure,” IBM Journal of Research and Development 45, no. 3/4 (2001): 439.

[26] Paul Davies, The Fifth Miracle, (New York: Simon & Schuster, 1999), 95.

[27] Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Colorado Springs, CO: NavPress, 2004), 164; Hubert P. Yockey, Information Theory and Molecular Biology, (Cambridge: Cambridge University Press, 1992). This book is highly recommended to those who wish to understand the origins of life question.

[28] Ibid.

[29] An order of magnitude equates to a factor of 10. One order of magnitude reduction from 1,000 is 100, and from 100, is 10. The reduction referenced here represents the difference between 85,000 multiplications of 10-77 (the improbability of biologically viable protein production inside an organism) and 85,000 multiplications of 10-125 (the improbability of biologically viable protein production outside an organism).

[30] Denton, Destiny.

[31] Jacques Monod, Chance and Necessity (New York: Vintage Books, 1972), 47; Andre R. O. Cavalcanti, Elisa Soares Leite, Benicio B. Neto, and Ricardo Ferreira, “On the Classes of Aminoacyl-tRNA Synthetases, Amino Acids and the Genetic Code,” Origins of Life and the Evolution of the Biosphere, 34, no. 4 (2004), 409; Sidney Fox, The Emergence of Life: Darwinian Evolution from the Inside, (New York: Basic Books, Inc. Publishers, 1988), 13.

[32] Gabriel Waksman, ed., Proteomics and Protein-Protein Interactions: Biology, Chemistry, Bioinformatics, and Drug Design, Protein Reviews, vol. 3 (New York: Springer Science+Business Media, Inc., 2005), vi. Also see Joseph D. Puglisi, ed., Structure and Biophysics – New Technologies for Current Challenges in Biology and Beyond (Dordrecht, Netherlands: Springer, 2005); Joe DeBartolo, et al., “Mimicking the Folding Pathway to Improve Homology-free Protein Structure Prediction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 10 (2009): 3734-3739, and Jin Wang, et al., “Uncovering the Rules for Protein-Protein Interactions from Yeast Genomic Data,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 10 (2009): 3752-3757 for a good indication of the astronomical complexity of physical protein folding, shape prediction, and related research.

[33] Sarah A. Harris and Vivien M. Kendon, “Quantum-assisted Biomolecular Modeling,” Philosophical Transactions of the Royal Society, Series A., vol. 368, no. 1924 (2010): 3581-3592; Tony R. Obalinsky, ed., Protein Folding: New Research (New York: Nova Science Publishers, Inc., 2006), viii-ix; Cathy H. Wu and Jerry W. McLarty. Neural Networks and Genome Informatics, Methods in Computational Biology and Biochemistry, vol. 1 (Amsterdam: Elsevier, 2000); Lev. A. Blumenfeld and Alexander N. Tikhonov, Biophysical Thermodynamics of Intracellular Processes: Molecular Machines of the Living Cell (New York: Springer-Verlag, 1994), 102-105. D. Bashford, “Macroscopic Electrostatics with Atomic Detail (MEAD): Applications to Biomacromolecules,” in Biomacromolecules: From 3-D Structure to Applications, edited by Rick L Ornstein (Columbus, OH: Battelle Press, 1995): 53-68.

[34] See the SETI@home Website at U. C. Berkeley,, and Stanford University’s and

[35] Amir Alexander and Charlene Anderson, “Searching for ET and the Cure for Cancer: The Planetary Society Helps Trigger a Computing Revolution,” published to the Web at

[36] William Dembski, et al., Unlocking the Mystery of Life, Illustra Media (DVD),

[37] Ada Yonath, "Ribosomal Crystallography: Peptide Bond Formation, Chaperone Assistance, and Antibiotics Inactivation", in Joseph D. Puglisi, ed., Structure and Biophysics – New Technologies for Current Challenges in Biology and Beyond (Dordrecht, Netherlands: Springer, 2005); Kathleen L. Triman, "Mutational Analysis of the Ribosome," in Jeffrey C. Hall, Jay C. Dunlap, Theodore Friedmann, and Veronica van Heyningen. Advances in Genetics, vol. 58 (Amsterdam: Elsevier, 2007); A. Liljas, Structural Aspects of Protein Synthesis (Singapore: World Scientific, 2004); R. A. Garrett, S. R. Douthwaite, A. Liljas, A. T. Matheson, P. B. Moore, and H. Noller, eds. The Ribosome: Structure, Function, Antibiotics and Cellular Interactions (Washington D.C.: ASM Press, 2000). Ribosomal DNA sequence size is given at, Michigan State University’s Ribosomal Database Project – II.

[38] Meyer, "Biological Information," 220; a DNA sequence length for a standard size gene across the tree of life is approximately 1,000 base pairs; human genes average around 5,000 bp. If we computed the probability for accidentally producing the 50 plus proteins involved in the ribosome more strictly, we must multiply 10-77 times itself 50 times for a total probability of 10-3,850! The total probability for accidental construction of a ribosome is then less than 10-3,927! This is a huge negative probability, equating to one chance in 10 followed by 3,926 zeroes!

[39] Edward A. Bayer, Jean-Pierre Belaich, Yuval Shoham, and Raphael Lamed “The Cellulosomes: Multienzyme Machines for Degradation of Plant Cell Wall Polysaccharides,” Annual Review of Microbiology, 58 (2004): 521-54.

[40] H. Wijnen and M. W. Young, “Interplay of Circadian Clocks and Metabolic Rhythms,” Annual Review of Genetics, vol. 40 (2006): 409-448.

[41] John B. Hogenesch, “It’s All in a Day’s Work: Regulation of DNA Excision Repair by the Circadian Clock,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 8 (2009): 2481-2482; Tae-Hong Kang, Joyce T. Reardon, Michael Kemp, and Aziz Sancar. “Circadian Oscillation of Nucleotide Excision Repair in Mammalian Brain.” Proceedings of the National Academy of Sciences of the United States of America. Vol. 106, no. 8 (2009): 2864-2867.

[42] Robert M. Macnab, “How Bacteria Assemble Flagella,” Annual Review of Microbiology, 57 (2003): 77-100; Christian Heintzen and Yi Liu, "The Neurospora crassa Circadian Clock," in Jeffrey C. Hall, Jay C. Dunlap, Theodore Friedmann, and Veronica van Heyningen, Advances in Genetics, vol. 58 (Amsterdam: Elsevier, 2007). Also see, Giovanni Meacci and Yuhai Tu, “Dynamics of the Bacterial Flagellar Motor with Multiple Stators,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 10 (2009): 3746-3751.

[43] Boyce Rensberger, Life Itself: Exploring the Realm of the Living Cell (Oxford: Oxford University Press, 1996), chap. 2.

[44] Behe, Black Box, 46.

[45] Michael J. Denton, Evolution: A Theory in Crisis, (Bethesda, MD: Adler & Adler, 1986), 223-225.

[46] For an overview of key selected systems within the human body, see Discover magazine’s special issue, Discover Presents: The Body, Summer 2008, 26-35.

[47] Behe, Black Box, chap. 6; Rensberger, Life Itself, chap. 11; Tak W. Mak and Mary E. Saunders, The Immune Response, (Burlington, MA: Elsevier Academic Press, 2006), 20.

[48] Barry J. Gibb, The Rough Guide to the Brain (London: Rough Guide, 2007), 31.

[49] Peter Kassan, “Duplicating Human Intelligence is a Mirage” in Artificial Intelligence, edited by Sylvia Engdahl (Farmington Hills, MI: Greenhaven Press, 2008), 112-122.

[50] Francis S. Collins, The Language of Life (New York: HarperCollins Publishers, 2010), 187; Luigi F. Agnati, Diego Guidolin, Michele Guescini, Susanna Genedani, and Kjell Fuxe, “Understanding Wiring and Volume Transmission,” Brain Research Reviews, volume 64, no. 1 (2010): 137-159.               

[51] Roger Penrose, Shadows of the Mind: Search for the Missing Science of Consciousness (Oxford, UK: Oxford University Press, 1994).

[52] David Faust, The Limitations of Scientific Reasoning (Minneapolis: University of Minnesota Press, 1984), 152.

[53] J. C. Eccles, The Understanding of the Brain (New York: McGraw-Hill Book Company, 1977), 204.

[54] Enrico Cherubini, S. Gustincich, and H. Robinson, “The Mammalian Transcriptome and the Cellular Complexity of the Brain,” Journal of Physiology-London, vol. 575, no. 2 (2005): 319-320; Stefano Gustincich, Albin Sandelin, Charles Plessy, Shintaro Katayama, Roberto Simone, Dejan Lazarevici, Yoshihide Hayashizaki and Piero Carnici, "The Complexity of the Mammalian Transcriptome," Journal of Physiology-London, vol. 575, no. 2 (2005): 321-332; Anthony R. Ruffa, Darwinism and Determinism: The Role of Direction in Evolution (Brookline Village, MA: Branden Press, Inc., 1983).

[55] Robert Pollack, Signs of Life: The Language and Meanings of DNA (Boston: Houghton Mifflin Co., 1994), chap. 1-5.

[56] “Ordering Genes,” Astrobiology Magazine, Dec 7, 2004.

[57] Anton Nekrutenko, “Reconciling the Numbers: ESTs Versus Protein-Coding Genes,” Molecular Biology and Evolution, vol. 21, no. 7 (2004): 1278-1282; Francis S. Collins, The Language of Life (New York: HarperCollins Publishers, 2010), 187. The estimate of the number of genes in the human genome has declined steadily since the initial estimates, which hovered around 40,000. Francis S. Collins, now the director of NIH, cites 20,000 in his highly acclaimed 2010 offering, The Language of Life, which makes it close to being official, but we are still learning. Why the decline? The answer appears to have more to do with discovering the increased complexity of single genes, than with overestimates of the complexity of genetic systems. DNA sequences integral to a given gene have been found to be scattered in fragments that occur throughout the chromosome instead of being confined to a single jelly-bean like contiguous stretch of nucleotides as was hypothesized in the early days of genetic science.

[58] Julian L. Griffin, “Metabolic Profiles to Define the Genome: Can We Hear the Phenotypes?” Philosophical Transactions of the Royal Society, B, Biological Sciences, vol. 359, no. 1446 (2004): 857-871.

[59] Mark J. Schofield and Peggy Hsieh, “DNA Mismatch Repair: Molecular Mechanisms and Biological Function,” Annual Review of Microbiology, 57 (2003); Wolfram Seide, Yoke Wah Kow, and Paul W. Doetsch, DNA Damage Recognition (New York: Taylor & Francis Group, 2006); Paul Nelson, “Uncovering the Hidden Meanings of the Genome,” Access Research Network, Literature Survey 19:1, published to the Internet at, citing Chiou-Hwa Yuh, Hamid Bolouri, and Eric H. Davidson, “Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene,” Science, vol. 279, no. 5358 (20 March 1998):1896-1902; Gil Ast, “The Alternative Genome,” Scientific American, vol. 292, no. 4 (2005): 58-65.

[60] G. Ledyard Stebbins, Processes of Organic Evolution (Englewood Cliffs, NJ: Prentice-Hall, 1971), 15, Fig.1-6.

[61]James W. Valentine, On the Origin of Phyla (Chicago: University of Chicago Press, 2004), 81-82; Anton Nekrutenko, “Reconciling the Numbers: ESTs Versus Protein-Coding Genes,” Molecular Biology and Evolution, vol. 21, no. 7 (2204): 1278-1282. Published to the Internet at; Anton Nekrutenko, “Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames,” Trends in Genetics,  9 Oct 2006, an advance Epub published to the Internet at

[62] Helena Curtis and N. Sue Barnes, Biology (New York: Worth Publishers, Inc., 1989), 115.

[63] Tiffany D. Miles, Jelena Jakovljevic, Edward W. Horsey, Piyanun Harnpicharnchai, Lan Tang, and John L. Woolford, Jr., “Ytm1, Nop7, and erb1 Form a Complex Necessary for Maturation of Yeast 66S Preribosomes,” Molecular and Cellular Biology, vol. 25, no. 23 (2005): 10419-10432.

[64] Valentine, Phyla, 40-65.

[65] W. Ford Doolittle, “Evolutionary Creativity and Complex Adaptations: A Molecular Biologist’s Perspective,” in John H. Campbell and J. William Schopf, ed., Creative Evolution (Boston: Jane and Bartlett Publishers, 1994), 50.

[66] Eva Jablonka and Marion J. Lamb, Epigenetic Inheritance and Evolution: The Lamarckian Dimension (Oxford: Oxford University Press, 1995), 86-90.

[67] Jonathan Wells, “Making Sense of Biology” in Dembski, Intelligence, 120-122.

[68] Wistar Institute, "Gene Activation: It's Quite Dynamic!" published to the Internet at; Richard C. Francis, Epigenetics: The Ultimate Mystery of Inheritance (New York: W. W. Norton & Company, 2011), 61; Thomas  Woodward and James Gills, The Mysterious Epigenome: What Lies Beyond DNA (Grand Rapids, MI: Kregel, 2012).

[69] Valentine, Phyla, chap. 5.

[70] Robert F. Dehaan and John L. Wiester “The Cambrian Explosion” in Dembski, Intelligence, 148; Meyer “Biological Information,” 214.

[71] Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, vol. 25, no, 1 (2012): 41-47.

[72] D. M. Raup, “Life, Terrestrial Environments, and Events in Space,” in David Milne et al. eds., The Evolution of Complex and Higher Organisms -NASA Special Publication 478 (Washington, DC: NASA, 1985), 14; Ross D. E. MacPhee, and Hans-Dieter Sues, eds., Extinctions in Near Time: Causes, Contexts, and Consequences (Advances in Vertebrate Paleobiology) (New York: Kluwer Academic, 1999).

[73] Valentine, Phyla, 66.

[74] John Gribbin, Q is for Quantum: An Encyclopedia of Particle Physics (New York: The Free Press, 1998), 77-79.

[75] Life on Earth is produced by BBC Natural History Unit in association with Warner Brothers and Reiner Moritz Productions, 1986. Distributed by Warner Home Video.

[76] Douglas J. Futuyma, Evolutionary Biology, 3rd ed., (Sunderland, MA: Sinauer Associates, Inc., 1998), 152-154.

[77] Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (Cambridge: Cambridge University Press, 2003).

[78] Schroeder, The Science of God, chap. 6.

[79] “Francis Crick Remembered,” Astrobiology Magazine, Jul 30, 2004. Also see Francis Crick and Leslie E. Orgel, “Directed Panspermia,” Icarus, vol. 19 (1973): 341-346.

[80] Geoffrey Zubay, Origins of Life on the Earth and in the Cosmos (San Diego: Academic Press, 2000), 496.

[81] Mayr, What Evolution Is, 98.

[82] Ibid, 108-109.

[83] Wildlife and Environmental Biologist Gary Jordan first brought this deficiency in neo-Darwinian theory to my attention circa 1998. He explained that the problem with accidental evolution, in addition to the fossil record not having the correct pattern and there not being enough time for accident to work, all seemed to boil down to neo-Darwinists having no explanation for the creation of new biologically meaningful information.

[84] See the Time Magazine article at

[85] “The Struggle of Ideas,” Time, 16 Jun 1941.

[86] James F. Crow and Carter Denniston, “Mutation in Human Populations,” Advances in Human Genetics 14 (1985): 61, 107. Robert Pollack, Signs of Life: The Language and Meanings of DNA (Boston: Houghton Mifflin Co., 1994), 32; Futuyma, Evolutionary Biology, 278; Margulis. Acquiring Genomes, 11-12.

[87] Pollack, Signs, 32.

[88] Wells, “Making Sense” in Dembski, Intelligence, 120.

[89] From the PBS Web site at

[90] Meyer, “Biological Information,” 218.

[91] Jonathan Wells, The Myth of Junk DNA. Seattle: Discovery Institute Press, 2011.

[92] Progressive is here defined to mean the organism survives the mutation moving towards an overall design improvement related to the journey toward some highly complex creature.

[93] Jonathan Wells, Icons of Evolution (Washington, DC: Regnery Publishing, Inc., 2002).

[94] Douglas J. Futuyma, Science on Trial (Sunderland, MA: Sinauer Associates, Inc., 1995), 138-139.

[95] Karl Popper, Objective Knowledge: An Evolutionary Approach (Oxford: Oxford University Press, 1972), 267.

[96] Jerry Bergman, “Darwinism and the Deterioration of the Genome,” Creation Research Society Quarterly, vol. 42, no. 2 (2005).

[97] Futuyma, Science on Trial, 141.

[98] Davison, “Instant Evolution,” a succinct and very readable article:

[99] Douglas J. Futuyma, Evolutionary Biology. 1st ed. Sunderland, MA: Sinauer Associates, Inc., 1979, 294.

[100] Susumu Ohno, “The Notion of the Cambrian Pananimalia Genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 16 (1996): 8475-8478.

[101] Mark Ridley, Evolution (Boston: Blackwell Scientific Publications, 1993), 76-78.

[102] A. Kumar and J. L. Bennetzen, “Plant Retrotransposons,” Annual Review of Genetics, vol. 33 (1999): 479-532.

[103] A. M. Lambowitz and S. Zimmerly, “Mobile Group II Introns,” Annual Review of Genetics, vol. 38 (2004): 1-35.

[104] Wu, Chengcang, Suojin Wang and Hong-Bin Zhang, “Interactions Among Genomic Structure, Function, and Evolution Revealed by Comprehensive Analysis of the Arabidopsis thaliana Genome,” Genomics, vol. 88, no. 4 (2006): 394-406.

[105] W. E. Lonnig and H. Saedler, “Chromosome Rearrangements and Transposable Elements,” Annual Review of Genetics, vol. 36 (2002): 389-410. Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, “Resynthesizing Evolutionary and Developmental Biology,” Developmental Biology, vol. 173, no. 2 (1996): 357-372. Gilbert et al. say that the emerging synthesis in evolutionary biology is that the classic Darwinian model for macroevolution that says population dynamics can explain macroevolutionary events has failed, and that a new dynamic is being invoked by a more robust model that posits special segments of the developmental genome, called “morphogenetic fields,” as the primary source of macroevolution.

[106] Michael Gleich, et al., Life Counts (New York: Atlantic Monthly Press, 2000), 28.

[107] L. Aravind, Kira S. Makarova and Eugene V. Koonin, “Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories,” Nucleic Acids Research, vol. 28, no. 18 (2000): 3417-3432.

[108] Don B. Clewell and Cynthia Gawron-Burke, “Conjugative Transposons and the Dissemination of Antibiotic Resistance in Streptococci,” Annual Review of Microbiology, vol. 40 (1986): 635-659; Gregory, Evolution of the Genome, 612.

[109] Gordon C. Mills, Malcolm Lancaster, and Walter L. Bradley “Origin of Life and Evolution in Biology Textbooks: A Critique,” in John Angus Campbell and Stephen C. Meyer ed., Darwinism, Design, and Public Education (East Lansing: Michigan State University Press, 2003), 214.

[110] Kassan, “Mirage,” 121.

[111] Aravind, “Holliday,” 3417-3432.

[112] Mayr, What Evolution Is, 106.

[113] See the NewScientist Blog article at

[114] See the San Diego Earth Times article at

[115] See “How Many Species of Bacteria Are There?” published on the WiseGeek Web site,

[116] Ohno, “Pananimalia,” 8475-8478.

[117] Martin Jones, The Molecule Hunt: Archaeology and the Search for Ancient DNA (New York: Arcade Publishing, 2001).

[118] Raup, “Terrestrial Environments,” 11.

[119] Dehaan, “Cambrian,” 147-154.

[120] Michael Denton, Evolution: A Theory in Crisis (Bethesda, Maryland: Adler & Adler, 1986), 191-2; In-Young Chang and Jennifer Curry ed., Evolution, The Reference Shelf, vol. 78, no. 5 (New York: The H. W. Wilson Company, 2006), chap. IV.

[121] See Stephen Jones “Evolution Quotes” Web site at

[122] Raup, “Terrestrial Environments,” 12; Chang, Evolution, chap. IV; Meyer “Biological Information,” 215.

[123] Meyer “Biological Information,” 215.

[124] Richard C. Lewontin, “Adaptation” in The Fossil Record and Evolution (San Francisco: W. H. Freeman and Company, 1982).

[125] A sampling-standardized analysis of Phanerozoic marine diversification and extinction,” a working group proposed by John Alroy, Department of Paleobiology Smithsonian Institution MRC 121 Washington, DC 20560 & Charles R. Marshall, Department of Earth and Space Sciences, Molecular Biology Institute, and Institute for Geophysics and Planetary Physics University of California Los Angeles, CA 90095-1567, published as an Adobe PDF document at

[126] Duane T. Gish, Evolution: The Fossils Still Say No! (El Cajon, Calif.: Institute for Creation Research, 1995), 53, 55, 59; Dehaan, “Cambrian,” 149-154.

[127] Wells, Icons, 35.

[128] R. K. Bamback, et al.  “Geologic History of Complex Organisms” in David Milne et al., eds., The Evolution of Complex and Higher Organisms (Washington, DC: NASA, 1985): 29-30.

[129] Charles R. Marshall, “Missing Links in the History of Life,” in J. William Schopf, ed., Evolution Facts and Fallacies (San Diego: Academic Press, 1999), 43.

[130] C. R. C. Paul “The Adequacy of the Fossil Record” in K. A. Joysey and A. E. Friday, eds., Problems of Phylogenetic Reconstruction, 75-117 (London: Academic, 1982); David S. Woodruff, "Evolution: A Paleobiological View," Science, vol. 208. no. 4445 (1980): 717. Gee, Deep Time.